coverage.py v7.6.7, - created at 2024-11-19 08:32 +0000 + created at 2024-11-19 08:51 +0000
From 3fc132470ca072663f28f3df8ec449816c9ffd88 Mon Sep 17 00:00:00 2001
From: FynnBe Contents
-
Python specific core utilities for bioimage.io resources (in particular models).
+Python specific core utilities for bioimage.io resources (in particular DL models).
coverage.py v7.6.7, - created at 2024-11-19 08:32 +0000 + created at 2024-11-19 08:51 +0000
coverage.py v7.6.7, - created at 2024-11-19 08:32 +0000 + created at 2024-11-19 08:51 +0000
coverage.py v7.6.7, - created at 2024-11-19 08:32 +0000 + created at 2024-11-19 08:51 +0000
coverage.py v7.6.7, - created at 2024-11-19 08:32 +0000 + created at 2024-11-19 08:51 +0000
Python specific core utilities for bioimage.io resources (in particular models).
\n\nTo get started we recommend installing bioimageio.core with conda together with a deep\nlearning framework, e.g. pytorch, and run a few bioimageio
commands to see what\nbioimage.core has to offer:
install with conda (for more details on conda environments, checkout the conda docs)
\n\nconda install -c conda-forge bioimageio.core pytorch\n
\ntest a model
\n\n$ bioimageio test powerful-chipmunk\n...\n
\n(Click to expand output)
\u2714\ufe0f bioimageio validation passed\n\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\n source https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/powerful-chipmunk/1/files/rdf.yaml\n format version model 0.4.10\n bioimageio.spec 0.5.3post4\n bioimageio.core 0.6.8\n\n\n\n \u2753 location detail\n\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\n \u2714\ufe0f initialized ModelDescr to describe model 0.4.10\n\n \u2714\ufe0f bioimageio.spec format validation model 0.4.10\n \ud83d\udd0d context.perform_io_checks True\n \ud83d\udd0d context.root https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/powerful-chipmunk/1/files\n \ud83d\udd0d context.known_files.weights.pt 3bd9c518c8473f1e35abb7624f82f3aa92f1015e66fb1f6a9d08444e1f2f5698\n \ud83d\udd0d context.known_files.weights-torchscript.pt 4e568fd81c0ffa06ce13061327c3f673e1bac808891135badd3b0fcdacee086b\n \ud83d\udd0d context.warning_level error\n\n \u2714\ufe0f Reproduce test outputs from test inputs\n\n \u2714\ufe0f Reproduce test outputs from test inputs\n
\nor
\n\n$ bioimageio test impartial-shrimp\n...\n
\n(Click to expand output)
\u2714\ufe0f bioimageio validation passed\n\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\n source https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/impartial-shrimp/1.1/files/rdf.yaml\n format version model 0.5.3\n bioimageio.spec 0.5.3.2\n bioimageio.core 0.6.9\n\n\n \u2753 location detail\n\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\n \u2714\ufe0f initialized ModelDescr to describe model 0.5.3\n\n\n \u2714\ufe0f bioimageio.spec format validation model 0.5.3\n\n \ud83d\udd0d context.perform_io_checks False\n \ud83d\udd0d context.warning_level error\n\n \u2714\ufe0f Reproduce test outputs from test inputs (pytorch_state_dict)\n\n\n \u2714\ufe0f Run pytorch_state_dict inference for inputs with batch_size: 1 and size parameter n:\n\n 0\n\n \u2714\ufe0f Run pytorch_state_dict inference for inputs with batch_size: 2 and size parameter n:\n\n 0\n\n \u2714\ufe0f Run pytorch_state_dict inference for inputs with batch_size: 1 and size parameter n:\n\n 1\n\n \u2714\ufe0f Run pytorch_state_dict inference for inputs with batch_size: 2 and size parameter n:\n\n 1\n\n \u2714\ufe0f Run pytorch_state_dict inference for inputs with batch_size: 1 and size parameter n:\n\n 2\n\n \u2714\ufe0f Run pytorch_state_dict inference for inputs with batch_size: 2 and size parameter n:\n\n 2\n\n \u2714\ufe0f Reproduce test outputs from test inputs (torchscript)\n\n\n \u2714\ufe0f Run torchscript inference for inputs with batch_size: 1 and size parameter n: 0\n\n\n \u2714\ufe0f Run torchscript inference for inputs with batch_size: 2 and size parameter n: 0\n\n\n \u2714\ufe0f Run torchscript inference for inputs with batch_size: 1 and size parameter n: 1\n\n\n \u2714\ufe0f Run torchscript inference for inputs with batch_size: 2 and size parameter n: 1\n\n\n \u2714\ufe0f Run torchscript inference for inputs with batch_size: 1 and size parameter n: 2\n\n\n \u2714\ufe0f Run torchscript inference for inputs with batch_size: 2 and size parameter n: 2\n
\ndisplay the bioimageio-predict
command help to get an overview:
$ bioimageio predict --help\n...\n
\n(Click to expand output)
usage: bioimageio predict [-h] [--inputs Sequence[Union[str,Annotated[Tuple[str,...],MinLenmin_length=1]]]]\n [--outputs {str,Tuple[str,...]}] [--overwrite bool] [--blockwise bool] [--stats Path]\n [--preview bool]\n [--weight_format {typing.Literal['keras_hdf5','onnx','pytorch_state_dict','tensorflow_js','tensorflow_saved_model_bundle','torchscript'],any}]\n [--example bool]\n SOURCE\n\nbioimageio-predict - Run inference on your data with a bioimage.io model.\n\npositional arguments:\n SOURCE Url/path to a bioimageio.yaml/rdf.yaml file\n or a bioimage.io resource identifier, e.g. 'affable-shark'\n\noptional arguments:\n -h, --help show this help message and exit\n --inputs Sequence[Union[str,Annotated[Tuple[str,...],MinLen(min_length=1)]]]\n Model input sample paths (for each input tensor)\n\n The input paths are expected to have shape...\n - (n_samples,) or (n_samples,1) for models expecting a single input tensor\n - (n_samples,) containing the substring '{input_id}', or\n - (n_samples, n_model_inputs) to provide each input tensor path explicitly.\n\n All substrings that are replaced by metadata from the model description:\n - '{model_id}'\n - '{input_id}'\n\n Example inputs to process sample 'a' and 'b'\n for a model expecting a 'raw' and a 'mask' input tensor:\n --inputs="[["a_raw.tif","a_mask.tif"],["b_raw.tif","b_mask.tif"]]"\n (Note that JSON double quotes need to be escaped.)\n\n Alternatively a `bioimageio-cli.yaml` (or `bioimageio-cli.json`) file\n may provide the arguments, e.g.:\n ```yaml\n inputs:\n - [a_raw.tif, a_mask.tif]\n - [b_raw.tif, b_mask.tif]\n \n
\n `.npy` and any file extension supported by imageio are supported.\n Aavailable formats are listed at\n https://imageio.readthedocs.io/en/stable/formats/index.html#all-formats.\n Some formats have additional dependencies.\n\n \u200a (default: ('{input_id}/001.tif',))\n
\n\n--outputs {str,Tuple[str,...]}\n Model output path pattern (per output tensor)
\n\n All substrings that are replaced:\n - '{model_id}' (from model description)\n - '{output_id}' (from model description)\n - '{sample_id}' (extracted from input paths)\n\n \u200a (default: outputs_{model_id}/{output_id}/{sample_id}.tif)\n
\n\n--overwrite bool allow overwriting existing output files (default: False)\n --blockwise bool process inputs blockwise (default: False)\n --stats Path path to dataset statistics\n (will be written if it does not exist,\n but the model requires statistical dataset measures)\n \u200a (default: dataset_statistics.json)\n --preview bool preview which files would be processed\n and what outputs would be generated. (default: False)\n --weight_format {typing.Literal['keras_hdf5','onnx','pytorch_state_dict','tensorflow_js','tensorflow_saved_model_bundle','torchscript'],any}\n The weight format to use. (default: any)\n --example bool generate and run an example
\n\n 1. downloads example model inputs\n 2. creates a `{model_id}_example` folder\n 3. writes input arguments to `{model_id}_example/bioimageio-cli.yaml`\n 4. executes a preview dry-run\n 5. executes prediction with example input\n\n \u200a (default: False)\n
\n </details>\n\n- create an example and run prediction locally!\n\n ```console\n $ bioimageio predict impartial-shrimp --example=True\n ...\n
\n\n<details>\n<summary>(Click to expand output)</summary>\n\n```console\n\ud83d\udec8 bioimageio prediction preview structure:\n{'{sample_id}': {'inputs': {'{input_id}': '<input path>'},\n 'outputs': {'{output_id}': '<output path>'}}}\n\ud83d\udd0e bioimageio prediction preview output:\n{'1': {'inputs': {'input0': 'impartial-shrimp_example/input0/001.tif'},\n 'outputs': {'output0': 'impartial-shrimp_example/outputs/output0/1.tif'}}}\npredict with impartial-shrimp: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 1/1 [00:21<00:00, 21.76s/sample]\n\ud83c\udf89 Sucessfully ran example prediction!\nTo predict the example input using the CLI example config file impartial-shrimp_example\\bioimageio-cli.yaml, execute `bioimageio predict` from impartial-shrimp_example:\n$ cd impartial-shrimp_example\n$ bioimageio predict \"impartial-shrimp\"\n\nAlternatively run the following command in the current workind directory, not the example folder:\n$ bioimageio predict --preview=False --overwrite=True --stats=\"impartial-shrimp_example/dataset_statistics.json\" --inputs=\"[[\\\"impartial-shrimp_example/input0/001.tif\\\"]]\" --outputs=\"impartial-shrimp_example/outputs/{output_id}/{sample_id}.tif\" \"impartial-shrimp\"\n(note that a local 'bioimageio-cli.json' or 'bioimageio-cli.yaml' may interfere with this)\n
\n\n\n </details>\n\n## Installation\n\n### Via Mamba/Conda\n\nThe `bioimageio.core` package can be installed from conda-forge via\n\n```console\nmamba install -c conda-forge bioimageio.core\n```\n\nIf you do not install any additional deep learning libraries, you will only be able to use general convenience\nfunctionality, but not any functionality for model prediction.\nTo install additional deep learning libraries use:\n\n- Pytorch/Torchscript:\n\n CPU installation (if you don't have an nvidia graphics card):\n\n ```console\n mamba install -c pytorch -c conda-forge bioimageio.core pytorch torchvision cpuonly\n
\n\nGPU installation (for cuda 11.6, please choose the appropriate cuda version for your system):
\n\nmamba install -c pytorch -c nvidia -c conda-forge bioimageio.core pytorch torchvision pytorch-cuda=11.8\n
\nNote that the pytorch installation instructions may change in the future. For the latest instructions please refer to pytorch.org.
\n\nTensorflow
\n\nCurrently only CPU version supported
\n\nmamba install -c conda-forge bioimageio.core tensorflow\n
\nONNXRuntime
\n\nCurrently only cpu version supported
\n\nmamba install -c conda-forge bioimageio.core onnxruntime\n
\nThe package is also available via pip\n(e.g. with recommended extras onnx
and pytorch
):
pip install "bioimageio.core[onnx,pytorch]"\n
\nTo set up a development conda environment run the following commands:
\n\nmamba env create -f dev/env.yaml\nmamba activate core\npip install -e . --no-deps\n
\nThere are different environment files available that only install tensorflow or pytorch as dependencies.
\n\nbioimageio.core
installs a command line interface (CLI) for testing models and other functionality.\nYou can list all the available commands via:
bioimageio\n
\nFor convenience the command line options (not arguments) may be given in a bioimageio-cli.json
\nor bioimageio-cli.yaml
file, e.g.:
# bioimageio-cli.yaml\ninputs: inputs/*_{tensor_id}.h5\noutputs: outputs_{model_id}/{sample_id}_{tensor_id}.h5\noverwrite: true\nblockwise: true\nstats: inputs/dataset_statistics.json\n
\nbioimageio.core
is a python package that implements prediction with bioimageio models\nincluding standardized pre- and postprocessing operations.\nThese models are described by---and can be loaded with---the bioimageio.spec package.
In addition bioimageio.core provides functionality to convert model weight formats.
\n\nTo get an overview of this functionality, check out these example notebooks:
\n\n\n\nand the developer documentation.
\n\nbioimageio.spec
and bioimageio.core
use loguru for logging, hence the logging level\nmay be controlled with the LOGURU_LEVEL
environment variable.
The model specification and its validation tools can be found at https://github.com/bioimage-io/spec-bioimage-io.
\n\nValidationDetail.recommended_env
in ValidationSummary
get_io_sample_block_metas()
\nzipfile.ZipFile
object with bioimageio.spec==0.5.3.5resolve
and resolve_and_extract
enable_determinism
function and determinism input argument for testing with seeded\nrandom generators and optionally (determinsim==\"full\") instructing DL frameworks to use\ndeterministic algorithms.predict
commandpath
is now requiredpredict()
argument inputs
may be samplebioimageio validate-format
commandstr(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec._internal.types.LowerCaseIdentifier"}, "bioimageio.core.AxisId.root_model": {"fullname": "bioimageio.core.AxisId.root_model", "modulename": "bioimageio.core", "qualname": "AxisId.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[str, MinLen, AfterValidator, AfterValidator, Annotated[TypeVar, Predicate], MaxLen]]'>"}, "bioimageio.core.BlockMeta": {"fullname": "bioimageio.core.BlockMeta", "modulename": "bioimageio.core", "qualname": "BlockMeta", "kind": "class", "doc": "Block meta data of a sample member (a tensor in a sample)
\n\nFigure for illustration:\nThe first 2d block (dashed) of a sample member (bold).\nThe inner slice (thin) is expanded by a halo in both dimensions on both sides.\nThe outer slice reaches from the sample member origin (0, 0) to the right halo point.
\n\n\u250c \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2510\n\u2577 halo(left) \u2577\n\u2577 \u2577\n\u2577 (0, 0)\u250f\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u252f\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u252f\u2501\u2501\u2501\u2794\n\u2577 \u2503 \u2502 \u2577 sample member\n\u2577 \u2503 inner \u2502 \u2577\n\u2577 \u2503 (and outer) \u2502 outer \u2577\n\u2577 \u2503 slice \u2502 slice \u2577\n\u2577 \u2503 \u2502 \u2577\n\u2577 \u2523\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518 \u2577\n\u2577 \u2503 outer slice \u2577\n\u2577 \u2503 halo(right) \u2577\n\u2514 \u2500 \u2500 \u2500 \u2500\u2503\u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500\u2518\n \u2b07\n
\n\nnote:
\n\nthe axis sizes of the whole (unblocked) sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.BlockMeta.inner_slice": {"fullname": "bioimageio.core.BlockMeta.inner_slice", "modulename": "bioimageio.core", "qualname": "BlockMeta.inner_slice", "kind": "variable", "doc": "inner region (without halo) wrt the sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.SliceInfo]"}, "bioimageio.core.BlockMeta.halo": {"fullname": "bioimageio.core.BlockMeta.halo", "modulename": "bioimageio.core", "qualname": "BlockMeta.halo", "kind": "variable", "doc": "halo enlarging the inner region to the block's sizes
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.Halo]"}, "bioimageio.core.BlockMeta.block_index": {"fullname": "bioimageio.core.BlockMeta.block_index", "modulename": "bioimageio.core", "qualname": "BlockMeta.block_index", "kind": "variable", "doc": "the i-th block of the sample
\n", "annotation": ": int"}, "bioimageio.core.BlockMeta.blocks_in_sample": {"fullname": "bioimageio.core.BlockMeta.blocks_in_sample", "modulename": "bioimageio.core", "qualname": "BlockMeta.blocks_in_sample", "kind": "variable", "doc": "total number of blocks in the sample
\n", "annotation": ": int"}, "bioimageio.core.BlockMeta.shape": {"fullname": "bioimageio.core.BlockMeta.shape", "modulename": "bioimageio.core", "qualname": "BlockMeta.shape", "kind": "variable", "doc": "axis lengths of the block
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.BlockMeta.padding": {"fullname": "bioimageio.core.BlockMeta.padding", "modulename": "bioimageio.core", "qualname": "BlockMeta.padding", "kind": "variable", "doc": "padding to realize the halo at the sample edge\nwhere we cannot simply enlarge the inner slice
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.PadWidth]"}, "bioimageio.core.BlockMeta.outer_slice": {"fullname": "bioimageio.core.BlockMeta.outer_slice", "modulename": "bioimageio.core", "qualname": "BlockMeta.outer_slice", "kind": "variable", "doc": "slice of the outer block (without padding) wrt the sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.SliceInfo]"}, "bioimageio.core.BlockMeta.inner_shape": {"fullname": "bioimageio.core.BlockMeta.inner_shape", "modulename": "bioimageio.core", "qualname": "BlockMeta.inner_shape", "kind": "variable", "doc": "axis lengths of the inner region (without halo)
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.BlockMeta.local_slice": {"fullname": "bioimageio.core.BlockMeta.local_slice", "modulename": "bioimageio.core", "qualname": "BlockMeta.local_slice", "kind": "variable", "doc": "inner slice wrt the block, not the sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.SliceInfo]"}, "bioimageio.core.BlockMeta.dims": {"fullname": "bioimageio.core.BlockMeta.dims", "modulename": "bioimageio.core", "qualname": "BlockMeta.dims", "kind": "variable", "doc": "\n", "annotation": ": Collection[bioimageio.spec.model.v0_5.AxisId]"}, "bioimageio.core.BlockMeta.tagged_shape": {"fullname": "bioimageio.core.BlockMeta.tagged_shape", "modulename": "bioimageio.core", "qualname": "BlockMeta.tagged_shape", "kind": "variable", "doc": "alias for shape
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.BlockMeta.inner_slice_wo_overlap": {"fullname": "bioimageio.core.BlockMeta.inner_slice_wo_overlap", "modulename": "bioimageio.core", "qualname": "BlockMeta.inner_slice_wo_overlap", "kind": "variable", "doc": "subslice of the inner slice, such that all inner_slice_wo_overlap
can be\nstiched together trivially to form the original sample.
This can also be used to calculate statistics\nwithout overrepresenting block edge regions.
\n"}, "bioimageio.core.BlockMeta.get_transformed": {"fullname": "bioimageio.core.BlockMeta.get_transformed", "modulename": "bioimageio.core", "qualname": "BlockMeta.get_transformed", "kind": "function", "doc": "\n", "signature": "(\tself,\tnew_axes: Mapping[bioimageio.spec.model.v0_5.AxisId, Union[bioimageio.core.block_meta.LinearAxisTransform, int]]) -> Self:", "funcdef": "def"}, "bioimageio.core.build_description": {"fullname": "bioimageio.core.build_description", "modulename": "bioimageio.core", "qualname": "build_description", "kind": "function", "doc": "build a bioimage.io resource description from an RDF's content.
\n\nUse load_description
if you want to build a resource description from an rdf.yaml\nor bioimage.io zip-package.
\n\n", "signature": "(\tcontent: Dict[str, YamlValue],\t/,\t*,\tcontext: Optional[bioimageio.spec._internal.validation_context.ValidationContext] = None,\tformat_version: Union[Literal['latest', 'discover'], str] = 'discover') -> Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec._internal.common_nodes.InvalidDescr]:", "funcdef": "def"}, "bioimageio.core.compute_dataset_measures": {"fullname": "bioimageio.core.compute_dataset_measures", "modulename": "bioimageio.core", "qualname": "compute_dataset_measures", "kind": "function", "doc": "An object holding all metadata of the bioimage.io resource
\n
compute all dataset measures
for the given dataset
Creates prediction pipeline which includes:
\n\nConverts a resource to a dictionary containing only simple types that can directly be serialzed to YAML.
\n", "signature": "(\trd: Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec._internal.common_nodes.InvalidDescr],\texclude_unset: bool = True) -> Dict[str, YamlValue]:", "funcdef": "def"}, "bioimageio.core.enable_determinism": {"fullname": "bioimageio.core.enable_determinism", "modulename": "bioimageio.core", "qualname": "enable_determinism", "kind": "function", "doc": "Seed and configure ML frameworks for maximum reproducibility.\nMay degrade performance. Only recommended for testing reproducibility!
\n\nSeed any random generators and (if mode==\"full\") request ML frameworks to use\ndeterministic algorithms.
\n\n\n \n\n", "signature": "(mode: Literal['seed_only', 'full']):", "funcdef": "def"}, "bioimageio.core.load_dataset_description": {"fullname": "bioimageio.core.load_dataset_description", "modulename": "bioimageio.core", "qualname": "load_dataset_description", "kind": "function", "doc": "
same as load_description
, but addtionally ensures that the loaded\ndescription is valid and of type 'dataset'.
Test RDF dynamically, e.g. model inference of test inputs
\n", "signature": "(\tsource: Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], Dict[str, YamlValue]],\t*,\tformat_version: Union[Literal['discover', 'latest'], str] = 'discover',\tweight_format: Optional[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']] = None,\tdevices: Optional[Sequence[str]] = None,\tabsolute_tolerance: float = 0.00015,\trelative_tolerance: float = 0.0001,\tdecimal: Optional[int] = None,\tdeterminism: Literal['seed_only', 'full'] = 'seed_only',\texpected_type: Optional[str] = None) -> Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec._internal.common_nodes.InvalidDescr]:", "funcdef": "def"}, "bioimageio.core.load_description_and_validate_format_only": {"fullname": "bioimageio.core.load_description_and_validate_format_only", "modulename": "bioimageio.core", "qualname": "load_description_and_validate_format_only", "kind": "function", "doc": "load a bioimage.io resource description
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], zipfile.ZipFile],\t/,\t*,\tformat_version: Union[Literal['discover'], Literal['latest'], str] = 'discover',\tperform_io_checks: bool = True,\tknown_files: Optional[Dict[str, bioimageio.spec._internal.io_basics.Sha256]] = None) -> bioimageio.spec.summary.ValidationSummary:", "funcdef": "def"}, "bioimageio.core.load_description": {"fullname": "bioimageio.core.load_description", "modulename": "bioimageio.core", "qualname": "load_description", "kind": "function", "doc": "Validation summary of the bioimage.io resource found at
\nsource
.
load a bioimage.io resource description
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], zipfile.ZipFile],\t/,\t*,\tformat_version: Union[Literal['discover'], Literal['latest'], str] = 'discover',\tperform_io_checks: bool = True,\tknown_files: Optional[Dict[str, bioimageio.spec._internal.io_basics.Sha256]] = None) -> Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec._internal.common_nodes.InvalidDescr]:", "funcdef": "def"}, "bioimageio.core.load_model_description": {"fullname": "bioimageio.core.load_model_description", "modulename": "bioimageio.core", "qualname": "load_model_description", "kind": "function", "doc": "An object holding all metadata of the bioimage.io resource
\n
same as load_description
, but addtionally ensures that the loaded\ndescription is valid and of type 'model'.
alias of load_model_description
alias of load_description
Run prediction for a multiple sets of inputs with a bioimage.io model
\n\n{i}
will be formatted as the i-th sample.\nIf {i}
(or {i:
) is not present and inputs
is an iterable {i:03}
is appended.{member_id}
{sample_id}
in it\nto save the output to.Run prediction for a single set of input(s) with a bioimage.io model
\n\ninput_block_shape
blocksize_parameter
.{member_id}
{sample_id}
in it\nto save the output to.Represents model computation including preprocessing and postprocessing\nNote: Ideally use the PredictionPipeline as a context manager
\n"}, "bioimageio.core.PredictionPipeline.__init__": {"fullname": "bioimageio.core.PredictionPipeline.__init__", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.__init__", "kind": "function", "doc": "\n", "signature": "(\t*,\tname: str,\tmodel_description: Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)],\tpreprocessing: List[Union[bioimageio.core.proc_ops.AddKnownDatasetStats, bioimageio.core.proc_ops.Binarize, bioimageio.core.proc_ops.Clip, bioimageio.core.proc_ops.EnsureDtype, bioimageio.core.proc_ops.FixedZeroMeanUnitVariance, bioimageio.core.proc_ops.ScaleLinear, bioimageio.core.proc_ops.ScaleMeanVariance, bioimageio.core.proc_ops.ScaleRange, bioimageio.core.proc_ops.Sigmoid, bioimageio.core.proc_ops.UpdateStats, bioimageio.core.proc_ops.ZeroMeanUnitVariance]],\tpostprocessing: List[Union[bioimageio.core.proc_ops.AddKnownDatasetStats, bioimageio.core.proc_ops.Binarize, bioimageio.core.proc_ops.Clip, bioimageio.core.proc_ops.EnsureDtype, bioimageio.core.proc_ops.FixedZeroMeanUnitVariance, bioimageio.core.proc_ops.ScaleLinear, bioimageio.core.proc_ops.ScaleMeanVariance, bioimageio.core.proc_ops.ScaleRange, bioimageio.core.proc_ops.Sigmoid, bioimageio.core.proc_ops.UpdateStats, bioimageio.core.proc_ops.ZeroMeanUnitVariance]],\tmodel_adapter: bioimageio.core.model_adapters._model_adapter.ModelAdapter,\tdefault_ns: Union[int, Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int]] = 10,\tdefault_batch_size: int = 1)"}, "bioimageio.core.PredictionPipeline.name": {"fullname": "bioimageio.core.PredictionPipeline.name", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.name", "kind": "variable", "doc": "\n"}, "bioimageio.core.PredictionPipeline.model_description": {"fullname": "bioimageio.core.PredictionPipeline.model_description", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.model_description", "kind": "variable", "doc": "\n"}, "bioimageio.core.PredictionPipeline.predict_sample_block": {"fullname": "bioimageio.core.PredictionPipeline.predict_sample_block", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.predict_sample_block", "kind": "function", "doc": "\n", "signature": "(\tself,\tsample_block: bioimageio.core.sample.SampleBlockWithOrigin,\tskip_preprocessing: bool = False,\tskip_postprocessing: bool = False) -> bioimageio.core.sample.SampleBlock:", "funcdef": "def"}, "bioimageio.core.PredictionPipeline.predict_sample_without_blocking": {"fullname": "bioimageio.core.PredictionPipeline.predict_sample_without_blocking", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.predict_sample_without_blocking", "kind": "function", "doc": "predict a sample.\nThe sample's tensor shapes have to match the model's input tensor description.\nIf that is not the case, consider predict_sample_with_blocking
predict a sample by splitting it into blocks according to the model and the ns
parameter
apply preprocessing in-place, also updates sample stats
\n", "signature": "(\tself,\tsample: Union[bioimageio.core.sample.Sample, bioimageio.core.sample.SampleBlockWithOrigin]) -> None:", "funcdef": "def"}, "bioimageio.core.PredictionPipeline.apply_postprocessing": {"fullname": "bioimageio.core.PredictionPipeline.apply_postprocessing", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.apply_postprocessing", "kind": "function", "doc": "apply postprocessing in-place, also updates samples stats
\n", "signature": "(\tself,\tsample: Union[bioimageio.core.sample.Sample, bioimageio.core.sample.SampleBlock, bioimageio.core.sample.SampleBlockWithOrigin]) -> None:", "funcdef": "def"}, "bioimageio.core.PredictionPipeline.load": {"fullname": "bioimageio.core.PredictionPipeline.load", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.load", "kind": "function", "doc": "optional step: load model onto devices before calling forward if not using it as context manager
\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.PredictionPipeline.unload": {"fullname": "bioimageio.core.PredictionPipeline.unload", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.unload", "kind": "function", "doc": "free any device memory in use
\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.Sample": {"fullname": "bioimageio.core.Sample", "modulename": "bioimageio.core", "qualname": "Sample", "kind": "class", "doc": "A dataset sample
\n"}, "bioimageio.core.Sample.__init__": {"fullname": "bioimageio.core.Sample.__init__", "modulename": "bioimageio.core", "qualname": "Sample.__init__", "kind": "function", "doc": "\n", "signature": "(\tmembers: Dict[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.tensor.Tensor],\tstat: Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer>, return_type=PydanticUndefined, when_used='always')]]],\tid: Hashable)"}, "bioimageio.core.Sample.members": {"fullname": "bioimageio.core.Sample.members", "modulename": "bioimageio.core", "qualname": "Sample.members", "kind": "variable", "doc": "the sample's tensors
\n", "annotation": ": Dict[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.tensor.Tensor]"}, "bioimageio.core.Sample.stat": {"fullname": "bioimageio.core.Sample.stat", "modulename": "bioimageio.core", "qualname": "Sample.stat", "kind": "variable", "doc": "sample and dataset statistics
\n", "annotation": ": Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]"}, "bioimageio.core.Sample.id": {"fullname": "bioimageio.core.Sample.id", "modulename": "bioimageio.core", "qualname": "Sample.id", "kind": "variable", "doc": "identifier within the sample's dataset
\n", "annotation": ": Hashable"}, "bioimageio.core.Sample.shape": {"fullname": "bioimageio.core.Sample.shape", "modulename": "bioimageio.core", "qualname": "Sample.shape", "kind": "variable", "doc": "\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]"}, "bioimageio.core.Sample.split_into_blocks": {"fullname": "bioimageio.core.Sample.split_into_blocks", "modulename": "bioimageio.core", "qualname": "Sample.split_into_blocks", "kind": "function", "doc": "\n", "signature": "(\tself,\tblock_shapes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\thalo: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, Union[int, Tuple[int, int], bioimageio.core.common.Halo]]],\tpad_mode: Literal['edge', 'reflect', 'symmetric'],\tbroadcast: bool = False) -> Tuple[int, Iterable[bioimageio.core.sample.SampleBlockWithOrigin]]:", "funcdef": "def"}, "bioimageio.core.Sample.as_single_block": {"fullname": "bioimageio.core.Sample.as_single_block", "modulename": "bioimageio.core", "qualname": "Sample.as_single_block", "kind": "function", "doc": "\n", "signature": "(\tself,\thalo: Optional[Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.Halo]]] = None):", "funcdef": "def"}, "bioimageio.core.Sample.from_blocks": {"fullname": "bioimageio.core.Sample.from_blocks", "modulename": "bioimageio.core", "qualname": "Sample.from_blocks", "kind": "function", "doc": "\n", "signature": "(\tcls,\tsample_blocks: Iterable[bioimageio.core.sample.SampleBlock],\t*,\tfill_value: float = nan) -> Self:", "funcdef": "def"}, "bioimageio.core.save_bioimageio_package_as_folder": {"fullname": "bioimageio.core.save_bioimageio_package_as_folder", "modulename": "bioimageio.core", "qualname": "save_bioimageio_package_as_folder", "kind": "function", "doc": "Write the content of a bioimage.io resource package to a folder.
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], Dict[str, YamlValue], Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\t/,\t*,\toutput_path: Union[Annotated[pathlib.Path, PathType(path_type='new')], Annotated[pathlib.Path, PathType(path_type='dir')], NoneType] = None,\tweights_priority_order: Optional[Sequence[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]] = None) -> Annotated[pathlib.Path, PathType(path_type='dir')]:", "funcdef": "def"}, "bioimageio.core.save_bioimageio_package": {"fullname": "bioimageio.core.save_bioimageio_package", "modulename": "bioimageio.core", "qualname": "save_bioimageio_package", "kind": "function", "doc": "directory path to bioimageio package folder
\n
Package a bioimageio resource as a zip file.
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], Dict[str, YamlValue], Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\t/,\t*,\tcompression: int = 8,\tcompression_level: int = 1,\toutput_path: Union[Annotated[pathlib.Path, PathType(path_type='new')], Annotated[pathlib.Path, PathType(path_type='file')], NoneType] = None,\tweights_priority_order: Optional[Sequence[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]] = None) -> Annotated[pathlib.Path, PathType(path_type='file')]:", "funcdef": "def"}, "bioimageio.core.save_bioimageio_yaml_only": {"fullname": "bioimageio.core.save_bioimageio_yaml_only", "modulename": "bioimageio.core", "qualname": "save_bioimageio_yaml_only", "kind": "function", "doc": "path to zipped bioimageio package
\n
write the metadata of a resource description (rd
) to file
\nwithout writing any of the referenced files in it.
Note: To save a resource description with its associated files as a package,\nuse save_bioimageio_package
or save_bioimageio_package_as_folder
.
A wrapper around an xr.DataArray for better integration with bioimageio.spec\nand improved type annotations.
\n", "bases": "bioimageio.core._magic_tensor_ops.MagicTensorOpsMixin"}, "bioimageio.core.Tensor.__init__": {"fullname": "bioimageio.core.Tensor.__init__", "modulename": "bioimageio.core", "qualname": "Tensor.__init__", "kind": "function", "doc": "\n", "signature": "(\tarray: numpy.ndarray[typing.Any, numpy.dtype[typing.Any]],\tdims: Sequence[Union[bioimageio.spec.model.v0_5.AxisId, Literal['b', 'i', 't', 'c', 'z', 'y', 'x'], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexInputAxis, bioimageio.spec.model.v0_5.TimeInputAxis, bioimageio.spec.model.v0_5.SpaceInputAxis], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexOutputAxis, Annotated[Union[Annotated[bioimageio.spec.model.v0_5.TimeOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.core.axis.Axis]])"}, "bioimageio.core.Tensor.from_xarray": {"fullname": "bioimageio.core.Tensor.from_xarray", "modulename": "bioimageio.core", "qualname": "Tensor.from_xarray", "kind": "function", "doc": "create a Tensor
from an xarray data array
note for internal use: this factory method is round-trip save\n for any Tensor
's data
property (an xarray.DataArray).
create a Tensor
from a numpy array
axes
is None and axes guessing fails.Tuple of dimension names associated with this tensor.
\n"}, "bioimageio.core.Tensor.tagged_shape": {"fullname": "bioimageio.core.Tensor.tagged_shape", "modulename": "bioimageio.core", "qualname": "Tensor.tagged_shape", "kind": "variable", "doc": "(alias for sizes
) Ordered, immutable mapping from axis ids to lengths.
Tuple of tensor axes lengths
\n"}, "bioimageio.core.Tensor.size": {"fullname": "bioimageio.core.Tensor.size", "modulename": "bioimageio.core", "qualname": "Tensor.size", "kind": "variable", "doc": "Number of elements in the tensor.
\n\nEqual to math.prod(tensor.shape), i.e., the product of the tensors\u2019 dimensions.
\n"}, "bioimageio.core.Tensor.sum": {"fullname": "bioimageio.core.Tensor.sum", "modulename": "bioimageio.core", "qualname": "Tensor.sum", "kind": "function", "doc": "Reduce this Tensor's data by applying sum along some dimension(s).
\n", "signature": "(\tself,\tdim: Union[bioimageio.spec.model.v0_5.AxisId, Sequence[bioimageio.spec.model.v0_5.AxisId], NoneType] = None) -> Self:", "funcdef": "def"}, "bioimageio.core.Tensor.ndim": {"fullname": "bioimageio.core.Tensor.ndim", "modulename": "bioimageio.core", "qualname": "Tensor.ndim", "kind": "variable", "doc": "Number of tensor dimensions.
\n"}, "bioimageio.core.Tensor.dtype": {"fullname": "bioimageio.core.Tensor.dtype", "modulename": "bioimageio.core", "qualname": "Tensor.dtype", "kind": "variable", "doc": "\n", "annotation": ": Literal['bool', 'float32', 'float64', 'int8', 'int16', 'int32', 'int64', 'uint8', 'uint16', 'uint32', 'uint64']"}, "bioimageio.core.Tensor.sizes": {"fullname": "bioimageio.core.Tensor.sizes", "modulename": "bioimageio.core", "qualname": "Tensor.sizes", "kind": "variable", "doc": "Ordered, immutable mapping from axis ids to axis lengths.
\n"}, "bioimageio.core.Tensor.astype": {"fullname": "bioimageio.core.Tensor.astype", "modulename": "bioimageio.core", "qualname": "Tensor.astype", "kind": "function", "doc": "Return tensor cast to dtype
note: if dtype is already satisfied copy if copy
Return a tensor whose values are limited to [min, max].\nAt least one of max or min must be given.
\n", "signature": "(self, min: Optional[float] = None, max: Optional[float] = None):", "funcdef": "def"}, "bioimageio.core.Tensor.crop_to": {"fullname": "bioimageio.core.Tensor.crop_to", "modulename": "bioimageio.core", "qualname": "Tensor.crop_to", "kind": "function", "doc": "crop to match sizes
pad tensor
to match sizes
return cropped/padded tensor with sizes
return a transposed tensor
\n\nTest a bioimage.io resource dynamically, e.g. prediction of test tensors for models
\n", "signature": "(\tsource: Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], Dict[str, YamlValue]],\t*,\tformat_version: Union[Literal['discover', 'latest'], str] = 'discover',\tweight_format: Optional[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']] = None,\tdevices: Optional[Sequence[str]] = None,\tabsolute_tolerance: float = 0.00015,\trelative_tolerance: float = 0.0001,\tdecimal: Optional[int] = None,\tdeterminism: Literal['seed_only', 'full'] = 'seed_only',\texpected_type: Optional[str] = None) -> bioimageio.spec.summary.ValidationSummary:", "funcdef": "def"}, "bioimageio.core.test_model": {"fullname": "bioimageio.core.test_model", "modulename": "bioimageio.core", "qualname": "test_model", "kind": "function", "doc": "Test model inference
\n", "signature": "(\tsource: Union[bioimageio.spec.model.v0_5.ModelDescr, Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)]],\tweight_format: Optional[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']] = None,\tdevices: Optional[List[str]] = None,\tabsolute_tolerance: float = 0.00015,\trelative_tolerance: float = 0.0001,\tdecimal: Optional[int] = None,\t*,\tdeterminism: Literal['seed_only', 'full'] = 'seed_only') -> bioimageio.spec.summary.ValidationSummary:", "funcdef": "def"}, "bioimageio.core.test_resource": {"fullname": "bioimageio.core.test_resource", "modulename": "bioimageio.core", "qualname": "test_resource", "kind": "function", "doc": "alias of test_description
validate a bioimageio.yaml file (RDF)
\n", "signature": "(\tdata: Dict[str, YamlValue],\t/,\t*,\tformat_version: Union[Literal['latest', 'discover'], str] = 'discover',\tcontext: Optional[bioimageio.spec._internal.validation_context.ValidationContext] = None) -> bioimageio.spec.summary.ValidationSummary:", "funcdef": "def"}, "bioimageio.core.axis": {"fullname": "bioimageio.core.axis", "modulename": "bioimageio.core.axis", "kind": "module", "doc": "\n"}, "bioimageio.core.axis.AxisId": {"fullname": "bioimageio.core.axis.AxisId", "modulename": "bioimageio.core.axis", "qualname": "AxisId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec._internal.types.LowerCaseIdentifier"}, "bioimageio.core.axis.AxisId.root_model": {"fullname": "bioimageio.core.axis.AxisId.root_model", "modulename": "bioimageio.core.axis", "qualname": "AxisId.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[str, MinLen, AfterValidator, AfterValidator, Annotated[TypeVar, Predicate], MaxLen]]'>"}, "bioimageio.core.axis.PerAxis": {"fullname": "bioimageio.core.axis.PerAxis", "modulename": "bioimageio.core.axis", "qualname": "PerAxis", "kind": "variable", "doc": "\n", "default_value": "typing.Mapping[bioimageio.spec.model.v0_5.AxisId, ~T]"}, "bioimageio.core.axis.BatchSize": {"fullname": "bioimageio.core.axis.BatchSize", "modulename": "bioimageio.core.axis", "qualname": "BatchSize", "kind": "variable", "doc": "\n", "default_value": "<class 'int'>"}, "bioimageio.core.axis.AxisLetter": {"fullname": "bioimageio.core.axis.AxisLetter", "modulename": "bioimageio.core.axis", "qualname": "AxisLetter", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['b', 'i', 't', 'c', 'z', 'y', 'x']"}, "bioimageio.core.axis.AxisLike": {"fullname": "bioimageio.core.axis.AxisLike", "modulename": "bioimageio.core.axis", "qualname": "AxisLike", "kind": "variable", "doc": "\n", "default_value": "typing.Union[bioimageio.spec.model.v0_5.AxisId, typing.Literal['b', 'i', 't', 'c', 'z', 'y', 'x'], typing.Annotated[typing.Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexInputAxis, bioimageio.spec.model.v0_5.TimeInputAxis, bioimageio.spec.model.v0_5.SpaceInputAxis], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexOutputAxis, typing.Annotated[typing.Union[typing.Annotated[bioimageio.spec.model.v0_5.TimeOutputAxis, Tag(tag='wo_halo')], typing.Annotated[bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[typing.Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxis, Tag(tag='wo_halo')], typing.Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], ForwardRef('Axis')]"}, "bioimageio.core.axis.Axis": {"fullname": "bioimageio.core.axis.Axis", "modulename": "bioimageio.core.axis", "qualname": "Axis", "kind": "class", "doc": "\n"}, "bioimageio.core.axis.Axis.__init__": {"fullname": "bioimageio.core.axis.Axis.__init__", "modulename": "bioimageio.core.axis", "qualname": "Axis.__init__", "kind": "function", "doc": "\n", "signature": "(\tid: bioimageio.spec.model.v0_5.AxisId,\ttype: Literal['batch', 'channel', 'index', 'space', 'time'])"}, "bioimageio.core.axis.Axis.id": {"fullname": "bioimageio.core.axis.Axis.id", "modulename": "bioimageio.core.axis", "qualname": "Axis.id", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_5.AxisId"}, "bioimageio.core.axis.Axis.type": {"fullname": "bioimageio.core.axis.Axis.type", "modulename": "bioimageio.core.axis", "qualname": "Axis.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['batch', 'channel', 'index', 'space', 'time']"}, "bioimageio.core.axis.Axis.create": {"fullname": "bioimageio.core.axis.Axis.create", "modulename": "bioimageio.core.axis", "qualname": "Axis.create", "kind": "function", "doc": "\n", "signature": "(\tcls,\taxis: Union[bioimageio.spec.model.v0_5.AxisId, Literal['b', 'i', 't', 'c', 'z', 'y', 'x'], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexInputAxis, bioimageio.spec.model.v0_5.TimeInputAxis, bioimageio.spec.model.v0_5.SpaceInputAxis], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexOutputAxis, Annotated[Union[Annotated[bioimageio.spec.model.v0_5.TimeOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.core.axis.Axis]) -> bioimageio.core.axis.Axis:", "funcdef": "def"}, "bioimageio.core.axis.AxisInfo": {"fullname": "bioimageio.core.axis.AxisInfo", "modulename": "bioimageio.core.axis", "qualname": "AxisInfo", "kind": "class", "doc": "\n", "bases": "Axis"}, "bioimageio.core.axis.AxisInfo.__init__": {"fullname": "bioimageio.core.axis.AxisInfo.__init__", "modulename": "bioimageio.core.axis", "qualname": "AxisInfo.__init__", "kind": "function", "doc": "\n", "signature": "(\tid: bioimageio.spec.model.v0_5.AxisId,\ttype: Literal['batch', 'channel', 'index', 'space', 'time'],\tmaybe_singleton: bool)"}, "bioimageio.core.axis.AxisInfo.maybe_singleton": {"fullname": "bioimageio.core.axis.AxisInfo.maybe_singleton", "modulename": "bioimageio.core.axis", "qualname": "AxisInfo.maybe_singleton", "kind": "variable", "doc": "\n", "annotation": ": bool"}, "bioimageio.core.axis.AxisInfo.create": {"fullname": "bioimageio.core.axis.AxisInfo.create", "modulename": "bioimageio.core.axis", "qualname": "AxisInfo.create", "kind": "function", "doc": "\n", "signature": "(\tcls,\taxis: Union[bioimageio.spec.model.v0_5.AxisId, Literal['b', 'i', 't', 'c', 'z', 'y', 'x'], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexInputAxis, bioimageio.spec.model.v0_5.TimeInputAxis, bioimageio.spec.model.v0_5.SpaceInputAxis], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexOutputAxis, Annotated[Union[Annotated[bioimageio.spec.model.v0_5.TimeOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.core.axis.Axis],\tmaybe_singleton: Optional[bool] = None) -> bioimageio.core.axis.AxisInfo:", "funcdef": "def"}, "bioimageio.core.block_meta": {"fullname": "bioimageio.core.block_meta", "modulename": "bioimageio.core.block_meta", "kind": "module", "doc": "\n"}, "bioimageio.core.block_meta.LinearAxisTransform": {"fullname": "bioimageio.core.block_meta.LinearAxisTransform", "modulename": "bioimageio.core.block_meta", "qualname": "LinearAxisTransform", "kind": "class", "doc": "\n"}, "bioimageio.core.block_meta.LinearAxisTransform.__init__": {"fullname": "bioimageio.core.block_meta.LinearAxisTransform.__init__", "modulename": "bioimageio.core.block_meta", "qualname": "LinearAxisTransform.__init__", "kind": "function", "doc": "\n", "signature": "(axis: bioimageio.spec.model.v0_5.AxisId, scale: float, offset: int)"}, "bioimageio.core.block_meta.LinearAxisTransform.axis": {"fullname": "bioimageio.core.block_meta.LinearAxisTransform.axis", "modulename": "bioimageio.core.block_meta", "qualname": "LinearAxisTransform.axis", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_5.AxisId"}, "bioimageio.core.block_meta.LinearAxisTransform.scale": {"fullname": "bioimageio.core.block_meta.LinearAxisTransform.scale", "modulename": "bioimageio.core.block_meta", "qualname": "LinearAxisTransform.scale", "kind": "variable", "doc": "\n", "annotation": ": float"}, "bioimageio.core.block_meta.LinearAxisTransform.offset": {"fullname": "bioimageio.core.block_meta.LinearAxisTransform.offset", "modulename": "bioimageio.core.block_meta", "qualname": "LinearAxisTransform.offset", "kind": "variable", "doc": "\n", "annotation": ": int"}, "bioimageio.core.block_meta.LinearAxisTransform.compute": {"fullname": "bioimageio.core.block_meta.LinearAxisTransform.compute", "modulename": "bioimageio.core.block_meta", "qualname": "LinearAxisTransform.compute", "kind": "function", "doc": "\n", "signature": "(\tself,\ts: int,\tround: Callable[[float], int] = <built-in function floor>) -> int:", "funcdef": "def"}, "bioimageio.core.block_meta.BlockMeta": {"fullname": "bioimageio.core.block_meta.BlockMeta", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta", "kind": "class", "doc": "Block meta data of a sample member (a tensor in a sample)
\n\nFigure for illustration:\nThe first 2d block (dashed) of a sample member (bold).\nThe inner slice (thin) is expanded by a halo in both dimensions on both sides.\nThe outer slice reaches from the sample member origin (0, 0) to the right halo point.
\n\n\u250c \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2510\n\u2577 halo(left) \u2577\n\u2577 \u2577\n\u2577 (0, 0)\u250f\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u252f\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u252f\u2501\u2501\u2501\u2794\n\u2577 \u2503 \u2502 \u2577 sample member\n\u2577 \u2503 inner \u2502 \u2577\n\u2577 \u2503 (and outer) \u2502 outer \u2577\n\u2577 \u2503 slice \u2502 slice \u2577\n\u2577 \u2503 \u2502 \u2577\n\u2577 \u2523\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518 \u2577\n\u2577 \u2503 outer slice \u2577\n\u2577 \u2503 halo(right) \u2577\n\u2514 \u2500 \u2500 \u2500 \u2500\u2503\u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500\u2518\n \u2b07\n
\n\nnote:
\n\nthe axis sizes of the whole (unblocked) sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.block_meta.BlockMeta.inner_slice": {"fullname": "bioimageio.core.block_meta.BlockMeta.inner_slice", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.inner_slice", "kind": "variable", "doc": "inner region (without halo) wrt the sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.SliceInfo]"}, "bioimageio.core.block_meta.BlockMeta.halo": {"fullname": "bioimageio.core.block_meta.BlockMeta.halo", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.halo", "kind": "variable", "doc": "halo enlarging the inner region to the block's sizes
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.Halo]"}, "bioimageio.core.block_meta.BlockMeta.block_index": {"fullname": "bioimageio.core.block_meta.BlockMeta.block_index", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.block_index", "kind": "variable", "doc": "the i-th block of the sample
\n", "annotation": ": int"}, "bioimageio.core.block_meta.BlockMeta.blocks_in_sample": {"fullname": "bioimageio.core.block_meta.BlockMeta.blocks_in_sample", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.blocks_in_sample", "kind": "variable", "doc": "total number of blocks in the sample
\n", "annotation": ": int"}, "bioimageio.core.block_meta.BlockMeta.shape": {"fullname": "bioimageio.core.block_meta.BlockMeta.shape", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.shape", "kind": "variable", "doc": "axis lengths of the block
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.block_meta.BlockMeta.padding": {"fullname": "bioimageio.core.block_meta.BlockMeta.padding", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.padding", "kind": "variable", "doc": "padding to realize the halo at the sample edge\nwhere we cannot simply enlarge the inner slice
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.PadWidth]"}, "bioimageio.core.block_meta.BlockMeta.outer_slice": {"fullname": "bioimageio.core.block_meta.BlockMeta.outer_slice", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.outer_slice", "kind": "variable", "doc": "slice of the outer block (without padding) wrt the sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.SliceInfo]"}, "bioimageio.core.block_meta.BlockMeta.inner_shape": {"fullname": "bioimageio.core.block_meta.BlockMeta.inner_shape", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.inner_shape", "kind": "variable", "doc": "axis lengths of the inner region (without halo)
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.block_meta.BlockMeta.local_slice": {"fullname": "bioimageio.core.block_meta.BlockMeta.local_slice", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.local_slice", "kind": "variable", "doc": "inner slice wrt the block, not the sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.SliceInfo]"}, "bioimageio.core.block_meta.BlockMeta.dims": {"fullname": "bioimageio.core.block_meta.BlockMeta.dims", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.dims", "kind": "variable", "doc": "\n", "annotation": ": Collection[bioimageio.spec.model.v0_5.AxisId]"}, "bioimageio.core.block_meta.BlockMeta.tagged_shape": {"fullname": "bioimageio.core.block_meta.BlockMeta.tagged_shape", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.tagged_shape", "kind": "variable", "doc": "alias for shape
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.block_meta.BlockMeta.inner_slice_wo_overlap": {"fullname": "bioimageio.core.block_meta.BlockMeta.inner_slice_wo_overlap", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.inner_slice_wo_overlap", "kind": "variable", "doc": "subslice of the inner slice, such that all inner_slice_wo_overlap
can be\nstiched together trivially to form the original sample.
This can also be used to calculate statistics\nwithout overrepresenting block edge regions.
\n"}, "bioimageio.core.block_meta.BlockMeta.get_transformed": {"fullname": "bioimageio.core.block_meta.BlockMeta.get_transformed", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.get_transformed", "kind": "function", "doc": "\n", "signature": "(\tself,\tnew_axes: Mapping[bioimageio.spec.model.v0_5.AxisId, Union[bioimageio.core.block_meta.LinearAxisTransform, int]]) -> Self:", "funcdef": "def"}, "bioimageio.core.block_meta.split_shape_into_blocks": {"fullname": "bioimageio.core.block_meta.split_shape_into_blocks", "modulename": "bioimageio.core.block_meta", "qualname": "split_shape_into_blocks", "kind": "function", "doc": "\n", "signature": "(\tshape: Mapping[bioimageio.spec.model.v0_5.AxisId, int],\tblock_shape: Mapping[bioimageio.spec.model.v0_5.AxisId, int],\thalo: Mapping[bioimageio.spec.model.v0_5.AxisId, Union[int, Tuple[int, int], bioimageio.core.common.Halo]],\tstride: Optional[Mapping[bioimageio.spec.model.v0_5.AxisId, int]] = None) -> Tuple[int, Generator[bioimageio.core.block_meta.BlockMeta, Any, NoneType]]:", "funcdef": "def"}, "bioimageio.core.block_meta.split_multiple_shapes_into_blocks": {"fullname": "bioimageio.core.block_meta.split_multiple_shapes_into_blocks", "modulename": "bioimageio.core.block_meta", "qualname": "split_multiple_shapes_into_blocks", "kind": "function", "doc": "\n", "signature": "(\tshapes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\tblock_shapes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\t*,\thalo: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, Union[int, Tuple[int, int], bioimageio.core.common.Halo]]],\tstrides: Optional[Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]] = None,\tbroadcast: bool = False) -> Tuple[int, Iterable[Mapping[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.block_meta.BlockMeta]]]:", "funcdef": "def"}, "bioimageio.core.cli": {"fullname": "bioimageio.core.cli", "modulename": "bioimageio.core.cli", "kind": "module", "doc": "bioimageio CLI
\n\nNote: Some docstrings use a hair space '\u200a'\n to place the added '(default: ...)' on a new line.
\n"}, "bioimageio.core.cli.yaml": {"fullname": "bioimageio.core.cli.yaml", "modulename": "bioimageio.core.cli", "qualname": "yaml", "kind": "variable", "doc": "\n", "default_value": "<ruyaml.main.YAML object>"}, "bioimageio.core.cli.CmdBase": {"fullname": "bioimageio.core.cli.CmdBase", "modulename": "bioimageio.core.cli", "qualname": "CmdBase", "kind": "class", "doc": "Usage docs: https://docs.pydantic.dev/2.9/concepts/models/
\n\nA base class for creating Pydantic models.
\n\n__init__
[Signature
][inspect.Signature] of the model.__init__
function.Model.__validators__
and Model.__root_validators__
from Pydantic V1.RootModel
][pydantic.root_model.RootModel].pydantic-core
SchemaSerializer
used to dump instances of the model.pydantic-core
SchemaValidator
used to validate instances of the model.extra
][pydantic.config.ConfigDict.extra]\nis set to 'allow'
.Usage docs: https://docs.pydantic.dev/2.9/concepts/models/
\n\nA base class for creating Pydantic models.
\n\n__init__
[Signature
][inspect.Signature] of the model.__init__
function.Model.__validators__
and Model.__root_validators__
from Pydantic V1.RootModel
][pydantic.root_model.RootModel].pydantic-core
SchemaSerializer
used to dump instances of the model.pydantic-core
SchemaValidator
used to validate instances of the model.extra
][pydantic.config.ConfigDict.extra]\nis set to 'allow'
.Usage docs: https://docs.pydantic.dev/2.9/concepts/models/
\n\nA base class for creating Pydantic models.
\n\n__init__
[Signature
][inspect.Signature] of the model.__init__
function.Model.__validators__
and Model.__root_validators__
from Pydantic V1.RootModel
][pydantic.root_model.RootModel].pydantic-core
SchemaSerializer
used to dump instances of the model.pydantic-core
SchemaValidator
used to validate instances of the model.extra
][pydantic.config.ConfigDict.extra]\nis set to 'allow'
.Url/path to a bioimageio.yaml/rdf.yaml file\nor a bioimage.io resource identifier, e.g. 'affable-shark'
\n", "annotation": ": Annotated[str, <class 'pydantic_settings.sources._CliPositionalArg'>]"}, "bioimageio.core.cli.WithSource.descr": {"fullname": "bioimageio.core.cli.WithSource.descr", "modulename": "bioimageio.core.cli", "qualname": "WithSource.descr", "kind": "variable", "doc": "\n"}, "bioimageio.core.cli.WithSource.descr_id": {"fullname": "bioimageio.core.cli.WithSource.descr_id", "modulename": "bioimageio.core.cli", "qualname": "WithSource.descr_id", "kind": "variable", "doc": "a more user-friendly description id\n(replacing legacy ids with their nicknames)
\n", "annotation": ": str"}, "bioimageio.core.cli.ValidateFormatCmd": {"fullname": "bioimageio.core.cli.ValidateFormatCmd", "modulename": "bioimageio.core.cli", "qualname": "ValidateFormatCmd", "kind": "class", "doc": "validate the meta data format of a bioimageio resource.
\n", "bases": "CmdBase, WithSource"}, "bioimageio.core.cli.ValidateFormatCmd.run": {"fullname": "bioimageio.core.cli.ValidateFormatCmd.run", "modulename": "bioimageio.core.cli", "qualname": "ValidateFormatCmd.run", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.cli.TestCmd": {"fullname": "bioimageio.core.cli.TestCmd", "modulename": "bioimageio.core.cli", "qualname": "TestCmd", "kind": "class", "doc": "Test a bioimageio resource (beyond meta data formatting)
\n", "bases": "CmdBase, WithSource"}, "bioimageio.core.cli.TestCmd.weight_format": {"fullname": "bioimageio.core.cli.TestCmd.weight_format", "modulename": "bioimageio.core.cli", "qualname": "TestCmd.weight_format", "kind": "variable", "doc": "The weight format to limit testing to.
\n\n(only relevant for model resources)
\n", "annotation": ": Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript', 'all']"}, "bioimageio.core.cli.TestCmd.devices": {"fullname": "bioimageio.core.cli.TestCmd.devices", "modulename": "bioimageio.core.cli", "qualname": "TestCmd.devices", "kind": "variable", "doc": "Device(s) to use for testing
\n", "annotation": ": Union[str, Sequence[str], NoneType]"}, "bioimageio.core.cli.TestCmd.decimal": {"fullname": "bioimageio.core.cli.TestCmd.decimal", "modulename": "bioimageio.core.cli", "qualname": "TestCmd.decimal", "kind": "variable", "doc": "Precision for numerical comparisons
\n", "annotation": ": int"}, "bioimageio.core.cli.TestCmd.run": {"fullname": "bioimageio.core.cli.TestCmd.run", "modulename": "bioimageio.core.cli", "qualname": "TestCmd.run", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.cli.PackageCmd": {"fullname": "bioimageio.core.cli.PackageCmd", "modulename": "bioimageio.core.cli", "qualname": "PackageCmd", "kind": "class", "doc": "save a resource's metadata with its associated files.
\n", "bases": "CmdBase, WithSource"}, "bioimageio.core.cli.PackageCmd.path": {"fullname": "bioimageio.core.cli.PackageCmd.path", "modulename": "bioimageio.core.cli", "qualname": "PackageCmd.path", "kind": "variable", "doc": "The path to write the (zipped) package to.\nIf it does not have a .zip
suffix\nthis command will save the package as an unzipped folder instead.
The weight format to include in the package (for model descriptions only).
\n", "annotation": ": Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript', 'all']"}, "bioimageio.core.cli.PackageCmd.run": {"fullname": "bioimageio.core.cli.PackageCmd.run", "modulename": "bioimageio.core.cli", "qualname": "PackageCmd.run", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.cli.PredictCmd": {"fullname": "bioimageio.core.cli.PredictCmd", "modulename": "bioimageio.core.cli", "qualname": "PredictCmd", "kind": "class", "doc": "Run inference on your data with a bioimage.io model.
\n", "bases": "CmdBase, WithSource"}, "bioimageio.core.cli.PredictCmd.inputs": {"fullname": "bioimageio.core.cli.PredictCmd.inputs", "modulename": "bioimageio.core.cli", "qualname": "PredictCmd.inputs", "kind": "variable", "doc": "Model input sample paths (for each input tensor)
\n\nThe input paths are expected to have shape...
\n\nAll substrings that are replaced by metadata from the model description:
\n\nExample inputs to process sample 'a' and 'b'\nfor a model expecting a 'raw' and a 'mask' input tensor:\n--inputs=\"[[\"a_raw.tif\",\"a_mask.tif\"],[\"b_raw.tif\",\"b_mask.tif\"]]\"\n(Note that JSON double quotes need to be escaped.)
\n\nAlternatively a bioimageio-cli.yaml
(or bioimageio-cli.json
) file\nmay provide the arguments, e.g.:
inputs:\n- [a_raw.tif, a_mask.tif]\n- [b_raw.tif, b_mask.tif]\n
\n.npy
and any file extension supported by imageio are supported.\n Aavailable formats are listed at\nhttps://imageio.readthedocs.io/en/stable/formats/index.html#all-formats.\nSome formats have additional dependencies.
Model output path pattern (per output tensor)
\n\nAll substrings that are replaced:
\n\nallow overwriting existing output files
\n", "annotation": ": bool"}, "bioimageio.core.cli.PredictCmd.blockwise": {"fullname": "bioimageio.core.cli.PredictCmd.blockwise", "modulename": "bioimageio.core.cli", "qualname": "PredictCmd.blockwise", "kind": "variable", "doc": "process inputs blockwise
\n", "annotation": ": bool"}, "bioimageio.core.cli.PredictCmd.stats": {"fullname": "bioimageio.core.cli.PredictCmd.stats", "modulename": "bioimageio.core.cli", "qualname": "PredictCmd.stats", "kind": "variable", "doc": "path to dataset statistics\n(will be written if it does not exist,\nbut the model requires statistical dataset measures)
\n", "annotation": ": pathlib.Path"}, "bioimageio.core.cli.PredictCmd.preview": {"fullname": "bioimageio.core.cli.PredictCmd.preview", "modulename": "bioimageio.core.cli", "qualname": "PredictCmd.preview", "kind": "variable", "doc": "preview which files would be processed\nand what outputs would be generated.
\n", "annotation": ": bool"}, "bioimageio.core.cli.PredictCmd.weight_format": {"fullname": "bioimageio.core.cli.PredictCmd.weight_format", "modulename": "bioimageio.core.cli", "qualname": "PredictCmd.weight_format", "kind": "variable", "doc": "The weight format to use.
\n", "annotation": ": Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript', 'any']"}, "bioimageio.core.cli.PredictCmd.example": {"fullname": "bioimageio.core.cli.PredictCmd.example", "modulename": "bioimageio.core.cli", "qualname": "PredictCmd.example", "kind": "variable", "doc": "generate and run an example
\n\n{model_id}_example
folder{model_id}_example/bioimageio-cli.yaml
bioimageio - CLI for bioimage.io resources \ud83e\udd92
\n\nlibrary versions:\n bioimageio.core 0.7.0\n bioimageio.spec 0.7.0
\n\nspec format versions:\n model RDF 0.5.3\n dataset RDF 0.3.0\n notebook RDF 0.3.0
\n", "bases": "pydantic_settings.main.BaseSettings"}, "bioimageio.core.cli.Bioimageio.validate_format": {"fullname": "bioimageio.core.cli.Bioimageio.validate_format", "modulename": "bioimageio.core.cli", "qualname": "Bioimageio.validate_format", "kind": "variable", "doc": "Check a resource's metadata format
\n", "annotation": ": Annotated[Optional[bioimageio.core.cli.ValidateFormatCmd], <class 'pydantic_settings.sources._CliSubCommand'>]"}, "bioimageio.core.cli.Bioimageio.test": {"fullname": "bioimageio.core.cli.Bioimageio.test", "modulename": "bioimageio.core.cli", "qualname": "Bioimageio.test", "kind": "variable", "doc": "Test a bioimageio resource (beyond meta data formatting)
\n", "annotation": ": Annotated[Optional[bioimageio.core.cli.TestCmd], <class 'pydantic_settings.sources._CliSubCommand'>]"}, "bioimageio.core.cli.Bioimageio.package": {"fullname": "bioimageio.core.cli.Bioimageio.package", "modulename": "bioimageio.core.cli", "qualname": "Bioimageio.package", "kind": "variable", "doc": "Package a resource
\n", "annotation": ": Annotated[Optional[bioimageio.core.cli.PackageCmd], <class 'pydantic_settings.sources._CliSubCommand'>]"}, "bioimageio.core.cli.Bioimageio.predict": {"fullname": "bioimageio.core.cli.Bioimageio.predict", "modulename": "bioimageio.core.cli", "qualname": "Bioimageio.predict", "kind": "variable", "doc": "Predict with a model resource
\n", "annotation": ": Annotated[Optional[bioimageio.core.cli.PredictCmd], <class 'pydantic_settings.sources._CliSubCommand'>]"}, "bioimageio.core.cli.Bioimageio.settings_customise_sources": {"fullname": "bioimageio.core.cli.Bioimageio.settings_customise_sources", "modulename": "bioimageio.core.cli", "qualname": "Bioimageio.settings_customise_sources", "kind": "function", "doc": "Define the sources and their order for loading the settings values.
\n\nInitSettingsSource
instance.EnvSettingsSource
instance.DotEnvSettingsSource
instance.SecretsSettingsSource
instance.\n\n", "signature": "(\tcls,\tsettings_cls: Type[pydantic_settings.main.BaseSettings],\tinit_settings: pydantic_settings.sources.PydanticBaseSettingsSource,\tenv_settings: pydantic_settings.sources.PydanticBaseSettingsSource,\tdotenv_settings: pydantic_settings.sources.PydanticBaseSettingsSource,\tfile_secret_settings: pydantic_settings.sources.PydanticBaseSettingsSource) -> Tuple[pydantic_settings.sources.PydanticBaseSettingsSource, ...]:", "funcdef": "def"}, "bioimageio.core.cli.Bioimageio.run": {"fullname": "bioimageio.core.cli.Bioimageio.run", "modulename": "bioimageio.core.cli", "qualname": "Bioimageio.run", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.commands": {"fullname": "bioimageio.core.commands", "modulename": "bioimageio.core.commands", "kind": "module", "doc": "A tuple containing the sources and their order for loading the settings values.
\n
These functions implement the logic of the bioimageio command line interface\ndefined in bioimageio.core.cli
.
test a bioimageio resource
\n\nvalidate the meta data format of a bioimageio resource
\n\nSave a resource's metadata with its associated files.
\n\nNote: If path
does not have a .zip
suffix this command will save the\n package as an unzipped folder instead.
_LeftRight(left, right)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.common.CropWidth.__init__": {"fullname": "bioimageio.core.common.CropWidth.__init__", "modulename": "bioimageio.core.common", "qualname": "CropWidth.__init__", "kind": "function", "doc": "Create new instance of _LeftRight(left, right)
\n", "signature": "(left: int, right: int)"}, "bioimageio.core.common.CropWidthLike": {"fullname": "bioimageio.core.common.CropWidthLike", "modulename": "bioimageio.core.common", "qualname": "CropWidthLike", "kind": "variable", "doc": "\n", "default_value": "typing.Union[int, typing.Tuple[int, int], bioimageio.core.common.CropWidth]"}, "bioimageio.core.common.CropWhere": {"fullname": "bioimageio.core.common.CropWhere", "modulename": "bioimageio.core.common", "qualname": "CropWhere", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['left', 'right', 'left_and_right']"}, "bioimageio.core.common.Halo": {"fullname": "bioimageio.core.common.Halo", "modulename": "bioimageio.core.common", "qualname": "Halo", "kind": "class", "doc": "_LeftRight(left, right)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.common.Halo.__init__": {"fullname": "bioimageio.core.common.Halo.__init__", "modulename": "bioimageio.core.common", "qualname": "Halo.__init__", "kind": "function", "doc": "Create new instance of _LeftRight(left, right)
\n", "signature": "(left: int, right: int)"}, "bioimageio.core.common.HaloLike": {"fullname": "bioimageio.core.common.HaloLike", "modulename": "bioimageio.core.common", "qualname": "HaloLike", "kind": "variable", "doc": "\n", "default_value": "typing.Union[int, typing.Tuple[int, int], bioimageio.core.common.Halo]"}, "bioimageio.core.common.OverlapWidth": {"fullname": "bioimageio.core.common.OverlapWidth", "modulename": "bioimageio.core.common", "qualname": "OverlapWidth", "kind": "class", "doc": "_LeftRight(left, right)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.common.OverlapWidth.__init__": {"fullname": "bioimageio.core.common.OverlapWidth.__init__", "modulename": "bioimageio.core.common", "qualname": "OverlapWidth.__init__", "kind": "function", "doc": "Create new instance of _LeftRight(left, right)
\n", "signature": "(left: int, right: int)"}, "bioimageio.core.common.PadWidth": {"fullname": "bioimageio.core.common.PadWidth", "modulename": "bioimageio.core.common", "qualname": "PadWidth", "kind": "class", "doc": "_LeftRight(left, right)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.common.PadWidth.__init__": {"fullname": "bioimageio.core.common.PadWidth.__init__", "modulename": "bioimageio.core.common", "qualname": "PadWidth.__init__", "kind": "function", "doc": "Create new instance of _LeftRight(left, right)
\n", "signature": "(left: int, right: int)"}, "bioimageio.core.common.PadWidthLike": {"fullname": "bioimageio.core.common.PadWidthLike", "modulename": "bioimageio.core.common", "qualname": "PadWidthLike", "kind": "variable", "doc": "\n", "default_value": "typing.Union[int, typing.Tuple[int, int], bioimageio.core.common.PadWidth]"}, "bioimageio.core.common.PadMode": {"fullname": "bioimageio.core.common.PadMode", "modulename": "bioimageio.core.common", "qualname": "PadMode", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['edge', 'reflect', 'symmetric']"}, "bioimageio.core.common.PadWhere": {"fullname": "bioimageio.core.common.PadWhere", "modulename": "bioimageio.core.common", "qualname": "PadWhere", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['left', 'right', 'left_and_right']"}, "bioimageio.core.common.SliceInfo": {"fullname": "bioimageio.core.common.SliceInfo", "modulename": "bioimageio.core.common", "qualname": "SliceInfo", "kind": "class", "doc": "SliceInfo(start, stop)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.common.SliceInfo.__init__": {"fullname": "bioimageio.core.common.SliceInfo.__init__", "modulename": "bioimageio.core.common", "qualname": "SliceInfo.__init__", "kind": "function", "doc": "Create new instance of SliceInfo(start, stop)
\n", "signature": "(start: int, stop: int)"}, "bioimageio.core.common.SliceInfo.start": {"fullname": "bioimageio.core.common.SliceInfo.start", "modulename": "bioimageio.core.common", "qualname": "SliceInfo.start", "kind": "variable", "doc": "Alias for field number 0
\n", "annotation": ": int"}, "bioimageio.core.common.SliceInfo.stop": {"fullname": "bioimageio.core.common.SliceInfo.stop", "modulename": "bioimageio.core.common", "qualname": "SliceInfo.stop", "kind": "variable", "doc": "Alias for field number 1
\n", "annotation": ": int"}, "bioimageio.core.common.SampleId": {"fullname": "bioimageio.core.common.SampleId", "modulename": "bioimageio.core.common", "qualname": "SampleId", "kind": "variable", "doc": "\n", "default_value": "typing.Hashable"}, "bioimageio.core.common.MemberId": {"fullname": "bioimageio.core.common.MemberId", "modulename": "bioimageio.core.common", "qualname": "MemberId", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.model.v0_5.TensorId'>"}, "bioimageio.core.common.PerMember": {"fullname": "bioimageio.core.common.PerMember", "modulename": "bioimageio.core.common", "qualname": "PerMember", "kind": "variable", "doc": "\n", "default_value": "typing.Mapping[bioimageio.spec.model.v0_5.TensorId, ~T]"}, "bioimageio.core.common.BlockIndex": {"fullname": "bioimageio.core.common.BlockIndex", "modulename": "bioimageio.core.common", "qualname": "BlockIndex", "kind": "variable", "doc": "\n", "default_value": "<class 'int'>"}, "bioimageio.core.common.TotalNumberOfBlocks": {"fullname": "bioimageio.core.common.TotalNumberOfBlocks", "modulename": "bioimageio.core.common", "qualname": "TotalNumberOfBlocks", "kind": "variable", "doc": "\n", "default_value": "<class 'int'>"}, "bioimageio.core.common.Frozen": {"fullname": "bioimageio.core.common.Frozen", "modulename": "bioimageio.core.common", "qualname": "Frozen", "kind": "variable", "doc": "\n", "default_value": "<class 'mappingproxy'>"}, "bioimageio.core.digest_spec": {"fullname": "bioimageio.core.digest_spec", "modulename": "bioimageio.core.digest_spec", "kind": "module", "doc": "\n"}, "bioimageio.core.digest_spec.import_callable": {"fullname": "bioimageio.core.digest_spec.import_callable", "modulename": "bioimageio.core.digest_spec", "qualname": "import_callable", "kind": "function", "doc": "import a callable (e.g. a torch.nn.Module) from a spec node describing it
\n", "signature": "(\tnode: Union[bioimageio.spec.model.v0_4.CallableFromDepencency, bioimageio.spec.model.v0_5.ArchitectureFromLibraryDescr],\t/,\t**kwargs: Unpack[bioimageio.spec._internal.io.HashKwargs]) -> Callable[..., Any]:", "funcdef": "def"}, "bioimageio.core.digest_spec.get_axes_infos": {"fullname": "bioimageio.core.digest_spec.get_axes_infos", "modulename": "bioimageio.core.digest_spec", "qualname": "get_axes_infos", "kind": "function", "doc": "get a unified, simplified axis representation from spec axes
\n", "signature": "(\tio_descr: Union[bioimageio.spec.model.v0_4.InputTensorDescr, bioimageio.spec.model.v0_4.OutputTensorDescr, bioimageio.spec.model.v0_5.InputTensorDescr, bioimageio.spec.model.v0_5.OutputTensorDescr]) -> List[bioimageio.core.axis.AxisInfo]:", "funcdef": "def"}, "bioimageio.core.digest_spec.get_member_id": {"fullname": "bioimageio.core.digest_spec.get_member_id", "modulename": "bioimageio.core.digest_spec", "qualname": "get_member_id", "kind": "function", "doc": "get the normalized tensor ID, usable as a sample member ID
\n", "signature": "(\ttensor_description: Union[bioimageio.spec.model.v0_4.InputTensorDescr, bioimageio.spec.model.v0_4.OutputTensorDescr, bioimageio.spec.model.v0_5.InputTensorDescr, bioimageio.spec.model.v0_5.OutputTensorDescr]) -> bioimageio.spec.model.v0_5.TensorId:", "funcdef": "def"}, "bioimageio.core.digest_spec.get_member_ids": {"fullname": "bioimageio.core.digest_spec.get_member_ids", "modulename": "bioimageio.core.digest_spec", "qualname": "get_member_ids", "kind": "function", "doc": "get normalized tensor IDs to be used as sample member IDs
\n", "signature": "(\ttensor_descriptions: Sequence[Union[bioimageio.spec.model.v0_4.InputTensorDescr, bioimageio.spec.model.v0_4.OutputTensorDescr, bioimageio.spec.model.v0_5.InputTensorDescr, bioimageio.spec.model.v0_5.OutputTensorDescr]]) -> List[bioimageio.spec.model.v0_5.TensorId]:", "funcdef": "def"}, "bioimageio.core.digest_spec.get_test_inputs": {"fullname": "bioimageio.core.digest_spec.get_test_inputs", "modulename": "bioimageio.core.digest_spec", "qualname": "get_test_inputs", "kind": "function", "doc": "returns a model's test input sample
\n", "signature": "(\tmodel: Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]) -> bioimageio.core.sample.Sample:", "funcdef": "def"}, "bioimageio.core.digest_spec.get_test_outputs": {"fullname": "bioimageio.core.digest_spec.get_test_outputs", "modulename": "bioimageio.core.digest_spec", "qualname": "get_test_outputs", "kind": "function", "doc": "returns a model's test output sample
\n", "signature": "(\tmodel: Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]) -> bioimageio.core.sample.Sample:", "funcdef": "def"}, "bioimageio.core.digest_spec.IO_SampleBlockMeta": {"fullname": "bioimageio.core.digest_spec.IO_SampleBlockMeta", "modulename": "bioimageio.core.digest_spec", "qualname": "IO_SampleBlockMeta", "kind": "class", "doc": "IO_SampleBlockMeta(input, output)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.digest_spec.IO_SampleBlockMeta.__init__": {"fullname": "bioimageio.core.digest_spec.IO_SampleBlockMeta.__init__", "modulename": "bioimageio.core.digest_spec", "qualname": "IO_SampleBlockMeta.__init__", "kind": "function", "doc": "Create new instance of IO_SampleBlockMeta(input, output)
\n", "signature": "(\tinput: ForwardRef('SampleBlockMeta'),\toutput: ForwardRef('SampleBlockMeta'))"}, "bioimageio.core.digest_spec.IO_SampleBlockMeta.input": {"fullname": "bioimageio.core.digest_spec.IO_SampleBlockMeta.input", "modulename": "bioimageio.core.digest_spec", "qualname": "IO_SampleBlockMeta.input", "kind": "variable", "doc": "Alias for field number 0
\n", "annotation": ": bioimageio.core.sample.SampleBlockMeta"}, "bioimageio.core.digest_spec.IO_SampleBlockMeta.output": {"fullname": "bioimageio.core.digest_spec.IO_SampleBlockMeta.output", "modulename": "bioimageio.core.digest_spec", "qualname": "IO_SampleBlockMeta.output", "kind": "variable", "doc": "Alias for field number 1
\n", "annotation": ": bioimageio.core.sample.SampleBlockMeta"}, "bioimageio.core.digest_spec.get_input_halo": {"fullname": "bioimageio.core.digest_spec.get_input_halo", "modulename": "bioimageio.core.digest_spec", "qualname": "get_input_halo", "kind": "function", "doc": "returns which halo input tensors need to be divided into blocks with, such that\noutput_halo
can be cropped from their outputs without introducing gaps.
returns how a model's output tensor shapes relates to its input shapes
\n", "signature": "(\tmodel: bioimageio.spec.model.v0_5.ModelDescr) -> Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, Union[bioimageio.core.sample.LinearSampleAxisTransform, int]]]:", "funcdef": "def"}, "bioimageio.core.digest_spec.get_io_sample_block_metas": {"fullname": "bioimageio.core.digest_spec.get_io_sample_block_metas", "modulename": "bioimageio.core.digest_spec", "qualname": "get_io_sample_block_metas", "kind": "function", "doc": "returns an iterable yielding meta data for corresponding input and output samples
\n", "signature": "(\tmodel: bioimageio.spec.model.v0_5.ModelDescr,\tinput_sample_shape: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\tns: Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int],\tbatch_size: int = 1) -> Tuple[int, Iterable[bioimageio.core.digest_spec.IO_SampleBlockMeta]]:", "funcdef": "def"}, "bioimageio.core.digest_spec.get_tensor": {"fullname": "bioimageio.core.digest_spec.get_tensor", "modulename": "bioimageio.core.digest_spec", "qualname": "get_tensor", "kind": "function", "doc": "helper to cast/load various tensor sources
\n", "signature": "(\tsrc: Union[bioimageio.core.tensor.Tensor, xarray.core.dataarray.DataArray, numpy.ndarray[Any, numpy.dtype[Any]], pathlib.Path],\tipt: Union[bioimageio.spec.model.v0_4.InputTensorDescr, bioimageio.spec.model.v0_5.InputTensorDescr]):", "funcdef": "def"}, "bioimageio.core.digest_spec.create_sample_for_model": {"fullname": "bioimageio.core.digest_spec.create_sample_for_model", "modulename": "bioimageio.core.digest_spec", "qualname": "create_sample_for_model", "kind": "function", "doc": "Create a sample from a single set of input(s) for a specific bioimage.io model
\n\nload a single sample from paths
that can be processed by model
load a single image as numpy array
\n\nsave a sample to path
\n\nIf path
is a pathlib.Path or a string it must contain {member_id}
and may contain {sample_id}
,\nwhich are resolved with the sample
object.
Represents model without any preprocessing or postprocessing.
\n\nfrom bioimageio.core import load_description\n\nmodel = load_description(...)\n\n# option 1:\nadapter = ModelAdapter.create(model)\nadapter.forward(...)\nadapter.unload()\n\n# option 2:\nwith ModelAdapter.create(model) as adapter:\n adapter.forward(...)\n
\n", "bases": "abc.ABC"}, "bioimageio.core.model_adapters.ModelAdapter.create": {"fullname": "bioimageio.core.model_adapters.ModelAdapter.create", "modulename": "bioimageio.core.model_adapters", "qualname": "ModelAdapter.create", "kind": "function", "doc": "Creates model adapter based on the passed spec\nNote: All specific adapters should happen inside this function to prevent different framework\ninitializations interfering with each other
\n", "signature": "(\tcls,\tmodel_description: Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr],\t*,\tdevices: Optional[Sequence[str]] = None,\tweight_format_priority_order: Optional[Sequence[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]] = None):", "funcdef": "def"}, "bioimageio.core.model_adapters.ModelAdapter.load": {"fullname": "bioimageio.core.model_adapters.ModelAdapter.load", "modulename": "bioimageio.core.model_adapters", "qualname": "ModelAdapter.load", "kind": "function", "doc": "\n", "signature": "(self, *, devices: Optional[Sequence[str]] = None) -> None:", "funcdef": "def"}, "bioimageio.core.model_adapters.ModelAdapter.forward": {"fullname": "bioimageio.core.model_adapters.ModelAdapter.forward", "modulename": "bioimageio.core.model_adapters", "qualname": "ModelAdapter.forward", "kind": "function", "doc": "Run forward pass of model to get model predictions
\n", "signature": "(\tself,\t*input_tensors: Optional[bioimageio.core.tensor.Tensor]) -> List[Optional[bioimageio.core.tensor.Tensor]]:", "funcdef": "def"}, "bioimageio.core.model_adapters.ModelAdapter.unload": {"fullname": "bioimageio.core.model_adapters.ModelAdapter.unload", "modulename": "bioimageio.core.model_adapters", "qualname": "ModelAdapter.unload", "kind": "function", "doc": "Unload model from any devices, freeing their memory.\nThe moder adapter should be considered unusable afterwards.
\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.model_adapters.create_model_adapter": {"fullname": "bioimageio.core.model_adapters.create_model_adapter", "modulename": "bioimageio.core.model_adapters", "qualname": "create_model_adapter", "kind": "function", "doc": "Creates model adapter based on the passed spec\nNote: All specific adapters should happen inside this function to prevent different framework\ninitializations interfering with each other
\n", "signature": "(\tmodel_description: Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr],\t*,\tdevices: Optional[Sequence[str]] = None,\tweight_format_priority_order: Optional[Sequence[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]] = None):", "funcdef": "def"}, "bioimageio.core.model_adapters.get_weight_formats": {"fullname": "bioimageio.core.model_adapters.get_weight_formats", "modulename": "bioimageio.core.model_adapters", "qualname": "get_weight_formats", "kind": "function", "doc": "Return list of supported weight types
\n", "signature": "() -> List[str]:", "funcdef": "def"}, "bioimageio.core.prediction": {"fullname": "bioimageio.core.prediction", "modulename": "bioimageio.core.prediction", "kind": "module", "doc": "\n"}, "bioimageio.core.prediction.predict": {"fullname": "bioimageio.core.prediction.predict", "modulename": "bioimageio.core.prediction", "qualname": "predict", "kind": "function", "doc": "Run prediction for a single set of input(s) with a bioimage.io model
\n\ninput_block_shape
blocksize_parameter
.{member_id}
{sample_id}
in it\nto save the output to.Run prediction for a multiple sets of inputs with a bioimage.io model
\n\n{i}
will be formatted as the i-th sample.\nIf {i}
(or {i:
) is not present and inputs
is an iterable {i:03}
is appended.{member_id}
{sample_id}
in it\nto save the output to.Calculates sample and/or dataset measures
\n", "bases": "bioimageio.core._op_base.Operator"}, "bioimageio.core.proc_ops.UpdateStats.__init__": {"fullname": "bioimageio.core.proc_ops.UpdateStats.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "UpdateStats.__init__", "kind": "function", "doc": "\n", "signature": "(\tstats_calculator: bioimageio.core.stat_calculators.StatsCalculator,\tkeep_updating_initial_dataset_stats: bool = False)"}, "bioimageio.core.proc_ops.UpdateStats.stats_calculator": {"fullname": "bioimageio.core.proc_ops.UpdateStats.stats_calculator", "modulename": "bioimageio.core.proc_ops", "qualname": "UpdateStats.stats_calculator", "kind": "variable", "doc": "StatsCalculator
to be used by this operator.
indicates if operator calls should keep updating initial dataset statistics or not;\nif the stats_calculator
was not provided with any initial dataset statistics,\nthese are always updated with every new sample.
'output = tensor > threshold'.
\n", "bases": "_SimpleOperator"}, "bioimageio.core.proc_ops.Binarize.__init__": {"fullname": "bioimageio.core.proc_ops.Binarize.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "Binarize.__init__", "kind": "function", "doc": "\n", "signature": "(\tinput: bioimageio.spec.model.v0_5.TensorId,\toutput: bioimageio.spec.model.v0_5.TensorId,\tthreshold: Union[float, Sequence[float]],\taxis: Optional[bioimageio.spec.model.v0_5.AxisId] = None)"}, "bioimageio.core.proc_ops.Binarize.threshold": {"fullname": "bioimageio.core.proc_ops.Binarize.threshold", "modulename": "bioimageio.core.proc_ops", "qualname": "Binarize.threshold", "kind": "variable", "doc": "\n", "annotation": ": Union[float, Sequence[float]]"}, "bioimageio.core.proc_ops.Binarize.axis": {"fullname": "bioimageio.core.proc_ops.Binarize.axis", "modulename": "bioimageio.core.proc_ops", "qualname": "Binarize.axis", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.AxisId]", "default_value": "None"}, "bioimageio.core.proc_ops.Binarize.get_output_shape": {"fullname": "bioimageio.core.proc_ops.Binarize.get_output_shape", "modulename": "bioimageio.core.proc_ops", "qualname": "Binarize.get_output_shape", "kind": "function", "doc": "\n", "signature": "(\tself,\tinput_shape: Mapping[bioimageio.spec.model.v0_5.AxisId, int]) -> Mapping[bioimageio.spec.model.v0_5.AxisId, int]:", "funcdef": "def"}, "bioimageio.core.proc_ops.Binarize.from_proc_descr": {"fullname": "bioimageio.core.proc_ops.Binarize.from_proc_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "Binarize.from_proc_descr", "kind": "function", "doc": "\n", "signature": "(\tcls,\tdescr: Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_5.BinarizeDescr],\tmember_id: bioimageio.spec.model.v0_5.TensorId) -> Self:", "funcdef": "def"}, "bioimageio.core.proc_ops.Clip": {"fullname": "bioimageio.core.proc_ops.Clip", "modulename": "bioimageio.core.proc_ops", "qualname": "Clip", "kind": "class", "doc": "\n", "bases": "_SimpleOperator"}, "bioimageio.core.proc_ops.Clip.__init__": {"fullname": "bioimageio.core.proc_ops.Clip.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "Clip.__init__", "kind": "function", "doc": "\n", "signature": "(\tinput: bioimageio.spec.model.v0_5.TensorId,\toutput: bioimageio.spec.model.v0_5.TensorId,\tmin: Optional[float] = None,\tmax: Optional[float] = None)"}, "bioimageio.core.proc_ops.Clip.min": {"fullname": "bioimageio.core.proc_ops.Clip.min", "modulename": "bioimageio.core.proc_ops", "qualname": "Clip.min", "kind": "variable", "doc": "minimum value for clipping
\n", "annotation": ": Optional[float]", "default_value": "None"}, "bioimageio.core.proc_ops.Clip.max": {"fullname": "bioimageio.core.proc_ops.Clip.max", "modulename": "bioimageio.core.proc_ops", "qualname": "Clip.max", "kind": "variable", "doc": "maximum value for clipping
\n", "annotation": ": Optional[float]", "default_value": "None"}, "bioimageio.core.proc_ops.Clip.get_output_shape": {"fullname": "bioimageio.core.proc_ops.Clip.get_output_shape", "modulename": "bioimageio.core.proc_ops", "qualname": "Clip.get_output_shape", "kind": "function", "doc": "\n", "signature": "(\tself,\tinput_shape: Mapping[bioimageio.spec.model.v0_5.AxisId, int]) -> Mapping[bioimageio.spec.model.v0_5.AxisId, int]:", "funcdef": "def"}, "bioimageio.core.proc_ops.Clip.from_proc_descr": {"fullname": "bioimageio.core.proc_ops.Clip.from_proc_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "Clip.from_proc_descr", "kind": "function", "doc": "\n", "signature": "(\tcls,\tdescr: Union[bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_5.ClipDescr],\tmember_id: bioimageio.spec.model.v0_5.TensorId) -> Self:", "funcdef": "def"}, "bioimageio.core.proc_ops.EnsureDtype": {"fullname": "bioimageio.core.proc_ops.EnsureDtype", "modulename": "bioimageio.core.proc_ops", "qualname": "EnsureDtype", "kind": "class", "doc": "\n", "bases": "_SimpleOperator"}, "bioimageio.core.proc_ops.EnsureDtype.__init__": {"fullname": "bioimageio.core.proc_ops.EnsureDtype.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "EnsureDtype.__init__", "kind": "function", "doc": "\n", "signature": "(\tinput: bioimageio.spec.model.v0_5.TensorId,\toutput: bioimageio.spec.model.v0_5.TensorId,\tdtype: Literal['bool', 'float32', 'float64', 'int8', 'int16', 'int32', 'int64', 'uint8', 'uint16', 'uint32', 'uint64'])"}, "bioimageio.core.proc_ops.EnsureDtype.dtype": {"fullname": "bioimageio.core.proc_ops.EnsureDtype.dtype", "modulename": "bioimageio.core.proc_ops", "qualname": "EnsureDtype.dtype", "kind": "variable", "doc": "\n", "annotation": ": Literal['bool', 'float32', 'float64', 'int8', 'int16', 'int32', 'int64', 'uint8', 'uint16', 'uint32', 'uint64']"}, "bioimageio.core.proc_ops.EnsureDtype.from_proc_descr": {"fullname": "bioimageio.core.proc_ops.EnsureDtype.from_proc_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "EnsureDtype.from_proc_descr", "kind": "function", "doc": "\n", "signature": "(\tcls,\tdescr: bioimageio.spec.model.v0_5.EnsureDtypeDescr,\tmember_id: bioimageio.spec.model.v0_5.TensorId):", "funcdef": "def"}, "bioimageio.core.proc_ops.EnsureDtype.get_descr": {"fullname": "bioimageio.core.proc_ops.EnsureDtype.get_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "EnsureDtype.get_descr", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.proc_ops.EnsureDtype.get_output_shape": {"fullname": "bioimageio.core.proc_ops.EnsureDtype.get_output_shape", "modulename": "bioimageio.core.proc_ops", "qualname": "EnsureDtype.get_output_shape", "kind": "function", "doc": "\n", "signature": "(\tself,\tinput_shape: Mapping[bioimageio.spec.model.v0_5.AxisId, int]) -> Mapping[bioimageio.spec.model.v0_5.AxisId, int]:", "funcdef": "def"}, "bioimageio.core.proc_ops.ScaleLinear": {"fullname": "bioimageio.core.proc_ops.ScaleLinear", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleLinear", "kind": "class", "doc": "\n", "bases": "_SimpleOperator"}, "bioimageio.core.proc_ops.ScaleLinear.__init__": {"fullname": "bioimageio.core.proc_ops.ScaleLinear.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleLinear.__init__", "kind": "function", "doc": "\n", "signature": "(\tinput: bioimageio.spec.model.v0_5.TensorId,\toutput: bioimageio.spec.model.v0_5.TensorId,\tgain: Union[float, xarray.core.dataarray.DataArray] = 1.0,\toffset: Union[float, xarray.core.dataarray.DataArray] = 0.0)"}, "bioimageio.core.proc_ops.ScaleLinear.gain": {"fullname": "bioimageio.core.proc_ops.ScaleLinear.gain", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleLinear.gain", "kind": "variable", "doc": "multiplicative factor
\n", "annotation": ": Union[float, xarray.core.dataarray.DataArray]", "default_value": "1.0"}, "bioimageio.core.proc_ops.ScaleLinear.offset": {"fullname": "bioimageio.core.proc_ops.ScaleLinear.offset", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleLinear.offset", "kind": "variable", "doc": "additive term
\n", "annotation": ": Union[float, xarray.core.dataarray.DataArray]", "default_value": "0.0"}, "bioimageio.core.proc_ops.ScaleLinear.get_output_shape": {"fullname": "bioimageio.core.proc_ops.ScaleLinear.get_output_shape", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleLinear.get_output_shape", "kind": "function", "doc": "\n", "signature": "(\tself,\tinput_shape: Mapping[bioimageio.spec.model.v0_5.AxisId, int]) -> Mapping[bioimageio.spec.model.v0_5.AxisId, int]:", "funcdef": "def"}, "bioimageio.core.proc_ops.ScaleLinear.from_proc_descr": {"fullname": "bioimageio.core.proc_ops.ScaleLinear.from_proc_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleLinear.from_proc_descr", "kind": "function", "doc": "\n", "signature": "(\tcls,\tdescr: Union[bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_5.ScaleLinearDescr],\tmember_id: bioimageio.spec.model.v0_5.TensorId) -> Self:", "funcdef": "def"}, "bioimageio.core.proc_ops.ScaleMeanVariance": {"fullname": "bioimageio.core.proc_ops.ScaleMeanVariance", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleMeanVariance", "kind": "class", "doc": "\n", "bases": "_SimpleOperator"}, "bioimageio.core.proc_ops.ScaleMeanVariance.__init__": {"fullname": "bioimageio.core.proc_ops.ScaleMeanVariance.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleMeanVariance.__init__", "kind": "function", "doc": "\n", "signature": "(\tinput: bioimageio.spec.model.v0_5.TensorId,\toutput: bioimageio.spec.model.v0_5.TensorId,\taxes: Optional[Sequence[bioimageio.spec.model.v0_5.AxisId]] = None,\treference_tensor: Optional[bioimageio.spec.model.v0_5.TensorId] = None,\teps: float = 1e-06)"}, "bioimageio.core.proc_ops.ScaleMeanVariance.axes": {"fullname": "bioimageio.core.proc_ops.ScaleMeanVariance.axes", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleMeanVariance.axes", "kind": "variable", "doc": "\n", "annotation": ": Optional[Sequence[bioimageio.spec.model.v0_5.AxisId]]", "default_value": "None"}, "bioimageio.core.proc_ops.ScaleMeanVariance.reference_tensor": {"fullname": "bioimageio.core.proc_ops.ScaleMeanVariance.reference_tensor", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleMeanVariance.reference_tensor", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.TensorId]", "default_value": "None"}, "bioimageio.core.proc_ops.ScaleMeanVariance.eps": {"fullname": "bioimageio.core.proc_ops.ScaleMeanVariance.eps", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleMeanVariance.eps", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1e-06"}, "bioimageio.core.proc_ops.ScaleMeanVariance.mean": {"fullname": "bioimageio.core.proc_ops.ScaleMeanVariance.mean", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleMeanVariance.mean", "kind": "variable", "doc": "\n", "annotation": ": Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.DatasetMean]"}, "bioimageio.core.proc_ops.ScaleMeanVariance.std": {"fullname": "bioimageio.core.proc_ops.ScaleMeanVariance.std", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleMeanVariance.std", "kind": "variable", "doc": "\n", "annotation": ": Union[bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.DatasetStd]"}, "bioimageio.core.proc_ops.ScaleMeanVariance.ref_mean": {"fullname": "bioimageio.core.proc_ops.ScaleMeanVariance.ref_mean", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleMeanVariance.ref_mean", "kind": "variable", "doc": "\n", "annotation": ": Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.DatasetMean]"}, "bioimageio.core.proc_ops.ScaleMeanVariance.ref_std": {"fullname": "bioimageio.core.proc_ops.ScaleMeanVariance.ref_std", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleMeanVariance.ref_std", "kind": "variable", "doc": "\n", "annotation": ": Union[bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.DatasetStd]"}, "bioimageio.core.proc_ops.ScaleMeanVariance.required_measures": {"fullname": "bioimageio.core.proc_ops.ScaleMeanVariance.required_measures", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleMeanVariance.required_measures", "kind": "variable", "doc": "\n"}, "bioimageio.core.proc_ops.ScaleMeanVariance.get_output_shape": {"fullname": "bioimageio.core.proc_ops.ScaleMeanVariance.get_output_shape", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleMeanVariance.get_output_shape", "kind": "function", "doc": "\n", "signature": "(\tself,\tinput_shape: Mapping[bioimageio.spec.model.v0_5.AxisId, int]) -> Mapping[bioimageio.spec.model.v0_5.AxisId, int]:", "funcdef": "def"}, "bioimageio.core.proc_ops.ScaleMeanVariance.from_proc_descr": {"fullname": "bioimageio.core.proc_ops.ScaleMeanVariance.from_proc_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleMeanVariance.from_proc_descr", "kind": "function", "doc": "\n", "signature": "(\tcls,\tdescr: Union[bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr, bioimageio.spec.model.v0_5.ScaleMeanVarianceDescr],\tmember_id: bioimageio.spec.model.v0_5.TensorId) -> Self:", "funcdef": "def"}, "bioimageio.core.proc_ops.ScaleRange": {"fullname": "bioimageio.core.proc_ops.ScaleRange", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleRange", "kind": "class", "doc": "\n", "bases": "_SimpleOperator"}, "bioimageio.core.proc_ops.ScaleRange.__init__": {"fullname": "bioimageio.core.proc_ops.ScaleRange.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleRange.__init__", "kind": "function", "doc": "\n", "signature": "(\tinput: bioimageio.spec.model.v0_5.TensorId,\toutput: bioimageio.spec.model.v0_5.TensorId,\tlower_percentile: dataclasses.InitVar[typing.Union[bioimageio.core.stat_measures.SampleQuantile, bioimageio.core.stat_measures.DatasetPercentile, NoneType]] = None,\tupper_percentile: dataclasses.InitVar[typing.Union[bioimageio.core.stat_measures.SampleQuantile, bioimageio.core.stat_measures.DatasetPercentile, NoneType]] = None,\teps: float = 1e-06)"}, "bioimageio.core.proc_ops.ScaleRange.lower_percentile": {"fullname": "bioimageio.core.proc_ops.ScaleRange.lower_percentile", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleRange.lower_percentile", "kind": "variable", "doc": "\n", "annotation": ": dataclasses.InitVar[typing.Union[bioimageio.core.stat_measures.SampleQuantile, bioimageio.core.stat_measures.DatasetPercentile, NoneType]]", "default_value": "None"}, "bioimageio.core.proc_ops.ScaleRange.upper_percentile": {"fullname": "bioimageio.core.proc_ops.ScaleRange.upper_percentile", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleRange.upper_percentile", "kind": "variable", "doc": "\n", "annotation": ": dataclasses.InitVar[typing.Union[bioimageio.core.stat_measures.SampleQuantile, bioimageio.core.stat_measures.DatasetPercentile, NoneType]]", "default_value": "None"}, "bioimageio.core.proc_ops.ScaleRange.lower": {"fullname": "bioimageio.core.proc_ops.ScaleRange.lower", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleRange.lower", "kind": "variable", "doc": "\n", "annotation": ": Union[bioimageio.core.stat_measures.SampleQuantile, bioimageio.core.stat_measures.DatasetPercentile]"}, "bioimageio.core.proc_ops.ScaleRange.upper": {"fullname": "bioimageio.core.proc_ops.ScaleRange.upper", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleRange.upper", "kind": "variable", "doc": "\n", "annotation": ": Union[bioimageio.core.stat_measures.SampleQuantile, bioimageio.core.stat_measures.DatasetPercentile]"}, "bioimageio.core.proc_ops.ScaleRange.eps": {"fullname": "bioimageio.core.proc_ops.ScaleRange.eps", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleRange.eps", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1e-06"}, "bioimageio.core.proc_ops.ScaleRange.required_measures": {"fullname": "bioimageio.core.proc_ops.ScaleRange.required_measures", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleRange.required_measures", "kind": "variable", "doc": "\n"}, "bioimageio.core.proc_ops.ScaleRange.get_output_shape": {"fullname": "bioimageio.core.proc_ops.ScaleRange.get_output_shape", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleRange.get_output_shape", "kind": "function", "doc": "\n", "signature": "(\tself,\tinput_shape: Mapping[bioimageio.spec.model.v0_5.AxisId, int]) -> Mapping[bioimageio.spec.model.v0_5.AxisId, int]:", "funcdef": "def"}, "bioimageio.core.proc_ops.ScaleRange.from_proc_descr": {"fullname": "bioimageio.core.proc_ops.ScaleRange.from_proc_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleRange.from_proc_descr", "kind": "function", "doc": "\n", "signature": "(\tcls,\tdescr: Union[bioimageio.spec.model.v0_4.ScaleRangeDescr, bioimageio.spec.model.v0_5.ScaleRangeDescr],\tmember_id: bioimageio.spec.model.v0_5.TensorId):", "funcdef": "def"}, "bioimageio.core.proc_ops.ScaleRange.get_descr": {"fullname": "bioimageio.core.proc_ops.ScaleRange.get_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleRange.get_descr", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.proc_ops.Sigmoid": {"fullname": "bioimageio.core.proc_ops.Sigmoid", "modulename": "bioimageio.core.proc_ops", "qualname": "Sigmoid", "kind": "class", "doc": "1 / (1 + e^(-input)).
\n", "bases": "_SimpleOperator"}, "bioimageio.core.proc_ops.Sigmoid.__init__": {"fullname": "bioimageio.core.proc_ops.Sigmoid.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "Sigmoid.__init__", "kind": "function", "doc": "\n", "signature": "(\tinput: bioimageio.spec.model.v0_5.TensorId,\toutput: bioimageio.spec.model.v0_5.TensorId)"}, "bioimageio.core.proc_ops.Sigmoid.required_measures": {"fullname": "bioimageio.core.proc_ops.Sigmoid.required_measures", "modulename": "bioimageio.core.proc_ops", "qualname": "Sigmoid.required_measures", "kind": "variable", "doc": "\n", "annotation": ": Collection[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.core.proc_ops.Sigmoid.get_output_shape": {"fullname": "bioimageio.core.proc_ops.Sigmoid.get_output_shape", "modulename": "bioimageio.core.proc_ops", "qualname": "Sigmoid.get_output_shape", "kind": "function", "doc": "\n", "signature": "(\tself,\tinput_shape: Mapping[bioimageio.spec.model.v0_5.AxisId, int]) -> Mapping[bioimageio.spec.model.v0_5.AxisId, int]:", "funcdef": "def"}, "bioimageio.core.proc_ops.Sigmoid.from_proc_descr": {"fullname": "bioimageio.core.proc_ops.Sigmoid.from_proc_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "Sigmoid.from_proc_descr", "kind": "function", "doc": "\n", "signature": "(\tcls,\tdescr: Union[bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_5.SigmoidDescr],\tmember_id: bioimageio.spec.model.v0_5.TensorId) -> Self:", "funcdef": "def"}, "bioimageio.core.proc_ops.Sigmoid.get_descr": {"fullname": "bioimageio.core.proc_ops.Sigmoid.get_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "Sigmoid.get_descr", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.proc_ops.ZeroMeanUnitVariance": {"fullname": "bioimageio.core.proc_ops.ZeroMeanUnitVariance", "modulename": "bioimageio.core.proc_ops", "qualname": "ZeroMeanUnitVariance", "kind": "class", "doc": "normalize to zero mean, unit variance.
\n", "bases": "_SimpleOperator"}, "bioimageio.core.proc_ops.ZeroMeanUnitVariance.__init__": {"fullname": "bioimageio.core.proc_ops.ZeroMeanUnitVariance.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "ZeroMeanUnitVariance.__init__", "kind": "function", "doc": "\n", "signature": "(\tinput: bioimageio.spec.model.v0_5.TensorId,\toutput: bioimageio.spec.model.v0_5.TensorId,\tmean: Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.DatasetMean],\tstd: Union[bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.DatasetStd],\teps: float = 1e-06)"}, "bioimageio.core.proc_ops.ZeroMeanUnitVariance.mean": {"fullname": "bioimageio.core.proc_ops.ZeroMeanUnitVariance.mean", "modulename": "bioimageio.core.proc_ops", "qualname": "ZeroMeanUnitVariance.mean", "kind": "variable", "doc": "\n", "annotation": ": Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.DatasetMean]"}, "bioimageio.core.proc_ops.ZeroMeanUnitVariance.std": {"fullname": "bioimageio.core.proc_ops.ZeroMeanUnitVariance.std", "modulename": "bioimageio.core.proc_ops", "qualname": "ZeroMeanUnitVariance.std", "kind": "variable", "doc": "\n", "annotation": ": Union[bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.DatasetStd]"}, "bioimageio.core.proc_ops.ZeroMeanUnitVariance.eps": {"fullname": "bioimageio.core.proc_ops.ZeroMeanUnitVariance.eps", "modulename": "bioimageio.core.proc_ops", "qualname": "ZeroMeanUnitVariance.eps", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1e-06"}, "bioimageio.core.proc_ops.ZeroMeanUnitVariance.required_measures": {"fullname": "bioimageio.core.proc_ops.ZeroMeanUnitVariance.required_measures", "modulename": "bioimageio.core.proc_ops", "qualname": "ZeroMeanUnitVariance.required_measures", "kind": "variable", "doc": "\n", "annotation": ": Set[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.DatasetStd]]"}, "bioimageio.core.proc_ops.ZeroMeanUnitVariance.get_output_shape": {"fullname": "bioimageio.core.proc_ops.ZeroMeanUnitVariance.get_output_shape", "modulename": "bioimageio.core.proc_ops", "qualname": "ZeroMeanUnitVariance.get_output_shape", "kind": "function", "doc": "\n", "signature": "(\tself,\tinput_shape: Mapping[bioimageio.spec.model.v0_5.AxisId, int]) -> Mapping[bioimageio.spec.model.v0_5.AxisId, int]:", "funcdef": "def"}, "bioimageio.core.proc_ops.ZeroMeanUnitVariance.from_proc_descr": {"fullname": "bioimageio.core.proc_ops.ZeroMeanUnitVariance.from_proc_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "ZeroMeanUnitVariance.from_proc_descr", "kind": "function", "doc": "\n", "signature": "(\tcls,\tdescr: Union[bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr],\tmember_id: bioimageio.spec.model.v0_5.TensorId):", "funcdef": "def"}, "bioimageio.core.proc_ops.ZeroMeanUnitVariance.get_descr": {"fullname": "bioimageio.core.proc_ops.ZeroMeanUnitVariance.get_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "ZeroMeanUnitVariance.get_descr", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance": {"fullname": "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance", "modulename": "bioimageio.core.proc_ops", "qualname": "FixedZeroMeanUnitVariance", "kind": "class", "doc": "normalize to zero mean, unit variance with precomputed values.
\n", "bases": "_SimpleOperator"}, "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.__init__": {"fullname": "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "FixedZeroMeanUnitVariance.__init__", "kind": "function", "doc": "\n", "signature": "(\tinput: bioimageio.spec.model.v0_5.TensorId,\toutput: bioimageio.spec.model.v0_5.TensorId,\tmean: Union[float, xarray.core.dataarray.DataArray],\tstd: Union[float, xarray.core.dataarray.DataArray],\teps: float = 1e-06)"}, "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.mean": {"fullname": "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.mean", "modulename": "bioimageio.core.proc_ops", "qualname": "FixedZeroMeanUnitVariance.mean", "kind": "variable", "doc": "\n", "annotation": ": Union[float, xarray.core.dataarray.DataArray]"}, "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.std": {"fullname": "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.std", "modulename": "bioimageio.core.proc_ops", "qualname": "FixedZeroMeanUnitVariance.std", "kind": "variable", "doc": "\n", "annotation": ": Union[float, xarray.core.dataarray.DataArray]"}, "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.eps": {"fullname": "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.eps", "modulename": "bioimageio.core.proc_ops", "qualname": "FixedZeroMeanUnitVariance.eps", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1e-06"}, "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.get_output_shape": {"fullname": "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.get_output_shape", "modulename": "bioimageio.core.proc_ops", "qualname": "FixedZeroMeanUnitVariance.get_output_shape", "kind": "function", "doc": "\n", "signature": "(\tself,\tinput_shape: Mapping[bioimageio.spec.model.v0_5.AxisId, int]) -> Mapping[bioimageio.spec.model.v0_5.AxisId, int]:", "funcdef": "def"}, "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.from_proc_descr": {"fullname": "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.from_proc_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "FixedZeroMeanUnitVariance.from_proc_descr", "kind": "function", "doc": "\n", "signature": "(\tcls,\tdescr: bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceDescr,\tmember_id: bioimageio.spec.model.v0_5.TensorId) -> Self:", "funcdef": "def"}, "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.get_descr": {"fullname": "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.get_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "FixedZeroMeanUnitVariance.get_descr", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.proc_ops.ProcDescr": {"fullname": "bioimageio.core.proc_ops.ProcDescr", "modulename": "bioimageio.core.proc_ops", "qualname": "ProcDescr", "kind": "variable", "doc": "\n", "default_value": "typing.Union[typing.Annotated[typing.Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr, bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.model.v0_5.BinarizeDescr, bioimageio.spec.model.v0_5.ClipDescr, bioimageio.spec.model.v0_5.EnsureDtypeDescr, bioimageio.spec.model.v0_5.ScaleLinearDescr, bioimageio.spec.model.v0_5.SigmoidDescr, bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ScaleRangeDescr], Discriminator(discriminator='id', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.model.v0_5.BinarizeDescr, bioimageio.spec.model.v0_5.ClipDescr, bioimageio.spec.model.v0_5.EnsureDtypeDescr, bioimageio.spec.model.v0_5.ScaleLinearDescr, bioimageio.spec.model.v0_5.SigmoidDescr, bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ScaleRangeDescr, bioimageio.spec.model.v0_5.ScaleMeanVarianceDescr], Discriminator(discriminator='id', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.core.proc_ops.Processing": {"fullname": "bioimageio.core.proc_ops.Processing", "modulename": "bioimageio.core.proc_ops", "qualname": "Processing", "kind": "variable", "doc": "\n", "default_value": "typing.Union[bioimageio.core.proc_ops.AddKnownDatasetStats, bioimageio.core.proc_ops.Binarize, bioimageio.core.proc_ops.Clip, bioimageio.core.proc_ops.EnsureDtype, bioimageio.core.proc_ops.FixedZeroMeanUnitVariance, bioimageio.core.proc_ops.ScaleLinear, bioimageio.core.proc_ops.ScaleMeanVariance, bioimageio.core.proc_ops.ScaleRange, bioimageio.core.proc_ops.Sigmoid, bioimageio.core.proc_ops.UpdateStats, bioimageio.core.proc_ops.ZeroMeanUnitVariance]"}, "bioimageio.core.proc_ops.get_proc_class": {"fullname": "bioimageio.core.proc_ops.get_proc_class", "modulename": "bioimageio.core.proc_ops", "qualname": "get_proc_class", "kind": "function", "doc": "\n", "signature": "(\tproc_spec: Union[Annotated[Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr, bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_5.BinarizeDescr, bioimageio.spec.model.v0_5.ClipDescr, bioimageio.spec.model.v0_5.EnsureDtypeDescr, bioimageio.spec.model.v0_5.ScaleLinearDescr, bioimageio.spec.model.v0_5.SigmoidDescr, bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ScaleRangeDescr], Discriminator(discriminator='id', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_5.BinarizeDescr, bioimageio.spec.model.v0_5.ClipDescr, bioimageio.spec.model.v0_5.EnsureDtypeDescr, bioimageio.spec.model.v0_5.ScaleLinearDescr, bioimageio.spec.model.v0_5.SigmoidDescr, bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ScaleRangeDescr, bioimageio.spec.model.v0_5.ScaleMeanVarianceDescr], Discriminator(discriminator='id', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]):", "funcdef": "def"}, "bioimageio.core.proc_setup": {"fullname": "bioimageio.core.proc_setup", "modulename": "bioimageio.core.proc_setup", "kind": "module", "doc": "\n"}, "bioimageio.core.proc_setup.TensorDescr": {"fullname": "bioimageio.core.proc_setup.TensorDescr", "modulename": "bioimageio.core.proc_setup", "qualname": "TensorDescr", "kind": "variable", "doc": "\n", "default_value": "typing.Union[bioimageio.spec.model.v0_4.InputTensorDescr, bioimageio.spec.model.v0_4.OutputTensorDescr, bioimageio.spec.model.v0_5.InputTensorDescr, bioimageio.spec.model.v0_5.OutputTensorDescr]"}, "bioimageio.core.proc_setup.PreAndPostprocessing": {"fullname": "bioimageio.core.proc_setup.PreAndPostprocessing", "modulename": "bioimageio.core.proc_setup", "qualname": "PreAndPostprocessing", "kind": "class", "doc": "PreAndPostprocessing(pre, post)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.proc_setup.PreAndPostprocessing.__init__": {"fullname": "bioimageio.core.proc_setup.PreAndPostprocessing.__init__", "modulename": "bioimageio.core.proc_setup", "qualname": "PreAndPostprocessing.__init__", "kind": "function", "doc": "Create new instance of PreAndPostprocessing(pre, post)
\n", "signature": "(\tpre: List[Union[bioimageio.core.proc_ops.AddKnownDatasetStats, bioimageio.core.proc_ops.Binarize, bioimageio.core.proc_ops.Clip, bioimageio.core.proc_ops.EnsureDtype, bioimageio.core.proc_ops.FixedZeroMeanUnitVariance, bioimageio.core.proc_ops.ScaleLinear, bioimageio.core.proc_ops.ScaleMeanVariance, bioimageio.core.proc_ops.ScaleRange, bioimageio.core.proc_ops.Sigmoid, bioimageio.core.proc_ops.UpdateStats, bioimageio.core.proc_ops.ZeroMeanUnitVariance]],\tpost: List[Union[bioimageio.core.proc_ops.AddKnownDatasetStats, bioimageio.core.proc_ops.Binarize, bioimageio.core.proc_ops.Clip, bioimageio.core.proc_ops.EnsureDtype, bioimageio.core.proc_ops.FixedZeroMeanUnitVariance, bioimageio.core.proc_ops.ScaleLinear, bioimageio.core.proc_ops.ScaleMeanVariance, bioimageio.core.proc_ops.ScaleRange, bioimageio.core.proc_ops.Sigmoid, bioimageio.core.proc_ops.UpdateStats, bioimageio.core.proc_ops.ZeroMeanUnitVariance]])"}, "bioimageio.core.proc_setup.PreAndPostprocessing.pre": {"fullname": "bioimageio.core.proc_setup.PreAndPostprocessing.pre", "modulename": "bioimageio.core.proc_setup", "qualname": "PreAndPostprocessing.pre", "kind": "variable", "doc": "Alias for field number 0
\n", "annotation": ": List[Union[bioimageio.core.proc_ops.AddKnownDatasetStats, bioimageio.core.proc_ops.Binarize, bioimageio.core.proc_ops.Clip, bioimageio.core.proc_ops.EnsureDtype, bioimageio.core.proc_ops.FixedZeroMeanUnitVariance, bioimageio.core.proc_ops.ScaleLinear, bioimageio.core.proc_ops.ScaleMeanVariance, bioimageio.core.proc_ops.ScaleRange, bioimageio.core.proc_ops.Sigmoid, bioimageio.core.proc_ops.UpdateStats, bioimageio.core.proc_ops.ZeroMeanUnitVariance]]"}, "bioimageio.core.proc_setup.PreAndPostprocessing.post": {"fullname": "bioimageio.core.proc_setup.PreAndPostprocessing.post", "modulename": "bioimageio.core.proc_setup", "qualname": "PreAndPostprocessing.post", "kind": "variable", "doc": "Alias for field number 1
\n", "annotation": ": List[Union[bioimageio.core.proc_ops.AddKnownDatasetStats, bioimageio.core.proc_ops.Binarize, bioimageio.core.proc_ops.Clip, bioimageio.core.proc_ops.EnsureDtype, bioimageio.core.proc_ops.FixedZeroMeanUnitVariance, bioimageio.core.proc_ops.ScaleLinear, bioimageio.core.proc_ops.ScaleMeanVariance, bioimageio.core.proc_ops.ScaleRange, bioimageio.core.proc_ops.Sigmoid, bioimageio.core.proc_ops.UpdateStats, bioimageio.core.proc_ops.ZeroMeanUnitVariance]]"}, "bioimageio.core.proc_setup.setup_pre_and_postprocessing": {"fullname": "bioimageio.core.proc_setup.setup_pre_and_postprocessing", "modulename": "bioimageio.core.proc_setup", "qualname": "setup_pre_and_postprocessing", "kind": "function", "doc": "Get pre- and postprocessing operators for a model
description.\nuserd in `bioimageio.core.create_prediction_pipeline
RequiredMeasures(pre, post)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.proc_setup.RequiredMeasures.__init__": {"fullname": "bioimageio.core.proc_setup.RequiredMeasures.__init__", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredMeasures.__init__", "kind": "function", "doc": "Create new instance of RequiredMeasures(pre, post)
\n", "signature": "(\tpre: Set[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\tpost: Set[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)]])"}, "bioimageio.core.proc_setup.RequiredMeasures.pre": {"fullname": "bioimageio.core.proc_setup.RequiredMeasures.pre", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredMeasures.pre", "kind": "variable", "doc": "Alias for field number 0
\n", "annotation": ": Set[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.core.proc_setup.RequiredMeasures.post": {"fullname": "bioimageio.core.proc_setup.RequiredMeasures.post", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredMeasures.post", "kind": "variable", "doc": "Alias for field number 1
\n", "annotation": ": Set[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.core.proc_setup.RequiredDatasetMeasures": {"fullname": "bioimageio.core.proc_setup.RequiredDatasetMeasures", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredDatasetMeasures", "kind": "class", "doc": "RequiredDatasetMeasures(pre, post)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.proc_setup.RequiredDatasetMeasures.__init__": {"fullname": "bioimageio.core.proc_setup.RequiredDatasetMeasures.__init__", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredDatasetMeasures.__init__", "kind": "function", "doc": "Create new instance of RequiredDatasetMeasures(pre, post)
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\n", "annotation": ": Set[Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.core.proc_setup.RequiredSampleMeasures": {"fullname": "bioimageio.core.proc_setup.RequiredSampleMeasures", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredSampleMeasures", "kind": "class", "doc": "RequiredSampleMeasures(pre, post)
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\n", "annotation": ": Set[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.core.proc_setup.get_requried_measures": {"fullname": "bioimageio.core.proc_setup.get_requried_measures", "modulename": "bioimageio.core.proc_setup", "qualname": "get_requried_measures", "kind": "function", "doc": "\n", "signature": "(\tmodel: Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]) -> bioimageio.core.proc_setup.RequiredMeasures:", "funcdef": "def"}, "bioimageio.core.proc_setup.get_required_dataset_measures": {"fullname": "bioimageio.core.proc_setup.get_required_dataset_measures", "modulename": "bioimageio.core.proc_setup", "qualname": "get_required_dataset_measures", "kind": "function", "doc": "\n", "signature": "(\tmodel: Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]) -> bioimageio.core.proc_setup.RequiredDatasetMeasures:", "funcdef": "def"}, "bioimageio.core.proc_setup.get_requried_sample_measures": {"fullname": "bioimageio.core.proc_setup.get_requried_sample_measures", "modulename": "bioimageio.core.proc_setup", "qualname": "get_requried_sample_measures", "kind": "function", "doc": "\n", "signature": "(\tmodel: Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]) -> bioimageio.core.proc_setup.RequiredSampleMeasures:", "funcdef": "def"}, "bioimageio.core.sample": {"fullname": "bioimageio.core.sample", "modulename": "bioimageio.core.sample", "kind": "module", "doc": "\n"}, "bioimageio.core.sample.Sample": {"fullname": "bioimageio.core.sample.Sample", "modulename": "bioimageio.core.sample", "qualname": "Sample", "kind": "class", "doc": "A dataset sample
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\n", "annotation": ": Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]"}, "bioimageio.core.sample.Sample.id": {"fullname": "bioimageio.core.sample.Sample.id", "modulename": "bioimageio.core.sample", "qualname": "Sample.id", "kind": "variable", "doc": "identifier within the sample's dataset
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\n", "annotation": ": Hashable"}, "bioimageio.core.sample.SampleBlockBase.blocks": {"fullname": "bioimageio.core.sample.SampleBlockBase.blocks", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockBase.blocks", "kind": "variable", "doc": "Individual tensor blocks comprising this sample block
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\n", "annotation": ": int"}, "bioimageio.core.sample.SampleBlockBase.blocks_in_sample": {"fullname": "bioimageio.core.sample.SampleBlockBase.blocks_in_sample", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockBase.blocks_in_sample", "kind": "variable", "doc": "total number of blocks in the sample
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\n", "bases": "bioimageio.core.sample.SampleBlockBase[bioimageio.core.block_meta.BlockMeta]"}, "bioimageio.core.sample.SampleBlockMeta.__init__": {"fullname": "bioimageio.core.sample.SampleBlockMeta.__init__", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockMeta.__init__", "kind": "function", "doc": "\n", "signature": "(\tsample_shape: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\tsample_id: Hashable,\tblocks: Dict[bioimageio.spec.model.v0_5.TensorId, ~BlockT],\tblock_index: int,\tblocks_in_sample: int)"}, "bioimageio.core.sample.SampleBlockMeta.get_transformed": {"fullname": "bioimageio.core.sample.SampleBlockMeta.get_transformed", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockMeta.get_transformed", "kind": "function", "doc": "\n", "signature": "(\tself,\tnew_axes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, Union[bioimageio.core.sample.LinearSampleAxisTransform, int]]]) -> Self:", "funcdef": "def"}, "bioimageio.core.sample.SampleBlockMeta.with_data": {"fullname": "bioimageio.core.sample.SampleBlockMeta.with_data", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockMeta.with_data", "kind": "function", "doc": "\n", "signature": "(\tself,\tdata: Mapping[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.tensor.Tensor],\t*,\tstat: Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer>, return_type=PydanticUndefined, when_used='always')]]]) -> bioimageio.core.sample.SampleBlock:", "funcdef": "def"}, "bioimageio.core.sample.SampleBlock": {"fullname": "bioimageio.core.sample.SampleBlock", "modulename": "bioimageio.core.sample", "qualname": "SampleBlock", "kind": "class", "doc": "A block of a dataset sample
\n", "bases": "bioimageio.core.sample.SampleBlockBase[bioimageio.core.block.Block]"}, "bioimageio.core.sample.SampleBlock.__init__": {"fullname": "bioimageio.core.sample.SampleBlock.__init__", "modulename": "bioimageio.core.sample", "qualname": "SampleBlock.__init__", "kind": "function", "doc": "\n", "signature": "(\tsample_shape: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\tsample_id: Hashable,\tblocks: Dict[bioimageio.spec.model.v0_5.TensorId, ~BlockT],\tblock_index: int,\tblocks_in_sample: int,\tstat: Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer>, return_type=PydanticUndefined, when_used='always')]]])"}, "bioimageio.core.sample.SampleBlock.stat": {"fullname": "bioimageio.core.sample.SampleBlock.stat", "modulename": "bioimageio.core.sample", "qualname": "SampleBlock.stat", "kind": "variable", "doc": "computed statistics
\n", "annotation": ": Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]"}, "bioimageio.core.sample.SampleBlock.members": {"fullname": "bioimageio.core.sample.SampleBlock.members", "modulename": "bioimageio.core.sample", "qualname": "SampleBlock.members", "kind": "variable", "doc": "the sample block's tensors
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.tensor.Tensor]"}, "bioimageio.core.sample.SampleBlock.get_transformed_meta": {"fullname": "bioimageio.core.sample.SampleBlock.get_transformed_meta", "modulename": "bioimageio.core.sample", "qualname": "SampleBlock.get_transformed_meta", "kind": "function", "doc": "\n", "signature": "(\tself,\tnew_axes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, Union[bioimageio.core.sample.LinearSampleAxisTransform, int]]]) -> bioimageio.core.sample.SampleBlockMeta:", "funcdef": "def"}, "bioimageio.core.sample.SampleBlockWithOrigin": {"fullname": "bioimageio.core.sample.SampleBlockWithOrigin", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockWithOrigin", "kind": "class", "doc": "A SampleBlock
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) to the whole Sample
the sample this sample block was taken from
\n", "annotation": ": bioimageio.core.sample.Sample"}, "bioimageio.core.sample.sample_block_meta_generator": {"fullname": "bioimageio.core.sample.sample_block_meta_generator", "modulename": "bioimageio.core.sample", "qualname": "sample_block_meta_generator", "kind": "function", "doc": "\n", "signature": "(\tblocks: Iterable[Mapping[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.block_meta.BlockMeta]],\t*,\tsample_shape: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\tsample_id: Hashable):", "funcdef": "def"}, "bioimageio.core.sample.sample_block_generator": {"fullname": "bioimageio.core.sample.sample_block_generator", "modulename": "bioimageio.core.sample", "qualname": "sample_block_generator", "kind": "function", "doc": "\n", "signature": "(\tblocks: Iterable[Mapping[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.block_meta.BlockMeta]],\t*,\torigin: bioimageio.core.sample.Sample,\tpad_mode: Literal['edge', 'reflect', 'symmetric']) -> Iterable[bioimageio.core.sample.SampleBlockWithOrigin]:", "funcdef": "def"}, "bioimageio.core.stat_calculators": {"fullname": "bioimageio.core.stat_calculators", "modulename": "bioimageio.core.stat_calculators", "kind": "module", "doc": "\n"}, "bioimageio.core.stat_calculators.MeanCalculator": {"fullname": "bioimageio.core.stat_calculators.MeanCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanCalculator", "kind": "class", "doc": "to calculate sample and dataset mean for in-memory samples
\n"}, "bioimageio.core.stat_calculators.MeanCalculator.__init__": {"fullname": "bioimageio.core.stat_calculators.MeanCalculator.__init__", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanCalculator.__init__", "kind": "function", "doc": "\n", "signature": "(\tmember_id: bioimageio.spec.model.v0_5.TensorId,\taxes: Optional[Sequence[bioimageio.spec.model.v0_5.AxisId]])"}, "bioimageio.core.stat_calculators.MeanCalculator.compute": {"fullname": "bioimageio.core.stat_calculators.MeanCalculator.compute", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanCalculator.compute", "kind": "function", "doc": "\n", "signature": "(\tself,\tsample: bioimageio.core.sample.Sample) -> Dict[bioimageio.core.stat_measures.SampleMean, Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanCalculator.update": {"fullname": "bioimageio.core.stat_calculators.MeanCalculator.update", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanCalculator.update", "kind": "function", "doc": "\n", "signature": "(self, sample: bioimageio.core.sample.Sample) -> None:", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanCalculator.compute_and_update": {"fullname": "bioimageio.core.stat_calculators.MeanCalculator.compute_and_update", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanCalculator.compute_and_update", "kind": "function", "doc": "\n", "signature": "(\tself,\tsample: bioimageio.core.sample.Sample) -> Dict[bioimageio.core.stat_measures.SampleMean, Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanCalculator.finalize": {"fullname": "bioimageio.core.stat_calculators.MeanCalculator.finalize", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanCalculator.finalize", "kind": "function", "doc": "\n", "signature": "(\tself) -> Dict[bioimageio.core.stat_measures.DatasetMean, Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanVarStdCalculator": {"fullname": "bioimageio.core.stat_calculators.MeanVarStdCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanVarStdCalculator", "kind": "class", "doc": "to calculate sample and dataset mean, variance or standard deviation
\n"}, "bioimageio.core.stat_calculators.MeanVarStdCalculator.__init__": {"fullname": "bioimageio.core.stat_calculators.MeanVarStdCalculator.__init__", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanVarStdCalculator.__init__", "kind": "function", "doc": "\n", "signature": "(\tmember_id: bioimageio.spec.model.v0_5.TensorId,\taxes: Optional[Sequence[bioimageio.spec.model.v0_5.AxisId]])"}, "bioimageio.core.stat_calculators.MeanVarStdCalculator.compute": {"fullname": "bioimageio.core.stat_calculators.MeanVarStdCalculator.compute", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanVarStdCalculator.compute", "kind": "function", "doc": "\n", "signature": "(\tself,\tsample: bioimageio.core.sample.Sample) -> Dict[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleStd], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanVarStdCalculator.update": {"fullname": "bioimageio.core.stat_calculators.MeanVarStdCalculator.update", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanVarStdCalculator.update", "kind": "function", "doc": "\n", "signature": "(self, sample: bioimageio.core.sample.Sample):", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanVarStdCalculator.finalize": {"fullname": "bioimageio.core.stat_calculators.MeanVarStdCalculator.finalize", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanVarStdCalculator.finalize", "kind": "function", "doc": "\n", "signature": "(\tself) -> Dict[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetStd], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.SamplePercentilesCalculator": {"fullname": "bioimageio.core.stat_calculators.SamplePercentilesCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "SamplePercentilesCalculator", "kind": "class", "doc": "to calculate sample percentiles
\n"}, "bioimageio.core.stat_calculators.SamplePercentilesCalculator.__init__": {"fullname": "bioimageio.core.stat_calculators.SamplePercentilesCalculator.__init__", "modulename": "bioimageio.core.stat_calculators", "qualname": "SamplePercentilesCalculator.__init__", "kind": "function", "doc": "\n", "signature": "(\tmember_id: bioimageio.spec.model.v0_5.TensorId,\taxes: Optional[Sequence[bioimageio.spec.model.v0_5.AxisId]],\tqs: Collection[float])"}, "bioimageio.core.stat_calculators.SamplePercentilesCalculator.compute": {"fullname": "bioimageio.core.stat_calculators.SamplePercentilesCalculator.compute", "modulename": "bioimageio.core.stat_calculators", "qualname": "SamplePercentilesCalculator.compute", "kind": "function", "doc": "\n", "signature": "(\tself,\tsample: bioimageio.core.sample.Sample) -> Dict[bioimageio.core.stat_measures.SampleQuantile, Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanPercentilesCalculator": {"fullname": "bioimageio.core.stat_calculators.MeanPercentilesCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanPercentilesCalculator", "kind": "class", "doc": "to calculate dataset percentiles heuristically by averaging across samples\nnote: the returned dataset percentiles are an estiamte and not mathematically correct
\n"}, "bioimageio.core.stat_calculators.MeanPercentilesCalculator.__init__": {"fullname": "bioimageio.core.stat_calculators.MeanPercentilesCalculator.__init__", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanPercentilesCalculator.__init__", "kind": "function", "doc": "\n", "signature": "(\tmember_id: bioimageio.spec.model.v0_5.TensorId,\taxes: Optional[Sequence[bioimageio.spec.model.v0_5.AxisId]],\tqs: Collection[float])"}, "bioimageio.core.stat_calculators.MeanPercentilesCalculator.update": {"fullname": "bioimageio.core.stat_calculators.MeanPercentilesCalculator.update", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanPercentilesCalculator.update", "kind": "function", "doc": "\n", "signature": "(self, sample: bioimageio.core.sample.Sample):", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanPercentilesCalculator.finalize": {"fullname": "bioimageio.core.stat_calculators.MeanPercentilesCalculator.finalize", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanPercentilesCalculator.finalize", "kind": "function", "doc": "\n", "signature": "(\tself) -> Dict[bioimageio.core.stat_measures.DatasetPercentile, Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.CrickPercentilesCalculator": {"fullname": "bioimageio.core.stat_calculators.CrickPercentilesCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "CrickPercentilesCalculator", "kind": "class", "doc": "to calculate dataset percentiles with the experimental crick libray
\n"}, "bioimageio.core.stat_calculators.CrickPercentilesCalculator.__init__": {"fullname": "bioimageio.core.stat_calculators.CrickPercentilesCalculator.__init__", "modulename": "bioimageio.core.stat_calculators", "qualname": "CrickPercentilesCalculator.__init__", "kind": "function", "doc": "\n", "signature": "(\tmember_id: bioimageio.spec.model.v0_5.TensorId,\taxes: Optional[Sequence[bioimageio.spec.model.v0_5.AxisId]],\tqs: Collection[float])"}, "bioimageio.core.stat_calculators.CrickPercentilesCalculator.update": {"fullname": "bioimageio.core.stat_calculators.CrickPercentilesCalculator.update", "modulename": "bioimageio.core.stat_calculators", "qualname": "CrickPercentilesCalculator.update", "kind": "function", "doc": "\n", "signature": "(self, part: bioimageio.core.sample.Sample):", "funcdef": "def"}, "bioimageio.core.stat_calculators.CrickPercentilesCalculator.finalize": {"fullname": "bioimageio.core.stat_calculators.CrickPercentilesCalculator.finalize", "modulename": "bioimageio.core.stat_calculators", "qualname": "CrickPercentilesCalculator.finalize", "kind": "function", "doc": "\n", "signature": "(\tself) -> Dict[bioimageio.core.stat_measures.DatasetPercentile, Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator": {"fullname": "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "NaiveSampleMeasureCalculator", "kind": "class", "doc": "wrapper for measures to match interface of other sample measure calculators
\n"}, "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.__init__": {"fullname": "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.__init__", "modulename": "bioimageio.core.stat_calculators", "qualname": "NaiveSampleMeasureCalculator.__init__", "kind": "function", "doc": "\n", "signature": "(\tmember_id: bioimageio.spec.model.v0_5.TensorId,\tmeasure: Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)])"}, "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.tensor_name": {"fullname": "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.tensor_name", "modulename": "bioimageio.core.stat_calculators", "qualname": "NaiveSampleMeasureCalculator.tensor_name", "kind": "variable", "doc": "\n"}, "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.measure": {"fullname": "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.measure", "modulename": "bioimageio.core.stat_calculators", "qualname": "NaiveSampleMeasureCalculator.measure", "kind": "variable", "doc": "\n"}, "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.compute": {"fullname": "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.compute", "modulename": "bioimageio.core.stat_calculators", "qualname": "NaiveSampleMeasureCalculator.compute", "kind": "function", "doc": "\n", "signature": "(\tself,\tsample: bioimageio.core.sample.Sample) -> Dict[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.SampleMeasureCalculator": {"fullname": "bioimageio.core.stat_calculators.SampleMeasureCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "SampleMeasureCalculator", "kind": "variable", "doc": "\n", "default_value": "typing.Union[bioimageio.core.stat_calculators.MeanCalculator, bioimageio.core.stat_calculators.MeanVarStdCalculator, bioimageio.core.stat_calculators.SamplePercentilesCalculator, bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator]"}, "bioimageio.core.stat_calculators.DatasetMeasureCalculator": {"fullname": "bioimageio.core.stat_calculators.DatasetMeasureCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "DatasetMeasureCalculator", "kind": "variable", "doc": "\n", "default_value": "typing.Union[bioimageio.core.stat_calculators.MeanCalculator, bioimageio.core.stat_calculators.MeanVarStdCalculator, bioimageio.core.stat_calculators.MeanPercentilesCalculator]"}, "bioimageio.core.stat_calculators.StatsCalculator": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator", "kind": "class", "doc": "Estimates dataset statistics and computes sample statistics efficiently
\n"}, "bioimageio.core.stat_calculators.StatsCalculator.__init__": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator.__init__", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator.__init__", "kind": "function", "doc": "\n", "signature": "(\tmeasures: Collection[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\tinitial_dataset_measures: Optional[Mapping[Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer>, return_type=PydanticUndefined, when_used='always')]]]] = None)"}, "bioimageio.core.stat_calculators.StatsCalculator.sample_count": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator.sample_count", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator.sample_count", "kind": "variable", "doc": "\n"}, "bioimageio.core.stat_calculators.StatsCalculator.has_dataset_measures": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator.has_dataset_measures", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator.has_dataset_measures", "kind": "variable", "doc": "\n"}, "bioimageio.core.stat_calculators.StatsCalculator.update": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator.update", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator.update", "kind": "function", "doc": "\n", "signature": "(\tself,\tsample: Union[bioimageio.core.sample.Sample, Iterable[bioimageio.core.sample.Sample]]) -> None:", "funcdef": "def"}, "bioimageio.core.stat_calculators.StatsCalculator.finalize": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator.finalize", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator.finalize", "kind": "function", "doc": "returns aggregated dataset statistics
\n", "signature": "(\tself) -> Dict[Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.StatsCalculator.update_and_get_all": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator.update_and_get_all", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator.update_and_get_all", "kind": "function", "doc": "Returns sample as well as updated dataset statistics
\n", "signature": "(\tself,\tsample: Union[bioimageio.core.sample.Sample, Iterable[bioimageio.core.sample.Sample]]) -> Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.StatsCalculator.skip_update_and_get_all": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator.skip_update_and_get_all", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator.skip_update_and_get_all", "kind": "function", "doc": "Returns sample as well as previously computed dataset statistics
\n", "signature": "(\tself,\tsample: bioimageio.core.sample.Sample) -> Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.get_measure_calculators": {"fullname": "bioimageio.core.stat_calculators.get_measure_calculators", "modulename": "bioimageio.core.stat_calculators", "qualname": "get_measure_calculators", "kind": "function", "doc": "determines which calculators are needed to compute the required measures efficiently
\n", "signature": "(\trequired_measures: Iterable[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]) -> Tuple[List[Union[bioimageio.core.stat_calculators.MeanCalculator, bioimageio.core.stat_calculators.MeanVarStdCalculator, bioimageio.core.stat_calculators.SamplePercentilesCalculator, bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator]], List[Union[bioimageio.core.stat_calculators.MeanCalculator, bioimageio.core.stat_calculators.MeanVarStdCalculator, bioimageio.core.stat_calculators.MeanPercentilesCalculator]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.compute_dataset_measures": {"fullname": "bioimageio.core.stat_calculators.compute_dataset_measures", "modulename": "bioimageio.core.stat_calculators", "qualname": "compute_dataset_measures", "kind": "function", "doc": "compute all dataset measures
for the given dataset
compute all sample measures
for the given sample
compute all measures
for the given dataset
\nsample measures are computed for the last sample in dataset
Base class for protocol classes.
\n\nProtocol classes are defined as::
\n\nclass Proto(Protocol):\n def meth(self) -> int:\n ...\n
\n\nSuch classes are primarily used with static type checkers that recognize\nstructural subtyping (static duck-typing).
\n\nFor example::
\n\nclass C:\n def meth(self) -> int:\n return 0\n\ndef func(x: Proto) -> int:\n return x.meth()\n\nfunc(C()) # Passes static type check\n
\n\nSee PEP 544 for details. Protocol classes decorated with\n@typing.runtime_checkable act as simple-minded runtime protocols that check\nonly the presence of given attributes, ignoring their type signatures.\nProtocol classes can be generic, they are defined as::
\n\nclass GenProto[T](Protocol):\n def meth(self) -> T:\n ...\n
\n", "bases": "typing.Protocol"}, "bioimageio.core.stat_measures.SampleLike.__init__": {"fullname": "bioimageio.core.stat_measures.SampleLike.__init__", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleLike.__init__", "kind": "function", "doc": "\n", "signature": "(*args, **kwargs)"}, "bioimageio.core.stat_measures.SampleLike.members": {"fullname": "bioimageio.core.stat_measures.SampleLike.members", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleLike.members", "kind": "variable", "doc": "\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.tensor.Tensor]"}, "bioimageio.core.stat_measures.MeasureBase": {"fullname": "bioimageio.core.stat_measures.MeasureBase", "modulename": "bioimageio.core.stat_measures", "qualname": "MeasureBase", "kind": "class", "doc": "Usage docs: https://docs.pydantic.dev/2.9/concepts/models/
\n\nA base class for creating Pydantic models.
\n\n__init__
[Signature
][inspect.Signature] of the model.__init__
function.Model.__validators__
and Model.__root_validators__
from Pydantic V1.RootModel
][pydantic.root_model.RootModel].pydantic-core
SchemaSerializer
used to dump instances of the model.pydantic-core
SchemaValidator
used to validate instances of the model.extra
][pydantic.config.ConfigDict.extra]\nis set to 'allow'
.Usage docs: https://docs.pydantic.dev/2.9/concepts/models/
\n\nA base class for creating Pydantic models.
\n\n__init__
[Signature
][inspect.Signature] of the model.__init__
function.Model.__validators__
and Model.__root_validators__
from Pydantic V1.RootModel
][pydantic.root_model.RootModel].pydantic-core
SchemaSerializer
used to dump instances of the model.pydantic-core
SchemaValidator
used to validate instances of the model.extra
][pydantic.config.ConfigDict.extra]\nis set to 'allow'
.compute the measure
\n", "signature": "(\tself,\tsample: bioimageio.core.stat_measures.SampleLike) -> Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]:", "funcdef": "def"}, "bioimageio.core.stat_measures.DatasetMeasureBase": {"fullname": "bioimageio.core.stat_measures.DatasetMeasureBase", "modulename": "bioimageio.core.stat_measures", "qualname": "DatasetMeasureBase", "kind": "class", "doc": "Usage docs: https://docs.pydantic.dev/2.9/concepts/models/
\n\nA base class for creating Pydantic models.
\n\n__init__
[Signature
][inspect.Signature] of the model.__init__
function.Model.__validators__
and Model.__root_validators__
from Pydantic V1.RootModel
][pydantic.root_model.RootModel].pydantic-core
SchemaSerializer
used to dump instances of the model.pydantic-core
SchemaValidator
used to validate instances of the model.extra
][pydantic.config.ConfigDict.extra]\nis set to 'allow'
.The mean value of a single tensor
\n", "bases": "_Mean, SampleMeasureBase"}, "bioimageio.core.stat_measures.SampleMean.compute": {"fullname": "bioimageio.core.stat_measures.SampleMean.compute", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleMean.compute", "kind": "function", "doc": "compute the measure
\n", "signature": "(\tself,\tsample: bioimageio.core.stat_measures.SampleLike) -> Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]:", "funcdef": "def"}, "bioimageio.core.stat_measures.SampleMean.model_post_init": {"fullname": "bioimageio.core.stat_measures.SampleMean.model_post_init", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleMean.model_post_init", "kind": "function", "doc": "Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
The mean value across multiple samples
\n", "bases": "_Mean, DatasetMeasureBase"}, "bioimageio.core.stat_measures.DatasetMean.model_post_init": {"fullname": "bioimageio.core.stat_measures.DatasetMean.model_post_init", "modulename": "bioimageio.core.stat_measures", "qualname": "DatasetMean.model_post_init", "kind": "function", "doc": "Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
The standard deviation of a single tensor
\n", "bases": "_Std, SampleMeasureBase"}, "bioimageio.core.stat_measures.SampleStd.compute": {"fullname": "bioimageio.core.stat_measures.SampleStd.compute", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleStd.compute", "kind": "function", "doc": "compute the measure
\n", "signature": "(\tself,\tsample: bioimageio.core.stat_measures.SampleLike) -> Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]:", "funcdef": "def"}, "bioimageio.core.stat_measures.SampleStd.model_post_init": {"fullname": "bioimageio.core.stat_measures.SampleStd.model_post_init", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleStd.model_post_init", "kind": "function", "doc": "Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
The standard deviation across multiple samples
\n", "bases": "_Std, DatasetMeasureBase"}, "bioimageio.core.stat_measures.DatasetStd.model_post_init": {"fullname": "bioimageio.core.stat_measures.DatasetStd.model_post_init", "modulename": "bioimageio.core.stat_measures", "qualname": "DatasetStd.model_post_init", "kind": "function", "doc": "Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
The variance of a single tensor
\n", "bases": "_Var, SampleMeasureBase"}, "bioimageio.core.stat_measures.SampleVar.compute": {"fullname": "bioimageio.core.stat_measures.SampleVar.compute", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleVar.compute", "kind": "function", "doc": "compute the measure
\n", "signature": "(\tself,\tsample: bioimageio.core.stat_measures.SampleLike) -> Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]:", "funcdef": "def"}, "bioimageio.core.stat_measures.SampleVar.model_post_init": {"fullname": "bioimageio.core.stat_measures.SampleVar.model_post_init", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleVar.model_post_init", "kind": "function", "doc": "Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
The variance across multiple samples
\n", "bases": "_Var, DatasetMeasureBase"}, "bioimageio.core.stat_measures.DatasetVar.model_post_init": {"fullname": "bioimageio.core.stat_measures.DatasetVar.model_post_init", "modulename": "bioimageio.core.stat_measures", "qualname": "DatasetVar.model_post_init", "kind": "function", "doc": "Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
The n
th percentile of a single tensor
compute the measure
\n", "signature": "(\tself,\tsample: bioimageio.core.stat_measures.SampleLike) -> Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f4647f7a840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f4647f7aa20>, return_type=PydanticUndefined, when_used='always')]]:", "funcdef": "def"}, "bioimageio.core.stat_measures.SampleQuantile.model_post_init": {"fullname": "bioimageio.core.stat_measures.SampleQuantile.model_post_init", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleQuantile.model_post_init", "kind": "function", "doc": "Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
The n
th percentile across multiple samples
Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
A wrapper around an xr.DataArray for better integration with bioimageio.spec\nand improved type annotations.
\n", "bases": "bioimageio.core._magic_tensor_ops.MagicTensorOpsMixin"}, "bioimageio.core.tensor.Tensor.__init__": {"fullname": "bioimageio.core.tensor.Tensor.__init__", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.__init__", "kind": "function", "doc": "\n", "signature": "(\tarray: numpy.ndarray[typing.Any, numpy.dtype[typing.Any]],\tdims: Sequence[Union[bioimageio.spec.model.v0_5.AxisId, Literal['b', 'i', 't', 'c', 'z', 'y', 'x'], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexInputAxis, bioimageio.spec.model.v0_5.TimeInputAxis, bioimageio.spec.model.v0_5.SpaceInputAxis], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexOutputAxis, Annotated[Union[Annotated[bioimageio.spec.model.v0_5.TimeOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.core.axis.Axis]])"}, "bioimageio.core.tensor.Tensor.from_xarray": {"fullname": "bioimageio.core.tensor.Tensor.from_xarray", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.from_xarray", "kind": "function", "doc": "create a Tensor
from an xarray data array
note for internal use: this factory method is round-trip save\n for any Tensor
's data
property (an xarray.DataArray).
create a Tensor
from a numpy array
axes
is None and axes guessing fails.Tuple of dimension names associated with this tensor.
\n"}, "bioimageio.core.tensor.Tensor.tagged_shape": {"fullname": "bioimageio.core.tensor.Tensor.tagged_shape", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.tagged_shape", "kind": "variable", "doc": "(alias for sizes
) Ordered, immutable mapping from axis ids to lengths.
Tuple of tensor axes lengths
\n"}, "bioimageio.core.tensor.Tensor.size": {"fullname": "bioimageio.core.tensor.Tensor.size", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.size", "kind": "variable", "doc": "Number of elements in the tensor.
\n\nEqual to math.prod(tensor.shape), i.e., the product of the tensors\u2019 dimensions.
\n"}, "bioimageio.core.tensor.Tensor.sum": {"fullname": "bioimageio.core.tensor.Tensor.sum", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.sum", "kind": "function", "doc": "Reduce this Tensor's data by applying sum along some dimension(s).
\n", "signature": "(\tself,\tdim: Union[bioimageio.spec.model.v0_5.AxisId, Sequence[bioimageio.spec.model.v0_5.AxisId], NoneType] = None) -> Self:", "funcdef": "def"}, "bioimageio.core.tensor.Tensor.ndim": {"fullname": "bioimageio.core.tensor.Tensor.ndim", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.ndim", "kind": "variable", "doc": "Number of tensor dimensions.
\n"}, "bioimageio.core.tensor.Tensor.dtype": {"fullname": "bioimageio.core.tensor.Tensor.dtype", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.dtype", "kind": "variable", "doc": "\n", "annotation": ": Literal['bool', 'float32', 'float64', 'int8', 'int16', 'int32', 'int64', 'uint8', 'uint16', 'uint32', 'uint64']"}, "bioimageio.core.tensor.Tensor.sizes": {"fullname": "bioimageio.core.tensor.Tensor.sizes", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.sizes", "kind": "variable", "doc": "Ordered, immutable mapping from axis ids to axis lengths.
\n"}, "bioimageio.core.tensor.Tensor.astype": {"fullname": "bioimageio.core.tensor.Tensor.astype", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.astype", "kind": "function", "doc": "Return tensor cast to dtype
note: if dtype is already satisfied copy if copy
Return a tensor whose values are limited to [min, max].\nAt least one of max or min must be given.
\n", "signature": "(self, min: Optional[float] = None, max: Optional[float] = None):", "funcdef": "def"}, "bioimageio.core.tensor.Tensor.crop_to": {"fullname": "bioimageio.core.tensor.Tensor.crop_to", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.crop_to", "kind": "function", "doc": "crop to match sizes
pad tensor
to match sizes
return cropped/padded tensor with sizes
return a transposed tensor
\n\nBioimage.io description of an application.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.ApplicationDescr.type": {"fullname": "bioimageio.spec.ApplicationDescr.type", "modulename": "bioimageio.spec", "qualname": "ApplicationDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['application']"}, "bioimageio.spec.ApplicationDescr.id": {"fullname": "bioimageio.spec.ApplicationDescr.id", "modulename": "bioimageio.spec", "qualname": "ApplicationDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.application.v0_3.ApplicationId]"}, "bioimageio.spec.ApplicationDescr.parent": {"fullname": "bioimageio.spec.ApplicationDescr.parent", "modulename": "bioimageio.spec", "qualname": "ApplicationDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.application.v0_3.ApplicationId]"}, "bioimageio.spec.ApplicationDescr.source": {"fullname": "bioimageio.spec.ApplicationDescr.source", "modulename": "bioimageio.spec", "qualname": "ApplicationDescr.source", "kind": "variable", "doc": "The primary source of the application
\n", "annotation": ": Annotated[Optional[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')]], FieldInfo(annotation=NoneType, required=True, description='URL or path to the source of the application')]"}, "bioimageio.spec.ApplicationDescr.implemented_format_version": {"fullname": "bioimageio.spec.ApplicationDescr.implemented_format_version", "modulename": "bioimageio.spec", "qualname": "ApplicationDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.ApplicationDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.ApplicationDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec", "qualname": "ApplicationDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.ApplicationDescr.model_post_init": {"fullname": "bioimageio.spec.ApplicationDescr.model_post_init", "modulename": "bioimageio.spec", "qualname": "ApplicationDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.build_description": {"fullname": "bioimageio.spec.build_description", "modulename": "bioimageio.spec", "qualname": "build_description", "kind": "function", "doc": "build a bioimage.io resource description from an RDF's content.
\n\nUse load_description
if you want to build a resource description from an rdf.yaml\nor bioimage.io zip-package.
\n\n", "signature": "(\tcontent: Dict[str, YamlValue],\t/,\t*,\tcontext: Optional[bioimageio.spec._internal.validation_context.ValidationContext] = None,\tformat_version: Union[Literal['latest', 'discover'], str] = 'discover') -> Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec._internal.common_nodes.InvalidDescr]:", "funcdef": "def"}, "bioimageio.spec.DatasetDescr": {"fullname": "bioimageio.spec.DatasetDescr", "modulename": "bioimageio.spec", "qualname": "DatasetDescr", "kind": "class", "doc": "An object holding all metadata of the bioimage.io resource
\n
A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage\nprocessing.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.DatasetDescr.type": {"fullname": "bioimageio.spec.DatasetDescr.type", "modulename": "bioimageio.spec", "qualname": "DatasetDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['dataset']"}, "bioimageio.spec.DatasetDescr.id": {"fullname": "bioimageio.spec.DatasetDescr.id", "modulename": "bioimageio.spec", "qualname": "DatasetDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.dataset.v0_3.DatasetId]"}, "bioimageio.spec.DatasetDescr.parent": {"fullname": "bioimageio.spec.DatasetDescr.parent", "modulename": "bioimageio.spec", "qualname": "DatasetDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.dataset.v0_3.DatasetId]"}, "bioimageio.spec.DatasetDescr.source": {"fullname": "bioimageio.spec.DatasetDescr.source", "modulename": "bioimageio.spec", "qualname": "DatasetDescr.source", "kind": "variable", "doc": "\"URL to the source of the dataset.
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.DatasetDescr.implemented_format_version": {"fullname": "bioimageio.spec.DatasetDescr.implemented_format_version", "modulename": "bioimageio.spec", "qualname": "DatasetDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.DatasetDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.DatasetDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec", "qualname": "DatasetDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.DatasetDescr.model_post_init": {"fullname": "bioimageio.spec.DatasetDescr.model_post_init", "modulename": "bioimageio.spec", "qualname": "DatasetDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.dump_description": {"fullname": "bioimageio.spec.dump_description", "modulename": "bioimageio.spec", "qualname": "dump_description", "kind": "function", "doc": "Converts a resource to a dictionary containing only simple types that can directly be serialzed to YAML.
\n", "signature": "(\trd: Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec._internal.common_nodes.InvalidDescr],\texclude_unset: bool = True) -> Dict[str, YamlValue]:", "funcdef": "def"}, "bioimageio.spec.enable_pretty_validation_errors_in_ipynb": {"fullname": "bioimageio.spec.enable_pretty_validation_errors_in_ipynb", "modulename": "bioimageio.spec", "qualname": "enable_pretty_validation_errors_in_ipynb", "kind": "function", "doc": "A modestly hacky way to display prettified validaiton error messages and traceback\nin interactive Python notebooks
\n", "signature": "():", "funcdef": "def"}, "bioimageio.spec.GenericDescr": {"fullname": "bioimageio.spec.GenericDescr", "modulename": "bioimageio.spec", "qualname": "GenericDescr", "kind": "class", "doc": "Specification of the fields used in a generic bioimage.io-compliant resource description file (RDF).
\n\nAn RDF is a YAML file that describes a resource such as a model, a dataset, or a notebook.\nNote that those resources are described with a type-specific RDF.\nUse this generic resource description, if none of the known specific types matches your resource.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.GenericDescr.type": {"fullname": "bioimageio.spec.GenericDescr.type", "modulename": "bioimageio.spec", "qualname": "GenericDescr.type", "kind": "variable", "doc": "The resource type assigns a broad category to the resource.
\n", "annotation": ": Annotated[str, Annotated[~_StrType, Predicate(str.islower)]]"}, "bioimageio.spec.GenericDescr.id": {"fullname": "bioimageio.spec.GenericDescr.id", "modulename": "bioimageio.spec", "qualname": "GenericDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_3.ResourceId]"}, "bioimageio.spec.GenericDescr.parent": {"fullname": "bioimageio.spec.GenericDescr.parent", "modulename": "bioimageio.spec", "qualname": "GenericDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_3.ResourceId]"}, "bioimageio.spec.GenericDescr.source": {"fullname": "bioimageio.spec.GenericDescr.source", "modulename": "bioimageio.spec", "qualname": "GenericDescr.source", "kind": "variable", "doc": "The primary source of the resource
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.GenericDescr.check_specific_types": {"fullname": "bioimageio.spec.GenericDescr.check_specific_types", "modulename": "bioimageio.spec", "qualname": "GenericDescr.check_specific_types", "kind": "function", "doc": "\n", "signature": "(cls, value: str) -> str:", "funcdef": "def"}, "bioimageio.spec.GenericDescr.implemented_format_version": {"fullname": "bioimageio.spec.GenericDescr.implemented_format_version", "modulename": "bioimageio.spec", "qualname": "GenericDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.GenericDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.GenericDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec", "qualname": "GenericDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.GenericDescr.model_post_init": {"fullname": "bioimageio.spec.GenericDescr.model_post_init", "modulename": "bioimageio.spec", "qualname": "GenericDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.get_resource_package_content": {"fullname": "bioimageio.spec.get_resource_package_content", "modulename": "bioimageio.spec", "qualname": "get_resource_package_content", "kind": "function", "doc": "A representation of an invalid resource description
\n", "bases": "bioimageio.spec._internal.common_nodes.ResourceDescrBase"}, "bioimageio.spec.InvalidDescr.type": {"fullname": "bioimageio.spec.InvalidDescr.type", "modulename": "bioimageio.spec", "qualname": "InvalidDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Any"}, "bioimageio.spec.InvalidDescr.format_version": {"fullname": "bioimageio.spec.InvalidDescr.format_version", "modulename": "bioimageio.spec", "qualname": "InvalidDescr.format_version", "kind": "variable", "doc": "\n", "annotation": ": Any"}, "bioimageio.spec.InvalidDescr.fields_to_set_explicitly": {"fullname": "bioimageio.spec.InvalidDescr.fields_to_set_explicitly", "modulename": "bioimageio.spec", "qualname": "InvalidDescr.fields_to_set_explicitly", "kind": "variable", "doc": "set set these fields explicitly with their default value if they are not set,\nsuch that they are always included even when dumping with 'exlude_unset'
\n", "annotation": ": ClassVar[FrozenSet[LiteralString]]", "default_value": "frozenset()"}, "bioimageio.spec.InvalidDescr.implemented_format_version": {"fullname": "bioimageio.spec.InvalidDescr.implemented_format_version", "modulename": "bioimageio.spec", "qualname": "InvalidDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'unknown'"}, "bioimageio.spec.InvalidDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.InvalidDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec", "qualname": "InvalidDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 0, 0)"}, "bioimageio.spec.InvalidDescr.model_post_init": {"fullname": "bioimageio.spec.InvalidDescr.model_post_init", "modulename": "bioimageio.spec", "qualname": "InvalidDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.LatestResourceDescr": {"fullname": "bioimageio.spec.LatestResourceDescr", "modulename": "bioimageio.spec", "qualname": "LatestResourceDescr", "kind": "variable", "doc": "\n", "default_value": "typing.Union[typing.Annotated[typing.Union[bioimageio.spec.application.v0_3.ApplicationDescr, bioimageio.spec.dataset.v0_3.DatasetDescr, bioimageio.spec.model.v0_5.ModelDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec.generic.v0_3.GenericDescr]"}, "bioimageio.spec.load_dataset_description": {"fullname": "bioimageio.spec.load_dataset_description", "modulename": "bioimageio.spec", "qualname": "load_dataset_description", "kind": "function", "doc": "same as load_description
, but addtionally ensures that the loaded\ndescription is valid and of type 'dataset'.
load a bioimage.io resource description
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], zipfile.ZipFile],\t/,\t*,\tformat_version: Union[Literal['discover'], Literal['latest'], str] = 'discover',\tperform_io_checks: bool = True,\tknown_files: Optional[Dict[str, bioimageio.spec._internal.io_basics.Sha256]] = None) -> bioimageio.spec.summary.ValidationSummary:", "funcdef": "def"}, "bioimageio.spec.load_description": {"fullname": "bioimageio.spec.load_description", "modulename": "bioimageio.spec", "qualname": "load_description", "kind": "function", "doc": "Validation summary of the bioimage.io resource found at
\nsource
.
load a bioimage.io resource description
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], zipfile.ZipFile],\t/,\t*,\tformat_version: Union[Literal['discover'], Literal['latest'], str] = 'discover',\tperform_io_checks: bool = True,\tknown_files: Optional[Dict[str, bioimageio.spec._internal.io_basics.Sha256]] = None) -> Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec._internal.common_nodes.InvalidDescr]:", "funcdef": "def"}, "bioimageio.spec.load_model_description": {"fullname": "bioimageio.spec.load_model_description", "modulename": "bioimageio.spec", "qualname": "load_model_description", "kind": "function", "doc": "An object holding all metadata of the bioimage.io resource
\n
same as load_description
, but addtionally ensures that the loaded\ndescription is valid and of type 'model'.
Specification of the fields used in a bioimage.io-compliant RDF to describe AI models with pretrained weights.\nThese fields are typically stored in a YAML file which we call a model resource description file (model RDF).
\n", "bases": "bioimageio.spec.generic.v0_3.GenericModelDescrBase"}, "bioimageio.spec.ModelDescr.format_version": {"fullname": "bioimageio.spec.ModelDescr.format_version", "modulename": "bioimageio.spec", "qualname": "ModelDescr.format_version", "kind": "variable", "doc": "Version of the bioimage.io model description specification used.\nWhen creating a new model always use the latest micro/patch version described here.\nThe format_version
is important for any consumer software to understand how to parse the fields.
Specialized resource type 'model'
\n", "annotation": ": Literal['model']"}, "bioimageio.spec.ModelDescr.id": {"fullname": "bioimageio.spec.ModelDescr.id", "modulename": "bioimageio.spec", "qualname": "ModelDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.ModelId]"}, "bioimageio.spec.ModelDescr.authors": {"fullname": "bioimageio.spec.ModelDescr.authors", "modulename": "bioimageio.spec", "qualname": "ModelDescr.authors", "kind": "variable", "doc": "The authors are the creators of the model RDF and the primary points of contact.
\n", "annotation": ": Annotated[List[bioimageio.spec.generic.v0_3.Author], MinLen(min_length=1)]"}, "bioimageio.spec.ModelDescr.documentation": {"fullname": "bioimageio.spec.ModelDescr.documentation", "modulename": "bioimageio.spec", "qualname": "ModelDescr.documentation", "kind": "variable", "doc": "\u2208\ud83d\udce6 URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is README.md
. An .md
suffix is mandatory.\nThe documentation should include a '#[#] Validation' (sub)section\nwith details on how to quantitatively validate the model on unseen data.
Describes the input tensors expected by this model.
\n", "annotation": ": Annotated[Sequence[bioimageio.spec.model.v0_5.InputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.ModelDescr.name": {"fullname": "bioimageio.spec.ModelDescr.name", "modulename": "bioimageio.spec", "qualname": "ModelDescr.name", "kind": "variable", "doc": "A human-readable name of this model.\nIt should be no longer than 64 characters\nand may only contain letter, number, underscore, minus, parentheses and spaces.\nWe recommend to chose a name that refers to the model's task and image modality.
\n", "annotation": ": Annotated[str, RestrictCharacters(alphabet='abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_- ()'), MinLen(min_length=5), MaxLen(max_length=128), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f464562a0c0>, severity=20, msg='Name longer than 64 characters.', context={'typ': Annotated[Any, MaxLen(max_length=64)]})]"}, "bioimageio.spec.ModelDescr.outputs": {"fullname": "bioimageio.spec.ModelDescr.outputs", "modulename": "bioimageio.spec", "qualname": "ModelDescr.outputs", "kind": "variable", "doc": "Describes the output tensors.
\n", "annotation": ": Annotated[Sequence[bioimageio.spec.model.v0_5.OutputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.ModelDescr.packaged_by": {"fullname": "bioimageio.spec.ModelDescr.packaged_by", "modulename": "bioimageio.spec", "qualname": "ModelDescr.packaged_by", "kind": "variable", "doc": "The persons that have packaged and uploaded this model.\nOnly required if those persons differ from the authors
.
The model from which this model is derived, e.g. by fine-tuning the weights.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.LinkedModel]"}, "bioimageio.spec.ModelDescr.run_mode": {"fullname": "bioimageio.spec.ModelDescr.run_mode", "modulename": "bioimageio.spec", "qualname": "ModelDescr.run_mode", "kind": "variable", "doc": "Custom run mode for this model: for more complex prediction procedures like test time\ndata augmentation that currently cannot be expressed in the specification.\nNo standard run modes are defined yet.
\n", "annotation": ": Annotated[Optional[bioimageio.spec.model.v0_4.RunMode], AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f464562a520>, severity=30, msg="Run mode '{value}' has limited support across consumer softwares.", context={'typ': None})]"}, "bioimageio.spec.ModelDescr.timestamp": {"fullname": "bioimageio.spec.ModelDescr.timestamp", "modulename": "bioimageio.spec", "qualname": "ModelDescr.timestamp", "kind": "variable", "doc": "Timestamp in ISO 8601 format\nwith a few restrictions listed here.\n(In Python a datetime object is valid, too).
\n", "annotation": ": bioimageio.spec._internal.types.Datetime"}, "bioimageio.spec.ModelDescr.training_data": {"fullname": "bioimageio.spec.ModelDescr.training_data", "modulename": "bioimageio.spec", "qualname": "ModelDescr.training_data", "kind": "variable", "doc": "The dataset used to train this model
\n", "annotation": ": Annotated[Union[NoneType, bioimageio.spec.dataset.v0_3.LinkedDataset, bioimageio.spec.dataset.v0_3.DatasetDescr, bioimageio.spec.dataset.v0_2.DatasetDescr], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]"}, "bioimageio.spec.ModelDescr.weights": {"fullname": "bioimageio.spec.ModelDescr.weights", "modulename": "bioimageio.spec", "qualname": "ModelDescr.weights", "kind": "variable", "doc": "The weights for this model.\nWeights can be given for different formats, but should otherwise be equivalent.\nThe available weight formats determine which consumers can use this model.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.WeightsDescr, WrapSerializer(func=<function package_weights at 0x7f4654144360>, return_type=PydanticUndefined, when_used='always')]"}, "bioimageio.spec.ModelDescr.get_input_test_arrays": {"fullname": "bioimageio.spec.ModelDescr.get_input_test_arrays", "modulename": "bioimageio.spec", "qualname": "ModelDescr.get_input_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.ModelDescr.get_output_test_arrays": {"fullname": "bioimageio.spec.ModelDescr.get_output_test_arrays", "modulename": "bioimageio.spec", "qualname": "ModelDescr.get_output_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.ModelDescr.get_batch_size": {"fullname": "bioimageio.spec.ModelDescr.get_batch_size", "modulename": "bioimageio.spec", "qualname": "ModelDescr.get_batch_size", "kind": "function", "doc": "\n", "signature": "(\ttensor_sizes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]) -> int:", "funcdef": "def"}, "bioimageio.spec.ModelDescr.get_output_tensor_sizes": {"fullname": "bioimageio.spec.ModelDescr.get_output_tensor_sizes", "modulename": "bioimageio.spec", "qualname": "ModelDescr.get_output_tensor_sizes", "kind": "function", "doc": "Returns the tensor output sizes for given input_sizes.\nOnly if input_sizes has a valid input shape, the tensor output size is exact.\nOtherwise it might be larger than the actual (valid) output
\n", "signature": "(\tself,\tinput_sizes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]) -> Dict[bioimageio.spec.model.v0_5.TensorId, Dict[bioimageio.spec.model.v0_5.AxisId, Union[int, bioimageio.spec.model.v0_5._DataDepSize]]]:", "funcdef": "def"}, "bioimageio.spec.ModelDescr.get_ns": {"fullname": "bioimageio.spec.ModelDescr.get_ns", "modulename": "bioimageio.spec", "qualname": "ModelDescr.get_ns", "kind": "function", "doc": "get parameter n
for each parameterized axis\nsuch that the valid input size is >= the given input size
Determine input and output block shape for scale factors ns\nof parameterized input sizes.
\n\nn
for each axis (keyed by (tensor_id, axis_id))\nthat is parameterized as size = min + n * step
.n
, is larger\nthan max_input_shape is set to the minimal value n_min
for which\nthis is still true.\nUse this for small input samples or large values of ns.\nOr simply whenever you know the full input shape.\n\n", "signature": "(\tself,\tns: Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int],\tbatch_size: Optional[int] = None,\t*,\tmax_input_shape: Optional[Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int]] = None) -> bioimageio.spec.model.v0_5._AxisSizes:", "funcdef": "def"}, "bioimageio.spec.ModelDescr.implemented_format_version": {"fullname": "bioimageio.spec.ModelDescr.implemented_format_version", "modulename": "bioimageio.spec", "qualname": "ModelDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.5.3'"}, "bioimageio.spec.ModelDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.ModelDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec", "qualname": "ModelDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 5, 3)"}, "bioimageio.spec.ModelDescr.model_post_init": {"fullname": "bioimageio.spec.ModelDescr.model_post_init", "modulename": "bioimageio.spec", "qualname": "ModelDescr.model_post_init", "kind": "function", "doc": "Resolved axis sizes for model inputs and outputs.
\n
We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.NotebookDescr": {"fullname": "bioimageio.spec.NotebookDescr", "modulename": "bioimageio.spec", "qualname": "NotebookDescr", "kind": "class", "doc": "Bioimage.io description of a Jupyter notebook.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.NotebookDescr.type": {"fullname": "bioimageio.spec.NotebookDescr.type", "modulename": "bioimageio.spec", "qualname": "NotebookDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['notebook']"}, "bioimageio.spec.NotebookDescr.id": {"fullname": "bioimageio.spec.NotebookDescr.id", "modulename": "bioimageio.spec", "qualname": "NotebookDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.notebook.v0_3.NotebookId]"}, "bioimageio.spec.NotebookDescr.parent": {"fullname": "bioimageio.spec.NotebookDescr.parent", "modulename": "bioimageio.spec", "qualname": "NotebookDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.notebook.v0_3.NotebookId]"}, "bioimageio.spec.NotebookDescr.source": {"fullname": "bioimageio.spec.NotebookDescr.source", "modulename": "bioimageio.spec", "qualname": "NotebookDescr.source", "kind": "variable", "doc": "The Jupyter notebook
\n", "annotation": ": Union[Annotated[bioimageio.spec._internal.url.HttpUrl, WithSuffix(suffix='.ipynb', case_sensitive=True)], Annotated[pathlib.Path, PathType(path_type='file'), Predicate(is_absolute), WithSuffix(suffix='.ipynb', case_sensitive=True)], Annotated[bioimageio.spec._internal.io.RelativeFilePath, WithSuffix(suffix='.ipynb', case_sensitive=True)]]"}, "bioimageio.spec.NotebookDescr.implemented_format_version": {"fullname": "bioimageio.spec.NotebookDescr.implemented_format_version", "modulename": "bioimageio.spec", "qualname": "NotebookDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.NotebookDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.NotebookDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec", "qualname": "NotebookDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.NotebookDescr.model_post_init": {"fullname": "bioimageio.spec.NotebookDescr.model_post_init", "modulename": "bioimageio.spec", "qualname": "NotebookDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.ResourceDescr": {"fullname": "bioimageio.spec.ResourceDescr", "modulename": "bioimageio.spec", "qualname": "ResourceDescr", "kind": "variable", "doc": "\n", "default_value": "typing.Union[typing.Annotated[typing.Union[typing.Annotated[typing.Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.spec.save_bioimageio_package_as_folder": {"fullname": "bioimageio.spec.save_bioimageio_package_as_folder", "modulename": "bioimageio.spec", "qualname": "save_bioimageio_package_as_folder", "kind": "function", "doc": "Write the content of a bioimage.io resource package to a folder.
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], Dict[str, YamlValue], Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\t/,\t*,\toutput_path: Union[Annotated[pathlib.Path, PathType(path_type='new')], Annotated[pathlib.Path, PathType(path_type='dir')], NoneType] = None,\tweights_priority_order: Optional[Sequence[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]] = None) -> Annotated[pathlib.Path, PathType(path_type='dir')]:", "funcdef": "def"}, "bioimageio.spec.save_bioimageio_package_to_stream": {"fullname": "bioimageio.spec.save_bioimageio_package_to_stream", "modulename": "bioimageio.spec", "qualname": "save_bioimageio_package_to_stream", "kind": "function", "doc": "directory path to bioimageio package folder
\n
Package a bioimageio resource into a stream.
\n\nNote: this function bypasses safety checks and does not load/validate the model after writing.
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], Dict[str, YamlValue], Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\t/,\t*,\tcompression: int = 8,\tcompression_level: int = 1,\toutput_stream: Optional[IO[bytes]] = None,\tweights_priority_order: Optional[Sequence[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]] = None) -> IO[bytes]:", "funcdef": "def"}, "bioimageio.spec.save_bioimageio_package": {"fullname": "bioimageio.spec.save_bioimageio_package", "modulename": "bioimageio.spec", "qualname": "save_bioimageio_package", "kind": "function", "doc": "stream of zipped bioimageio package
\n
Package a bioimageio resource as a zip file.
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], Dict[str, YamlValue], Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\t/,\t*,\tcompression: int = 8,\tcompression_level: int = 1,\toutput_path: Union[Annotated[pathlib.Path, PathType(path_type='new')], Annotated[pathlib.Path, PathType(path_type='file')], NoneType] = None,\tweights_priority_order: Optional[Sequence[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]] = None) -> Annotated[pathlib.Path, PathType(path_type='file')]:", "funcdef": "def"}, "bioimageio.spec.save_bioimageio_yaml_only": {"fullname": "bioimageio.spec.save_bioimageio_yaml_only", "modulename": "bioimageio.spec", "qualname": "save_bioimageio_yaml_only", "kind": "function", "doc": "path to zipped bioimageio package
\n
write the metadata of a resource description (rd
) to file
\nwithout writing any of the referenced files in it.
Note: To save a resource description with its associated files as a package,\nuse save_bioimageio_package
or save_bioimageio_package_as_folder
.
validate a bioimageio.yaml file (RDF)
\n", "signature": "(\tdata: Dict[str, YamlValue],\t/,\t*,\tformat_version: Union[Literal['latest', 'discover'], str] = 'discover',\tcontext: Optional[bioimageio.spec._internal.validation_context.ValidationContext] = None) -> bioimageio.spec.summary.ValidationSummary:", "funcdef": "def"}, "bioimageio.spec.ValidationContext": {"fullname": "bioimageio.spec.ValidationContext", "modulename": "bioimageio.spec", "qualname": "ValidationContext", "kind": "class", "doc": "\n"}, "bioimageio.spec.ValidationContext.__init__": {"fullname": "bioimageio.spec.ValidationContext.__init__", "modulename": "bioimageio.spec", "qualname": "ValidationContext.__init__", "kind": "function", "doc": "\n", "signature": "(\troot: Union[bioimageio.spec._internal.root_url.RootHttpUrl, Annotated[pathlib.Path, PathType(path_type='dir'), Predicate(is_absolute)], zipfile.ZipFile] = PosixPath('.'),\twarning_level: Literal[20, 30, 35, 50] = 50,\tlog_warnings: bool = True,\tfile_name: Optional[str] = None,\tperform_io_checks: bool = True,\tknown_files: Dict[str, bioimageio.spec._internal.io_basics.Sha256] = <factory>)"}, "bioimageio.spec.ValidationContext.root": {"fullname": "bioimageio.spec.ValidationContext.root", "modulename": "bioimageio.spec", "qualname": "ValidationContext.root", "kind": "variable", "doc": "url/directory serving as base to resolve any relative file paths
\n", "annotation": ": Union[bioimageio.spec._internal.root_url.RootHttpUrl, Annotated[pathlib.Path, PathType(path_type='dir'), Predicate(is_absolute)], zipfile.ZipFile]", "default_value": "PosixPath('.')"}, "bioimageio.spec.ValidationContext.warning_level": {"fullname": "bioimageio.spec.ValidationContext.warning_level", "modulename": "bioimageio.spec", "qualname": "ValidationContext.warning_level", "kind": "variable", "doc": "raise warnings of severity s
as validation errors if s >= warning_level
if True
log warnings that are not raised to the console
file name of the bioimageio Yaml file
\n", "annotation": ": Optional[str]", "default_value": "None"}, "bioimageio.spec.ValidationContext.perform_io_checks": {"fullname": "bioimageio.spec.ValidationContext.perform_io_checks", "modulename": "bioimageio.spec", "qualname": "ValidationContext.perform_io_checks", "kind": "variable", "doc": "wether or not to perform validation that requires file io,\ne.g. downloading a remote files.
\n\nExistence of local absolute file paths is still being checked.
\n", "annotation": ": bool", "default_value": "True"}, "bioimageio.spec.ValidationContext.known_files": {"fullname": "bioimageio.spec.ValidationContext.known_files", "modulename": "bioimageio.spec", "qualname": "ValidationContext.known_files", "kind": "variable", "doc": "allows to bypass download and hashing of referenced files
\n", "annotation": ": Dict[str, bioimageio.spec._internal.io_basics.Sha256]"}, "bioimageio.spec.ValidationContext.replace": {"fullname": "bioimageio.spec.ValidationContext.replace", "modulename": "bioimageio.spec", "qualname": "ValidationContext.replace", "kind": "function", "doc": "\n", "signature": "(\tself,\troot: Union[bioimageio.spec._internal.root_url.RootHttpUrl, Annotated[pathlib.Path, PathType(path_type='dir')], zipfile.ZipFile, NoneType] = None,\twarning_level: Optional[Literal[20, 30, 35, 50]] = None,\tlog_warnings: Optional[bool] = None,\tfile_name: Optional[str] = None,\tperform_io_checks: Optional[bool] = None,\tknown_files: Optional[Dict[str, bioimageio.spec._internal.io_basics.Sha256]] = None) -> bioimageio.spec._internal.validation_context.ValidationContext:", "funcdef": "def"}, "bioimageio.spec.ValidationContext.source_name": {"fullname": "bioimageio.spec.ValidationContext.source_name", "modulename": "bioimageio.spec", "qualname": "ValidationContext.source_name", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.ValidationSummary": {"fullname": "bioimageio.spec.ValidationSummary", "modulename": "bioimageio.spec", "qualname": "ValidationSummary", "kind": "class", "doc": "Summarizes output of all bioimageio validations and tests\nfor one specific ResourceDescr
instance.
list of selected, relevant package versions
\n", "annotation": ": Set[bioimageio.spec.summary.InstalledPackage]"}, "bioimageio.spec.ValidationSummary.conda_list": {"fullname": "bioimageio.spec.ValidationSummary.conda_list", "modulename": "bioimageio.spec", "qualname": "ValidationSummary.conda_list", "kind": "variable", "doc": "parsed output of conda list
\n", "annotation": ": Optional[Sequence[bioimageio.spec.summary.InstalledPackage]]"}, "bioimageio.spec.ValidationSummary.status_icon": {"fullname": "bioimageio.spec.ValidationSummary.status_icon", "modulename": "bioimageio.spec", "qualname": "ValidationSummary.status_icon", "kind": "variable", "doc": "\n"}, "bioimageio.spec.ValidationSummary.errors": {"fullname": "bioimageio.spec.ValidationSummary.errors", "modulename": "bioimageio.spec", "qualname": "ValidationSummary.errors", "kind": "variable", "doc": "\n", "annotation": ": List[bioimageio.spec.summary.ErrorEntry]"}, "bioimageio.spec.ValidationSummary.warnings": {"fullname": "bioimageio.spec.ValidationSummary.warnings", "modulename": "bioimageio.spec", "qualname": "ValidationSummary.warnings", "kind": "variable", "doc": "\n", "annotation": ": List[bioimageio.spec.summary.WarningEntry]"}, "bioimageio.spec.ValidationSummary.format": {"fullname": "bioimageio.spec.ValidationSummary.format", "modulename": "bioimageio.spec", "qualname": "ValidationSummary.format", "kind": "function", "doc": "Format summary as Markdown string
\n\n Suitable to embed in HTML using '<br>' instead of '\n
\n\n'.
\n", "signature": "(\tself,\thide_tracebacks: bool = False,\thide_source: bool = False,\thide_env: bool = False,\troot_loc: Tuple[Union[int, str], ...] = ()) -> str:", "funcdef": "def"}, "bioimageio.spec.ValidationSummary.display": {"fullname": "bioimageio.spec.ValidationSummary.display", "modulename": "bioimageio.spec", "qualname": "ValidationSummary.display", "kind": "function", "doc": "\n", "signature": "(self) -> None:", "funcdef": "def"}, "bioimageio.spec.ValidationSummary.add_detail": {"fullname": "bioimageio.spec.ValidationSummary.add_detail", "modulename": "bioimageio.spec", "qualname": "ValidationSummary.add_detail", "kind": "function", "doc": "\n", "signature": "(self, detail: bioimageio.spec.summary.ValidationDetail):", "funcdef": "def"}, "bioimageio.spec.application": {"fullname": "bioimageio.spec.application", "modulename": "bioimageio.spec.application", "kind": "module", "doc": "implementaions of all released minor versions are available in submodules:
\n\nbioimageio.spec.application.v0_2.ApplicationDescr
bioimageio.spec.application.v0_3.ApplicationDescr
Bioimage.io description of an application.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.application.ApplicationDescr.type": {"fullname": "bioimageio.spec.application.ApplicationDescr.type", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['application']"}, "bioimageio.spec.application.ApplicationDescr.id": {"fullname": "bioimageio.spec.application.ApplicationDescr.id", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.application.v0_3.ApplicationId]"}, "bioimageio.spec.application.ApplicationDescr.parent": {"fullname": "bioimageio.spec.application.ApplicationDescr.parent", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.application.v0_3.ApplicationId]"}, "bioimageio.spec.application.ApplicationDescr.source": {"fullname": "bioimageio.spec.application.ApplicationDescr.source", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr.source", "kind": "variable", "doc": "The primary source of the application
\n", "annotation": ": Annotated[Optional[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')]], FieldInfo(annotation=NoneType, required=True, description='URL or path to the source of the application')]"}, "bioimageio.spec.application.ApplicationDescr.implemented_format_version": {"fullname": "bioimageio.spec.application.ApplicationDescr.implemented_format_version", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.application.ApplicationDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.application.ApplicationDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.application.ApplicationDescr.model_post_init": {"fullname": "bioimageio.spec.application.ApplicationDescr.model_post_init", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.application.ApplicationDescr_v0_2": {"fullname": "bioimageio.spec.application.ApplicationDescr_v0_2", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr_v0_2", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.application.v0_2.ApplicationDescr'>"}, "bioimageio.spec.application.ApplicationDescr_v0_3": {"fullname": "bioimageio.spec.application.ApplicationDescr_v0_3", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr_v0_3", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.application.v0_3.ApplicationDescr'>"}, "bioimageio.spec.application.AnyApplicationDescr": {"fullname": "bioimageio.spec.application.AnyApplicationDescr", "modulename": "bioimageio.spec.application", "qualname": "AnyApplicationDescr", "kind": "variable", "doc": "Union of any released application desription
\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]"}, "bioimageio.spec.application.v0_2": {"fullname": "bioimageio.spec.application.v0_2", "modulename": "bioimageio.spec.application.v0_2", "kind": "module", "doc": "\n"}, "bioimageio.spec.application.v0_2.ApplicationId": {"fullname": "bioimageio.spec.application.v0_2.ApplicationId", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec.generic.v0_2.ResourceId"}, "bioimageio.spec.application.v0_2.ApplicationDescr": {"fullname": "bioimageio.spec.application.v0_2.ApplicationDescr", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationDescr", "kind": "class", "doc": "Bioimage.io description of an application.
\n", "bases": "bioimageio.spec.generic.v0_2.GenericDescrBase"}, "bioimageio.spec.application.v0_2.ApplicationDescr.type": {"fullname": "bioimageio.spec.application.v0_2.ApplicationDescr.type", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['application']"}, "bioimageio.spec.application.v0_2.ApplicationDescr.id": {"fullname": "bioimageio.spec.application.v0_2.ApplicationDescr.id", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.application.v0_2.ApplicationId]"}, "bioimageio.spec.application.v0_2.ApplicationDescr.source": {"fullname": "bioimageio.spec.application.v0_2.ApplicationDescr.source", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationDescr.source", "kind": "variable", "doc": "The primary source of the application
\n", "annotation": ": Annotated[Optional[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')]], FieldInfo(annotation=NoneType, required=True, description='URL or path to the source of the application')]"}, "bioimageio.spec.application.v0_2.ApplicationDescr.implemented_format_version": {"fullname": "bioimageio.spec.application.v0_2.ApplicationDescr.implemented_format_version", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.2.4'"}, "bioimageio.spec.application.v0_2.ApplicationDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.application.v0_2.ApplicationDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 2, 4)"}, "bioimageio.spec.application.v0_2.ApplicationDescr.model_post_init": {"fullname": "bioimageio.spec.application.v0_2.ApplicationDescr.model_post_init", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.application.v0_2.LinkedApplication": {"fullname": "bioimageio.spec.application.v0_2.LinkedApplication", "modulename": "bioimageio.spec.application.v0_2", "qualname": "LinkedApplication", "kind": "class", "doc": "Reference to a bioimage.io application.
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.application.v0_2.LinkedApplication.id": {"fullname": "bioimageio.spec.application.v0_2.LinkedApplication.id", "modulename": "bioimageio.spec.application.v0_2", "qualname": "LinkedApplication.id", "kind": "variable", "doc": "A valid application id
from the bioimage.io collection.
version number (n-th published version, not the semantic version) of linked application
\n", "annotation": ": Optional[int]"}, "bioimageio.spec.application.v0_3": {"fullname": "bioimageio.spec.application.v0_3", "modulename": "bioimageio.spec.application.v0_3", "kind": "module", "doc": "\n"}, "bioimageio.spec.application.v0_3.ApplicationId": {"fullname": "bioimageio.spec.application.v0_3.ApplicationId", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec.generic.v0_3.ResourceId"}, "bioimageio.spec.application.v0_3.ApplicationDescr": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr", "kind": "class", "doc": "Bioimage.io description of an application.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.application.v0_3.ApplicationDescr.type": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr.type", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['application']"}, "bioimageio.spec.application.v0_3.ApplicationDescr.id": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr.id", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.application.v0_3.ApplicationId]"}, "bioimageio.spec.application.v0_3.ApplicationDescr.parent": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr.parent", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.application.v0_3.ApplicationId]"}, "bioimageio.spec.application.v0_3.ApplicationDescr.source": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr.source", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr.source", "kind": "variable", "doc": "The primary source of the application
\n", "annotation": ": Annotated[Optional[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')]], FieldInfo(annotation=NoneType, required=True, description='URL or path to the source of the application')]"}, "bioimageio.spec.application.v0_3.ApplicationDescr.implemented_format_version": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr.implemented_format_version", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.application.v0_3.ApplicationDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.application.v0_3.ApplicationDescr.model_post_init": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr.model_post_init", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.application.v0_3.LinkedApplication": {"fullname": "bioimageio.spec.application.v0_3.LinkedApplication", "modulename": "bioimageio.spec.application.v0_3", "qualname": "LinkedApplication", "kind": "class", "doc": "Reference to a bioimage.io application.
\n", "bases": "bioimageio.spec.generic.v0_3.LinkedResourceNode"}, "bioimageio.spec.application.v0_3.LinkedApplication.id": {"fullname": "bioimageio.spec.application.v0_3.LinkedApplication.id", "modulename": "bioimageio.spec.application.v0_3", "qualname": "LinkedApplication.id", "kind": "variable", "doc": "A valid application id
from the bioimage.io collection.
Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.common.FileDescr.source": {"fullname": "bioimageio.spec.common.FileDescr.source", "modulename": "bioimageio.spec.common", "qualname": "FileDescr.source", "kind": "variable", "doc": "\u2208\ud83d\udce6 file source
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.common.FileDescr.sha256": {"fullname": "bioimageio.spec.common.FileDescr.sha256", "modulename": "bioimageio.spec.common", "qualname": "FileDescr.sha256", "kind": "variable", "doc": "SHA256 checksum of the source file
\n", "annotation": ": Optional[bioimageio.spec._internal.io_basics.Sha256]"}, "bioimageio.spec.common.FileDescr.validate_sha256": {"fullname": "bioimageio.spec.common.FileDescr.validate_sha256", "modulename": "bioimageio.spec.common", "qualname": "FileDescr.validate_sha256", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.common.FileDescr.download": {"fullname": "bioimageio.spec.common.FileDescr.download", "modulename": "bioimageio.spec.common", "qualname": "FileDescr.download", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.spec.common.FileName": {"fullname": "bioimageio.spec.common.FileName", "modulename": "bioimageio.spec.common", "qualname": "FileName", "kind": "variable", "doc": "\n", "default_value": "<class 'str'>"}, "bioimageio.spec.common.FileSource": {"fullname": "bioimageio.spec.common.FileSource", "modulename": "bioimageio.spec.common", "qualname": "FileSource", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, typing.Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]"}, "bioimageio.spec.common.HttpUrl": {"fullname": "bioimageio.spec.common.HttpUrl", "modulename": "bioimageio.spec.common", "qualname": "HttpUrl", "kind": "class", "doc": "A 'URL folder', possibly an invalid http URL
\n", "bases": "bioimageio.spec._internal.root_url.RootHttpUrl"}, "bioimageio.spec.common.HttpUrl.root_model": {"fullname": "bioimageio.spec.common.HttpUrl.root_model", "modulename": "bioimageio.spec.common", "qualname": "HttpUrl.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)]]'>"}, "bioimageio.spec.common.HttpUrl.exists": {"fullname": "bioimageio.spec.common.HttpUrl.exists", "modulename": "bioimageio.spec.common", "qualname": "HttpUrl.exists", "kind": "function", "doc": "True if URL is available
\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.spec.common.InvalidDescr": {"fullname": "bioimageio.spec.common.InvalidDescr", "modulename": "bioimageio.spec.common", "qualname": "InvalidDescr", "kind": "class", "doc": "A representation of an invalid resource description
\n", "bases": "bioimageio.spec._internal.common_nodes.ResourceDescrBase"}, "bioimageio.spec.common.InvalidDescr.type": {"fullname": "bioimageio.spec.common.InvalidDescr.type", "modulename": "bioimageio.spec.common", "qualname": "InvalidDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Any"}, "bioimageio.spec.common.InvalidDescr.format_version": {"fullname": "bioimageio.spec.common.InvalidDescr.format_version", "modulename": "bioimageio.spec.common", "qualname": "InvalidDescr.format_version", "kind": "variable", "doc": "\n", "annotation": ": Any"}, "bioimageio.spec.common.InvalidDescr.fields_to_set_explicitly": {"fullname": "bioimageio.spec.common.InvalidDescr.fields_to_set_explicitly", "modulename": "bioimageio.spec.common", "qualname": "InvalidDescr.fields_to_set_explicitly", "kind": "variable", "doc": "set set these fields explicitly with their default value if they are not set,\nsuch that they are always included even when dumping with 'exlude_unset'
\n", "annotation": ": ClassVar[FrozenSet[LiteralString]]", "default_value": "frozenset()"}, "bioimageio.spec.common.InvalidDescr.implemented_format_version": {"fullname": "bioimageio.spec.common.InvalidDescr.implemented_format_version", "modulename": "bioimageio.spec.common", "qualname": "InvalidDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'unknown'"}, "bioimageio.spec.common.InvalidDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.common.InvalidDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.common", "qualname": "InvalidDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 0, 0)"}, "bioimageio.spec.common.InvalidDescr.model_post_init": {"fullname": "bioimageio.spec.common.InvalidDescr.model_post_init", "modulename": "bioimageio.spec.common", "qualname": "InvalidDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.common.PermissiveFileSource": {"fullname": "bioimageio.spec.common.PermissiveFileSource", "modulename": "bioimageio.spec.common", "qualname": "PermissiveFileSource", "kind": "variable", "doc": "\n", "default_value": "typing.Union[typing.Annotated[typing.Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, typing.Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, typing.Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)]]"}, "bioimageio.spec.common.RelativeFilePath": {"fullname": "bioimageio.spec.common.RelativeFilePath", "modulename": "bioimageio.spec.common", "qualname": "RelativeFilePath", "kind": "class", "doc": "A path relative to the rdf.yaml
file (also if the RDF source is a URL).
We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.common.RelativeFilePath.get_absolute": {"fullname": "bioimageio.spec.common.RelativeFilePath.get_absolute", "modulename": "bioimageio.spec.common", "qualname": "RelativeFilePath.get_absolute", "kind": "function", "doc": "\n", "signature": "(\tself,\troot: bioimageio.spec._internal.root_url.RootHttpUrl | pathlib.Path | pydantic_core._pydantic_core.Url | zipfile.ZipFile) -> Union[Annotated[pathlib.Path, PathType(path_type='file'), Predicate(is_absolute)], bioimageio.spec._internal.url.HttpUrl, zipp.Path]:", "funcdef": "def"}, "bioimageio.spec.common.RootHttpUrl": {"fullname": "bioimageio.spec.common.RootHttpUrl", "modulename": "bioimageio.spec.common", "qualname": "RootHttpUrl", "kind": "class", "doc": "A 'URL folder', possibly an invalid http URL
\n", "bases": "bioimageio.spec._internal.validated_string.ValidatedString"}, "bioimageio.spec.common.RootHttpUrl.root_model": {"fullname": "bioimageio.spec.common.RootHttpUrl.root_model", "modulename": "bioimageio.spec.common", "qualname": "RootHttpUrl.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)]]'>"}, "bioimageio.spec.common.RootHttpUrl.absolute": {"fullname": "bioimageio.spec.common.RootHttpUrl.absolute", "modulename": "bioimageio.spec.common", "qualname": "RootHttpUrl.absolute", "kind": "function", "doc": "analog to absolute
method of pathlib.
SHA-256 hash value
\n", "bases": "bioimageio.spec._internal.validated_string.ValidatedString"}, "bioimageio.spec.common.Sha256.root_model": {"fullname": "bioimageio.spec.common.Sha256.root_model", "modulename": "bioimageio.spec.common", "qualname": "Sha256.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[str, StringConstraints]]'>"}, "bioimageio.spec.common.ValidationError": {"fullname": "bioimageio.spec.common.ValidationError", "modulename": "bioimageio.spec.common", "qualname": "ValidationError", "kind": "class", "doc": "Inappropriate argument value (of correct type).
\n", "bases": "builtins.ValueError"}, "bioimageio.spec.common.ValidationError.from_exception_data": {"fullname": "bioimageio.spec.common.ValidationError.from_exception_data", "modulename": "bioimageio.spec.common", "qualname": "ValidationError.from_exception_data", "kind": "function", "doc": "\n", "signature": "(title, line_errors, input_type='python', hide_input=False):", "funcdef": "def"}, "bioimageio.spec.common.ValidationError.error_count": {"fullname": "bioimageio.spec.common.ValidationError.error_count", "modulename": "bioimageio.spec.common", "qualname": "ValidationError.error_count", "kind": "function", "doc": "\n", "signature": "(self, /):", "funcdef": "def"}, "bioimageio.spec.common.ValidationError.errors": {"fullname": "bioimageio.spec.common.ValidationError.errors", "modulename": "bioimageio.spec.common", "qualname": "ValidationError.errors", "kind": "function", "doc": "\n", "signature": "(\tself,\t/,\t*,\tinclude_url=True,\tinclude_context=True,\tinclude_input=True):", "funcdef": "def"}, "bioimageio.spec.common.ValidationError.json": {"fullname": "bioimageio.spec.common.ValidationError.json", "modulename": "bioimageio.spec.common", "qualname": "ValidationError.json", "kind": "function", "doc": "\n", "signature": "(\tself,\t/,\t*,\tindent=None,\tinclude_url=True,\tinclude_context=True,\tinclude_input=True):", "funcdef": "def"}, "bioimageio.spec.common.ValidationError.title": {"fullname": "bioimageio.spec.common.ValidationError.title", "modulename": "bioimageio.spec.common", "qualname": "ValidationError.title", "kind": "variable", "doc": "\n"}, "bioimageio.spec.common.YamlValue": {"fullname": "bioimageio.spec.common.YamlValue", "modulename": "bioimageio.spec.common", "qualname": "YamlValue", "kind": "variable", "doc": "\n", "default_value": "Union[bool, datetime.date, datetime.datetime, int, float, str, NoneType, List[ForwardRef('YamlValue')], Dict[Union[bool, datetime.date, datetime.datetime, int, float, str, NoneType, Tuple[Union[bool, datetime.date, datetime.datetime, int, float, str, NoneType], ...]], ForwardRef('YamlValue')]]"}, "bioimageio.spec.conda_env": {"fullname": "bioimageio.spec.conda_env", "modulename": "bioimageio.spec.conda_env", "kind": "module", "doc": "\n"}, "bioimageio.spec.conda_env.PipDeps": {"fullname": "bioimageio.spec.conda_env.PipDeps", "modulename": "bioimageio.spec.conda_env", "qualname": "PipDeps", "kind": "class", "doc": "Pip dependencies to include in conda dependecies
\n", "bases": "pydantic.main.BaseModel"}, "bioimageio.spec.conda_env.PipDeps.pip": {"fullname": "bioimageio.spec.conda_env.PipDeps.pip", "modulename": "bioimageio.spec.conda_env", "qualname": "PipDeps.pip", "kind": "variable", "doc": "\n", "annotation": ": List[str]"}, "bioimageio.spec.conda_env.CondaEnv": {"fullname": "bioimageio.spec.conda_env.CondaEnv", "modulename": "bioimageio.spec.conda_env", "qualname": "CondaEnv", "kind": "class", "doc": "Represenation of the content of a conda environment.yaml file
\n", "bases": "pydantic.main.BaseModel"}, "bioimageio.spec.conda_env.CondaEnv.name": {"fullname": "bioimageio.spec.conda_env.CondaEnv.name", "modulename": "bioimageio.spec.conda_env", "qualname": "CondaEnv.name", "kind": "variable", "doc": "\n", "annotation": ": Optional[str]"}, "bioimageio.spec.conda_env.CondaEnv.channels": {"fullname": "bioimageio.spec.conda_env.CondaEnv.channels", "modulename": "bioimageio.spec.conda_env", "qualname": "CondaEnv.channels", "kind": "variable", "doc": "\n", "annotation": ": List[str]"}, "bioimageio.spec.conda_env.CondaEnv.dependencies": {"fullname": "bioimageio.spec.conda_env.CondaEnv.dependencies", "modulename": "bioimageio.spec.conda_env", "qualname": "CondaEnv.dependencies", "kind": "variable", "doc": "\n", "annotation": ": List[Union[str, bioimageio.spec.conda_env.PipDeps]]"}, "bioimageio.spec.conda_env.CondaEnv.wo_name": {"fullname": "bioimageio.spec.conda_env.CondaEnv.wo_name", "modulename": "bioimageio.spec.conda_env", "qualname": "CondaEnv.wo_name", "kind": "variable", "doc": "\n"}, "bioimageio.spec.conda_env.BioimageioCondaEnv": {"fullname": "bioimageio.spec.conda_env.BioimageioCondaEnv", "modulename": "bioimageio.spec.conda_env", "qualname": "BioimageioCondaEnv", "kind": "class", "doc": "A special CondaEnv
that
implementaions of all released minor versions are available in submodules:
\n\nbioimageio.spec.dataset.v0_2.DatasetDescr
bioimageio.spec.dataset.v0_3.DatasetDescr
A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage\nprocessing.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.dataset.DatasetDescr.type": {"fullname": "bioimageio.spec.dataset.DatasetDescr.type", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['dataset']"}, "bioimageio.spec.dataset.DatasetDescr.id": {"fullname": "bioimageio.spec.dataset.DatasetDescr.id", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.dataset.v0_3.DatasetId]"}, "bioimageio.spec.dataset.DatasetDescr.parent": {"fullname": "bioimageio.spec.dataset.DatasetDescr.parent", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.dataset.v0_3.DatasetId]"}, "bioimageio.spec.dataset.DatasetDescr.source": {"fullname": "bioimageio.spec.dataset.DatasetDescr.source", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr.source", "kind": "variable", "doc": "\"URL to the source of the dataset.
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.dataset.DatasetDescr.implemented_format_version": {"fullname": "bioimageio.spec.dataset.DatasetDescr.implemented_format_version", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.dataset.DatasetDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.dataset.DatasetDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.dataset.DatasetDescr.model_post_init": {"fullname": "bioimageio.spec.dataset.DatasetDescr.model_post_init", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.dataset.DatasetDescr_v0_2": {"fullname": "bioimageio.spec.dataset.DatasetDescr_v0_2", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr_v0_2", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.dataset.v0_2.DatasetDescr'>"}, "bioimageio.spec.dataset.DatasetDescr_v0_3": {"fullname": "bioimageio.spec.dataset.DatasetDescr_v0_3", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr_v0_3", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.dataset.v0_3.DatasetDescr'>"}, "bioimageio.spec.dataset.AnyDatasetDescr": {"fullname": "bioimageio.spec.dataset.AnyDatasetDescr", "modulename": "bioimageio.spec.dataset", "qualname": "AnyDatasetDescr", "kind": "variable", "doc": "Union of any released dataset desription
\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]"}, "bioimageio.spec.dataset.v0_2": {"fullname": "bioimageio.spec.dataset.v0_2", "modulename": "bioimageio.spec.dataset.v0_2", "kind": "module", "doc": "\n"}, "bioimageio.spec.dataset.v0_2.DatasetId": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetId", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec.generic.v0_2.ResourceId"}, "bioimageio.spec.dataset.v0_2.DatasetDescr": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetDescr", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetDescr", "kind": "class", "doc": "A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage\nprocessing.
\n", "bases": "bioimageio.spec.generic.v0_2.GenericDescrBase"}, "bioimageio.spec.dataset.v0_2.DatasetDescr.type": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetDescr.type", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['dataset']"}, "bioimageio.spec.dataset.v0_2.DatasetDescr.id": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetDescr.id", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.dataset.v0_2.DatasetId]"}, "bioimageio.spec.dataset.v0_2.DatasetDescr.source": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetDescr.source", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetDescr.source", "kind": "variable", "doc": "\"URL to the source of the dataset.
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.dataset.v0_2.DatasetDescr.implemented_format_version": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetDescr.implemented_format_version", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.2.4'"}, "bioimageio.spec.dataset.v0_2.DatasetDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 2, 4)"}, "bioimageio.spec.dataset.v0_2.DatasetDescr.model_post_init": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetDescr.model_post_init", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.dataset.v0_2.LinkedDataset": {"fullname": "bioimageio.spec.dataset.v0_2.LinkedDataset", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "LinkedDataset", "kind": "class", "doc": "Reference to a bioimage.io dataset.
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.dataset.v0_2.LinkedDataset.id": {"fullname": "bioimageio.spec.dataset.v0_2.LinkedDataset.id", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "LinkedDataset.id", "kind": "variable", "doc": "A valid dataset id
from the bioimage.io collection.
version number (n-th published version, not the semantic version) of linked dataset
\n", "annotation": ": Optional[int]"}, "bioimageio.spec.dataset.v0_3": {"fullname": "bioimageio.spec.dataset.v0_3", "modulename": "bioimageio.spec.dataset.v0_3", "kind": "module", "doc": "\n"}, "bioimageio.spec.dataset.v0_3.DatasetId": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetId", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec.generic.v0_3.ResourceId"}, "bioimageio.spec.dataset.v0_3.DatasetDescr": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr", "kind": "class", "doc": "A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage\nprocessing.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.dataset.v0_3.DatasetDescr.type": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr.type", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['dataset']"}, "bioimageio.spec.dataset.v0_3.DatasetDescr.id": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr.id", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.dataset.v0_3.DatasetId]"}, "bioimageio.spec.dataset.v0_3.DatasetDescr.parent": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr.parent", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.dataset.v0_3.DatasetId]"}, "bioimageio.spec.dataset.v0_3.DatasetDescr.source": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr.source", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr.source", "kind": "variable", "doc": "\"URL to the source of the dataset.
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.dataset.v0_3.DatasetDescr.implemented_format_version": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr.implemented_format_version", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.dataset.v0_3.DatasetDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.dataset.v0_3.DatasetDescr.model_post_init": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr.model_post_init", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.dataset.v0_3.LinkedDataset": {"fullname": "bioimageio.spec.dataset.v0_3.LinkedDataset", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "LinkedDataset", "kind": "class", "doc": "Reference to a bioimage.io dataset.
\n", "bases": "bioimageio.spec.generic.v0_3.LinkedResourceNode"}, "bioimageio.spec.dataset.v0_3.LinkedDataset.id": {"fullname": "bioimageio.spec.dataset.v0_3.LinkedDataset.id", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "LinkedDataset.id", "kind": "variable", "doc": "A valid dataset id
from the bioimage.io collection.
implementaions of all released minor versions are available in submodules:
\n\nbioimageio.spec.generic.v0_2.GenericDescr
bioimageio.spec.generic.v0_3.GenericDescr
Specification of the fields used in a generic bioimage.io-compliant resource description file (RDF).
\n\nAn RDF is a YAML file that describes a resource such as a model, a dataset, or a notebook.\nNote that those resources are described with a type-specific RDF.\nUse this generic resource description, if none of the known specific types matches your resource.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.generic.GenericDescr.type": {"fullname": "bioimageio.spec.generic.GenericDescr.type", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.type", "kind": "variable", "doc": "The resource type assigns a broad category to the resource.
\n", "annotation": ": Annotated[str, Annotated[~_StrType, Predicate(str.islower)]]"}, "bioimageio.spec.generic.GenericDescr.id": {"fullname": "bioimageio.spec.generic.GenericDescr.id", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_3.ResourceId]"}, "bioimageio.spec.generic.GenericDescr.parent": {"fullname": "bioimageio.spec.generic.GenericDescr.parent", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_3.ResourceId]"}, "bioimageio.spec.generic.GenericDescr.source": {"fullname": "bioimageio.spec.generic.GenericDescr.source", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.source", "kind": "variable", "doc": "The primary source of the resource
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.generic.GenericDescr.check_specific_types": {"fullname": "bioimageio.spec.generic.GenericDescr.check_specific_types", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.check_specific_types", "kind": "function", "doc": "\n", "signature": "(cls, value: str) -> str:", "funcdef": "def"}, "bioimageio.spec.generic.GenericDescr.implemented_format_version": {"fullname": "bioimageio.spec.generic.GenericDescr.implemented_format_version", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.generic.GenericDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.generic.GenericDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.generic.GenericDescr.model_post_init": {"fullname": "bioimageio.spec.generic.GenericDescr.model_post_init", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.generic.GenericDescr_v0_2": {"fullname": "bioimageio.spec.generic.GenericDescr_v0_2", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr_v0_2", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.generic.v0_2.GenericDescr'>"}, "bioimageio.spec.generic.GenericDescr_v0_3": {"fullname": "bioimageio.spec.generic.GenericDescr_v0_3", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr_v0_3", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.generic.v0_3.GenericDescr'>"}, "bioimageio.spec.generic.AnyGenericDescr": {"fullname": "bioimageio.spec.generic.AnyGenericDescr", "modulename": "bioimageio.spec.generic", "qualname": "AnyGenericDescr", "kind": "variable", "doc": "Union of any released generic desription
\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]"}, "bioimageio.spec.generic.v0_2": {"fullname": "bioimageio.spec.generic.v0_2", "modulename": "bioimageio.spec.generic.v0_2", "kind": "module", "doc": "\n"}, "bioimageio.spec.generic.v0_2.ResourceId": {"fullname": "bioimageio.spec.generic.v0_2.ResourceId", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "ResourceId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec._internal.validated_string.ValidatedString"}, "bioimageio.spec.generic.v0_2.ResourceId.root_model": {"fullname": "bioimageio.spec.generic.v0_2.ResourceId.root_model", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "ResourceId.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[str, MinLen, AfterValidator, RestrictCharacters, Predicate]]'>"}, "bioimageio.spec.generic.v0_2.KNOWN_SPECIFIC_RESOURCE_TYPES": {"fullname": "bioimageio.spec.generic.v0_2.KNOWN_SPECIFIC_RESOURCE_TYPES", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "KNOWN_SPECIFIC_RESOURCE_TYPES", "kind": "variable", "doc": "\n", "default_value": "('application', 'collection', 'dataset', 'model', 'notebook')"}, "bioimageio.spec.generic.v0_2.VALID_COVER_IMAGE_EXTENSIONS": {"fullname": "bioimageio.spec.generic.v0_2.VALID_COVER_IMAGE_EXTENSIONS", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "VALID_COVER_IMAGE_EXTENSIONS", "kind": "variable", "doc": "\n", "default_value": "('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')"}, "bioimageio.spec.generic.v0_2.CoverImageSource": {"fullname": "bioimageio.spec.generic.v0_2.CoverImageSource", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "CoverImageSource", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[typing.Union[typing.Annotated[pathlib.Path, PathType(path_type='file'), Predicate(is_absolute)], bioimageio.spec._internal.io.RelativeFilePath, bioimageio.spec._internal.url.HttpUrl], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), WithSuffix(suffix=('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff'), case_sensitive=False), PlainSerializer(func=<function _package>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.generic.v0_2.AttachmentsDescr": {"fullname": "bioimageio.spec.generic.v0_2.AttachmentsDescr", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "AttachmentsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_2.AttachmentsDescr.model_config": {"fullname": "bioimageio.spec.generic.v0_2.AttachmentsDescr.model_config", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "AttachmentsDescr.model_config", "kind": "variable", "doc": "update pydantic model config to allow additional unknown keys
\n", "default_value": "{'extra': 'allow', 'frozen': False, 'populate_by_name': True, 'revalidate_instances': 'never', 'validate_assignment': True, 'validate_default': False, 'validate_return': True, 'use_attribute_docstrings': True}"}, "bioimageio.spec.generic.v0_2.AttachmentsDescr.files": {"fullname": "bioimageio.spec.generic.v0_2.AttachmentsDescr.files", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "AttachmentsDescr.files", "kind": "variable", "doc": "\u2208\ud83d\udce6 File attachments
\n", "annotation": ": List[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')]]"}, "bioimageio.spec.generic.v0_2.Uploader": {"fullname": "bioimageio.spec.generic.v0_2.Uploader", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Uploader", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_2.Uploader.email": {"fullname": "bioimageio.spec.generic.v0_2.Uploader.email", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Uploader.email", "kind": "variable", "doc": "name
\n", "annotation": ": Optional[Annotated[str, AfterValidator(func=<function _remove_slashes at 0x7f4654144680>)]]"}, "bioimageio.spec.generic.v0_2.Author": {"fullname": "bioimageio.spec.generic.v0_2.Author", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Author", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "_Person"}, "bioimageio.spec.generic.v0_2.Author.name": {"fullname": "bioimageio.spec.generic.v0_2.Author.name", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Author.name", "kind": "variable", "doc": "\n", "annotation": ": Annotated[str, AfterValidator(func=<function _remove_slashes at 0x7f4654144680>)]"}, "bioimageio.spec.generic.v0_2.Author.github_user": {"fullname": "bioimageio.spec.generic.v0_2.Author.github_user", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Author.github_user", "kind": "variable", "doc": "\n", "annotation": ": Optional[str]"}, "bioimageio.spec.generic.v0_2.Maintainer": {"fullname": "bioimageio.spec.generic.v0_2.Maintainer", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Maintainer", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "_Person"}, "bioimageio.spec.generic.v0_2.Maintainer.name": {"fullname": "bioimageio.spec.generic.v0_2.Maintainer.name", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Maintainer.name", "kind": "variable", "doc": "\n", "annotation": ": Optional[Annotated[str, AfterValidator(func=<function _remove_slashes at 0x7f4654144680>)]]"}, "bioimageio.spec.generic.v0_2.Maintainer.github_user": {"fullname": "bioimageio.spec.generic.v0_2.Maintainer.github_user", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Maintainer.github_user", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.generic.v0_2.BadgeDescr": {"fullname": "bioimageio.spec.generic.v0_2.BadgeDescr", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "BadgeDescr", "kind": "class", "doc": "A custom badge
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_2.BadgeDescr.label": {"fullname": "bioimageio.spec.generic.v0_2.BadgeDescr.label", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "BadgeDescr.label", "kind": "variable", "doc": "badge label to display on hover
\n", "annotation": ": Annotated[str, FieldInfo(annotation=NoneType, required=True, examples=['Open in Colab'])]"}, "bioimageio.spec.generic.v0_2.BadgeDescr.icon": {"fullname": "bioimageio.spec.generic.v0_2.BadgeDescr.icon", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "BadgeDescr.icon", "kind": "variable", "doc": "badge icon
\n", "annotation": ": Annotated[Union[Annotated[Union[Annotated[pathlib.Path, PathType(path_type='file')], bioimageio.spec._internal.io.RelativeFilePath], AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')], bioimageio.spec._internal.url.HttpUrl, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], NoneType], FieldInfo(annotation=NoneType, required=True, examples=['https://colab.research.google.com/assets/colab-badge.svg'])]"}, "bioimageio.spec.generic.v0_2.BadgeDescr.url": {"fullname": "bioimageio.spec.generic.v0_2.BadgeDescr.url", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "BadgeDescr.url", "kind": "variable", "doc": "target URL
\n", "annotation": ": Annotated[bioimageio.spec._internal.url.HttpUrl, FieldInfo(annotation=NoneType, required=True, examples=['https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb'])]"}, "bioimageio.spec.generic.v0_2.CiteEntry": {"fullname": "bioimageio.spec.generic.v0_2.CiteEntry", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "CiteEntry", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_2.CiteEntry.text": {"fullname": "bioimageio.spec.generic.v0_2.CiteEntry.text", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "CiteEntry.text", "kind": "variable", "doc": "free text description
\n", "annotation": ": str"}, "bioimageio.spec.generic.v0_2.CiteEntry.doi": {"fullname": "bioimageio.spec.generic.v0_2.CiteEntry.doi", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "CiteEntry.doi", "kind": "variable", "doc": "A digital object identifier (DOI) is the prefered citation reference.\nSee https://www.doi.org/ for details. (alternatively specify url
)
URL to cite (preferably specify a doi
instead)
Reference to a bioimage.io resource
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_2.LinkedResource.id": {"fullname": "bioimageio.spec.generic.v0_2.LinkedResource.id", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "LinkedResource.id", "kind": "variable", "doc": "A valid resource id
from the bioimage.io collection.
version number (n-th published version, not the semantic version) of linked resource
\n", "annotation": ": Optional[int]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase", "kind": "class", "doc": "Base for all resource descriptions including of model descriptions
\n", "bases": "bioimageio.spec._internal.common_nodes.ResourceDescrBase"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.name": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.name", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.name", "kind": "variable", "doc": "A human-friendly name of the resource description
\n", "annotation": ": Annotated[str, MinLen(min_length=1), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f4654117380>, severity=30, msg='Longer than 128 characters.', context={'typ': Annotated[Any, MaxLen(max_length=128)]})]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.description": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.description", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.description", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.covers": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.covers", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.covers", "kind": "variable", "doc": "\u2208\ud83d\udce6 Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.
\n", "annotation": ": Annotated[List[Annotated[Union[Annotated[pathlib.Path, PathType(path_type='file'), Predicate(is_absolute)], bioimageio.spec._internal.io.RelativeFilePath, bioimageio.spec._internal.url.HttpUrl], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), WithSuffix(suffix=('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff'), case_sensitive=False), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')]], FieldInfo(annotation=NoneType, required=True, description="Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.\\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')", examples=['cover.png'])]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.id_emoji": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.id_emoji", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.id_emoji", "kind": "variable", "doc": "UTF-8 emoji for display alongside the id
.
The authors are the creators of the RDF and the primary points of contact.
\n", "annotation": ": List[bioimageio.spec.generic.v0_2.Author]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.accept_author_strings": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.accept_author_strings", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.accept_author_strings", "kind": "function", "doc": "we unofficially accept strings as author entries
\n", "signature": "(cls, authors: Union[Any, Sequence[Any]]) -> Any:", "funcdef": "def"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.attachments": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.attachments", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.attachments", "kind": "variable", "doc": "file and other attachments
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_2.AttachmentsDescr]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.cite": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.cite", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.cite", "kind": "variable", "doc": "citations
\n", "annotation": ": List[bioimageio.spec.generic.v0_2.CiteEntry]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.config": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.config", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.config", "kind": "variable", "doc": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a github repo URL in config
since we already have the\ngit_repo
field defined in the spec.\nKeys in config
may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:
config:\n bioimageio: # here is the domain name\n my_custom_key: 3837283\n another_key:\n nested: value\n imagej: # config specific to ImageJ\n macro_dir: path/to/macro/file\n
\nIf possible, please use snake_case
for keys in config
.\nYou may want to list linked files additionally under attachments
to include them when packaging a resource\n(packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files)
URL to download the resource from (deprecated)
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.git_repo": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.git_repo", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.git_repo", "kind": "variable", "doc": "A URL to the Git repository where the resource is being developed.
\n", "annotation": ": Annotated[Optional[str], FieldInfo(annotation=NoneType, required=True, examples=['https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad'])]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.icon": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.icon", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.icon", "kind": "variable", "doc": "An icon for illustration
\n", "annotation": ": Union[Annotated[str, Len(min_length=1, max_length=2)], Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')], NoneType]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.links": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.links", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.links", "kind": "variable", "doc": "IDs of other bioimage.io resources
\n", "annotation": ": Annotated[List[str], FieldInfo(annotation=NoneType, required=True, examples=[('ilastik/ilastik', 'deepimagej/deepimagej', 'zero/notebook_u-net_3d_zerocostdl4mic')])]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.uploader": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.uploader", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.uploader", "kind": "variable", "doc": "The person who uploaded the model (e.g. to bioimage.io)
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_2.Uploader]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.maintainers": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.maintainers", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.maintainers", "kind": "variable", "doc": "Maintainers of this resource.\nIf not specified authors
are maintainers and at least some of them should specify their github_user
name
Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from.\nDo not set this field in a YAML file.
\n", "annotation": ": Optional[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.tags": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.tags", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.tags", "kind": "variable", "doc": "Associated tags
\n", "annotation": ": Annotated[List[str], FieldInfo(annotation=NoneType, required=True, examples=[('unet2d', 'pytorch', 'nucleus', 'segmentation', 'dsb2018')])]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.warn_about_tag_categories": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.warn_about_tag_categories", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.warn_about_tag_categories", "kind": "function", "doc": "\n", "signature": "(value: Any, info: pydantic_core.core_schema.ValidationInfo) -> Any:", "funcdef": "def"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.version": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.version", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.version", "kind": "variable", "doc": "The version of the resource following SemVer 2.0.
\n", "annotation": ": Optional[bioimageio.spec._internal.version_type.Version]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.version_number": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.version_number", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.version_number", "kind": "variable", "doc": "version number (n-th published version, not the semantic version)
\n", "annotation": ": Optional[int]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.model_post_init": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.model_post_init", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.generic.v0_2.GenericDescrBase": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescrBase", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescrBase", "kind": "class", "doc": "Base for all resource descriptions except for the model descriptions
\n", "bases": "GenericModelDescrBase"}, "bioimageio.spec.generic.v0_2.GenericDescrBase.format_version": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescrBase.format_version", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescrBase.format_version", "kind": "variable", "doc": "The format version of this resource specification\n(not the version
of the resource description)\nWhen creating a new resource always use the latest micro/patch version described here.\nThe format_version
is important for any consumer software to understand how to parse the fields.
badges associated with this resource
\n", "annotation": ": List[bioimageio.spec.generic.v0_2.BadgeDescr]"}, "bioimageio.spec.generic.v0_2.GenericDescrBase.documentation": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescrBase.documentation", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescrBase.documentation", "kind": "variable", "doc": "\u2208\ud83d\udce6 URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is README.md
. An .md
suffix is mandatory.
A SPDX license identifier.\nWe do not support custom license beyond the SPDX license list, if you need that please\nopen a GitHub issue to discuss your intentions with the community.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.license_id.LicenseId, bioimageio.spec._internal.license_id.DeprecatedLicenseId, str, NoneType], FieldInfo(annotation=NoneType, required=True, examples=['CC0-1.0', 'MIT', 'BSD-2-Clause'], metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]"}, "bioimageio.spec.generic.v0_2.GenericDescrBase.deprecated_spdx_license": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescrBase.deprecated_spdx_license", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescrBase.deprecated_spdx_license", "kind": "function", "doc": "\n", "signature": "(\tcls,\tvalue: Union[bioimageio.spec._internal.license_id.LicenseId, bioimageio.spec._internal.license_id.DeprecatedLicenseId, str, NoneType]):", "funcdef": "def"}, "bioimageio.spec.generic.v0_2.GenericDescrBase.implemented_format_version": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescrBase.implemented_format_version", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescrBase.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.2.4'"}, "bioimageio.spec.generic.v0_2.GenericDescrBase.implemented_format_version_tuple": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescrBase.implemented_format_version_tuple", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescrBase.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 2, 4)"}, "bioimageio.spec.generic.v0_2.GenericDescrBase.model_post_init": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescrBase.model_post_init", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescrBase.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.generic.v0_2.GenericDescr": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr", "kind": "class", "doc": "Specification of the fields used in a generic bioimage.io-compliant resource description file (RDF).
\n\nAn RDF is a YAML file that describes a resource such as a model, a dataset, or a notebook.\nNote that those resources are described with a type-specific RDF.\nUse this generic resource description, if none of the known specific types matches your resource.
\n", "bases": "GenericDescrBase"}, "bioimageio.spec.generic.v0_2.GenericDescr.type": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr.type", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr.type", "kind": "variable", "doc": "The resource type assigns a broad category to the resource.
\n", "annotation": ": Annotated[str, Annotated[~_StrType, Predicate(str.islower)], FieldInfo(annotation=NoneType, required=True, frozen=True)]"}, "bioimageio.spec.generic.v0_2.GenericDescr.id": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr.id", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_2.ResourceId]"}, "bioimageio.spec.generic.v0_2.GenericDescr.source": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr.source", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr.source", "kind": "variable", "doc": "The primary source of the resource
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.generic.v0_2.GenericDescr.check_specific_types": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr.check_specific_types", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr.check_specific_types", "kind": "function", "doc": "\n", "signature": "(cls, value: str) -> str:", "funcdef": "def"}, "bioimageio.spec.generic.v0_2.GenericDescr.implemented_format_version": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr.implemented_format_version", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.2.4'"}, "bioimageio.spec.generic.v0_2.GenericDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 2, 4)"}, "bioimageio.spec.generic.v0_2.GenericDescr.model_post_init": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr.model_post_init", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.generic.v0_3": {"fullname": "bioimageio.spec.generic.v0_3", "modulename": "bioimageio.spec.generic.v0_3", "kind": "module", "doc": "\n"}, "bioimageio.spec.generic.v0_3.KNOWN_SPECIFIC_RESOURCE_TYPES": {"fullname": "bioimageio.spec.generic.v0_3.KNOWN_SPECIFIC_RESOURCE_TYPES", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "KNOWN_SPECIFIC_RESOURCE_TYPES", "kind": "variable", "doc": "\n", "default_value": "('application', 'collection', 'dataset', 'model', 'notebook')"}, "bioimageio.spec.generic.v0_3.VALID_COVER_IMAGE_EXTENSIONS": {"fullname": "bioimageio.spec.generic.v0_3.VALID_COVER_IMAGE_EXTENSIONS", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "VALID_COVER_IMAGE_EXTENSIONS", "kind": "variable", "doc": "\n", "default_value": "('.gif', '.jpeg', '.jpg', '.png', '.svg')"}, "bioimageio.spec.generic.v0_3.ResourceId": {"fullname": "bioimageio.spec.generic.v0_3.ResourceId", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "ResourceId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec._internal.validated_string.ValidatedString"}, "bioimageio.spec.generic.v0_3.ResourceId.root_model": {"fullname": "bioimageio.spec.generic.v0_3.ResourceId.root_model", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "ResourceId.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[str, MinLen, RestrictCharacters, Predicate]]'>"}, "bioimageio.spec.generic.v0_3.DocumentationSource": {"fullname": "bioimageio.spec.generic.v0_3.DocumentationSource", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "DocumentationSource", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[typing.Union[typing.Annotated[pathlib.Path, PathType(path_type='file'), Predicate(is_absolute)], bioimageio.spec._internal.io.RelativeFilePath, bioimageio.spec._internal.url.HttpUrl], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function _validate_md_suffix>), PlainSerializer(func=<function _package>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.generic.v0_3.Author": {"fullname": "bioimageio.spec.generic.v0_3.Author", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "Author", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec.generic.v0_2.Author"}, "bioimageio.spec.generic.v0_3.Author.name": {"fullname": "bioimageio.spec.generic.v0_3.Author.name", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "Author.name", "kind": "variable", "doc": "\n", "annotation": ": Annotated[str, Predicate(func=<function _has_no_slash at 0x7f464ad8c040>)]"}, "bioimageio.spec.generic.v0_3.Author.github_user": {"fullname": "bioimageio.spec.generic.v0_3.Author.github_user", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "Author.github_user", "kind": "variable", "doc": "\n", "annotation": ": Optional[str]"}, "bioimageio.spec.generic.v0_3.Maintainer": {"fullname": "bioimageio.spec.generic.v0_3.Maintainer", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "Maintainer", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec.generic.v0_2.Maintainer"}, "bioimageio.spec.generic.v0_3.Maintainer.name": {"fullname": "bioimageio.spec.generic.v0_3.Maintainer.name", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "Maintainer.name", "kind": "variable", "doc": "\n", "annotation": ": Optional[Annotated[str, Predicate(func=<function _has_no_slash at 0x7f464ad8c040>)]]"}, "bioimageio.spec.generic.v0_3.Maintainer.github_user": {"fullname": "bioimageio.spec.generic.v0_3.Maintainer.github_user", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "Maintainer.github_user", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.generic.v0_3.Maintainer.validate_gh_user": {"fullname": "bioimageio.spec.generic.v0_3.Maintainer.validate_gh_user", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "Maintainer.validate_gh_user", "kind": "function", "doc": "\n", "signature": "(cls, value: str):", "funcdef": "def"}, "bioimageio.spec.generic.v0_3.CiteEntry": {"fullname": "bioimageio.spec.generic.v0_3.CiteEntry", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "CiteEntry", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_3.CiteEntry.text": {"fullname": "bioimageio.spec.generic.v0_3.CiteEntry.text", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "CiteEntry.text", "kind": "variable", "doc": "free text description
\n", "annotation": ": str"}, "bioimageio.spec.generic.v0_3.CiteEntry.doi": {"fullname": "bioimageio.spec.generic.v0_3.CiteEntry.doi", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "CiteEntry.doi", "kind": "variable", "doc": "A digital object identifier (DOI) is the prefered citation reference.\nSee https://www.doi.org/ for details. (alternatively specify url
)
URL to cite (preferably specify a doi
instead)
Reference to a bioimage.io resource
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_3.LinkedResource.id": {"fullname": "bioimageio.spec.generic.v0_3.LinkedResource.id", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "LinkedResource.id", "kind": "variable", "doc": "A valid resource id
from the official bioimage.io collection.
Base for all resource descriptions including of model descriptions
\n", "bases": "bioimageio.spec._internal.common_nodes.ResourceDescrBase"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.name": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.name", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.name", "kind": "variable", "doc": "A human-friendly name of the resource description.\nMay only contains letters, digits, underscore, minus, parentheses and spaces.
\n", "annotation": ": Annotated[str, MinLen(min_length=1), MaxLen(max_length=128)]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.description": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.description", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.description", "kind": "variable", "doc": "A string containing a brief description.
\n", "annotation": ": Annotated[str, MaxLen(max_length=1024), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f46463f5800>, severity=30, msg='Description longer than 512 characters.', context={'typ': Annotated[Any, MaxLen(max_length=512)]})]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.covers": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.covers", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.covers", "kind": "variable", "doc": "\u2208\ud83d\udce6 Cover images.
\n", "annotation": ": Annotated[List[Annotated[Union[Annotated[pathlib.Path, PathType(path_type='file'), Predicate(is_absolute)], bioimageio.spec._internal.io.RelativeFilePath, bioimageio.spec._internal.url.HttpUrl], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), WithSuffix(suffix=('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff'), case_sensitive=False), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')]], FieldInfo(annotation=NoneType, required=True, description="Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1 or 1:1.\\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg')", examples=[])]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.id_emoji": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.id_emoji", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.id_emoji", "kind": "variable", "doc": "UTF-8 emoji for display alongside the id
.
The authors are the creators of this resource description and the primary points of contact.
\n", "annotation": ": Annotated[List[bioimageio.spec.generic.v0_3.Author], MinLen(min_length=1)]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.attachments": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.attachments", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.attachments", "kind": "variable", "doc": "file attachments
\n", "annotation": ": List[bioimageio.spec._internal.io.FileDescr]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.cite": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.cite", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.cite", "kind": "variable", "doc": "citations
\n", "annotation": ": Annotated[List[bioimageio.spec.generic.v0_3.CiteEntry], MinLen(min_length=1)]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.license": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.license", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.license", "kind": "variable", "doc": "A SPDX license identifier.\nWe do not support custom license beyond the SPDX license list, if you need that please\nopen a GitHub issue\nto discuss your intentions with the community.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.license_id.LicenseId, bioimageio.spec._internal.license_id.DeprecatedLicenseId], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f46463f60c0>, severity=30, msg='{value} is deprecated, see https://spdx.org/licenses/{value}.html', context={'typ': <class 'bioimageio.spec._internal.license_id.LicenseId'>}), FieldInfo(annotation=NoneType, required=True, examples=['CC0-1.0', 'MIT', 'BSD-2-Clause'])]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.config": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.config", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.config", "kind": "variable", "doc": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a GitHub repo URL in config
since there is a git_repo
field.\nKeys in config
may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:
config:\n bioimageio: # here is the domain name\n my_custom_key: 3837283\n another_key:\n nested: value\n imagej: # config specific to ImageJ\n macro_dir: path/to/macro/file\n
\nIf possible, please use snake_case
for keys in config
.\nYou may want to list linked files additionally under attachments
to include them when packaging a resource.\n(Packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files.)
A URL to the Git repository where the resource is being developed.
\n", "annotation": ": Annotated[Optional[bioimageio.spec._internal.url.HttpUrl], FieldInfo(annotation=NoneType, required=True, examples=['https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad'])]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.icon": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.icon", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.icon", "kind": "variable", "doc": "An icon for illustration, e.g. on bioimage.io
\n", "annotation": ": Union[Annotated[str, Len(min_length=1, max_length=2)], Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')], NoneType]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.links": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.links", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.links", "kind": "variable", "doc": "IDs of other bioimage.io resources
\n", "annotation": ": Annotated[List[str], FieldInfo(annotation=NoneType, required=True, examples=[('ilastik/ilastik', 'deepimagej/deepimagej', 'zero/notebook_u-net_3d_zerocostdl4mic')])]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.uploader": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.uploader", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.uploader", "kind": "variable", "doc": "The person who uploaded the model (e.g. to bioimage.io)
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_2.Uploader]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.maintainers": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.maintainers", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.maintainers", "kind": "variable", "doc": "Maintainers of this resource.\nIf not specified, authors
are maintainers and at least some of them has to specify their github_user
name
Associated tags
\n", "annotation": ": Annotated[List[str], FieldInfo(annotation=NoneType, required=True, examples=[('unet2d', 'pytorch', 'nucleus', 'segmentation', 'dsb2018')])]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.warn_about_tag_categories": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.warn_about_tag_categories", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.warn_about_tag_categories", "kind": "function", "doc": "\n", "signature": "(value: Any, info: pydantic_core.core_schema.ValidationInfo) -> Any:", "funcdef": "def"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.version": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.version", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.version", "kind": "variable", "doc": "The version of the resource following SemVer 2.0.
\n", "annotation": ": Optional[bioimageio.spec._internal.version_type.Version]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.model_post_init": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.model_post_init", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.generic.v0_3.GenericDescrBase": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescrBase", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescrBase", "kind": "class", "doc": "Base for all resource descriptions except for the model descriptions
\n", "bases": "GenericModelDescrBase"}, "bioimageio.spec.generic.v0_3.GenericDescrBase.format_version": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescrBase.format_version", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescrBase.format_version", "kind": "variable", "doc": "The format version of this resource specification
\n", "annotation": ": Literal['0.3.0']"}, "bioimageio.spec.generic.v0_3.GenericDescrBase.documentation": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescrBase.documentation", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescrBase.documentation", "kind": "variable", "doc": "\u2208\ud83d\udce6 URL or relative path to a markdown file encoded in UTF-8 with additional documentation.\nThe recommended documentation file name is README.md
. An .md
suffix is mandatory.
badges associated with this resource
\n", "annotation": ": List[bioimageio.spec.generic.v0_2.BadgeDescr]"}, "bioimageio.spec.generic.v0_3.GenericDescrBase.implemented_format_version": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescrBase.implemented_format_version", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescrBase.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.generic.v0_3.GenericDescrBase.implemented_format_version_tuple": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescrBase.implemented_format_version_tuple", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescrBase.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.generic.v0_3.GenericDescrBase.model_post_init": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescrBase.model_post_init", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescrBase.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.generic.v0_3.GenericDescr": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr", "kind": "class", "doc": "Specification of the fields used in a generic bioimage.io-compliant resource description file (RDF).
\n\nAn RDF is a YAML file that describes a resource such as a model, a dataset, or a notebook.\nNote that those resources are described with a type-specific RDF.\nUse this generic resource description, if none of the known specific types matches your resource.
\n", "bases": "GenericDescrBase"}, "bioimageio.spec.generic.v0_3.GenericDescr.type": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.type", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.type", "kind": "variable", "doc": "The resource type assigns a broad category to the resource.
\n", "annotation": ": Annotated[str, Annotated[~_StrType, Predicate(str.islower)]]"}, "bioimageio.spec.generic.v0_3.GenericDescr.id": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.id", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_3.ResourceId]"}, "bioimageio.spec.generic.v0_3.GenericDescr.parent": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.parent", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_3.ResourceId]"}, "bioimageio.spec.generic.v0_3.GenericDescr.source": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.source", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.source", "kind": "variable", "doc": "The primary source of the resource
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.generic.v0_3.GenericDescr.check_specific_types": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.check_specific_types", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.check_specific_types", "kind": "function", "doc": "\n", "signature": "(cls, value: str) -> str:", "funcdef": "def"}, "bioimageio.spec.generic.v0_3.GenericDescr.implemented_format_version": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.implemented_format_version", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.generic.v0_3.GenericDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.generic.v0_3.GenericDescr.model_post_init": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.model_post_init", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.generic.v0_3.LinkedResourceNode": {"fullname": "bioimageio.spec.generic.v0_3.LinkedResourceNode", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "LinkedResourceNode", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_3.LinkedResourceNode.version": {"fullname": "bioimageio.spec.generic.v0_3.LinkedResourceNode.version", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "LinkedResourceNode.version", "kind": "variable", "doc": "The version of the linked resource following SemVer 2.0.
\n", "annotation": ": Optional[bioimageio.spec._internal.version_type.Version]"}, "bioimageio.spec.model": {"fullname": "bioimageio.spec.model", "modulename": "bioimageio.spec.model", "kind": "module", "doc": "implementaions of all released minor versions are available in submodules:
\n\nbioimageio.spec.model.v0_4.ModelDescr
bioimageio.spec.model.v0_5.ModelDescr
Specification of the fields used in a bioimage.io-compliant RDF to describe AI models with pretrained weights.\nThese fields are typically stored in a YAML file which we call a model resource description file (model RDF).
\n", "bases": "bioimageio.spec.generic.v0_3.GenericModelDescrBase"}, "bioimageio.spec.model.ModelDescr.format_version": {"fullname": "bioimageio.spec.model.ModelDescr.format_version", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.format_version", "kind": "variable", "doc": "Version of the bioimage.io model description specification used.\nWhen creating a new model always use the latest micro/patch version described here.\nThe format_version
is important for any consumer software to understand how to parse the fields.
Specialized resource type 'model'
\n", "annotation": ": Literal['model']"}, "bioimageio.spec.model.ModelDescr.id": {"fullname": "bioimageio.spec.model.ModelDescr.id", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.ModelId]"}, "bioimageio.spec.model.ModelDescr.authors": {"fullname": "bioimageio.spec.model.ModelDescr.authors", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.authors", "kind": "variable", "doc": "The authors are the creators of the model RDF and the primary points of contact.
\n", "annotation": ": Annotated[List[bioimageio.spec.generic.v0_3.Author], MinLen(min_length=1)]"}, "bioimageio.spec.model.ModelDescr.documentation": {"fullname": "bioimageio.spec.model.ModelDescr.documentation", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.documentation", "kind": "variable", "doc": "\u2208\ud83d\udce6 URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is README.md
. An .md
suffix is mandatory.\nThe documentation should include a '#[#] Validation' (sub)section\nwith details on how to quantitatively validate the model on unseen data.
Describes the input tensors expected by this model.
\n", "annotation": ": Annotated[Sequence[bioimageio.spec.model.v0_5.InputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.model.ModelDescr.name": {"fullname": "bioimageio.spec.model.ModelDescr.name", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.name", "kind": "variable", "doc": "A human-readable name of this model.\nIt should be no longer than 64 characters\nand may only contain letter, number, underscore, minus, parentheses and spaces.\nWe recommend to chose a name that refers to the model's task and image modality.
\n", "annotation": ": Annotated[str, RestrictCharacters(alphabet='abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_- ()'), MinLen(min_length=5), MaxLen(max_length=128), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f464516dc60>, severity=20, msg='Name longer than 64 characters.', context={'typ': Annotated[Any, MaxLen(max_length=64)]})]"}, "bioimageio.spec.model.ModelDescr.outputs": {"fullname": "bioimageio.spec.model.ModelDescr.outputs", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.outputs", "kind": "variable", "doc": "Describes the output tensors.
\n", "annotation": ": Annotated[Sequence[bioimageio.spec.model.v0_5.OutputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.model.ModelDescr.packaged_by": {"fullname": "bioimageio.spec.model.ModelDescr.packaged_by", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.packaged_by", "kind": "variable", "doc": "The persons that have packaged and uploaded this model.\nOnly required if those persons differ from the authors
.
The model from which this model is derived, e.g. by fine-tuning the weights.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.LinkedModel]"}, "bioimageio.spec.model.ModelDescr.run_mode": {"fullname": "bioimageio.spec.model.ModelDescr.run_mode", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.run_mode", "kind": "variable", "doc": "Custom run mode for this model: for more complex prediction procedures like test time\ndata augmentation that currently cannot be expressed in the specification.\nNo standard run modes are defined yet.
\n", "annotation": ": Annotated[Optional[bioimageio.spec.model.v0_4.RunMode], AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f464516ce00>, severity=30, msg="Run mode '{value}' has limited support across consumer softwares.", context={'typ': None})]"}, "bioimageio.spec.model.ModelDescr.timestamp": {"fullname": "bioimageio.spec.model.ModelDescr.timestamp", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.timestamp", "kind": "variable", "doc": "Timestamp in ISO 8601 format\nwith a few restrictions listed here.\n(In Python a datetime object is valid, too).
\n", "annotation": ": bioimageio.spec._internal.types.Datetime"}, "bioimageio.spec.model.ModelDescr.training_data": {"fullname": "bioimageio.spec.model.ModelDescr.training_data", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.training_data", "kind": "variable", "doc": "The dataset used to train this model
\n", "annotation": ": Annotated[Union[NoneType, bioimageio.spec.dataset.v0_3.LinkedDataset, bioimageio.spec.dataset.v0_3.DatasetDescr, bioimageio.spec.dataset.v0_2.DatasetDescr], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]"}, "bioimageio.spec.model.ModelDescr.weights": {"fullname": "bioimageio.spec.model.ModelDescr.weights", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.weights", "kind": "variable", "doc": "The weights for this model.\nWeights can be given for different formats, but should otherwise be equivalent.\nThe available weight formats determine which consumers can use this model.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.WeightsDescr, WrapSerializer(func=<function package_weights at 0x7f4654144360>, return_type=PydanticUndefined, when_used='always')]"}, "bioimageio.spec.model.ModelDescr.get_input_test_arrays": {"fullname": "bioimageio.spec.model.ModelDescr.get_input_test_arrays", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.get_input_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.model.ModelDescr.get_output_test_arrays": {"fullname": "bioimageio.spec.model.ModelDescr.get_output_test_arrays", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.get_output_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.model.ModelDescr.get_batch_size": {"fullname": "bioimageio.spec.model.ModelDescr.get_batch_size", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.get_batch_size", "kind": "function", "doc": "\n", "signature": "(\ttensor_sizes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]) -> int:", "funcdef": "def"}, "bioimageio.spec.model.ModelDescr.get_output_tensor_sizes": {"fullname": "bioimageio.spec.model.ModelDescr.get_output_tensor_sizes", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.get_output_tensor_sizes", "kind": "function", "doc": "Returns the tensor output sizes for given input_sizes.\nOnly if input_sizes has a valid input shape, the tensor output size is exact.\nOtherwise it might be larger than the actual (valid) output
\n", "signature": "(\tself,\tinput_sizes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]) -> Dict[bioimageio.spec.model.v0_5.TensorId, Dict[bioimageio.spec.model.v0_5.AxisId, Union[int, bioimageio.spec.model.v0_5._DataDepSize]]]:", "funcdef": "def"}, "bioimageio.spec.model.ModelDescr.get_ns": {"fullname": "bioimageio.spec.model.ModelDescr.get_ns", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.get_ns", "kind": "function", "doc": "get parameter n
for each parameterized axis\nsuch that the valid input size is >= the given input size
Determine input and output block shape for scale factors ns\nof parameterized input sizes.
\n\nn
for each axis (keyed by (tensor_id, axis_id))\nthat is parameterized as size = min + n * step
.n
, is larger\nthan max_input_shape is set to the minimal value n_min
for which\nthis is still true.\nUse this for small input samples or large values of ns.\nOr simply whenever you know the full input shape.\n\n", "signature": "(\tself,\tns: Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int],\tbatch_size: Optional[int] = None,\t*,\tmax_input_shape: Optional[Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int]] = None) -> bioimageio.spec.model.v0_5._AxisSizes:", "funcdef": "def"}, "bioimageio.spec.model.ModelDescr.implemented_format_version": {"fullname": "bioimageio.spec.model.ModelDescr.implemented_format_version", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.5.3'"}, "bioimageio.spec.model.ModelDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.model.ModelDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 5, 3)"}, "bioimageio.spec.model.ModelDescr.model_post_init": {"fullname": "bioimageio.spec.model.ModelDescr.model_post_init", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.model_post_init", "kind": "function", "doc": "Resolved axis sizes for model inputs and outputs.
\n
We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.model.ModelDescr_v0_4": {"fullname": "bioimageio.spec.model.ModelDescr_v0_4", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr_v0_4", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.model.v0_4.ModelDescr'>"}, "bioimageio.spec.model.ModelDescr_v0_5": {"fullname": "bioimageio.spec.model.ModelDescr_v0_5", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr_v0_5", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.model.v0_5.ModelDescr'>"}, "bioimageio.spec.model.AnyModelDescr": {"fullname": "bioimageio.spec.model.AnyModelDescr", "modulename": "bioimageio.spec.model", "qualname": "AnyModelDescr", "kind": "variable", "doc": "Union of any released model desription
\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]"}, "bioimageio.spec.model.v0_4": {"fullname": "bioimageio.spec.model.v0_4", "modulename": "bioimageio.spec.model.v0_4", "kind": "module", "doc": "\n"}, "bioimageio.spec.model.v0_4.ModelId": {"fullname": "bioimageio.spec.model.v0_4.ModelId", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec.generic.v0_2.ResourceId"}, "bioimageio.spec.model.v0_4.AxesStr": {"fullname": "bioimageio.spec.model.v0_4.AxesStr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "AxesStr", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[str, RestrictCharacters(alphabet='bitczyx'), AfterValidator(func=<function validate_unique_entries>)]"}, "bioimageio.spec.model.v0_4.AxesInCZYX": {"fullname": "bioimageio.spec.model.v0_4.AxesInCZYX", "modulename": "bioimageio.spec.model.v0_4", "qualname": "AxesInCZYX", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[str, RestrictCharacters(alphabet='czyx'), AfterValidator(func=<function validate_unique_entries>)]"}, "bioimageio.spec.model.v0_4.PostprocessingName": {"fullname": "bioimageio.spec.model.v0_4.PostprocessingName", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PostprocessingName", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['binarize', 'clip', 'scale_linear', 'sigmoid', 'zero_mean_unit_variance', 'scale_range', 'scale_mean_variance']"}, "bioimageio.spec.model.v0_4.PreprocessingName": {"fullname": "bioimageio.spec.model.v0_4.PreprocessingName", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PreprocessingName", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['binarize', 'clip', 'scale_linear', 'sigmoid', 'zero_mean_unit_variance', 'scale_range']"}, "bioimageio.spec.model.v0_4.TensorName": {"fullname": "bioimageio.spec.model.v0_4.TensorName", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorName", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec._internal.types.LowerCaseIdentifier"}, "bioimageio.spec.model.v0_4.CallableFromDepencency": {"fullname": "bioimageio.spec.model.v0_4.CallableFromDepencency", "modulename": "bioimageio.spec.model.v0_4", "qualname": "CallableFromDepencency", "kind": "class", "doc": "deprecated! don't use for new spec fields!
\n", "bases": "bioimageio.spec._internal.common_nodes.StringNode"}, "bioimageio.spec.model.v0_4.CallableFromDepencency.module_name": {"fullname": "bioimageio.spec.model.v0_4.CallableFromDepencency.module_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "CallableFromDepencency.module_name", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.model.v0_4.CallableFromDepencency.check_submodules": {"fullname": "bioimageio.spec.model.v0_4.CallableFromDepencency.check_submodules", "modulename": "bioimageio.spec.model.v0_4", "qualname": "CallableFromDepencency.check_submodules", "kind": "function", "doc": "\n", "signature": "(cls, module_name: str) -> str:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.CallableFromDepencency.callable_name": {"fullname": "bioimageio.spec.model.v0_4.CallableFromDepencency.callable_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "CallableFromDepencency.callable_name", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec._internal.types.Identifier"}, "bioimageio.spec.model.v0_4.CallableFromFile": {"fullname": "bioimageio.spec.model.v0_4.CallableFromFile", "modulename": "bioimageio.spec.model.v0_4", "qualname": "CallableFromFile", "kind": "class", "doc": "deprecated! don't use for new spec fields!
\n", "bases": "bioimageio.spec._internal.common_nodes.StringNode"}, "bioimageio.spec.model.v0_4.CallableFromFile.source_file": {"fullname": "bioimageio.spec.model.v0_4.CallableFromFile.source_file", "modulename": "bioimageio.spec.model.v0_4", "qualname": "CallableFromFile.source_file", "kind": "variable", "doc": "\u2208\ud83d\udce6 Python module that implements callable_name
The Python identifier of
\n", "annotation": ": bioimageio.spec._internal.types.Identifier"}, "bioimageio.spec.model.v0_4.CustomCallable": {"fullname": "bioimageio.spec.model.v0_4.CustomCallable", "modulename": "bioimageio.spec.model.v0_4", "qualname": "CustomCallable", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.model.v0_4.CallableFromFile, bioimageio.spec.model.v0_4.CallableFromDepencency], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]"}, "bioimageio.spec.model.v0_4.Dependencies": {"fullname": "bioimageio.spec.model.v0_4.Dependencies", "modulename": "bioimageio.spec.model.v0_4", "qualname": "Dependencies", "kind": "class", "doc": "deprecated! don't use for new spec fields!
\n", "bases": "bioimageio.spec._internal.common_nodes.StringNode"}, "bioimageio.spec.model.v0_4.Dependencies.manager": {"fullname": "bioimageio.spec.model.v0_4.Dependencies.manager", "modulename": "bioimageio.spec.model.v0_4", "qualname": "Dependencies.manager", "kind": "variable", "doc": "Dependency manager
\n", "annotation": ": Annotated[str, MinLen(min_length=1), FieldInfo(annotation=NoneType, required=True, examples=['conda', 'maven', 'pip'])]"}, "bioimageio.spec.model.v0_4.Dependencies.file": {"fullname": "bioimageio.spec.model.v0_4.Dependencies.file", "modulename": "bioimageio.spec.model.v0_4", "qualname": "Dependencies.file", "kind": "variable", "doc": "\u2208\ud83d\udce6 Dependency file
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none'), FieldInfo(annotation=NoneType, required=True, examples=['environment.yaml', 'pom.xml', 'requirements.txt'])]"}, "bioimageio.spec.model.v0_4.WeightsFormat": {"fullname": "bioimageio.spec.model.v0_4.WeightsFormat", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsFormat", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']"}, "bioimageio.spec.model.v0_4.WeightsDescr": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_4.WeightsDescr.keras_hdf5": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr.keras_hdf5", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr.keras_hdf5", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.KerasHdf5WeightsDescr]"}, "bioimageio.spec.model.v0_4.WeightsDescr.onnx": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr.onnx", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr.onnx", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.OnnxWeightsDescr]"}, "bioimageio.spec.model.v0_4.WeightsDescr.pytorch_state_dict": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr.pytorch_state_dict", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr.pytorch_state_dict", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr]"}, "bioimageio.spec.model.v0_4.WeightsDescr.tensorflow_js": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr.tensorflow_js", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr.tensorflow_js", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr]"}, "bioimageio.spec.model.v0_4.WeightsDescr.tensorflow_saved_model_bundle": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr.tensorflow_saved_model_bundle", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr.tensorflow_saved_model_bundle", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr]"}, "bioimageio.spec.model.v0_4.WeightsDescr.torchscript": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr.torchscript", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr.torchscript", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.TorchscriptWeightsDescr]"}, "bioimageio.spec.model.v0_4.WeightsDescr.check_one_entry": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr.check_one_entry", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr.check_one_entry", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.WeightsEntryDescrBase": {"fullname": "bioimageio.spec.model.v0_4.WeightsEntryDescrBase", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsEntryDescrBase", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.io.FileDescr"}, "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.type": {"fullname": "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsEntryDescrBase.type", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]"}, "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.weights_format_name": {"fullname": "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.weights_format_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsEntryDescrBase.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]"}, "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.source": {"fullname": "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.source", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsEntryDescrBase.source", "kind": "variable", "doc": "\u2208\ud83d\udce6 The weights file.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.attachments": {"fullname": "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.attachments", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsEntryDescrBase.attachments", "kind": "variable", "doc": "Attachments that are specific to this weights entry.
\n", "annotation": ": Annotated[Optional[bioimageio.spec.generic.v0_2.AttachmentsDescr], AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f4645628360>, severity=35, msg='Weights entry depends on additional attachments.', context={'typ': None})]"}, "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.authors": {"fullname": "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.authors", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsEntryDescrBase.authors", "kind": "variable", "doc": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a parent
)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a parent
field)
Dependency manager and dependency file, specified as <dependency manager>:<relative file path>
.
The source weights these weights were converted from.\nFor example, if a model's weights were converted from the pytorch_state_dict
format to torchscript
,\nThe pytorch_state_dict
weights entry has no parent
and is the parent of the torchscript
weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.
Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_4.KerasHdf5WeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_4.KerasHdf5WeightsDescr.type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "KerasHdf5WeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'keras_hdf5'"}, "bioimageio.spec.model.v0_4.KerasHdf5WeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_4.KerasHdf5WeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "KerasHdf5WeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Keras HDF5'"}, "bioimageio.spec.model.v0_4.KerasHdf5WeightsDescr.tensorflow_version": {"fullname": "bioimageio.spec.model.v0_4.KerasHdf5WeightsDescr.tensorflow_version", "modulename": "bioimageio.spec.model.v0_4", "qualname": "KerasHdf5WeightsDescr.tensorflow_version", "kind": "variable", "doc": "TensorFlow version used to create these weights
\n", "annotation": ": Optional[bioimageio.spec._internal.version_type.Version]"}, "bioimageio.spec.model.v0_4.OnnxWeightsDescr": {"fullname": "bioimageio.spec.model.v0_4.OnnxWeightsDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OnnxWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_4.OnnxWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_4.OnnxWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OnnxWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'onnx'"}, "bioimageio.spec.model.v0_4.OnnxWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_4.OnnxWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OnnxWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'ONNX'"}, "bioimageio.spec.model.v0_4.OnnxWeightsDescr.opset_version": {"fullname": "bioimageio.spec.model.v0_4.OnnxWeightsDescr.opset_version", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OnnxWeightsDescr.opset_version", "kind": "variable", "doc": "ONNX opset version
\n", "annotation": ": Optional[Annotated[int, Ge(ge=7)]]"}, "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr": {"fullname": "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PytorchStateDictWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PytorchStateDictWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'pytorch_state_dict'"}, "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PytorchStateDictWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Pytorch State Dict'"}, "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr.architecture": {"fullname": "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr.architecture", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PytorchStateDictWeightsDescr.architecture", "kind": "variable", "doc": "callable returning a torch.nn.Module instance.\nLocal implementation: <relative path to file>:<identifier of implementation within the file>
.\nImplementation in a dependency: <dependency-package>.<[dependency-module]>.<identifier>
.
The SHA256 of the architecture source file,\nif the architecture is not defined in a module listed in dependencies
key word arguments for the architecture
callable
Version of the PyTorch library used.\nIf depencencies
is specified it should include pytorch and the verison has to match.\n(dependencies
overrules pytorch_version
)
Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_4.TorchscriptWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_4.TorchscriptWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TorchscriptWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'torchscript'"}, "bioimageio.spec.model.v0_4.TorchscriptWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_4.TorchscriptWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TorchscriptWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'TorchScript'"}, "bioimageio.spec.model.v0_4.TorchscriptWeightsDescr.pytorch_version": {"fullname": "bioimageio.spec.model.v0_4.TorchscriptWeightsDescr.pytorch_version", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TorchscriptWeightsDescr.pytorch_version", "kind": "variable", "doc": "Version of the PyTorch library used.
\n", "annotation": ": Optional[bioimageio.spec._internal.version_type.Version]"}, "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr": {"fullname": "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowJsWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowJsWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'tensorflow_js'"}, "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowJsWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Tensorflow.js'"}, "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.tensorflow_version": {"fullname": "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.tensorflow_version", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowJsWeightsDescr.tensorflow_version", "kind": "variable", "doc": "Version of the TensorFlow library used.
\n", "annotation": ": Optional[bioimageio.spec._internal.version_type.Version]"}, "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.source": {"fullname": "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.source", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowJsWeightsDescr.source", "kind": "variable", "doc": "\u2208\ud83d\udce6 The multi-file weights.\nAll required files/folders should be a zip archive.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr": {"fullname": "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowSavedModelBundleWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowSavedModelBundleWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'tensorflow_saved_model_bundle'"}, "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowSavedModelBundleWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Tensorflow Saved Model'"}, "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr.tensorflow_version": {"fullname": "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr.tensorflow_version", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowSavedModelBundleWeightsDescr.tensorflow_version", "kind": "variable", "doc": "Version of the TensorFlow library used.
\n", "annotation": ": Optional[bioimageio.spec._internal.version_type.Version]"}, "bioimageio.spec.model.v0_4.ParameterizedInputShape": {"fullname": "bioimageio.spec.model.v0_4.ParameterizedInputShape", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ParameterizedInputShape", "kind": "class", "doc": "A sequence of valid shapes given by shape_k = min + k * step for k in {0, 1, ...}
.
The minimum input shape
\n", "annotation": ": Annotated[List[int], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_4.ParameterizedInputShape.step": {"fullname": "bioimageio.spec.model.v0_4.ParameterizedInputShape.step", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ParameterizedInputShape.step", "kind": "variable", "doc": "The minimum shape change
\n", "annotation": ": Annotated[List[int], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_4.ParameterizedInputShape.matching_lengths": {"fullname": "bioimageio.spec.model.v0_4.ParameterizedInputShape.matching_lengths", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ParameterizedInputShape.matching_lengths", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ImplicitOutputShape": {"fullname": "bioimageio.spec.model.v0_4.ImplicitOutputShape", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ImplicitOutputShape", "kind": "class", "doc": "Output tensor shape depending on an input tensor shape.\nshape(output_tensor) = shape(input_tensor) * scale + 2 * offset
Name of the reference tensor.
\n", "annotation": ": bioimageio.spec.model.v0_4.TensorName"}, "bioimageio.spec.model.v0_4.ImplicitOutputShape.scale": {"fullname": "bioimageio.spec.model.v0_4.ImplicitOutputShape.scale", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ImplicitOutputShape.scale", "kind": "variable", "doc": "output_pix/input_pix for each dimension.\n'null' values indicate new dimensions, whose length is defined by 2*offset
Position of origin wrt to input.
\n", "annotation": ": Annotated[List[Union[int, Annotated[float, MultipleOf(multiple_of=0.5)]]], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_4.ImplicitOutputShape.matching_lengths": {"fullname": "bioimageio.spec.model.v0_4.ImplicitOutputShape.matching_lengths", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ImplicitOutputShape.matching_lengths", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.TensorDescrBase": {"fullname": "bioimageio.spec.model.v0_4.TensorDescrBase", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorDescrBase", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_4.TensorDescrBase.name": {"fullname": "bioimageio.spec.model.v0_4.TensorDescrBase.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorDescrBase.name", "kind": "variable", "doc": "Tensor name. No duplicates are allowed.
\n", "annotation": ": bioimageio.spec.model.v0_4.TensorName"}, "bioimageio.spec.model.v0_4.TensorDescrBase.description": {"fullname": "bioimageio.spec.model.v0_4.TensorDescrBase.description", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorDescrBase.description", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.model.v0_4.TensorDescrBase.axes": {"fullname": "bioimageio.spec.model.v0_4.TensorDescrBase.axes", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorDescrBase.axes", "kind": "variable", "doc": "Axes identifying characters. Same length and order as the axes in shape
.
axis | \ndescription | \n
---|---|
b | \nbatch (groups multiple samples) | \n
i | \ninstance/index/element | \n
t | \ntime | \n
c | \nchannel | \n
z | \nspatial dimension z | \n
y | \nspatial dimension y | \n
x | \nspatial dimension x | \n
Tuple (minimum, maximum)
specifying the allowed range of the data in this tensor.\nIf not specified, the full data range that can be expressed in data_type
is allowed.
base class for pre-/postprocessing key word arguments
\n", "bases": "bioimageio.spec._internal.common_nodes.KwargsNode"}, "bioimageio.spec.model.v0_4.ProcessingDescrBase": {"fullname": "bioimageio.spec.model.v0_4.ProcessingDescrBase", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ProcessingDescrBase", "kind": "class", "doc": "processing base class
\n", "bases": "bioimageio.spec._internal.common_nodes.NodeWithExplicitlySetFields"}, "bioimageio.spec.model.v0_4.ProcessingDescrBase.fields_to_set_explicitly": {"fullname": "bioimageio.spec.model.v0_4.ProcessingDescrBase.fields_to_set_explicitly", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ProcessingDescrBase.fields_to_set_explicitly", "kind": "variable", "doc": "set set these fields explicitly with their default value if they are not set,\nsuch that they are always included even when dumping with 'exlude_unset'
\n", "annotation": ": ClassVar[FrozenSet[LiteralString]]", "default_value": "frozenset({'name'})"}, "bioimageio.spec.model.v0_4.BinarizeKwargs": {"fullname": "bioimageio.spec.model.v0_4.BinarizeKwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "BinarizeKwargs", "kind": "class", "doc": "key word arguments for BinarizeDescr
The fixed threshold
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_4.BinarizeDescr": {"fullname": "bioimageio.spec.model.v0_4.BinarizeDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "BinarizeDescr", "kind": "class", "doc": "BinarizeDescr the tensor with a fixed BinarizeKwargs.threshold
.\nValues above the threshold will be set to one, values below the threshold to zero.
key word arguments for ClipDescr
minimum value for clipping
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_4.ClipKwargs.max": {"fullname": "bioimageio.spec.model.v0_4.ClipKwargs.max", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ClipKwargs.max", "kind": "variable", "doc": "maximum value for clipping
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_4.ClipDescr": {"fullname": "bioimageio.spec.model.v0_4.ClipDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ClipDescr", "kind": "class", "doc": "Clip tensor values to a range.
\n\nSet tensor values below ClipKwargs.min
to ClipKwargs.min
\nand above ClipKwargs.max
to ClipKwargs.max
.
key word arguments for ScaleLinearDescr
The subset of axes to scale jointly.\nFor example xy to scale the two image axes for 2d data jointly.
\n", "annotation": ": Annotated[Optional[Annotated[str, RestrictCharacters(alphabet='czyx'), AfterValidator(func=<function validate_unique_entries at 0x7f465881eac0>)]], FieldInfo(annotation=NoneType, required=True, examples=['xy'])]"}, "bioimageio.spec.model.v0_4.ScaleLinearKwargs.gain": {"fullname": "bioimageio.spec.model.v0_4.ScaleLinearKwargs.gain", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleLinearKwargs.gain", "kind": "variable", "doc": "multiplicative factor
\n", "annotation": ": Union[float, List[float]]"}, "bioimageio.spec.model.v0_4.ScaleLinearKwargs.offset": {"fullname": "bioimageio.spec.model.v0_4.ScaleLinearKwargs.offset", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleLinearKwargs.offset", "kind": "variable", "doc": "additive term
\n", "annotation": ": Union[float, List[float]]"}, "bioimageio.spec.model.v0_4.ScaleLinearKwargs.either_gain_or_offset": {"fullname": "bioimageio.spec.model.v0_4.ScaleLinearKwargs.either_gain_or_offset", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleLinearKwargs.either_gain_or_offset", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ScaleLinearDescr": {"fullname": "bioimageio.spec.model.v0_4.ScaleLinearDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleLinearDescr", "kind": "class", "doc": "Fixed linear scaling.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_4.ScaleLinearDescr.name": {"fullname": "bioimageio.spec.model.v0_4.ScaleLinearDescr.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleLinearDescr.name", "kind": "variable", "doc": "\n", "annotation": ": Literal['scale_linear']"}, "bioimageio.spec.model.v0_4.ScaleLinearDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_4.ScaleLinearDescr.kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleLinearDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_4.ScaleLinearKwargs"}, "bioimageio.spec.model.v0_4.SigmoidDescr": {"fullname": "bioimageio.spec.model.v0_4.SigmoidDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "SigmoidDescr", "kind": "class", "doc": "The logistic sigmoid funciton, a.k.a. expit function.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_4.SigmoidDescr.name": {"fullname": "bioimageio.spec.model.v0_4.SigmoidDescr.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "SigmoidDescr.name", "kind": "variable", "doc": "\n", "annotation": ": Literal['sigmoid']"}, "bioimageio.spec.model.v0_4.SigmoidDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_4.SigmoidDescr.kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "SigmoidDescr.kwargs", "kind": "variable", "doc": "empty kwargs
\n", "annotation": ": bioimageio.spec.model.v0_4.ProcessingKwargs"}, "bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceKwargs": {"fullname": "bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceKwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ZeroMeanUnitVarianceKwargs", "kind": "class", "doc": "key word arguments for ZeroMeanUnitVarianceDescr
Mode for computing mean and variance.
\n\nmode | \ndescription | \n
---|---|
fixed | \nFixed values for mean and variance | \n
per_dataset | \nCompute for the entire dataset | \n
per_sample | \nCompute for each sample individually | \n
The subset of axes to normalize jointly.\nFor example xy
to normalize the two image axes for 2d data jointly.
The mean value(s) to use for mode: fixed
.\nFor example [1.1, 2.2, 3.3]
in the case of a 3 channel image with axes: xy
.
The standard deviation values to use for mode: fixed
. Analogous to mean.
epsilon for numeric stability: out = (tensor - mean) / (std + eps)
.
Subtract mean and divide by variance.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr.name": {"fullname": "bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ZeroMeanUnitVarianceDescr.name", "kind": "variable", "doc": "\n", "annotation": ": Literal['zero_mean_unit_variance']"}, "bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr.kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ZeroMeanUnitVarianceDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceKwargs"}, "bioimageio.spec.model.v0_4.ScaleRangeKwargs": {"fullname": "bioimageio.spec.model.v0_4.ScaleRangeKwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleRangeKwargs", "kind": "class", "doc": "key word arguments for ScaleRangeDescr
For min_percentile
=0.0 (the default) and max_percentile
=100 (the default)\nthis processing step normalizes data to the [0, 1] intervall.\nFor other percentiles the normalized values will partially be outside the [0, 1]\nintervall. Use ScaleRange
followed by ClipDescr
if you want to limit the\nnormalized values to a range.
Mode for computing percentiles.
\n\nmode | \ndescription | \n
---|---|
per_dataset | \ncompute for the entire dataset | \n
per_sample | \ncompute for each sample individually | \n
The subset of axes to normalize jointly.\nFor example xy to normalize the two image axes for 2d data jointly.
\n", "annotation": ": Annotated[str, RestrictCharacters(alphabet='czyx'), AfterValidator(func=<function validate_unique_entries at 0x7f465881eac0>), FieldInfo(annotation=NoneType, required=True, examples=['xy'])]"}, "bioimageio.spec.model.v0_4.ScaleRangeKwargs.min_percentile": {"fullname": "bioimageio.spec.model.v0_4.ScaleRangeKwargs.min_percentile", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleRangeKwargs.min_percentile", "kind": "variable", "doc": "The lower percentile used to determine the value to align with zero.
\n", "annotation": ": Annotated[Union[int, float], Interval(gt=None, ge=0, lt=100, le=None)]"}, "bioimageio.spec.model.v0_4.ScaleRangeKwargs.max_percentile": {"fullname": "bioimageio.spec.model.v0_4.ScaleRangeKwargs.max_percentile", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleRangeKwargs.max_percentile", "kind": "variable", "doc": "The upper percentile used to determine the value to align with one.\nHas to be bigger than min_percentile
.\nThe range is 1 to 100 instead of 0 to 100 to avoid mistakenly\naccepting percentiles specified in the range 0.0 to 1.0.
Epsilon for numeric stability.\nout = (tensor - v_lower) / (v_upper - v_lower + eps)
;\nwith v_lower,v_upper
values at the respective percentiles.
Tensor name to compute the percentiles from. Default: The tensor itself.\nFor any tensor in inputs
only input tensor references are allowed.\nFor a tensor in outputs
only input tensor refereences are allowed if mode: per_dataset
Scale with percentiles.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_4.ScaleRangeDescr.name": {"fullname": "bioimageio.spec.model.v0_4.ScaleRangeDescr.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleRangeDescr.name", "kind": "variable", "doc": "\n", "annotation": ": Literal['scale_range']"}, "bioimageio.spec.model.v0_4.ScaleRangeDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_4.ScaleRangeDescr.kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleRangeDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_4.ScaleRangeKwargs"}, "bioimageio.spec.model.v0_4.ScaleMeanVarianceKwargs": {"fullname": "bioimageio.spec.model.v0_4.ScaleMeanVarianceKwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleMeanVarianceKwargs", "kind": "class", "doc": "key word arguments for ScaleMeanVarianceDescr
Mode for computing mean and variance.
\n\nmode | \ndescription | \n
---|---|
per_dataset | \nCompute for the entire dataset | \n
per_sample | \nCompute for each sample individually | \n
Name of tensor to match.
\n", "annotation": ": bioimageio.spec.model.v0_4.TensorName"}, "bioimageio.spec.model.v0_4.ScaleMeanVarianceKwargs.axes": {"fullname": "bioimageio.spec.model.v0_4.ScaleMeanVarianceKwargs.axes", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleMeanVarianceKwargs.axes", "kind": "variable", "doc": "The subset of axes to scale jointly.\nFor example xy to normalize the two image axes for 2d data jointly.\nDefault: scale all non-batch axes jointly.
\n", "annotation": ": Annotated[Optional[Annotated[str, RestrictCharacters(alphabet='czyx'), AfterValidator(func=<function validate_unique_entries at 0x7f465881eac0>)]], FieldInfo(annotation=NoneType, required=True, examples=['xy'])]"}, "bioimageio.spec.model.v0_4.ScaleMeanVarianceKwargs.eps": {"fullname": "bioimageio.spec.model.v0_4.ScaleMeanVarianceKwargs.eps", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleMeanVarianceKwargs.eps", "kind": "variable", "doc": "Epsilon for numeric stability:\n\"`out = (tensor - mean) / (std + eps) * (ref_std + eps) + ref_mean.
\n", "annotation": ": Annotated[float, Interval(gt=0, ge=None, lt=None, le=0.1)]"}, "bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr": {"fullname": "bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleMeanVarianceDescr", "kind": "class", "doc": "Scale the tensor s.t. its mean and variance match a reference tensor.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr.name": {"fullname": "bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleMeanVarianceDescr.name", "kind": "variable", "doc": "\n", "annotation": ": Literal['scale_mean_variance']"}, "bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr.kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleMeanVarianceDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_4.ScaleMeanVarianceKwargs"}, "bioimageio.spec.model.v0_4.PreprocessingDescr": {"fullname": "bioimageio.spec.model.v0_4.PreprocessingDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PreprocessingDescr", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]"}, "bioimageio.spec.model.v0_4.PostprocessingDescr": {"fullname": "bioimageio.spec.model.v0_4.PostprocessingDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PostprocessingDescr", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr, bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]"}, "bioimageio.spec.model.v0_4.InputTensorDescr": {"fullname": "bioimageio.spec.model.v0_4.InputTensorDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "InputTensorDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "TensorDescrBase"}, "bioimageio.spec.model.v0_4.InputTensorDescr.data_type": {"fullname": "bioimageio.spec.model.v0_4.InputTensorDescr.data_type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "InputTensorDescr.data_type", "kind": "variable", "doc": "For now an input tensor is expected to be given as float32
.\nThe data flow in bioimage.io models is explained\nin this diagram..
Specification of input tensor shape.
\n", "annotation": ": Annotated[Union[Sequence[int], bioimageio.spec.model.v0_4.ParameterizedInputShape], FieldInfo(annotation=NoneType, required=True, examples=[(1, 512, 512, 1), {'min': (1, 64, 64, 1), 'step': (0, 32, 32, 0)}])]"}, "bioimageio.spec.model.v0_4.InputTensorDescr.preprocessing": {"fullname": "bioimageio.spec.model.v0_4.InputTensorDescr.preprocessing", "modulename": "bioimageio.spec.model.v0_4", "qualname": "InputTensorDescr.preprocessing", "kind": "variable", "doc": "Description of how this input should be preprocessed.
\n", "annotation": ": List[Annotated[Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.spec.model.v0_4.InputTensorDescr.zero_batch_step_and_one_batch_size": {"fullname": "bioimageio.spec.model.v0_4.InputTensorDescr.zero_batch_step_and_one_batch_size", "modulename": "bioimageio.spec.model.v0_4", "qualname": "InputTensorDescr.zero_batch_step_and_one_batch_size", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.InputTensorDescr.validate_preprocessing_kwargs": {"fullname": "bioimageio.spec.model.v0_4.InputTensorDescr.validate_preprocessing_kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "InputTensorDescr.validate_preprocessing_kwargs", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.OutputTensorDescr": {"fullname": "bioimageio.spec.model.v0_4.OutputTensorDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OutputTensorDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "TensorDescrBase"}, "bioimageio.spec.model.v0_4.OutputTensorDescr.data_type": {"fullname": "bioimageio.spec.model.v0_4.OutputTensorDescr.data_type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OutputTensorDescr.data_type", "kind": "variable", "doc": "Data type.\nThe data flow in bioimage.io models is explained\nin this diagram..
\n", "annotation": ": Literal['float32', 'float64', 'uint8', 'int8', 'uint16', 'int16', 'uint32', 'int32', 'uint64', 'int64', 'bool']"}, "bioimageio.spec.model.v0_4.OutputTensorDescr.shape": {"fullname": "bioimageio.spec.model.v0_4.OutputTensorDescr.shape", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OutputTensorDescr.shape", "kind": "variable", "doc": "Output tensor shape.
\n", "annotation": ": Union[Sequence[int], bioimageio.spec.model.v0_4.ImplicitOutputShape]"}, "bioimageio.spec.model.v0_4.OutputTensorDescr.halo": {"fullname": "bioimageio.spec.model.v0_4.OutputTensorDescr.halo", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OutputTensorDescr.halo", "kind": "variable", "doc": "The halo
that should be cropped from the output tensor to avoid boundary effects.\nThe halo
is to be cropped from both sides, i.e. shape_after_crop = shape - 2 * halo
.\nTo document a halo
that is already cropped by the model shape.offset
has to be used instead.
Description of how this output should be postprocessed.
\n", "annotation": ": List[Annotated[Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr, bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.spec.model.v0_4.OutputTensorDescr.matching_halo_length": {"fullname": "bioimageio.spec.model.v0_4.OutputTensorDescr.matching_halo_length", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OutputTensorDescr.matching_halo_length", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.OutputTensorDescr.validate_postprocessing_kwargs": {"fullname": "bioimageio.spec.model.v0_4.OutputTensorDescr.validate_postprocessing_kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OutputTensorDescr.validate_postprocessing_kwargs", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.KnownRunMode": {"fullname": "bioimageio.spec.model.v0_4.KnownRunMode", "modulename": "bioimageio.spec.model.v0_4", "qualname": "KnownRunMode", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['deepimagej']"}, "bioimageio.spec.model.v0_4.RunMode": {"fullname": "bioimageio.spec.model.v0_4.RunMode", "modulename": "bioimageio.spec.model.v0_4", "qualname": "RunMode", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_4.RunMode.name": {"fullname": "bioimageio.spec.model.v0_4.RunMode.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "RunMode.name", "kind": "variable", "doc": "Run mode name
\n", "annotation": ": Annotated[Union[Literal['deepimagej'], str], AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f4644a8aca0>, severity=30, msg="Unknown run mode '{value}'.", context={'typ': Literal['deepimagej']})]"}, "bioimageio.spec.model.v0_4.RunMode.kwargs": {"fullname": "bioimageio.spec.model.v0_4.RunMode.kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "RunMode.kwargs", "kind": "variable", "doc": "Run mode specific key word arguments
\n", "annotation": ": Dict[str, Any]"}, "bioimageio.spec.model.v0_4.LinkedModel": {"fullname": "bioimageio.spec.model.v0_4.LinkedModel", "modulename": "bioimageio.spec.model.v0_4", "qualname": "LinkedModel", "kind": "class", "doc": "Reference to a bioimage.io model.
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_4.LinkedModel.id": {"fullname": "bioimageio.spec.model.v0_4.LinkedModel.id", "modulename": "bioimageio.spec.model.v0_4", "qualname": "LinkedModel.id", "kind": "variable", "doc": "A valid model id
from the bioimage.io collection.
version number (n-th published version, not the semantic version) of linked model
\n", "annotation": ": Optional[int]"}, "bioimageio.spec.model.v0_4.package_weights": {"fullname": "bioimageio.spec.model.v0_4.package_weights", "modulename": "bioimageio.spec.model.v0_4", "qualname": "package_weights", "kind": "function", "doc": "\n", "signature": "(\tvalue: bioimageio.spec._internal.node.Node,\thandler: pydantic_core.core_schema.SerializerFunctionWrapHandler,\tinfo: pydantic_core.core_schema.SerializationInfo):", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr", "kind": "class", "doc": "Specification of the fields used in a bioimage.io-compliant RDF that describes AI models with pretrained weights.
\n\nThese fields are typically stored in a YAML file which we call a model resource description file (model RDF).
\n", "bases": "bioimageio.spec.generic.v0_2.GenericModelDescrBase"}, "bioimageio.spec.model.v0_4.ModelDescr.format_version": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.format_version", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.format_version", "kind": "variable", "doc": "Version of the bioimage.io model description specification used.\nWhen creating a new model always use the latest micro/patch version described here.\nThe format_version
is important for any consumer software to understand how to parse the fields.
Specialized resource type 'model'
\n", "annotation": ": Literal['model']"}, "bioimageio.spec.model.v0_4.ModelDescr.id": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.id", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.ModelId]"}, "bioimageio.spec.model.v0_4.ModelDescr.authors": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.authors", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.authors", "kind": "variable", "doc": "The authors are the creators of the model RDF and the primary points of contact.
\n", "annotation": ": Annotated[List[bioimageio.spec.generic.v0_2.Author], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_4.ModelDescr.documentation": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.documentation", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.documentation", "kind": "variable", "doc": "\u2208\ud83d\udce6 URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is README.md
. An .md
suffix is mandatory.\nThe documentation should include a '[#[#]]# Validation' (sub)section\nwith details on how to quantitatively validate the model on unseen data.
Describes the input tensors expected by this model.
\n", "annotation": ": Annotated[List[bioimageio.spec.model.v0_4.InputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_4.ModelDescr.license": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.license", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.license", "kind": "variable", "doc": "A SPDX license identifier.\nWe do notsupport custom license beyond the SPDX license list, if you need that please\nopen a GitHub issue to discuss your intentions with the community.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.license_id.LicenseId, str], AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f4644a89da0>, severity=30, msg="Unknown license id '{value}'.", context={'typ': <class 'bioimageio.spec._internal.license_id.LicenseId'>}), FieldInfo(annotation=NoneType, required=True, examples=['CC0-1.0', 'MIT', 'BSD-2-Clause'])]"}, "bioimageio.spec.model.v0_4.ModelDescr.name": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.name", "kind": "variable", "doc": "A human-readable name of this model.\nIt should be no longer than 64 characters and only contain letter, number, underscore, minus or space characters.
\n", "annotation": ": Annotated[str, MinLen(min_length=1), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f4644a8a7a0>, severity=20, msg='Name shorter than 5 characters.', context={'typ': Annotated[Any, MinLen(min_length=5)]}), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f4644a88540>, severity=20, msg='Name longer than 64 characters.', context={'typ': Annotated[Any, MaxLen(max_length=64)]})]"}, "bioimageio.spec.model.v0_4.ModelDescr.outputs": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.outputs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.outputs", "kind": "variable", "doc": "Describes the output tensors.
\n", "annotation": ": Annotated[List[bioimageio.spec.model.v0_4.OutputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_4.ModelDescr.unique_tensor_descr_names": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.unique_tensor_descr_names", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.unique_tensor_descr_names", "kind": "function", "doc": "\n", "signature": "(\tcls,\tvalue: Sequence[Union[bioimageio.spec.model.v0_4.InputTensorDescr, bioimageio.spec.model.v0_4.OutputTensorDescr]]) -> Sequence[Union[bioimageio.spec.model.v0_4.InputTensorDescr, bioimageio.spec.model.v0_4.OutputTensorDescr]]:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.unique_io_names": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.unique_io_names", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.unique_io_names", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.minimum_shape2valid_output": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.minimum_shape2valid_output", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.minimum_shape2valid_output", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.validate_tensor_references_in_inputs": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.validate_tensor_references_in_inputs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.validate_tensor_references_in_inputs", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.validate_tensor_references_in_outputs": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.validate_tensor_references_in_outputs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.validate_tensor_references_in_outputs", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.packaged_by": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.packaged_by", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.packaged_by", "kind": "variable", "doc": "The persons that have packaged and uploaded this model.\nOnly required if those persons differ from the authors
.
The model from which this model is derived, e.g. by fine-tuning the weights.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.LinkedModel]"}, "bioimageio.spec.model.v0_4.ModelDescr.ignore_url_parent": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.ignore_url_parent", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.ignore_url_parent", "kind": "function", "doc": "\n", "signature": "(cls, parent: Any):", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.run_mode": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.run_mode", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.run_mode", "kind": "variable", "doc": "Custom run mode for this model: for more complex prediction procedures like test time\ndata augmentation that currently cannot be expressed in the specification.\nNo standard run modes are defined yet.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.RunMode]"}, "bioimageio.spec.model.v0_4.ModelDescr.sample_inputs": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.sample_inputs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.sample_inputs", "kind": "variable", "doc": "\u2208\ud83d\udce6 URLs/relative paths to sample inputs to illustrate possible inputs for the model,\nfor example stored as PNG or TIFF images.\nThe sample files primarily serve to inform a human user about an example use case
\n", "annotation": ": List[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')]]"}, "bioimageio.spec.model.v0_4.ModelDescr.sample_outputs": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.sample_outputs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.sample_outputs", "kind": "variable", "doc": "\u2208\ud83d\udce6 URLs/relative paths to sample outputs corresponding to the sample_inputs
.
\u2208\ud83d\udce6 Test input tensors compatible with the inputs
description for a single test case.\nThis means if your model has more than one input, you should provide one URL/relative path for each input.\nEach test input should be a file with an ndarray in\nnumpy.lib file format.\nThe extension must be '.npy'.
\u2208\ud83d\udce6 Analog to test_inputs
.
Timestamp in ISO 8601 format\nwith a few restrictions listed here.
\n", "annotation": ": bioimageio.spec._internal.types.Datetime"}, "bioimageio.spec.model.v0_4.ModelDescr.training_data": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.training_data", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.training_data", "kind": "variable", "doc": "The dataset used to train this model
\n", "annotation": ": Union[bioimageio.spec.dataset.v0_2.LinkedDataset, bioimageio.spec.dataset.v0_2.DatasetDescr, NoneType]"}, "bioimageio.spec.model.v0_4.ModelDescr.weights": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.weights", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.weights", "kind": "variable", "doc": "The weights for this model.\nWeights can be given for different formats, but should otherwise be equivalent.\nThe available weight formats determine which consumers can use this model.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_4.WeightsDescr, WrapSerializer(func=<function package_weights at 0x7f4654144360>, return_type=PydanticUndefined, when_used='always')]"}, "bioimageio.spec.model.v0_4.ModelDescr.get_input_test_arrays": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.get_input_test_arrays", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.get_input_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.get_output_test_arrays": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.get_output_test_arrays", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.get_output_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.implemented_format_version": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.implemented_format_version", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.4.10'"}, "bioimageio.spec.model.v0_4.ModelDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 4, 10)"}, "bioimageio.spec.model.v0_4.ModelDescr.model_post_init": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.model_post_init", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.model.v0_5": {"fullname": "bioimageio.spec.model.v0_5", "modulename": "bioimageio.spec.model.v0_5", "kind": "module", "doc": "\n"}, "bioimageio.spec.model.v0_5.SpaceUnit": {"fullname": "bioimageio.spec.model.v0_5.SpaceUnit", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceUnit", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['attometer', 'angstrom', 'centimeter', 'decimeter', 'exameter', 'femtometer', 'foot', 'gigameter', 'hectometer', 'inch', 'kilometer', 'megameter', 'meter', 'micrometer', 'mile', 'millimeter', 'nanometer', 'parsec', 'petameter', 'picometer', 'terameter', 'yard', 'yoctometer', 'yottameter', 'zeptometer', 'zettameter']"}, "bioimageio.spec.model.v0_5.TimeUnit": {"fullname": "bioimageio.spec.model.v0_5.TimeUnit", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeUnit", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['attosecond', 'centisecond', 'day', 'decisecond', 'exasecond', 'femtosecond', 'gigasecond', 'hectosecond', 'hour', 'kilosecond', 'megasecond', 'microsecond', 'millisecond', 'minute', 'nanosecond', 'petasecond', 'picosecond', 'second', 'terasecond', 'yoctosecond', 'yottasecond', 'zeptosecond', 'zettasecond']"}, "bioimageio.spec.model.v0_5.AxisType": {"fullname": "bioimageio.spec.model.v0_5.AxisType", "modulename": "bioimageio.spec.model.v0_5", "qualname": "AxisType", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['batch', 'channel', 'index', 'time', 'space']"}, "bioimageio.spec.model.v0_5.TensorId": {"fullname": "bioimageio.spec.model.v0_5.TensorId", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec._internal.types.LowerCaseIdentifier"}, "bioimageio.spec.model.v0_5.TensorId.root_model": {"fullname": "bioimageio.spec.model.v0_5.TensorId.root_model", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorId.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[str, MinLen, AfterValidator, AfterValidator, Annotated[TypeVar, Predicate], MaxLen]]'>"}, "bioimageio.spec.model.v0_5.AxisId": {"fullname": "bioimageio.spec.model.v0_5.AxisId", "modulename": "bioimageio.spec.model.v0_5", "qualname": "AxisId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec._internal.types.LowerCaseIdentifier"}, "bioimageio.spec.model.v0_5.AxisId.root_model": {"fullname": "bioimageio.spec.model.v0_5.AxisId.root_model", "modulename": "bioimageio.spec.model.v0_5", "qualname": "AxisId.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[str, MinLen, AfterValidator, AfterValidator, Annotated[TypeVar, Predicate], MaxLen]]'>"}, "bioimageio.spec.model.v0_5.NonBatchAxisId": {"fullname": "bioimageio.spec.model.v0_5.NonBatchAxisId", "modulename": "bioimageio.spec.model.v0_5", "qualname": "NonBatchAxisId", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_not_batch)]"}, "bioimageio.spec.model.v0_5.PostprocessingId": {"fullname": "bioimageio.spec.model.v0_5.PostprocessingId", "modulename": "bioimageio.spec.model.v0_5", "qualname": "PostprocessingId", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['binarize', 'clip', 'ensure_dtype', 'fixed_zero_mean_unit_variance', 'scale_linear', 'scale_mean_variance', 'scale_range', 'sigmoid', 'zero_mean_unit_variance']"}, "bioimageio.spec.model.v0_5.PreprocessingId": {"fullname": "bioimageio.spec.model.v0_5.PreprocessingId", "modulename": "bioimageio.spec.model.v0_5", "qualname": "PreprocessingId", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['binarize', 'clip', 'ensure_dtype', 'scale_linear', 'sigmoid', 'zero_mean_unit_variance', 'scale_range']"}, "bioimageio.spec.model.v0_5.SAME_AS_TYPE": {"fullname": "bioimageio.spec.model.v0_5.SAME_AS_TYPE", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SAME_AS_TYPE", "kind": "variable", "doc": "\n", "default_value": "'<same as type>'"}, "bioimageio.spec.model.v0_5.ParameterizedSize_N": {"fullname": "bioimageio.spec.model.v0_5.ParameterizedSize_N", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ParameterizedSize_N", "kind": "variable", "doc": "\n", "default_value": "<class 'int'>"}, "bioimageio.spec.model.v0_5.ParameterizedSize": {"fullname": "bioimageio.spec.model.v0_5.ParameterizedSize", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ParameterizedSize", "kind": "class", "doc": "Describes a range of valid tensor axis sizes as size = min + n*step
.
integer to parameterize this axis
\n", "annotation": ": ClassVar[Type[int]]", "default_value": "<class 'int'>"}, "bioimageio.spec.model.v0_5.ParameterizedSize.min": {"fullname": "bioimageio.spec.model.v0_5.ParameterizedSize.min", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ParameterizedSize.min", "kind": "variable", "doc": "\n", "annotation": ": Annotated[int, Gt(gt=0)]"}, "bioimageio.spec.model.v0_5.ParameterizedSize.step": {"fullname": "bioimageio.spec.model.v0_5.ParameterizedSize.step", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ParameterizedSize.step", "kind": "variable", "doc": "\n", "annotation": ": Annotated[int, Gt(gt=0)]"}, "bioimageio.spec.model.v0_5.ParameterizedSize.validate_size": {"fullname": "bioimageio.spec.model.v0_5.ParameterizedSize.validate_size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ParameterizedSize.validate_size", "kind": "function", "doc": "\n", "signature": "(self, size: int) -> int:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ParameterizedSize.get_size": {"fullname": "bioimageio.spec.model.v0_5.ParameterizedSize.get_size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ParameterizedSize.get_size", "kind": "function", "doc": "\n", "signature": "(self, n: int) -> int:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ParameterizedSize.get_n": {"fullname": "bioimageio.spec.model.v0_5.ParameterizedSize.get_n", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ParameterizedSize.get_n", "kind": "function", "doc": "return smallest n parameterizing a size greater or equal than s
Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_5.DataDependentSize.min": {"fullname": "bioimageio.spec.model.v0_5.DataDependentSize.min", "modulename": "bioimageio.spec.model.v0_5", "qualname": "DataDependentSize.min", "kind": "variable", "doc": "\n", "annotation": ": Annotated[int, Gt(gt=0)]"}, "bioimageio.spec.model.v0_5.DataDependentSize.max": {"fullname": "bioimageio.spec.model.v0_5.DataDependentSize.max", "modulename": "bioimageio.spec.model.v0_5", "qualname": "DataDependentSize.max", "kind": "variable", "doc": "\n", "annotation": ": Annotated[Optional[int], Gt(gt=1)]"}, "bioimageio.spec.model.v0_5.DataDependentSize.validate_size": {"fullname": "bioimageio.spec.model.v0_5.DataDependentSize.validate_size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "DataDependentSize.validate_size", "kind": "function", "doc": "\n", "signature": "(self, size: int) -> int:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.SizeReference": {"fullname": "bioimageio.spec.model.v0_5.SizeReference", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SizeReference", "kind": "class", "doc": "A tensor axis size (extent in pixels/frames) defined in relation to a reference axis.
\n\naxis.size = reference.size * reference.scale / axis.scale + offset
note:
\n\nconcatenable
the referencing axis is assumed to be\nconcatenable
as well with the same block order.example:\nAn unisotropic input image of wh=10049 pixels depicts a phsical space of 200196mm\u00b2.\nLet's assume that we want to express the image height h in relation to its width w\ninstead of only accepting input images of exactly 10049 pixels\n(for example to express a range of valid image shapes by parametrizing w, see ParameterizedSize
).
>>> w = SpaceInputAxis(id=AxisId("w"), size=100, unit="millimeter", scale=2)\n>>> h = SpaceInputAxis(\n... id=AxisId("h"),\n... size=SizeReference(tensor_id=TensorId("input"), axis_id=AxisId("w"), offset=-1),\n... unit="millimeter",\n... scale=4,\n... )\n>>> print(h.size.compute(h, w))\n49\n
\n-> h = w * w.scale / h.scale + offset = 100 * 2mm / 4mm - 1 = 49
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_5.SizeReference.tensor_id": {"fullname": "bioimageio.spec.model.v0_5.SizeReference.tensor_id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SizeReference.tensor_id", "kind": "variable", "doc": "tensor id of the reference axis
\n", "annotation": ": bioimageio.spec.model.v0_5.TensorId"}, "bioimageio.spec.model.v0_5.SizeReference.axis_id": {"fullname": "bioimageio.spec.model.v0_5.SizeReference.axis_id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SizeReference.axis_id", "kind": "variable", "doc": "axis id of the reference axis
\n", "annotation": ": bioimageio.spec.model.v0_5.AxisId"}, "bioimageio.spec.model.v0_5.SizeReference.offset": {"fullname": "bioimageio.spec.model.v0_5.SizeReference.offset", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SizeReference.offset", "kind": "variable", "doc": "\n", "annotation": ": int"}, "bioimageio.spec.model.v0_5.SizeReference.get_size": {"fullname": "bioimageio.spec.model.v0_5.SizeReference.get_size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SizeReference.get_size", "kind": "function", "doc": "Compute the concrete size for a given axis and its reference axis.
\n\nSizeReference
is the size of.ParameterizedSize
)\nand no fixed ref_size is given,\nn is used to compute the size of the parameterized ref_axis.Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.common_nodes.NodeWithExplicitlySetFields"}, "bioimageio.spec.model.v0_5.AxisBase.fields_to_set_explicitly": {"fullname": "bioimageio.spec.model.v0_5.AxisBase.fields_to_set_explicitly", "modulename": "bioimageio.spec.model.v0_5", "qualname": "AxisBase.fields_to_set_explicitly", "kind": "variable", "doc": "set set these fields explicitly with their default value if they are not set,\nsuch that they are always included even when dumping with 'exlude_unset'
\n", "annotation": ": ClassVar[FrozenSet[LiteralString]]", "default_value": "frozenset({'type'})"}, "bioimageio.spec.model.v0_5.AxisBase.id": {"fullname": "bioimageio.spec.model.v0_5.AxisBase.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "AxisBase.id", "kind": "variable", "doc": "An axis id unique across all axes of one tensor.
\n", "annotation": ": bioimageio.spec.model.v0_5.AxisId"}, "bioimageio.spec.model.v0_5.AxisBase.description": {"fullname": "bioimageio.spec.model.v0_5.AxisBase.description", "modulename": "bioimageio.spec.model.v0_5", "qualname": "AxisBase.description", "kind": "variable", "doc": "\n", "annotation": ": Annotated[str, MaxLen(max_length=128)]"}, "bioimageio.spec.model.v0_5.WithHalo": {"fullname": "bioimageio.spec.model.v0_5.WithHalo", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WithHalo", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_5.WithHalo.halo": {"fullname": "bioimageio.spec.model.v0_5.WithHalo.halo", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WithHalo.halo", "kind": "variable", "doc": "The halo should be cropped from the output tensor to avoid boundary effects.\nIt is to be cropped from both sides, i.e. size_after_crop = size - 2 * halo
.\nTo document a halo that is already cropped by the model use size.offset
instead.
reference to another axis with an optional offset (see SizeReference
)
Subpart of a resource description
\n", "bases": "AxisBase"}, "bioimageio.spec.model.v0_5.BatchAxis.type": {"fullname": "bioimageio.spec.model.v0_5.BatchAxis.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BatchAxis.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['batch']"}, "bioimageio.spec.model.v0_5.BatchAxis.id": {"fullname": "bioimageio.spec.model.v0_5.BatchAxis.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BatchAxis.id", "kind": "variable", "doc": "An axis id unique across all axes of one tensor.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_batch)]"}, "bioimageio.spec.model.v0_5.BatchAxis.size": {"fullname": "bioimageio.spec.model.v0_5.BatchAxis.size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BatchAxis.size", "kind": "variable", "doc": "The batch size may be fixed to 1,\notherwise (the default) it may be chosen arbitrarily depending on available memory
\n", "annotation": ": Optional[Literal[1]]"}, "bioimageio.spec.model.v0_5.BatchAxis.scale": {"fullname": "bioimageio.spec.model.v0_5.BatchAxis.scale", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BatchAxis.scale", "kind": "variable", "doc": "\n"}, "bioimageio.spec.model.v0_5.BatchAxis.concatenable": {"fullname": "bioimageio.spec.model.v0_5.BatchAxis.concatenable", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BatchAxis.concatenable", "kind": "variable", "doc": "\n"}, "bioimageio.spec.model.v0_5.BatchAxis.unit": {"fullname": "bioimageio.spec.model.v0_5.BatchAxis.unit", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BatchAxis.unit", "kind": "variable", "doc": "\n"}, "bioimageio.spec.model.v0_5.ChannelAxis": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "AxisBase"}, "bioimageio.spec.model.v0_5.ChannelAxis.type": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['channel']"}, "bioimageio.spec.model.v0_5.ChannelAxis.id": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis.id", "kind": "variable", "doc": "An axis id unique across all axes of one tensor.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_not_batch)]"}, "bioimageio.spec.model.v0_5.ChannelAxis.channel_names": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis.channel_names", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis.channel_names", "kind": "variable", "doc": "\n", "annotation": ": Annotated[List[bioimageio.spec._internal.types.Identifier], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_5.ChannelAxis.size": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis.size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis.size", "kind": "variable", "doc": "\n", "annotation": ": int"}, "bioimageio.spec.model.v0_5.ChannelAxis.concatenable": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis.concatenable", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis.concatenable", "kind": "variable", "doc": "\n"}, "bioimageio.spec.model.v0_5.ChannelAxis.scale": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis.scale", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis.scale", "kind": "variable", "doc": "\n", "annotation": ": float"}, "bioimageio.spec.model.v0_5.ChannelAxis.unit": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis.unit", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis.unit", "kind": "variable", "doc": "\n"}, "bioimageio.spec.model.v0_5.IndexAxisBase": {"fullname": "bioimageio.spec.model.v0_5.IndexAxisBase", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexAxisBase", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "AxisBase"}, "bioimageio.spec.model.v0_5.IndexAxisBase.type": {"fullname": "bioimageio.spec.model.v0_5.IndexAxisBase.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexAxisBase.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['index']"}, "bioimageio.spec.model.v0_5.IndexAxisBase.id": {"fullname": "bioimageio.spec.model.v0_5.IndexAxisBase.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexAxisBase.id", "kind": "variable", "doc": "An axis id unique across all axes of one tensor.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_not_batch)]"}, "bioimageio.spec.model.v0_5.IndexAxisBase.scale": {"fullname": "bioimageio.spec.model.v0_5.IndexAxisBase.scale", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexAxisBase.scale", "kind": "variable", "doc": "\n", "annotation": ": float"}, "bioimageio.spec.model.v0_5.IndexAxisBase.unit": {"fullname": "bioimageio.spec.model.v0_5.IndexAxisBase.unit", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexAxisBase.unit", "kind": "variable", "doc": "\n"}, "bioimageio.spec.model.v0_5.IndexInputAxis": {"fullname": "bioimageio.spec.model.v0_5.IndexInputAxis", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexInputAxis", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "IndexAxisBase, _WithInputAxisSize"}, "bioimageio.spec.model.v0_5.IndexInputAxis.concatenable": {"fullname": "bioimageio.spec.model.v0_5.IndexInputAxis.concatenable", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexInputAxis.concatenable", "kind": "variable", "doc": "If a model has a concatenable
input axis, it can be processed blockwise,\nsplitting a longer sample axis into blocks matching its input tensor description.\nOutput axes are concatenable if they have a SizeReference
to a concatenable\ninput axis.
Subpart of a resource description
\n", "bases": "IndexAxisBase"}, "bioimageio.spec.model.v0_5.IndexOutputAxis.size": {"fullname": "bioimageio.spec.model.v0_5.IndexOutputAxis.size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexOutputAxis.size", "kind": "variable", "doc": "The size/length of this axis can be specified as
\n\nSizeReference
)DataDependentSize
(size is only known after model inference)Subpart of a resource description
\n", "bases": "AxisBase"}, "bioimageio.spec.model.v0_5.TimeAxisBase.type": {"fullname": "bioimageio.spec.model.v0_5.TimeAxisBase.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeAxisBase.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['time']"}, "bioimageio.spec.model.v0_5.TimeAxisBase.id": {"fullname": "bioimageio.spec.model.v0_5.TimeAxisBase.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeAxisBase.id", "kind": "variable", "doc": "An axis id unique across all axes of one tensor.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_not_batch)]"}, "bioimageio.spec.model.v0_5.TimeAxisBase.unit": {"fullname": "bioimageio.spec.model.v0_5.TimeAxisBase.unit", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeAxisBase.unit", "kind": "variable", "doc": "\n", "annotation": ": Optional[Literal['attosecond', 'centisecond', 'day', 'decisecond', 'exasecond', 'femtosecond', 'gigasecond', 'hectosecond', 'hour', 'kilosecond', 'megasecond', 'microsecond', 'millisecond', 'minute', 'nanosecond', 'petasecond', 'picosecond', 'second', 'terasecond', 'yoctosecond', 'yottasecond', 'zeptosecond', 'zettasecond']]"}, "bioimageio.spec.model.v0_5.TimeAxisBase.scale": {"fullname": "bioimageio.spec.model.v0_5.TimeAxisBase.scale", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeAxisBase.scale", "kind": "variable", "doc": "\n", "annotation": ": Annotated[float, Gt(gt=0)]"}, "bioimageio.spec.model.v0_5.TimeInputAxis": {"fullname": "bioimageio.spec.model.v0_5.TimeInputAxis", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeInputAxis", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "TimeAxisBase, _WithInputAxisSize"}, "bioimageio.spec.model.v0_5.TimeInputAxis.concatenable": {"fullname": "bioimageio.spec.model.v0_5.TimeInputAxis.concatenable", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeInputAxis.concatenable", "kind": "variable", "doc": "If a model has a concatenable
input axis, it can be processed blockwise,\nsplitting a longer sample axis into blocks matching its input tensor description.\nOutput axes are concatenable if they have a SizeReference
to a concatenable\ninput axis.
Subpart of a resource description
\n", "bases": "AxisBase"}, "bioimageio.spec.model.v0_5.SpaceAxisBase.type": {"fullname": "bioimageio.spec.model.v0_5.SpaceAxisBase.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceAxisBase.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['space']"}, "bioimageio.spec.model.v0_5.SpaceAxisBase.id": {"fullname": "bioimageio.spec.model.v0_5.SpaceAxisBase.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceAxisBase.id", "kind": "variable", "doc": "An axis id unique across all axes of one tensor.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_not_batch), FieldInfo(annotation=NoneType, required=True, examples=['x', 'y', 'z'])]"}, "bioimageio.spec.model.v0_5.SpaceAxisBase.unit": {"fullname": "bioimageio.spec.model.v0_5.SpaceAxisBase.unit", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceAxisBase.unit", "kind": "variable", "doc": "\n", "annotation": ": Optional[Literal['attometer', 'angstrom', 'centimeter', 'decimeter', 'exameter', 'femtometer', 'foot', 'gigameter', 'hectometer', 'inch', 'kilometer', 'megameter', 'meter', 'micrometer', 'mile', 'millimeter', 'nanometer', 'parsec', 'petameter', 'picometer', 'terameter', 'yard', 'yoctometer', 'yottameter', 'zeptometer', 'zettameter']]"}, "bioimageio.spec.model.v0_5.SpaceAxisBase.scale": {"fullname": "bioimageio.spec.model.v0_5.SpaceAxisBase.scale", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceAxisBase.scale", "kind": "variable", "doc": "\n", "annotation": ": Annotated[float, Gt(gt=0)]"}, "bioimageio.spec.model.v0_5.SpaceInputAxis": {"fullname": "bioimageio.spec.model.v0_5.SpaceInputAxis", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceInputAxis", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "SpaceAxisBase, _WithInputAxisSize"}, "bioimageio.spec.model.v0_5.SpaceInputAxis.concatenable": {"fullname": "bioimageio.spec.model.v0_5.SpaceInputAxis.concatenable", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceInputAxis.concatenable", "kind": "variable", "doc": "If a model has a concatenable
input axis, it can be processed blockwise,\nsplitting a longer sample axis into blocks matching its input tensor description.\nOutput axes are concatenable if they have a SizeReference
to a concatenable\ninput axis.
Subpart of a resource description
\n", "bases": "TimeAxisBase, _WithOutputAxisSize"}, "bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo": {"fullname": "bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeOutputAxisWithHalo", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "TimeAxisBase, WithHalo"}, "bioimageio.spec.model.v0_5.SpaceOutputAxis": {"fullname": "bioimageio.spec.model.v0_5.SpaceOutputAxis", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceOutputAxis", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "SpaceAxisBase, _WithOutputAxisSize"}, "bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo": {"fullname": "bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceOutputAxisWithHalo", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "SpaceAxisBase, WithHalo"}, "bioimageio.spec.model.v0_5.OutputAxis": {"fullname": "bioimageio.spec.model.v0_5.OutputAxis", "modulename": "bioimageio.spec.model.v0_5", "qualname": "OutputAxis", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexOutputAxis, typing.Annotated[typing.Union[typing.Annotated[bioimageio.spec.model.v0_5.TimeOutputAxis, Tag(tag='wo_halo')], typing.Annotated[bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[typing.Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxis, Tag(tag='wo_halo')], typing.Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)]"}, "bioimageio.spec.model.v0_5.AnyAxis": {"fullname": "bioimageio.spec.model.v0_5.AnyAxis", "modulename": "bioimageio.spec.model.v0_5", "qualname": "AnyAxis", "kind": "variable", "doc": "\n", "default_value": "typing.Union[typing.Annotated[typing.Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexInputAxis, bioimageio.spec.model.v0_5.TimeInputAxis, bioimageio.spec.model.v0_5.SpaceInputAxis], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexOutputAxis, typing.Annotated[typing.Union[typing.Annotated[bioimageio.spec.model.v0_5.TimeOutputAxis, Tag(tag='wo_halo')], typing.Annotated[bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[typing.Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxis, Tag(tag='wo_halo')], typing.Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.spec.model.v0_5.TVs": {"fullname": "bioimageio.spec.model.v0_5.TVs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TVs", "kind": "variable", "doc": "\n", "default_value": "typing.Union[typing.Annotated[typing.List[int], MinLen(min_length=1)], typing.Annotated[typing.List[float], MinLen(min_length=1)], typing.Annotated[typing.List[bool], MinLen(min_length=1)], typing.Annotated[typing.List[str], MinLen(min_length=1)]]"}, "bioimageio.spec.model.v0_5.NominalOrOrdinalDType": {"fullname": "bioimageio.spec.model.v0_5.NominalOrOrdinalDType", "modulename": "bioimageio.spec.model.v0_5", "qualname": "NominalOrOrdinalDType", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['float32', 'float64', 'uint8', 'int8', 'uint16', 'int16', 'uint32', 'int32', 'uint64', 'int64', 'bool']"}, "bioimageio.spec.model.v0_5.NominalOrOrdinalDataDescr": {"fullname": "bioimageio.spec.model.v0_5.NominalOrOrdinalDataDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "NominalOrOrdinalDataDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_5.NominalOrOrdinalDataDescr.values": {"fullname": "bioimageio.spec.model.v0_5.NominalOrOrdinalDataDescr.values", "modulename": "bioimageio.spec.model.v0_5", "qualname": "NominalOrOrdinalDataDescr.values", "kind": "variable", "doc": "A fixed set of nominal or an ascending sequence of ordinal values.\nIn this case data_type
is required to be an unsigend integer type, e.g. 'uint8'.\nString values
are interpreted as labels for tensor values 0, ..., N.\nNote: as YAML 1.2 does not natively support a \"set\" datatype,\nnominal values should be given as a sequence (aka list/array) as well.
Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_5.IntervalOrRatioDataDescr.type": {"fullname": "bioimageio.spec.model.v0_5.IntervalOrRatioDataDescr.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IntervalOrRatioDataDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Annotated[Literal['float32', 'float64', 'uint8', 'int8', 'uint16', 'int16', 'uint32', 'int32', 'uint64', 'int64'], FieldInfo(annotation=NoneType, required=True, examples=['float32', 'float64', 'uint8', 'uint16'])]"}, "bioimageio.spec.model.v0_5.IntervalOrRatioDataDescr.range": {"fullname": "bioimageio.spec.model.v0_5.IntervalOrRatioDataDescr.range", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IntervalOrRatioDataDescr.range", "kind": "variable", "doc": "Tuple (minimum, maximum)
specifying the allowed range of the data in this tensor.\nNone
corresponds to min/max of what can be expressed by data_type
.
Scale for data on an interval (or ratio) scale.
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_5.IntervalOrRatioDataDescr.offset": {"fullname": "bioimageio.spec.model.v0_5.IntervalOrRatioDataDescr.offset", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IntervalOrRatioDataDescr.offset", "kind": "variable", "doc": "Offset for data on a ratio scale.
\n", "annotation": ": Optional[float]"}, "bioimageio.spec.model.v0_5.TensorDataDescr": {"fullname": "bioimageio.spec.model.v0_5.TensorDataDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDataDescr", "kind": "variable", "doc": "\n", "default_value": "typing.Union[bioimageio.spec.model.v0_5.NominalOrOrdinalDataDescr, bioimageio.spec.model.v0_5.IntervalOrRatioDataDescr]"}, "bioimageio.spec.model.v0_5.ProcessingDescrBase": {"fullname": "bioimageio.spec.model.v0_5.ProcessingDescrBase", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ProcessingDescrBase", "kind": "class", "doc": "processing base class
\n", "bases": "bioimageio.spec._internal.common_nodes.NodeWithExplicitlySetFields, abc.ABC"}, "bioimageio.spec.model.v0_5.ProcessingDescrBase.fields_to_set_explicitly": {"fullname": "bioimageio.spec.model.v0_5.ProcessingDescrBase.fields_to_set_explicitly", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ProcessingDescrBase.fields_to_set_explicitly", "kind": "variable", "doc": "set set these fields explicitly with their default value if they are not set,\nsuch that they are always included even when dumping with 'exlude_unset'
\n", "annotation": ": ClassVar[FrozenSet[LiteralString]]", "default_value": "frozenset({'id'})"}, "bioimageio.spec.model.v0_5.BinarizeKwargs": {"fullname": "bioimageio.spec.model.v0_5.BinarizeKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BinarizeKwargs", "kind": "class", "doc": "key word arguments for BinarizeDescr
The fixed threshold
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_5.BinarizeAlongAxisKwargs": {"fullname": "bioimageio.spec.model.v0_5.BinarizeAlongAxisKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BinarizeAlongAxisKwargs", "kind": "class", "doc": "key word arguments for BinarizeDescr
The fixed threshold values along axis
The threshold
axis
Binarize the tensor with a fixed threshold.
\n\nValues above BinarizeKwargs.threshold
/BinarizeAlongAxisKwargs.threshold
\nwill be set to one, values below the threshold to zero.
Set tensor values below min to min and above max to max.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_5.ClipDescr.id": {"fullname": "bioimageio.spec.model.v0_5.ClipDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ClipDescr.id", "kind": "variable", "doc": "\n", "annotation": ": Literal['clip']"}, "bioimageio.spec.model.v0_5.ClipDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_5.ClipDescr.kwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ClipDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_4.ClipKwargs"}, "bioimageio.spec.model.v0_5.EnsureDtypeKwargs": {"fullname": "bioimageio.spec.model.v0_5.EnsureDtypeKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "EnsureDtypeKwargs", "kind": "class", "doc": "key word arguments for EnsureDtypeDescr
cast the tensor data type to EnsureDtypeKwargs.dtype
(if not matching)
key word arguments for ScaleLinearDescr
multiplicative factor
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_5.ScaleLinearKwargs.offset": {"fullname": "bioimageio.spec.model.v0_5.ScaleLinearKwargs.offset", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleLinearKwargs.offset", "kind": "variable", "doc": "additive term
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_5.ScaleLinearAlongAxisKwargs": {"fullname": "bioimageio.spec.model.v0_5.ScaleLinearAlongAxisKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleLinearAlongAxisKwargs", "kind": "class", "doc": "key word arguments for ScaleLinearDescr
The axis of of gains/offsets values.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_not_batch), FieldInfo(annotation=NoneType, required=True, examples=['channel'])]"}, "bioimageio.spec.model.v0_5.ScaleLinearAlongAxisKwargs.gain": {"fullname": "bioimageio.spec.model.v0_5.ScaleLinearAlongAxisKwargs.gain", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleLinearAlongAxisKwargs.gain", "kind": "variable", "doc": "multiplicative factor
\n", "annotation": ": Union[float, Annotated[List[float], MinLen(min_length=1)]]"}, "bioimageio.spec.model.v0_5.ScaleLinearAlongAxisKwargs.offset": {"fullname": "bioimageio.spec.model.v0_5.ScaleLinearAlongAxisKwargs.offset", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleLinearAlongAxisKwargs.offset", "kind": "variable", "doc": "additive term
\n", "annotation": ": Union[float, Annotated[List[float], MinLen(min_length=1)]]"}, "bioimageio.spec.model.v0_5.ScaleLinearDescr": {"fullname": "bioimageio.spec.model.v0_5.ScaleLinearDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleLinearDescr", "kind": "class", "doc": "Fixed linear scaling.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_5.ScaleLinearDescr.id": {"fullname": "bioimageio.spec.model.v0_5.ScaleLinearDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleLinearDescr.id", "kind": "variable", "doc": "\n", "annotation": ": Literal['scale_linear']"}, "bioimageio.spec.model.v0_5.ScaleLinearDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_5.ScaleLinearDescr.kwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleLinearDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": Union[bioimageio.spec.model.v0_5.ScaleLinearKwargs, bioimageio.spec.model.v0_5.ScaleLinearAlongAxisKwargs]"}, "bioimageio.spec.model.v0_5.SigmoidDescr": {"fullname": "bioimageio.spec.model.v0_5.SigmoidDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SigmoidDescr", "kind": "class", "doc": "The logistic sigmoid funciton, a.k.a. expit function.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_5.SigmoidDescr.id": {"fullname": "bioimageio.spec.model.v0_5.SigmoidDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SigmoidDescr.id", "kind": "variable", "doc": "\n", "annotation": ": Literal['sigmoid']"}, "bioimageio.spec.model.v0_5.SigmoidDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_5.SigmoidDescr.kwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SigmoidDescr.kwargs", "kind": "variable", "doc": "empty kwargs
\n", "annotation": ": bioimageio.spec.model.v0_4.ProcessingKwargs"}, "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceKwargs": {"fullname": "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "FixedZeroMeanUnitVarianceKwargs", "kind": "class", "doc": "key word arguments for FixedZeroMeanUnitVarianceDescr
The mean value to normalize with.
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceKwargs.std": {"fullname": "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceKwargs.std", "modulename": "bioimageio.spec.model.v0_5", "qualname": "FixedZeroMeanUnitVarianceKwargs.std", "kind": "variable", "doc": "The standard deviation value to normalize with.
\n", "annotation": ": Annotated[float, Ge(ge=1e-06)]"}, "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceAlongAxisKwargs": {"fullname": "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceAlongAxisKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "FixedZeroMeanUnitVarianceAlongAxisKwargs", "kind": "class", "doc": "key word arguments for FixedZeroMeanUnitVarianceDescr
The mean value(s) to normalize with.
\n", "annotation": ": Annotated[List[float], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceAlongAxisKwargs.std": {"fullname": "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceAlongAxisKwargs.std", "modulename": "bioimageio.spec.model.v0_5", "qualname": "FixedZeroMeanUnitVarianceAlongAxisKwargs.std", "kind": "variable", "doc": "The standard deviation value(s) to normalize with.\nSize must match mean
values.
The axis of the mean/std values to normalize each entry along that dimension\nseparately.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_not_batch), FieldInfo(annotation=NoneType, required=True, examples=['channel', 'index'])]"}, "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceDescr": {"fullname": "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "FixedZeroMeanUnitVarianceDescr", "kind": "class", "doc": "Subtract a given mean and divide by the standard deviation.
\n\nNormalize with fixed, precomputed values for\nFixedZeroMeanUnitVarianceKwargs.mean
and FixedZeroMeanUnitVarianceKwargs.std
\nUse FixedZeroMeanUnitVarianceAlongAxisKwargs
for independent scaling along given\naxes.
key word arguments for ZeroMeanUnitVarianceDescr
The subset of axes to normalize jointly, i.e. axes to reduce to compute mean/std.\nFor example to normalize 'batch', 'x' and 'y' jointly in a tensor ('batch', 'channel', 'y', 'x')\nresulting in a tensor of equal shape normalized per channel, specify axes=('batch', 'x', 'y')
.\nTo normalize each sample independently leave out the 'batch' axis.\nDefault: Scale all axes jointly.
epsilon for numeric stability: out = (tensor - mean) / (std + eps)
.
Subtract mean and divide by variance.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr.id": {"fullname": "bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ZeroMeanUnitVarianceDescr.id", "kind": "variable", "doc": "\n", "annotation": ": Literal['zero_mean_unit_variance']"}, "bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr.kwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ZeroMeanUnitVarianceDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceKwargs"}, "bioimageio.spec.model.v0_5.ScaleRangeKwargs": {"fullname": "bioimageio.spec.model.v0_5.ScaleRangeKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleRangeKwargs", "kind": "class", "doc": "key word arguments for ScaleRangeDescr
For min_percentile
=0.0 (the default) and max_percentile
=100 (the default)\nthis processing step normalizes data to the [0, 1] intervall.\nFor other percentiles the normalized values will partially be outside the [0, 1]\nintervall. Use ScaleRange
followed by ClipDescr
if you want to limit the\nnormalized values to a range.
The subset of axes to normalize jointly, i.e. axes to reduce to compute the min/max percentile value.\nFor example to normalize 'batch', 'x' and 'y' jointly in a tensor ('batch', 'channel', 'y', 'x')\nresulting in a tensor of equal shape normalized per channel, specify axes=('batch', 'x', 'y')
.\nTo normalize samples indepdencently, leave out the \"batch\" axis.\nDefault: Scale all axes jointly.
The lower percentile used to determine the value to align with zero.
\n", "annotation": ": Annotated[float, Interval(gt=None, ge=0, lt=100, le=None)]"}, "bioimageio.spec.model.v0_5.ScaleRangeKwargs.max_percentile": {"fullname": "bioimageio.spec.model.v0_5.ScaleRangeKwargs.max_percentile", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleRangeKwargs.max_percentile", "kind": "variable", "doc": "The upper percentile used to determine the value to align with one.\nHas to be bigger than min_percentile
.\nThe range is 1 to 100 instead of 0 to 100 to avoid mistakenly\naccepting percentiles specified in the range 0.0 to 1.0.
Epsilon for numeric stability.\nout = (tensor - v_lower) / (v_upper - v_lower + eps)
;\nwith v_lower,v_upper
values at the respective percentiles.
Tensor ID to compute the percentiles from. Default: The tensor itself.\nFor any tensor in inputs
only input tensor references are allowed.
Scale with percentiles.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_5.ScaleRangeDescr.id": {"fullname": "bioimageio.spec.model.v0_5.ScaleRangeDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleRangeDescr.id", "kind": "variable", "doc": "\n", "annotation": ": Literal['scale_range']"}, "bioimageio.spec.model.v0_5.ScaleRangeDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_5.ScaleRangeDescr.kwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleRangeDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_5.ScaleRangeKwargs"}, "bioimageio.spec.model.v0_5.ScaleMeanVarianceKwargs": {"fullname": "bioimageio.spec.model.v0_5.ScaleMeanVarianceKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleMeanVarianceKwargs", "kind": "class", "doc": "key word arguments for ScaleMeanVarianceKwargs
Name of tensor to match.
\n", "annotation": ": bioimageio.spec.model.v0_5.TensorId"}, "bioimageio.spec.model.v0_5.ScaleMeanVarianceKwargs.axes": {"fullname": "bioimageio.spec.model.v0_5.ScaleMeanVarianceKwargs.axes", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleMeanVarianceKwargs.axes", "kind": "variable", "doc": "The subset of axes to normalize jointly, i.e. axes to reduce to compute mean/std.\nFor example to normalize 'batch', 'x' and 'y' jointly in a tensor ('batch', 'channel', 'y', 'x')\nresulting in a tensor of equal shape normalized per channel, specify axes=('batch', 'x', 'y')
.\nTo normalize samples independently, leave out the 'batch' axis.\nDefault: Scale all axes jointly.
Epsilon for numeric stability:\nout = (tensor - mean) / (std + eps) * (ref_std + eps) + ref_mean.
Scale a tensor's data distribution to match another tensor's mean/std.\nout = (tensor - mean) / (std + eps) * (ref_std + eps) + ref_mean.
Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node, typing.Generic[~IO_AxisT]"}, "bioimageio.spec.model.v0_5.TensorDescrBase.id": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase.id", "kind": "variable", "doc": "Tensor id. No duplicates are allowed.
\n", "annotation": ": bioimageio.spec.model.v0_5.TensorId"}, "bioimageio.spec.model.v0_5.TensorDescrBase.description": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase.description", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase.description", "kind": "variable", "doc": "free text description
\n", "annotation": ": Annotated[str, MaxLen(max_length=128)]"}, "bioimageio.spec.model.v0_5.TensorDescrBase.axes": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase.axes", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase.axes", "kind": "variable", "doc": "tensor axes
\n", "annotation": ": Annotated[Sequence[~IO_AxisT], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_5.TensorDescrBase.shape": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase.shape", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase.shape", "kind": "variable", "doc": "\n"}, "bioimageio.spec.model.v0_5.TensorDescrBase.test_tensor": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase.test_tensor", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase.test_tensor", "kind": "variable", "doc": "An example tensor to use for testing.\nUsing the model with the test input tensors is expected to yield the test output tensors.\nEach test tensor has be a an ndarray in the\nnumpy.lib file format.\nThe file extension must be '.npy'.
\n", "annotation": ": bioimageio.spec._internal.io.FileDescr"}, "bioimageio.spec.model.v0_5.TensorDescrBase.sample_tensor": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase.sample_tensor", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase.sample_tensor", "kind": "variable", "doc": "A sample tensor to illustrate a possible input/output for the model,\nThe sample image primarily serves to inform a human user about an example use case\nand is typically stored as .hdf5, .png or .tiff.\nIt has to be readable by the imageio library\n(numpy's .npy
format is not supported).\nThe image dimensionality has to match the number of axes specified in this tensor description.
Description of the tensor's data values, optionally per channel.\nIf specified per channel, the data type
needs to match across channels.
dtype as specified under data.type
or data[i].type
Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node, typing.Generic[~IO_AxisT]"}, "bioimageio.spec.model.v0_5.InputTensorDescr.id": {"fullname": "bioimageio.spec.model.v0_5.InputTensorDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "InputTensorDescr.id", "kind": "variable", "doc": "Input tensor id.\nNo duplicates are allowed across all inputs and outputs.
\n", "annotation": ": bioimageio.spec.model.v0_5.TensorId"}, "bioimageio.spec.model.v0_5.InputTensorDescr.optional": {"fullname": "bioimageio.spec.model.v0_5.InputTensorDescr.optional", "modulename": "bioimageio.spec.model.v0_5", "qualname": "InputTensorDescr.optional", "kind": "variable", "doc": "indicates that this tensor may be None
Description of how this input should be preprocessed.
\n\nnotes:
\n\nSubpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node, typing.Generic[~IO_AxisT]"}, "bioimageio.spec.model.v0_5.OutputTensorDescr.id": {"fullname": "bioimageio.spec.model.v0_5.OutputTensorDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "OutputTensorDescr.id", "kind": "variable", "doc": "Output tensor id.\nNo duplicates are allowed across all inputs and outputs.
\n", "annotation": ": bioimageio.spec.model.v0_5.TensorId"}, "bioimageio.spec.model.v0_5.OutputTensorDescr.postprocessing": {"fullname": "bioimageio.spec.model.v0_5.OutputTensorDescr.postprocessing", "modulename": "bioimageio.spec.model.v0_5", "qualname": "OutputTensorDescr.postprocessing", "kind": "variable", "doc": "Description of how this output should be postprocessed.
\n\nnote: postprocessing
always ends with an 'ensure_dtype' operation.\n If not given this is added to cast to this tensor's data.type
.
Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.io.FileDescr"}, "bioimageio.spec.model.v0_5.EnvironmentFileDescr.source": {"fullname": "bioimageio.spec.model.v0_5.EnvironmentFileDescr.source", "modulename": "bioimageio.spec.model.v0_5", "qualname": "EnvironmentFileDescr.source", "kind": "variable", "doc": "\u2208\ud83d\udce6 Conda environment file.\nAllows to specify custom dependencies, see conda docs:
\n\n\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none'), WithSuffix(suffix=('.yaml', '.yml'), case_sensitive=True), FieldInfo(annotation=NoneType, required=True, examples=['environment.yaml'])]"}, "bioimageio.spec.model.v0_5.ArchitectureFromFileDescr": {"fullname": "bioimageio.spec.model.v0_5.ArchitectureFromFileDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ArchitectureFromFileDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "_ArchitectureCallableDescr, bioimageio.spec._internal.io.FileDescr"}, "bioimageio.spec.model.v0_5.ArchitectureFromLibraryDescr": {"fullname": "bioimageio.spec.model.v0_5.ArchitectureFromLibraryDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ArchitectureFromLibraryDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "_ArchitectureCallableDescr"}, "bioimageio.spec.model.v0_5.ArchitectureFromLibraryDescr.import_from": {"fullname": "bioimageio.spec.model.v0_5.ArchitectureFromLibraryDescr.import_from", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ArchitectureFromLibraryDescr.import_from", "kind": "variable", "doc": "Where to import the callable from, i.e. from <import_from> import <callable>
Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.io.FileDescr"}, "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.type": {"fullname": "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsEntryDescrBase.type", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]"}, "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.weights_format_name": {"fullname": "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.weights_format_name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsEntryDescrBase.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]"}, "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.source": {"fullname": "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.source", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsEntryDescrBase.source", "kind": "variable", "doc": "\u2208\ud83d\udce6 The weights file.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.authors": {"fullname": "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.authors", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsEntryDescrBase.authors", "kind": "variable", "doc": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a parent
)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a parent
field)
The source weights these weights were converted from.\nFor example, if a model's weights were converted from the pytorch_state_dict
format to torchscript
,\nThe pytorch_state_dict
weights entry has no parent
and is the parent of the torchscript
weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.
Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_5.KerasHdf5WeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_5.KerasHdf5WeightsDescr.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "KerasHdf5WeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'keras_hdf5'"}, "bioimageio.spec.model.v0_5.KerasHdf5WeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_5.KerasHdf5WeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "KerasHdf5WeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Keras HDF5'"}, "bioimageio.spec.model.v0_5.KerasHdf5WeightsDescr.tensorflow_version": {"fullname": "bioimageio.spec.model.v0_5.KerasHdf5WeightsDescr.tensorflow_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "KerasHdf5WeightsDescr.tensorflow_version", "kind": "variable", "doc": "TensorFlow version used to create these weights.
\n", "annotation": ": bioimageio.spec._internal.version_type.Version"}, "bioimageio.spec.model.v0_5.OnnxWeightsDescr": {"fullname": "bioimageio.spec.model.v0_5.OnnxWeightsDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "OnnxWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_5.OnnxWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_5.OnnxWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "OnnxWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'onnx'"}, "bioimageio.spec.model.v0_5.OnnxWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_5.OnnxWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "OnnxWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'ONNX'"}, "bioimageio.spec.model.v0_5.OnnxWeightsDescr.opset_version": {"fullname": "bioimageio.spec.model.v0_5.OnnxWeightsDescr.opset_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "OnnxWeightsDescr.opset_version", "kind": "variable", "doc": "ONNX opset version
\n", "annotation": ": Annotated[int, Ge(ge=7)]"}, "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr": {"fullname": "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "PytorchStateDictWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "PytorchStateDictWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'pytorch_state_dict'"}, "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "PytorchStateDictWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Pytorch State Dict'"}, "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.architecture": {"fullname": "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.architecture", "modulename": "bioimageio.spec.model.v0_5", "qualname": "PytorchStateDictWeightsDescr.architecture", "kind": "variable", "doc": "\n", "annotation": ": Annotated[Union[bioimageio.spec.model.v0_5.ArchitectureFromFileDescr, bioimageio.spec.model.v0_5.ArchitectureFromLibraryDescr], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]"}, "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.pytorch_version": {"fullname": "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.pytorch_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "PytorchStateDictWeightsDescr.pytorch_version", "kind": "variable", "doc": "Version of the PyTorch library used.\nIf architecture.depencencies
is specified it has to include pytorch and any version pinning has to be compatible.
Custom depencies beyond pytorch.\nThe conda environment file should include pytorch and any version pinning has to be compatible with\npytorch_version
.
Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowJsWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'tensorflow_js'"}, "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowJsWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Tensorflow.js'"}, "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.tensorflow_version": {"fullname": "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.tensorflow_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowJsWeightsDescr.tensorflow_version", "kind": "variable", "doc": "Version of the TensorFlow library used.
\n", "annotation": ": bioimageio.spec._internal.version_type.Version"}, "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.source": {"fullname": "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.source", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowJsWeightsDescr.source", "kind": "variable", "doc": "\u2208\ud83d\udce6 The multi-file weights.\nAll required files/folders should be a zip archive.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr": {"fullname": "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowSavedModelBundleWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowSavedModelBundleWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'tensorflow_saved_model_bundle'"}, "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowSavedModelBundleWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Tensorflow Saved Model'"}, "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.tensorflow_version": {"fullname": "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.tensorflow_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowSavedModelBundleWeightsDescr.tensorflow_version", "kind": "variable", "doc": "Version of the TensorFlow library used.
\n", "annotation": ": bioimageio.spec._internal.version_type.Version"}, "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.dependencies": {"fullname": "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.dependencies", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowSavedModelBundleWeightsDescr.dependencies", "kind": "variable", "doc": "Custom dependencies beyond tensorflow.\nShould include tensorflow and any version pinning has to be compatible with tensorflow_version
.
\u2208\ud83d\udce6 The multi-file weights.\nAll required files/folders should be a zip archive.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f46569b0ea0>), PlainSerializer(func=<function _package at 0x7f46569b1620>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr": {"fullname": "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TorchscriptWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TorchscriptWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'torchscript'"}, "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TorchscriptWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'TorchScript'"}, "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr.pytorch_version": {"fullname": "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr.pytorch_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TorchscriptWeightsDescr.pytorch_version", "kind": "variable", "doc": "Version of the PyTorch library used.
\n", "annotation": ": bioimageio.spec._internal.version_type.Version"}, "bioimageio.spec.model.v0_5.WeightsDescr": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_5.WeightsDescr.keras_hdf5": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr.keras_hdf5", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr.keras_hdf5", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.KerasHdf5WeightsDescr]"}, "bioimageio.spec.model.v0_5.WeightsDescr.onnx": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr.onnx", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr.onnx", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.OnnxWeightsDescr]"}, "bioimageio.spec.model.v0_5.WeightsDescr.pytorch_state_dict": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr.pytorch_state_dict", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr.pytorch_state_dict", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr]"}, "bioimageio.spec.model.v0_5.WeightsDescr.tensorflow_js": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr.tensorflow_js", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr.tensorflow_js", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr]"}, "bioimageio.spec.model.v0_5.WeightsDescr.tensorflow_saved_model_bundle": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr.tensorflow_saved_model_bundle", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr.tensorflow_saved_model_bundle", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr]"}, "bioimageio.spec.model.v0_5.WeightsDescr.torchscript": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr.torchscript", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr.torchscript", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.TorchscriptWeightsDescr]"}, "bioimageio.spec.model.v0_5.WeightsDescr.check_entries": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr.check_entries", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr.check_entries", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ModelId": {"fullname": "bioimageio.spec.model.v0_5.ModelId", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec.generic.v0_3.ResourceId"}, "bioimageio.spec.model.v0_5.LinkedModel": {"fullname": "bioimageio.spec.model.v0_5.LinkedModel", "modulename": "bioimageio.spec.model.v0_5", "qualname": "LinkedModel", "kind": "class", "doc": "Reference to a bioimage.io model.
\n", "bases": "bioimageio.spec.generic.v0_3.LinkedResourceNode"}, "bioimageio.spec.model.v0_5.LinkedModel.id": {"fullname": "bioimageio.spec.model.v0_5.LinkedModel.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "LinkedModel.id", "kind": "variable", "doc": "A valid model id
from the bioimage.io collection.
Specification of the fields used in a bioimage.io-compliant RDF to describe AI models with pretrained weights.\nThese fields are typically stored in a YAML file which we call a model resource description file (model RDF).
\n", "bases": "bioimageio.spec.generic.v0_3.GenericModelDescrBase"}, "bioimageio.spec.model.v0_5.ModelDescr.format_version": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.format_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.format_version", "kind": "variable", "doc": "Version of the bioimage.io model description specification used.\nWhen creating a new model always use the latest micro/patch version described here.\nThe format_version
is important for any consumer software to understand how to parse the fields.
Specialized resource type 'model'
\n", "annotation": ": Literal['model']"}, "bioimageio.spec.model.v0_5.ModelDescr.id": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.ModelId]"}, "bioimageio.spec.model.v0_5.ModelDescr.authors": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.authors", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.authors", "kind": "variable", "doc": "The authors are the creators of the model RDF and the primary points of contact.
\n", "annotation": ": Annotated[List[bioimageio.spec.generic.v0_3.Author], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_5.ModelDescr.documentation": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.documentation", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.documentation", "kind": "variable", "doc": "\u2208\ud83d\udce6 URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is README.md
. An .md
suffix is mandatory.\nThe documentation should include a '#[#] Validation' (sub)section\nwith details on how to quantitatively validate the model on unseen data.
Describes the input tensors expected by this model.
\n", "annotation": ": Annotated[Sequence[bioimageio.spec.model.v0_5.InputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_5.ModelDescr.name": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.name", "kind": "variable", "doc": "A human-readable name of this model.\nIt should be no longer than 64 characters\nand may only contain letter, number, underscore, minus, parentheses and spaces.\nWe recommend to chose a name that refers to the model's task and image modality.
\n", "annotation": ": Annotated[str, RestrictCharacters(alphabet='abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_- ()'), MinLen(min_length=5), MaxLen(max_length=128), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f4645e98040>, severity=20, msg='Name longer than 64 characters.', context={'typ': Annotated[Any, MaxLen(max_length=64)]})]"}, "bioimageio.spec.model.v0_5.ModelDescr.outputs": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.outputs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.outputs", "kind": "variable", "doc": "Describes the output tensors.
\n", "annotation": ": Annotated[Sequence[bioimageio.spec.model.v0_5.OutputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_5.ModelDescr.packaged_by": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.packaged_by", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.packaged_by", "kind": "variable", "doc": "The persons that have packaged and uploaded this model.\nOnly required if those persons differ from the authors
.
The model from which this model is derived, e.g. by fine-tuning the weights.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.LinkedModel]"}, "bioimageio.spec.model.v0_5.ModelDescr.run_mode": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.run_mode", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.run_mode", "kind": "variable", "doc": "Custom run mode for this model: for more complex prediction procedures like test time\ndata augmentation that currently cannot be expressed in the specification.\nNo standard run modes are defined yet.
\n", "annotation": ": Annotated[Optional[bioimageio.spec.model.v0_4.RunMode], AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f46473f5ee0>, severity=30, msg="Run mode '{value}' has limited support across consumer softwares.", context={'typ': None})]"}, "bioimageio.spec.model.v0_5.ModelDescr.timestamp": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.timestamp", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.timestamp", "kind": "variable", "doc": "Timestamp in ISO 8601 format\nwith a few restrictions listed here.\n(In Python a datetime object is valid, too).
\n", "annotation": ": bioimageio.spec._internal.types.Datetime"}, "bioimageio.spec.model.v0_5.ModelDescr.training_data": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.training_data", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.training_data", "kind": "variable", "doc": "The dataset used to train this model
\n", "annotation": ": Annotated[Union[NoneType, bioimageio.spec.dataset.v0_3.LinkedDataset, bioimageio.spec.dataset.v0_3.DatasetDescr, bioimageio.spec.dataset.v0_2.DatasetDescr], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]"}, "bioimageio.spec.model.v0_5.ModelDescr.weights": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.weights", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.weights", "kind": "variable", "doc": "The weights for this model.\nWeights can be given for different formats, but should otherwise be equivalent.\nThe available weight formats determine which consumers can use this model.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.WeightsDescr, WrapSerializer(func=<function package_weights at 0x7f4654144360>, return_type=PydanticUndefined, when_used='always')]"}, "bioimageio.spec.model.v0_5.ModelDescr.get_input_test_arrays": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.get_input_test_arrays", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.get_input_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ModelDescr.get_output_test_arrays": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.get_output_test_arrays", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.get_output_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ModelDescr.get_batch_size": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.get_batch_size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.get_batch_size", "kind": "function", "doc": "\n", "signature": "(\ttensor_sizes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]) -> int:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ModelDescr.get_output_tensor_sizes": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.get_output_tensor_sizes", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.get_output_tensor_sizes", "kind": "function", "doc": "Returns the tensor output sizes for given input_sizes.\nOnly if input_sizes has a valid input shape, the tensor output size is exact.\nOtherwise it might be larger than the actual (valid) output
\n", "signature": "(\tself,\tinput_sizes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]) -> Dict[bioimageio.spec.model.v0_5.TensorId, Dict[bioimageio.spec.model.v0_5.AxisId, Union[int, bioimageio.spec.model.v0_5._DataDepSize]]]:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ModelDescr.get_ns": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.get_ns", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.get_ns", "kind": "function", "doc": "get parameter n
for each parameterized axis\nsuch that the valid input size is >= the given input size
Determine input and output block shape for scale factors ns\nof parameterized input sizes.
\n\nn
for each axis (keyed by (tensor_id, axis_id))\nthat is parameterized as size = min + n * step
.n
, is larger\nthan max_input_shape is set to the minimal value n_min
for which\nthis is still true.\nUse this for small input samples or large values of ns.\nOr simply whenever you know the full input shape.\n\n", "signature": "(\tself,\tns: Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int],\tbatch_size: Optional[int] = None,\t*,\tmax_input_shape: Optional[Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int]] = None) -> bioimageio.spec.model.v0_5._AxisSizes:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ModelDescr.implemented_format_version": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.implemented_format_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.5.3'"}, "bioimageio.spec.model.v0_5.ModelDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 5, 3)"}, "bioimageio.spec.model.v0_5.ModelDescr.model_post_init": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.model_post_init", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.model_post_init", "kind": "function", "doc": "Resolved axis sizes for model inputs and outputs.
\n
We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.generate_covers": {"fullname": "bioimageio.spec.model.v0_5.generate_covers", "modulename": "bioimageio.spec.model.v0_5", "qualname": "generate_covers", "kind": "function", "doc": "\n", "signature": "(\tinputs: Sequence[Tuple[bioimageio.spec.model.v0_5.InputTensorDescr, numpy.ndarray[Any, numpy.dtype[Any]]]],\toutputs: Sequence[Tuple[bioimageio.spec.model.v0_5.OutputTensorDescr, numpy.ndarray[Any, numpy.dtype[Any]]]]) -> List[pathlib.Path]:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.TensorDescrBase[Annotated[Union[BatchAxis, ChannelAxis, IndexInputAxis, TimeInputAxis, SpaceInputAxis], Discriminator]]": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase[Annotated[Union[BatchAxis, ChannelAxis, IndexInputAxis, TimeInputAxis, SpaceInputAxis], Discriminator]]", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase[Annotated[Union[BatchAxis, ChannelAxis, IndexInputAxis, TimeInputAxis, SpaceInputAxis], Discriminator]]", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node, typing.Generic[~IO_AxisT]"}, "bioimageio.spec.model.v0_5.TensorDescrBase[Annotated[Union[BatchAxis, ChannelAxis, IndexOutputAxis, Annotated[Union[Annotated[TimeOutputAxis, Tag], Annotated[TimeOutputAxisWithHalo, Tag]], Discriminator], Annotated[Union[Annotated[SpaceOutputAxis, Tag], Annotated[SpaceOutputAxisWithHalo, Tag]], Discriminator]], Discriminator]]": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase[Annotated[Union[BatchAxis, ChannelAxis, IndexOutputAxis, Annotated[Union[Annotated[TimeOutputAxis, Tag], Annotated[TimeOutputAxisWithHalo, Tag]], Discriminator], Annotated[Union[Annotated[SpaceOutputAxis, Tag], Annotated[SpaceOutputAxisWithHalo, Tag]], Discriminator]], Discriminator]]", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase[Annotated[Union[BatchAxis, ChannelAxis, IndexOutputAxis, Annotated[Union[Annotated[TimeOutputAxis, Tag], Annotated[TimeOutputAxisWithHalo, Tag]], Discriminator], Annotated[Union[Annotated[SpaceOutputAxis, Tag], Annotated[SpaceOutputAxisWithHalo, Tag]], Discriminator]], Discriminator]]", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node, typing.Generic[~IO_AxisT]"}, "bioimageio.spec.pretty_validation_errors": {"fullname": "bioimageio.spec.pretty_validation_errors", "modulename": "bioimageio.spec.pretty_validation_errors", "kind": "module", "doc": "\n"}, "bioimageio.spec.pretty_validation_errors.PrettyValidationError": {"fullname": "bioimageio.spec.pretty_validation_errors.PrettyValidationError", "modulename": "bioimageio.spec.pretty_validation_errors", "qualname": "PrettyValidationError", "kind": "class", "doc": "Wrap a pydantic.ValidationError to custumize formatting.
\n", "bases": "builtins.ValueError"}, "bioimageio.spec.pretty_validation_errors.PrettyValidationError.__init__": {"fullname": "bioimageio.spec.pretty_validation_errors.PrettyValidationError.__init__", "modulename": "bioimageio.spec.pretty_validation_errors", "qualname": "PrettyValidationError.__init__", "kind": "function", "doc": "\n", "signature": "(validation_error: pydantic_core._pydantic_core.ValidationError)"}, "bioimageio.spec.pretty_validation_errors.PrettyValidationError.error": {"fullname": "bioimageio.spec.pretty_validation_errors.PrettyValidationError.error", "modulename": "bioimageio.spec.pretty_validation_errors", "qualname": "PrettyValidationError.error", "kind": "variable", "doc": "\n"}, "bioimageio.spec.pretty_validation_errors.enable_pretty_validation_errors_in_ipynb": {"fullname": "bioimageio.spec.pretty_validation_errors.enable_pretty_validation_errors_in_ipynb", "modulename": "bioimageio.spec.pretty_validation_errors", "qualname": "enable_pretty_validation_errors_in_ipynb", "kind": "function", "doc": "A modestly hacky way to display prettified validaiton error messages and traceback\nin interactive Python notebooks
\n", "signature": "():", "funcdef": "def"}, "bioimageio.spec.summary": {"fullname": "bioimageio.spec.summary", "modulename": "bioimageio.spec.summary", "kind": "module", "doc": "\n"}, "bioimageio.spec.summary.Loc": {"fullname": "bioimageio.spec.summary.Loc", "modulename": "bioimageio.spec.summary", "qualname": "Loc", "kind": "variable", "doc": "location of error/warning in a nested data structure
\n", "default_value": "typing.Tuple[typing.Union[int, str], ...]"}, "bioimageio.spec.summary.WarningSeverityName": {"fullname": "bioimageio.spec.summary.WarningSeverityName", "modulename": "bioimageio.spec.summary", "qualname": "WarningSeverityName", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['info', 'warning', 'alert']"}, "bioimageio.spec.summary.WarningLevelName": {"fullname": "bioimageio.spec.summary.WarningLevelName", "modulename": "bioimageio.spec.summary", "qualname": "WarningLevelName", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['info', 'warning', 'alert', 'error']"}, "bioimageio.spec.summary.WARNING_SEVERITY_TO_NAME": {"fullname": "bioimageio.spec.summary.WARNING_SEVERITY_TO_NAME", "modulename": "bioimageio.spec.summary", "qualname": "WARNING_SEVERITY_TO_NAME", "kind": "variable", "doc": "\n", "annotation": ": Mapping[Literal[20, 30, 35], Literal['info', 'warning', 'alert']]", "default_value": "mappingproxy({20: 'info', 30: 'warning', 35: 'alert'})"}, "bioimageio.spec.summary.WARNING_LEVEL_TO_NAME": {"fullname": "bioimageio.spec.summary.WARNING_LEVEL_TO_NAME", "modulename": "bioimageio.spec.summary", "qualname": "WARNING_LEVEL_TO_NAME", "kind": "variable", "doc": "\n", "annotation": ": Mapping[Literal[20, 30, 35, 50], Literal['info', 'warning', 'alert', 'error']]", "default_value": "mappingproxy({20: 'info', 30: 'warning', 35: 'alert', 50: 'error'})"}, "bioimageio.spec.summary.WARNING_NAME_TO_LEVEL": {"fullname": "bioimageio.spec.summary.WARNING_NAME_TO_LEVEL", "modulename": "bioimageio.spec.summary", "qualname": "WARNING_NAME_TO_LEVEL", "kind": "variable", "doc": "\n", "annotation": ": Mapping[Literal['info', 'warning', 'alert', 'error'], Literal[20, 30, 35, 50]]", "default_value": "mappingproxy({'info': 20, 'warning': 30, 'alert': 35, 'error': 50})"}, "bioimageio.spec.summary.ValidationEntry": {"fullname": "bioimageio.spec.summary.ValidationEntry", "modulename": "bioimageio.spec.summary", "qualname": "ValidationEntry", "kind": "class", "doc": "Base of ErrorEntry
and WarningEntry
An error in a ValidationDetail
A warning in a ValidationDetail
helper to format a location tuple Loc
as Markdown string
InstalledPackage(name, version, build, channel)
\n", "bases": "typing.NamedTuple"}, "bioimageio.spec.summary.InstalledPackage.__init__": {"fullname": "bioimageio.spec.summary.InstalledPackage.__init__", "modulename": "bioimageio.spec.summary", "qualname": "InstalledPackage.__init__", "kind": "function", "doc": "Create new instance of InstalledPackage(name, version, build, channel)
\n", "signature": "(name: str, version: str, build: str = '', channel: str = '')"}, "bioimageio.spec.summary.InstalledPackage.name": {"fullname": "bioimageio.spec.summary.InstalledPackage.name", "modulename": "bioimageio.spec.summary", "qualname": "InstalledPackage.name", "kind": "variable", "doc": "Alias for field number 0
\n", "annotation": ": str"}, "bioimageio.spec.summary.InstalledPackage.version": {"fullname": "bioimageio.spec.summary.InstalledPackage.version", "modulename": "bioimageio.spec.summary", "qualname": "InstalledPackage.version", "kind": "variable", "doc": "Alias for field number 1
\n", "annotation": ": str"}, "bioimageio.spec.summary.InstalledPackage.build": {"fullname": "bioimageio.spec.summary.InstalledPackage.build", "modulename": "bioimageio.spec.summary", "qualname": "InstalledPackage.build", "kind": "variable", "doc": "Alias for field number 2
\n", "annotation": ": str"}, "bioimageio.spec.summary.InstalledPackage.channel": {"fullname": "bioimageio.spec.summary.InstalledPackage.channel", "modulename": "bioimageio.spec.summary", "qualname": "InstalledPackage.channel", "kind": "variable", "doc": "Alias for field number 3
\n", "annotation": ": str"}, "bioimageio.spec.summary.ValidationContextSummary": {"fullname": "bioimageio.spec.summary.ValidationContextSummary", "modulename": "bioimageio.spec.summary", "qualname": "ValidationContextSummary", "kind": "class", "doc": "\n", "bases": "typing_extensions.TypedDict"}, "bioimageio.spec.summary.ValidationContextSummary.perform_io_checks": {"fullname": "bioimageio.spec.summary.ValidationContextSummary.perform_io_checks", "modulename": "bioimageio.spec.summary", "qualname": "ValidationContextSummary.perform_io_checks", "kind": "variable", "doc": "\n", "annotation": ": bool"}, "bioimageio.spec.summary.ValidationContextSummary.known_files": {"fullname": "bioimageio.spec.summary.ValidationContextSummary.known_files", "modulename": "bioimageio.spec.summary", "qualname": "ValidationContextSummary.known_files", "kind": "variable", "doc": "\n", "annotation": ": Mapping[str, str]"}, "bioimageio.spec.summary.ValidationContextSummary.root": {"fullname": "bioimageio.spec.summary.ValidationContextSummary.root", "modulename": "bioimageio.spec.summary", "qualname": "ValidationContextSummary.root", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.summary.ValidationContextSummary.warning_level": {"fullname": "bioimageio.spec.summary.ValidationContextSummary.warning_level", "modulename": "bioimageio.spec.summary", "qualname": "ValidationContextSummary.warning_level", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.summary.ValidationDetail": {"fullname": "bioimageio.spec.summary.ValidationDetail", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail", "kind": "class", "doc": "a detail in a validation summary
\n", "bases": "pydantic.main.BaseModel"}, "bioimageio.spec.summary.ValidationDetail.name": {"fullname": "bioimageio.spec.summary.ValidationDetail.name", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.name", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.summary.ValidationDetail.status": {"fullname": "bioimageio.spec.summary.ValidationDetail.status", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.status", "kind": "variable", "doc": "\n", "annotation": ": Literal['passed', 'failed']"}, "bioimageio.spec.summary.ValidationDetail.loc": {"fullname": "bioimageio.spec.summary.ValidationDetail.loc", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.loc", "kind": "variable", "doc": "location in the RDF that this detail applies to
\n", "annotation": ": Tuple[Union[int, str], ...]"}, "bioimageio.spec.summary.ValidationDetail.errors": {"fullname": "bioimageio.spec.summary.ValidationDetail.errors", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.errors", "kind": "variable", "doc": "\n", "annotation": ": List[bioimageio.spec.summary.ErrorEntry]"}, "bioimageio.spec.summary.ValidationDetail.warnings": {"fullname": "bioimageio.spec.summary.ValidationDetail.warnings", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.warnings", "kind": "variable", "doc": "\n", "annotation": ": List[bioimageio.spec.summary.WarningEntry]"}, "bioimageio.spec.summary.ValidationDetail.context": {"fullname": "bioimageio.spec.summary.ValidationDetail.context", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.context", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.summary.ValidationContextSummary]"}, "bioimageio.spec.summary.ValidationDetail.recommended_env": {"fullname": "bioimageio.spec.summary.ValidationDetail.recommended_env", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.recommended_env", "kind": "variable", "doc": "recommended conda environemnt for this validation detail
\n", "annotation": ": Optional[bioimageio.spec.conda_env.CondaEnv]"}, "bioimageio.spec.summary.ValidationDetail.conda_compare": {"fullname": "bioimageio.spec.summary.ValidationDetail.conda_compare", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.conda_compare", "kind": "variable", "doc": "output of conda compare <recommended env>
create conda_compare
default value if needed
format as Markdown string
\n", "signature": "(\tself,\thide_tracebacks: bool = False,\troot_loc: Tuple[Union[int, str], ...] = ()) -> str:", "funcdef": "def"}, "bioimageio.spec.summary.ValidationSummary": {"fullname": "bioimageio.spec.summary.ValidationSummary", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary", "kind": "class", "doc": "Summarizes output of all bioimageio validations and tests\nfor one specific ResourceDescr
instance.
list of selected, relevant package versions
\n", "annotation": ": Set[bioimageio.spec.summary.InstalledPackage]"}, "bioimageio.spec.summary.ValidationSummary.conda_list": {"fullname": "bioimageio.spec.summary.ValidationSummary.conda_list", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary.conda_list", "kind": "variable", "doc": "parsed output of conda list
\n", "annotation": ": Optional[Sequence[bioimageio.spec.summary.InstalledPackage]]"}, "bioimageio.spec.summary.ValidationSummary.status_icon": {"fullname": "bioimageio.spec.summary.ValidationSummary.status_icon", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary.status_icon", "kind": "variable", "doc": "\n"}, "bioimageio.spec.summary.ValidationSummary.errors": {"fullname": "bioimageio.spec.summary.ValidationSummary.errors", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary.errors", "kind": "variable", "doc": "\n", "annotation": ": List[bioimageio.spec.summary.ErrorEntry]"}, "bioimageio.spec.summary.ValidationSummary.warnings": {"fullname": "bioimageio.spec.summary.ValidationSummary.warnings", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary.warnings", "kind": "variable", "doc": "\n", "annotation": ": List[bioimageio.spec.summary.WarningEntry]"}, "bioimageio.spec.summary.ValidationSummary.format": {"fullname": "bioimageio.spec.summary.ValidationSummary.format", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary.format", "kind": "function", "doc": "Format summary as Markdown string
\n\n Suitable to embed in HTML using '<br>' instead of '\n
\n\n'.
\n", "signature": "(\tself,\thide_tracebacks: bool = False,\thide_source: bool = False,\thide_env: bool = False,\troot_loc: Tuple[Union[int, str], ...] = ()) -> str:", "funcdef": "def"}, "bioimageio.spec.summary.ValidationSummary.display": {"fullname": "bioimageio.spec.summary.ValidationSummary.display", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary.display", "kind": "function", "doc": "\n", "signature": "(self) -> None:", "funcdef": "def"}, "bioimageio.spec.summary.ValidationSummary.add_detail": {"fullname": "bioimageio.spec.summary.ValidationSummary.add_detail", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary.add_detail", "kind": "function", "doc": "\n", "signature": "(self, detail: bioimageio.spec.summary.ValidationDetail):", "funcdef": "def"}, "bioimageio.spec.utils": {"fullname": "bioimageio.spec.utils", "modulename": "bioimageio.spec.utils", "kind": "module", "doc": "\n"}, "bioimageio.spec.utils.download": {"fullname": "bioimageio.spec.utils.download", "modulename": "bioimageio.spec.utils", "qualname": "download", "kind": "function", "doc": "Resolve file source
(download if needed)
from https://stackoverflow.com/a/44873382
\n", "signature": "(\tpath: Union[pathlib.Path, zipp.Path]) -> bioimageio.spec._internal.io_basics.Sha256:", "funcdef": "def"}, "bioimageio.spec.utils.get_spdx_licenses": {"fullname": "bioimageio.spec.utils.get_spdx_licenses", "modulename": "bioimageio.spec.utils", "qualname": "get_spdx_licenses", "kind": "function", "doc": "get details of the SPDX licenses known to bioimageio.spec
\n", "signature": "() -> bioimageio.spec.utils.SpdxLicenses:", "funcdef": "def"}, "bioimageio.spec.utils.identify_bioimageio_yaml_file_name": {"fullname": "bioimageio.spec.utils.identify_bioimageio_yaml_file_name", "modulename": "bioimageio.spec.utils", "qualname": "identify_bioimageio_yaml_file_name", "kind": "function", "doc": "\n", "signature": "(file_names: Iterable[str]) -> str:", "funcdef": "def"}, "bioimageio.spec.utils.is_valid_bioimageio_yaml_name": {"fullname": "bioimageio.spec.utils.is_valid_bioimageio_yaml_name", "modulename": "bioimageio.spec.utils", "qualname": "is_valid_bioimageio_yaml_name", "kind": "function", "doc": "\n", "signature": "(file_name: str) -> bool:", "funcdef": "def"}, "bioimageio.spec.utils.load_array": {"fullname": "bioimageio.spec.utils.load_array", "modulename": "bioimageio.spec.utils", "qualname": "load_array", "kind": "function", "doc": "\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], bioimageio.spec._internal.io.FileDescr, zipp.Path]) -> numpy.ndarray[typing.Any, numpy.dtype[typing.Any]]:", "funcdef": "def"}, "bioimageio.spec.utils.save_array": {"fullname": "bioimageio.spec.utils.save_array", "modulename": "bioimageio.spec.utils", "qualname": "save_array", "kind": "function", "doc": "\n", "signature": "(\tpath: Union[pathlib.Path, zipp.Path],\tarray: numpy.ndarray[typing.Any, numpy.dtype[typing.Any]]) -> None:", "funcdef": "def"}, "bioimageio.spec.utils.SpdxLicenseEntry": {"fullname": "bioimageio.spec.utils.SpdxLicenseEntry", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenseEntry", "kind": "class", "doc": "\n", "bases": "typing.TypedDict"}, "bioimageio.spec.utils.SpdxLicenseEntry.isDeprecatedLicenseId": {"fullname": "bioimageio.spec.utils.SpdxLicenseEntry.isDeprecatedLicenseId", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenseEntry.isDeprecatedLicenseId", "kind": "variable", "doc": "\n", "annotation": ": bool"}, "bioimageio.spec.utils.SpdxLicenseEntry.isKnownByZenodo": {"fullname": "bioimageio.spec.utils.SpdxLicenseEntry.isKnownByZenodo", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenseEntry.isKnownByZenodo", "kind": "variable", "doc": "\n", "annotation": ": bool"}, "bioimageio.spec.utils.SpdxLicenseEntry.isOsiApproved": {"fullname": "bioimageio.spec.utils.SpdxLicenseEntry.isOsiApproved", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenseEntry.isOsiApproved", "kind": "variable", "doc": "\n", "annotation": ": bool"}, "bioimageio.spec.utils.SpdxLicenseEntry.licenseId": {"fullname": "bioimageio.spec.utils.SpdxLicenseEntry.licenseId", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenseEntry.licenseId", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.utils.SpdxLicenseEntry.name": {"fullname": "bioimageio.spec.utils.SpdxLicenseEntry.name", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenseEntry.name", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.utils.SpdxLicenseEntry.reference": {"fullname": "bioimageio.spec.utils.SpdxLicenseEntry.reference", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenseEntry.reference", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.utils.SpdxLicenses": {"fullname": "bioimageio.spec.utils.SpdxLicenses", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenses", "kind": "class", "doc": "\n", "bases": "typing.TypedDict"}, "bioimageio.spec.utils.SpdxLicenses.licenseListVersion": {"fullname": "bioimageio.spec.utils.SpdxLicenses.licenseListVersion", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenses.licenseListVersion", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.utils.SpdxLicenses.licenses": {"fullname": "bioimageio.spec.utils.SpdxLicenses.licenses", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenses.licenses", "kind": "variable", "doc": "\n", "annotation": ": List[bioimageio.spec.utils.SpdxLicenseEntry]"}, "bioimageio.spec.utils.SpdxLicenses.releaseDate": {"fullname": "bioimageio.spec.utils.SpdxLicenses.releaseDate", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenses.releaseDate", "kind": "variable", "doc": "\n", "annotation": ": str"}}, "docInfo": {"bioimageio.core": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 2771}, "bioimageio.core.Axis": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "bioimageio.core.Axis.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 97, "bases": 0, "doc": 3}, "bioimageio.core.Axis.id": {"qualname": 2, "fullname": 4, "annotation": 7, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "bioimageio.core.Axis.type": {"qualname": 2, "fullname": 4, "annotation": 18, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "bioimageio.core.Axis.create": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 881, "bases": 0, "doc": 3}, "bioimageio.core.AxisId": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 5, "doc": 72}, "bioimageio.core.AxisId.root_model": {"qualname": 3, "fullname": 5, "annotation": 5, "default_value": 17, "signature": 0, "bases": 0, "doc": 10}, "bioimageio.core.BlockMeta": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 209}, "bioimageio.core.BlockMeta.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 193, "bases": 0, "doc": 3}, "bioimageio.core.BlockMeta.sample_shape": {"qualname": 3, "fullname": 5, "annotation": 8, "default_value": 0, "signature": 0, "bases": 0, "doc": 10}, "bioimageio.core.BlockMeta.inner_slice": {"qualname": 3, "fullname": 5, "annotation": 11, "default_value": 0, "signature": 0, "bases": 0, "doc": 9}, "bioimageio.core.BlockMeta.halo": {"qualname": 2, "fullname": 4, "annotation": 11, "default_value": 0, "signature": 0, "bases": 0, "doc": 12}, "bioimageio.core.BlockMeta.block_index": {"qualname": 3, "fullname": 5, "annotation": 2, "default_value": 0, "signature": 0, "bases": 0, "doc": 9}, "bioimageio.core.BlockMeta.blocks_in_sample": {"qualname": 4, "fullname": 6, "annotation": 2, "default_value": 0, "signature": 0, "bases": 0, "doc": 9}, "bioimageio.core.BlockMeta.shape": {"qualname": 2, "fullname": 4, "annotation": 8, "default_value": 0, "signature": 0, "bases": 0, "doc": 7}, "bioimageio.core.BlockMeta.padding": {"qualname": 2, "fullname": 4, "annotation": 11, "default_value": 0, "signature": 0, "bases": 0, "doc": 19}, "bioimageio.core.BlockMeta.outer_slice": {"qualname": 3, "fullname": 5, "annotation": 11, "default_value": 0, "signature": 0, "bases": 0, "doc": 12}, "bioimageio.core.BlockMeta.inner_shape": {"qualname": 3, "fullname": 5, "annotation": 8, "default_value": 0, "signature": 0, "bases": 0, "doc": 11}, "bioimageio.core.BlockMeta.local_slice": {"qualname": 3, "fullname": 5, "annotation": 11, "default_value": 0, "signature": 0, "bases": 0, "doc": 12}, "bioimageio.core.BlockMeta.dims": {"qualname": 2, "fullname": 4, "annotation": 7, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "bioimageio.core.BlockMeta.tagged_shape": {"qualname": 3, "fullname": 5, "annotation": 8, "default_value": 0, "signature": 0, "bases": 0, "doc": 5}, "bioimageio.core.BlockMeta.inner_slice_wo_overlap": {"qualname": 5, "fullname": 7, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 43}, "bioimageio.core.BlockMeta.get_transformed": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 86, "bases": 0, "doc": 3}, "bioimageio.core.build_description": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 854, "bases": 0, "doc": 115}, "bioimageio.core.compute_dataset_measures": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 507, "bases": 0, "doc": 14}, "bioimageio.core.create_prediction_pipeline": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 930, "bases": 0, "doc": 33}, "bioimageio.core.dump_description": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 762, "bases": 0, "doc": 20}, "bioimageio.core.enable_determinism": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 37, "bases": 0, "doc": 113}, "bioimageio.core.load_dataset_description": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 578, "bases": 0, "doc": 22}, "bioimageio.core.load_description_and_test": {"qualname": 4, "fullname": 6, "annotation": 0, "default_value": 0, "signature": 2022, "bases": 0, "doc": 12}, "bioimageio.core.load_description_and_validate_format_only": {"qualname": 6, "fullname": 8, "annotation": 0, "default_value": 0, "signature": 474, "bases": 0, "doc": 144}, "bioimageio.core.load_description": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 1170, "bases": 0, "doc": 141}, "bioimageio.core.load_model_description": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 578, "bases": 0, "doc": 40}, "bioimageio.core.load_model": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 578, "bases": 0, "doc": 9}, "bioimageio.core.load_resource": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 1170, "bases": 0, "doc": 8}, "bioimageio.core.MemberId": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 13, "signature": 0, "bases": 0, "doc": 3}, "bioimageio.core.predict_many": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 742, "bases": 0, "doc": 185}, "bioimageio.core.predict": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 841, "bases": 0, "doc": 198}, "bioimageio.core.PredictionPipeline": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 18}, "bioimageio.core.PredictionPipeline.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 814, "bases": 0, "doc": 3}, "bioimageio.core.PredictionPipeline.name": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "bioimageio.core.PredictionPipeline.model_description": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "bioimageio.core.PredictionPipeline.predict_sample_block": {"qualname": 4, "fullname": 6, "annotation": 0, "default_value": 0, "signature": 95, "bases": 0, "doc": 3}, "bioimageio.core.PredictionPipeline.predict_sample_without_blocking": {"qualname": 5, "fullname": 7, "annotation": 0, "default_value": 0, "signature": 94, "bases": 0, "doc": 32}, "bioimageio.core.PredictionPipeline.get_output_sample_id": {"qualname": 5, "fullname": 7, "annotation": 0, "default_value": 0, "signature": 23, "bases": 0, "doc": 3}, "bioimageio.core.PredictionPipeline.predict_sample_with_fixed_blocking": {"qualname": 6, "fullname": 8, "annotation": 0, "default_value": 0, "signature": 177, "bases": 0, "doc": 3}, "bioimageio.core.PredictionPipeline.predict_sample_with_blocking": {"qualname": 5, "fullname": 7, "annotation": 0, "default_value": 0, "signature": 217, "bases": 0, "doc": 20}, "bioimageio.core.PredictionPipeline.apply_preprocessing": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 68, "bases": 0, "doc": 10}, "bioimageio.core.PredictionPipeline.apply_postprocessing": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 89, "bases": 0, "doc": 10}, "bioimageio.core.PredictionPipeline.load": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 11, "bases": 0, "doc": 18}, "bioimageio.core.PredictionPipeline.unload": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 11, "bases": 0, "doc": 8}, "bioimageio.core.Sample": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 5}, "bioimageio.core.Sample.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 596, "bases": 0, "doc": 3}, "bioimageio.core.Sample.members": {"qualname": 2, "fullname": 4, "annotation": 11, "default_value": 0, "signature": 0, "bases": 0, "doc": 6}, "bioimageio.core.Sample.stat": {"qualname": 2, "fullname": 4, 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particular DL models).
\n\nTo get started we recommend installing bioimageio.core with conda together with a deep\nlearning framework, e.g. pytorch, and run a few bioimageio
commands to see what\nbioimage.core has to offer:
install with conda (for more details on conda environments, checkout the conda docs)
\n\nconda install -c conda-forge bioimageio.core pytorch\n
\ntest a model
\n\n$ bioimageio test powerful-chipmunk\n...\n
\n(Click to expand output)
\u2714\ufe0f bioimageio validation passed\n\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\n source https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/powerful-chipmunk/1/files/rdf.yaml\n format version model 0.4.10\n bioimageio.spec 0.5.3post4\n bioimageio.core 0.6.8\n\n\n\n \u2753 location detail\n\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\n \u2714\ufe0f initialized ModelDescr to describe model 0.4.10\n\n \u2714\ufe0f bioimageio.spec format validation model 0.4.10\n \ud83d\udd0d context.perform_io_checks True\n \ud83d\udd0d context.root https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/powerful-chipmunk/1/files\n \ud83d\udd0d context.known_files.weights.pt 3bd9c518c8473f1e35abb7624f82f3aa92f1015e66fb1f6a9d08444e1f2f5698\n \ud83d\udd0d context.known_files.weights-torchscript.pt 4e568fd81c0ffa06ce13061327c3f673e1bac808891135badd3b0fcdacee086b\n \ud83d\udd0d context.warning_level error\n\n \u2714\ufe0f Reproduce test outputs from test inputs\n\n \u2714\ufe0f Reproduce test outputs from test inputs\n
\nor
\n\n$ bioimageio test impartial-shrimp\n...\n
\n(Click to expand output)
\u2714\ufe0f bioimageio validation passed\n\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\n source https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/impartial-shrimp/1.1/files/rdf.yaml\n format version model 0.5.3\n bioimageio.spec 0.5.3.2\n bioimageio.core 0.6.9\n\n\n \u2753 location detail\n\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\n \u2714\ufe0f initialized ModelDescr to describe model 0.5.3\n\n\n \u2714\ufe0f bioimageio.spec format validation model 0.5.3\n\n \ud83d\udd0d context.perform_io_checks False\n \ud83d\udd0d context.warning_level error\n\n \u2714\ufe0f Reproduce test outputs from test inputs (pytorch_state_dict)\n\n\n \u2714\ufe0f Run pytorch_state_dict inference for inputs with batch_size: 1 and size parameter n:\n\n 0\n\n \u2714\ufe0f Run pytorch_state_dict inference for inputs with batch_size: 2 and size parameter n:\n\n 0\n\n \u2714\ufe0f Run pytorch_state_dict inference for inputs with batch_size: 1 and size parameter n:\n\n 1\n\n \u2714\ufe0f Run pytorch_state_dict inference for inputs with batch_size: 2 and size parameter n:\n\n 1\n\n \u2714\ufe0f Run pytorch_state_dict inference for inputs with batch_size: 1 and size parameter n:\n\n 2\n\n \u2714\ufe0f Run pytorch_state_dict inference for inputs with batch_size: 2 and size parameter n:\n\n 2\n\n \u2714\ufe0f Reproduce test outputs from test inputs (torchscript)\n\n\n \u2714\ufe0f Run torchscript inference for inputs with batch_size: 1 and size parameter n: 0\n\n\n \u2714\ufe0f Run torchscript inference for inputs with batch_size: 2 and size parameter n: 0\n\n\n \u2714\ufe0f Run torchscript inference for inputs with batch_size: 1 and size parameter n: 1\n\n\n \u2714\ufe0f Run torchscript inference for inputs with batch_size: 2 and size parameter n: 1\n\n\n \u2714\ufe0f Run torchscript inference for inputs with batch_size: 1 and size parameter n: 2\n\n\n \u2714\ufe0f Run torchscript inference for inputs with batch_size: 2 and size parameter n: 2\n
\ndisplay the bioimageio-predict
command help to get an overview:
$ bioimageio predict --help\n...\n
\n(Click to expand output)
usage: bioimageio predict [-h] [--inputs Sequence[Union[str,Annotated[Tuple[str,...],MinLenmin_length=1]]]]\n [--outputs {str,Tuple[str,...]}] [--overwrite bool] [--blockwise bool] [--stats Path]\n [--preview bool]\n [--weight_format {typing.Literal['keras_hdf5','onnx','pytorch_state_dict','tensorflow_js','tensorflow_saved_model_bundle','torchscript'],any}]\n [--example bool]\n SOURCE\n\nbioimageio-predict - Run inference on your data with a bioimage.io model.\n\npositional arguments:\n SOURCE Url/path to a bioimageio.yaml/rdf.yaml file\n or a bioimage.io resource identifier, e.g. 'affable-shark'\n\noptional arguments:\n -h, --help show this help message and exit\n --inputs Sequence[Union[str,Annotated[Tuple[str,...],MinLen(min_length=1)]]]\n Model input sample paths (for each input tensor)\n\n The input paths are expected to have shape...\n - (n_samples,) or (n_samples,1) for models expecting a single input tensor\n - (n_samples,) containing the substring '{input_id}', or\n - (n_samples, n_model_inputs) to provide each input tensor path explicitly.\n\n All substrings that are replaced by metadata from the model description:\n - '{model_id}'\n - '{input_id}'\n\n Example inputs to process sample 'a' and 'b'\n for a model expecting a 'raw' and a 'mask' input tensor:\n --inputs="[["a_raw.tif","a_mask.tif"],["b_raw.tif","b_mask.tif"]]"\n (Note that JSON double quotes need to be escaped.)\n\n Alternatively a `bioimageio-cli.yaml` (or `bioimageio-cli.json`) file\n may provide the arguments, e.g.:\n ```yaml\n inputs:\n - [a_raw.tif, a_mask.tif]\n - [b_raw.tif, b_mask.tif]\n \n
\n `.npy` and any file extension supported by imageio are supported.\n Aavailable formats are listed at\n https://imageio.readthedocs.io/en/stable/formats/index.html#all-formats.\n Some formats have additional dependencies.\n\n \u200a (default: ('{input_id}/001.tif',))\n
\n\n--outputs {str,Tuple[str,...]}\n Model output path pattern (per output tensor)
\n\n All substrings that are replaced:\n - '{model_id}' (from model description)\n - '{output_id}' (from model description)\n - '{sample_id}' (extracted from input paths)\n\n \u200a (default: outputs_{model_id}/{output_id}/{sample_id}.tif)\n
\n\n--overwrite bool allow overwriting existing output files (default: False)\n --blockwise bool process inputs blockwise (default: False)\n --stats Path path to dataset statistics\n (will be written if it does not exist,\n but the model requires statistical dataset measures)\n \u200a (default: dataset_statistics.json)\n --preview bool preview which files would be processed\n and what outputs would be generated. (default: False)\n --weight_format {typing.Literal['keras_hdf5','onnx','pytorch_state_dict','tensorflow_js','tensorflow_saved_model_bundle','torchscript'],any}\n The weight format to use. (default: any)\n --example bool generate and run an example
\n\n 1. downloads example model inputs\n 2. creates a `{model_id}_example` folder\n 3. writes input arguments to `{model_id}_example/bioimageio-cli.yaml`\n 4. executes a preview dry-run\n 5. executes prediction with example input\n\n \u200a (default: False)\n
\n </details>\n\n- create an example and run prediction locally!\n\n ```console\n $ bioimageio predict impartial-shrimp --example=True\n ...\n
\n\n<details>\n<summary>(Click to expand output)</summary>\n\n```console\n\ud83d\udec8 bioimageio prediction preview structure:\n{'{sample_id}': {'inputs': {'{input_id}': '<input path>'},\n 'outputs': {'{output_id}': '<output path>'}}}\n\ud83d\udd0e bioimageio prediction preview output:\n{'1': {'inputs': {'input0': 'impartial-shrimp_example/input0/001.tif'},\n 'outputs': {'output0': 'impartial-shrimp_example/outputs/output0/1.tif'}}}\npredict with impartial-shrimp: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 1/1 [00:21<00:00, 21.76s/sample]\n\ud83c\udf89 Sucessfully ran example prediction!\nTo predict the example input using the CLI example config file impartial-shrimp_example\\bioimageio-cli.yaml, execute `bioimageio predict` from impartial-shrimp_example:\n$ cd impartial-shrimp_example\n$ bioimageio predict \"impartial-shrimp\"\n\nAlternatively run the following command in the current workind directory, not the example folder:\n$ bioimageio predict --preview=False --overwrite=True --stats=\"impartial-shrimp_example/dataset_statistics.json\" --inputs=\"[[\\\"impartial-shrimp_example/input0/001.tif\\\"]]\" --outputs=\"impartial-shrimp_example/outputs/{output_id}/{sample_id}.tif\" \"impartial-shrimp\"\n(note that a local 'bioimageio-cli.json' or 'bioimageio-cli.yaml' may interfere with this)\n
\n\n\n </details>\n\n## Installation\n\n### Via Mamba/Conda\n\nThe `bioimageio.core` package can be installed from conda-forge via\n\n```console\nmamba install -c conda-forge bioimageio.core\n```\n\nIf you do not install any additional deep learning libraries, you will only be able to use general convenience\nfunctionality, but not any functionality for model prediction.\nTo install additional deep learning libraries use:\n\n- Pytorch/Torchscript:\n\n CPU installation (if you don't have an nvidia graphics card):\n\n ```console\n mamba install -c pytorch -c conda-forge bioimageio.core pytorch torchvision cpuonly\n
\n\nGPU installation (for cuda 11.6, please choose the appropriate cuda version for your system):
\n\nmamba install -c pytorch -c nvidia -c conda-forge bioimageio.core pytorch torchvision pytorch-cuda=11.8\n
\nNote that the pytorch installation instructions may change in the future. For the latest instructions please refer to pytorch.org.
\n\nTensorflow
\n\nCurrently only CPU version supported
\n\nmamba install -c conda-forge bioimageio.core tensorflow\n
\nONNXRuntime
\n\nCurrently only cpu version supported
\n\nmamba install -c conda-forge bioimageio.core onnxruntime\n
\nThe package is also available via pip\n(e.g. with recommended extras onnx
and pytorch
):
pip install "bioimageio.core[onnx,pytorch]"\n
\nTo set up a development conda environment run the following commands:
\n\nmamba env create -f dev/env.yaml\nmamba activate core\npip install -e . --no-deps\n
\nThere are different environment files available that only install tensorflow or pytorch as dependencies.
\n\nbioimageio.core
installs a command line interface (CLI) for testing models and other functionality.\nYou can list all the available commands via:
bioimageio\n
\nFor convenience the command line options (not arguments) may be given in a bioimageio-cli.json
\nor bioimageio-cli.yaml
file, e.g.:
# bioimageio-cli.yaml\ninputs: inputs/*_{tensor_id}.h5\noutputs: outputs_{model_id}/{sample_id}_{tensor_id}.h5\noverwrite: true\nblockwise: true\nstats: inputs/dataset_statistics.json\n
\nbioimageio.core
is a python package that implements prediction with bioimageio models\nincluding standardized pre- and postprocessing operations.\nThese models are described by---and can be loaded with---the bioimageio.spec package.
In addition bioimageio.core provides functionality to convert model weight formats.
\n\nTo get an overview of this functionality, check out these example notebooks:
\n\n\n\nand the developer documentation.
\n\nbioimageio.spec
and bioimageio.core
use loguru for logging, hence the logging level\nmay be controlled with the LOGURU_LEVEL
environment variable.
The model specification and its validation tools can be found at https://github.com/bioimage-io/spec-bioimage-io.
\n\nValidationDetail.recommended_env
in ValidationSummary
get_io_sample_block_metas()
\nzipfile.ZipFile
object with bioimageio.spec==0.5.3.5resolve
and resolve_and_extract
enable_determinism
function and determinism input argument for testing with seeded\nrandom generators and optionally (determinsim==\"full\") instructing DL frameworks to use\ndeterministic algorithms.predict
commandpath
is now requiredpredict()
argument inputs
may be samplebioimageio validate-format
commandstr(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec._internal.types.LowerCaseIdentifier"}, "bioimageio.core.AxisId.root_model": {"fullname": "bioimageio.core.AxisId.root_model", "modulename": "bioimageio.core", "qualname": "AxisId.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[str, MinLen, AfterValidator, AfterValidator, Annotated[TypeVar, Predicate], MaxLen]]'>"}, "bioimageio.core.BlockMeta": {"fullname": "bioimageio.core.BlockMeta", "modulename": "bioimageio.core", "qualname": "BlockMeta", "kind": "class", "doc": "Block meta data of a sample member (a tensor in a sample)
\n\nFigure for illustration:\nThe first 2d block (dashed) of a sample member (bold).\nThe inner slice (thin) is expanded by a halo in both dimensions on both sides.\nThe outer slice reaches from the sample member origin (0, 0) to the right halo point.
\n\n\u250c \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2510\n\u2577 halo(left) \u2577\n\u2577 \u2577\n\u2577 (0, 0)\u250f\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u252f\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u252f\u2501\u2501\u2501\u2794\n\u2577 \u2503 \u2502 \u2577 sample member\n\u2577 \u2503 inner \u2502 \u2577\n\u2577 \u2503 (and outer) \u2502 outer \u2577\n\u2577 \u2503 slice \u2502 slice \u2577\n\u2577 \u2503 \u2502 \u2577\n\u2577 \u2523\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518 \u2577\n\u2577 \u2503 outer slice \u2577\n\u2577 \u2503 halo(right) \u2577\n\u2514 \u2500 \u2500 \u2500 \u2500\u2503\u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500\u2518\n \u2b07\n
\n\nnote:
\n\nthe axis sizes of the whole (unblocked) sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.BlockMeta.inner_slice": {"fullname": "bioimageio.core.BlockMeta.inner_slice", "modulename": "bioimageio.core", "qualname": "BlockMeta.inner_slice", "kind": "variable", "doc": "inner region (without halo) wrt the sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.SliceInfo]"}, "bioimageio.core.BlockMeta.halo": {"fullname": "bioimageio.core.BlockMeta.halo", "modulename": "bioimageio.core", "qualname": "BlockMeta.halo", "kind": "variable", "doc": "halo enlarging the inner region to the block's sizes
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.Halo]"}, "bioimageio.core.BlockMeta.block_index": {"fullname": "bioimageio.core.BlockMeta.block_index", "modulename": "bioimageio.core", "qualname": "BlockMeta.block_index", "kind": "variable", "doc": "the i-th block of the sample
\n", "annotation": ": int"}, "bioimageio.core.BlockMeta.blocks_in_sample": {"fullname": "bioimageio.core.BlockMeta.blocks_in_sample", "modulename": "bioimageio.core", "qualname": "BlockMeta.blocks_in_sample", "kind": "variable", "doc": "total number of blocks in the sample
\n", "annotation": ": int"}, "bioimageio.core.BlockMeta.shape": {"fullname": "bioimageio.core.BlockMeta.shape", "modulename": "bioimageio.core", "qualname": "BlockMeta.shape", "kind": "variable", "doc": "axis lengths of the block
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.BlockMeta.padding": {"fullname": "bioimageio.core.BlockMeta.padding", "modulename": "bioimageio.core", "qualname": "BlockMeta.padding", "kind": "variable", "doc": "padding to realize the halo at the sample edge\nwhere we cannot simply enlarge the inner slice
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.PadWidth]"}, "bioimageio.core.BlockMeta.outer_slice": {"fullname": "bioimageio.core.BlockMeta.outer_slice", "modulename": "bioimageio.core", "qualname": "BlockMeta.outer_slice", "kind": "variable", "doc": "slice of the outer block (without padding) wrt the sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.SliceInfo]"}, "bioimageio.core.BlockMeta.inner_shape": {"fullname": "bioimageio.core.BlockMeta.inner_shape", "modulename": "bioimageio.core", "qualname": "BlockMeta.inner_shape", "kind": "variable", "doc": "axis lengths of the inner region (without halo)
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.BlockMeta.local_slice": {"fullname": "bioimageio.core.BlockMeta.local_slice", "modulename": "bioimageio.core", "qualname": "BlockMeta.local_slice", "kind": "variable", "doc": "inner slice wrt the block, not the sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.SliceInfo]"}, "bioimageio.core.BlockMeta.dims": {"fullname": "bioimageio.core.BlockMeta.dims", "modulename": "bioimageio.core", "qualname": "BlockMeta.dims", "kind": "variable", "doc": "\n", "annotation": ": Collection[bioimageio.spec.model.v0_5.AxisId]"}, "bioimageio.core.BlockMeta.tagged_shape": {"fullname": "bioimageio.core.BlockMeta.tagged_shape", "modulename": "bioimageio.core", "qualname": "BlockMeta.tagged_shape", "kind": "variable", "doc": "alias for shape
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.BlockMeta.inner_slice_wo_overlap": {"fullname": "bioimageio.core.BlockMeta.inner_slice_wo_overlap", "modulename": "bioimageio.core", "qualname": "BlockMeta.inner_slice_wo_overlap", "kind": "variable", "doc": "subslice of the inner slice, such that all inner_slice_wo_overlap
can be\nstiched together trivially to form the original sample.
This can also be used to calculate statistics\nwithout overrepresenting block edge regions.
\n"}, "bioimageio.core.BlockMeta.get_transformed": {"fullname": "bioimageio.core.BlockMeta.get_transformed", "modulename": "bioimageio.core", "qualname": "BlockMeta.get_transformed", "kind": "function", "doc": "\n", "signature": "(\tself,\tnew_axes: Mapping[bioimageio.spec.model.v0_5.AxisId, Union[bioimageio.core.block_meta.LinearAxisTransform, int]]) -> Self:", "funcdef": "def"}, "bioimageio.core.build_description": {"fullname": "bioimageio.core.build_description", "modulename": "bioimageio.core", "qualname": "build_description", "kind": "function", "doc": "build a bioimage.io resource description from an RDF's content.
\n\nUse load_description
if you want to build a resource description from an rdf.yaml\nor bioimage.io zip-package.
\n\n", "signature": "(\tcontent: Dict[str, YamlValue],\t/,\t*,\tcontext: Optional[bioimageio.spec._internal.validation_context.ValidationContext] = None,\tformat_version: Union[Literal['latest', 'discover'], str] = 'discover') -> Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec._internal.common_nodes.InvalidDescr]:", "funcdef": "def"}, "bioimageio.core.compute_dataset_measures": {"fullname": "bioimageio.core.compute_dataset_measures", "modulename": "bioimageio.core", "qualname": "compute_dataset_measures", "kind": "function", "doc": "An object holding all metadata of the bioimage.io resource
\n
compute all dataset measures
for the given dataset
Creates prediction pipeline which includes:
\n\nConverts a resource to a dictionary containing only simple types that can directly be serialzed to YAML.
\n", "signature": "(\trd: Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec._internal.common_nodes.InvalidDescr],\texclude_unset: bool = True) -> Dict[str, YamlValue]:", "funcdef": "def"}, "bioimageio.core.enable_determinism": {"fullname": "bioimageio.core.enable_determinism", "modulename": "bioimageio.core", "qualname": "enable_determinism", "kind": "function", "doc": "Seed and configure ML frameworks for maximum reproducibility.\nMay degrade performance. Only recommended for testing reproducibility!
\n\nSeed any random generators and (if mode==\"full\") request ML frameworks to use\ndeterministic algorithms.
\n\n\n \n\n", "signature": "(mode: Literal['seed_only', 'full']):", "funcdef": "def"}, "bioimageio.core.load_dataset_description": {"fullname": "bioimageio.core.load_dataset_description", "modulename": "bioimageio.core", "qualname": "load_dataset_description", "kind": "function", "doc": "
same as load_description
, but addtionally ensures that the loaded\ndescription is valid and of type 'dataset'.
Test RDF dynamically, e.g. model inference of test inputs
\n", "signature": "(\tsource: Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], Dict[str, YamlValue]],\t*,\tformat_version: Union[Literal['discover', 'latest'], str] = 'discover',\tweight_format: Optional[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']] = None,\tdevices: Optional[Sequence[str]] = None,\tabsolute_tolerance: float = 0.00015,\trelative_tolerance: float = 0.0001,\tdecimal: Optional[int] = None,\tdeterminism: Literal['seed_only', 'full'] = 'seed_only',\texpected_type: Optional[str] = None) -> Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec._internal.common_nodes.InvalidDescr]:", "funcdef": "def"}, "bioimageio.core.load_description_and_validate_format_only": {"fullname": "bioimageio.core.load_description_and_validate_format_only", "modulename": "bioimageio.core", "qualname": "load_description_and_validate_format_only", "kind": "function", "doc": "load a bioimage.io resource description
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], zipfile.ZipFile],\t/,\t*,\tformat_version: Union[Literal['discover'], Literal['latest'], str] = 'discover',\tperform_io_checks: bool = True,\tknown_files: Optional[Dict[str, bioimageio.spec._internal.io_basics.Sha256]] = None) -> bioimageio.spec.summary.ValidationSummary:", "funcdef": "def"}, "bioimageio.core.load_description": {"fullname": "bioimageio.core.load_description", "modulename": "bioimageio.core", "qualname": "load_description", "kind": "function", "doc": "Validation summary of the bioimage.io resource found at
\nsource
.
load a bioimage.io resource description
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], zipfile.ZipFile],\t/,\t*,\tformat_version: Union[Literal['discover'], Literal['latest'], str] = 'discover',\tperform_io_checks: bool = True,\tknown_files: Optional[Dict[str, bioimageio.spec._internal.io_basics.Sha256]] = None) -> Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec._internal.common_nodes.InvalidDescr]:", "funcdef": "def"}, "bioimageio.core.load_model_description": {"fullname": "bioimageio.core.load_model_description", "modulename": "bioimageio.core", "qualname": "load_model_description", "kind": "function", "doc": "An object holding all metadata of the bioimage.io resource
\n
same as load_description
, but addtionally ensures that the loaded\ndescription is valid and of type 'model'.
alias of load_model_description
alias of load_description
Run prediction for a multiple sets of inputs with a bioimage.io model
\n\n{i}
will be formatted as the i-th sample.\nIf {i}
(or {i:
) is not present and inputs
is an iterable {i:03}
is appended.{member_id}
{sample_id}
in it\nto save the output to.Run prediction for a single set of input(s) with a bioimage.io model
\n\ninput_block_shape
blocksize_parameter
.{member_id}
{sample_id}
in it\nto save the output to.Represents model computation including preprocessing and postprocessing\nNote: Ideally use the PredictionPipeline as a context manager
\n"}, "bioimageio.core.PredictionPipeline.__init__": {"fullname": "bioimageio.core.PredictionPipeline.__init__", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.__init__", "kind": "function", "doc": "\n", "signature": "(\t*,\tname: str,\tmodel_description: Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)],\tpreprocessing: List[Union[bioimageio.core.proc_ops.AddKnownDatasetStats, bioimageio.core.proc_ops.Binarize, bioimageio.core.proc_ops.Clip, bioimageio.core.proc_ops.EnsureDtype, bioimageio.core.proc_ops.FixedZeroMeanUnitVariance, bioimageio.core.proc_ops.ScaleLinear, bioimageio.core.proc_ops.ScaleMeanVariance, bioimageio.core.proc_ops.ScaleRange, bioimageio.core.proc_ops.Sigmoid, bioimageio.core.proc_ops.UpdateStats, bioimageio.core.proc_ops.ZeroMeanUnitVariance]],\tpostprocessing: List[Union[bioimageio.core.proc_ops.AddKnownDatasetStats, bioimageio.core.proc_ops.Binarize, bioimageio.core.proc_ops.Clip, bioimageio.core.proc_ops.EnsureDtype, bioimageio.core.proc_ops.FixedZeroMeanUnitVariance, bioimageio.core.proc_ops.ScaleLinear, bioimageio.core.proc_ops.ScaleMeanVariance, bioimageio.core.proc_ops.ScaleRange, bioimageio.core.proc_ops.Sigmoid, bioimageio.core.proc_ops.UpdateStats, bioimageio.core.proc_ops.ZeroMeanUnitVariance]],\tmodel_adapter: bioimageio.core.model_adapters._model_adapter.ModelAdapter,\tdefault_ns: Union[int, Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int]] = 10,\tdefault_batch_size: int = 1)"}, "bioimageio.core.PredictionPipeline.name": {"fullname": "bioimageio.core.PredictionPipeline.name", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.name", "kind": "variable", "doc": "\n"}, "bioimageio.core.PredictionPipeline.model_description": {"fullname": "bioimageio.core.PredictionPipeline.model_description", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.model_description", "kind": "variable", "doc": "\n"}, "bioimageio.core.PredictionPipeline.predict_sample_block": {"fullname": "bioimageio.core.PredictionPipeline.predict_sample_block", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.predict_sample_block", "kind": "function", "doc": "\n", "signature": "(\tself,\tsample_block: bioimageio.core.sample.SampleBlockWithOrigin,\tskip_preprocessing: bool = False,\tskip_postprocessing: bool = False) -> bioimageio.core.sample.SampleBlock:", "funcdef": "def"}, "bioimageio.core.PredictionPipeline.predict_sample_without_blocking": {"fullname": "bioimageio.core.PredictionPipeline.predict_sample_without_blocking", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.predict_sample_without_blocking", "kind": "function", "doc": "predict a sample.\nThe sample's tensor shapes have to match the model's input tensor description.\nIf that is not the case, consider predict_sample_with_blocking
predict a sample by splitting it into blocks according to the model and the ns
parameter
apply preprocessing in-place, also updates sample stats
\n", "signature": "(\tself,\tsample: Union[bioimageio.core.sample.Sample, bioimageio.core.sample.SampleBlockWithOrigin]) -> None:", "funcdef": "def"}, "bioimageio.core.PredictionPipeline.apply_postprocessing": {"fullname": "bioimageio.core.PredictionPipeline.apply_postprocessing", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.apply_postprocessing", "kind": "function", "doc": "apply postprocessing in-place, also updates samples stats
\n", "signature": "(\tself,\tsample: Union[bioimageio.core.sample.Sample, bioimageio.core.sample.SampleBlock, bioimageio.core.sample.SampleBlockWithOrigin]) -> None:", "funcdef": "def"}, "bioimageio.core.PredictionPipeline.load": {"fullname": "bioimageio.core.PredictionPipeline.load", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.load", "kind": "function", "doc": "optional step: load model onto devices before calling forward if not using it as context manager
\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.PredictionPipeline.unload": {"fullname": "bioimageio.core.PredictionPipeline.unload", "modulename": "bioimageio.core", "qualname": "PredictionPipeline.unload", "kind": "function", "doc": "free any device memory in use
\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.Sample": {"fullname": "bioimageio.core.Sample", "modulename": "bioimageio.core", "qualname": "Sample", "kind": "class", "doc": "A dataset sample
\n"}, "bioimageio.core.Sample.__init__": {"fullname": "bioimageio.core.Sample.__init__", "modulename": "bioimageio.core", "qualname": "Sample.__init__", "kind": "function", "doc": "\n", "signature": "(\tmembers: Dict[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.tensor.Tensor],\tstat: Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer>, return_type=PydanticUndefined, when_used='always')]]],\tid: Hashable)"}, "bioimageio.core.Sample.members": {"fullname": "bioimageio.core.Sample.members", "modulename": "bioimageio.core", "qualname": "Sample.members", "kind": "variable", "doc": "the sample's tensors
\n", "annotation": ": Dict[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.tensor.Tensor]"}, "bioimageio.core.Sample.stat": {"fullname": "bioimageio.core.Sample.stat", "modulename": "bioimageio.core", "qualname": "Sample.stat", "kind": "variable", "doc": "sample and dataset statistics
\n", "annotation": ": Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]"}, "bioimageio.core.Sample.id": {"fullname": "bioimageio.core.Sample.id", "modulename": "bioimageio.core", "qualname": "Sample.id", "kind": "variable", "doc": "identifier within the sample's dataset
\n", "annotation": ": Hashable"}, "bioimageio.core.Sample.shape": {"fullname": "bioimageio.core.Sample.shape", "modulename": "bioimageio.core", "qualname": "Sample.shape", "kind": "variable", "doc": "\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]"}, "bioimageio.core.Sample.split_into_blocks": {"fullname": "bioimageio.core.Sample.split_into_blocks", "modulename": "bioimageio.core", "qualname": "Sample.split_into_blocks", "kind": "function", "doc": "\n", "signature": "(\tself,\tblock_shapes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\thalo: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, Union[int, Tuple[int, int], bioimageio.core.common.Halo]]],\tpad_mode: Literal['edge', 'reflect', 'symmetric'],\tbroadcast: bool = False) -> Tuple[int, Iterable[bioimageio.core.sample.SampleBlockWithOrigin]]:", "funcdef": "def"}, "bioimageio.core.Sample.as_single_block": {"fullname": "bioimageio.core.Sample.as_single_block", "modulename": "bioimageio.core", "qualname": "Sample.as_single_block", "kind": "function", "doc": "\n", "signature": "(\tself,\thalo: Optional[Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.Halo]]] = None):", "funcdef": "def"}, "bioimageio.core.Sample.from_blocks": {"fullname": "bioimageio.core.Sample.from_blocks", "modulename": "bioimageio.core", "qualname": "Sample.from_blocks", "kind": "function", "doc": "\n", "signature": "(\tcls,\tsample_blocks: Iterable[bioimageio.core.sample.SampleBlock],\t*,\tfill_value: float = nan) -> Self:", "funcdef": "def"}, "bioimageio.core.save_bioimageio_package_as_folder": {"fullname": "bioimageio.core.save_bioimageio_package_as_folder", "modulename": "bioimageio.core", "qualname": "save_bioimageio_package_as_folder", "kind": "function", "doc": "Write the content of a bioimage.io resource package to a folder.
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], Dict[str, YamlValue], Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\t/,\t*,\toutput_path: Union[Annotated[pathlib.Path, PathType(path_type='new')], Annotated[pathlib.Path, PathType(path_type='dir')], NoneType] = None,\tweights_priority_order: Optional[Sequence[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]] = None) -> Annotated[pathlib.Path, PathType(path_type='dir')]:", "funcdef": "def"}, "bioimageio.core.save_bioimageio_package": {"fullname": "bioimageio.core.save_bioimageio_package", "modulename": "bioimageio.core", "qualname": "save_bioimageio_package", "kind": "function", "doc": "directory path to bioimageio package folder
\n
Package a bioimageio resource as a zip file.
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], Dict[str, YamlValue], Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\t/,\t*,\tcompression: int = 8,\tcompression_level: int = 1,\toutput_path: Union[Annotated[pathlib.Path, PathType(path_type='new')], Annotated[pathlib.Path, PathType(path_type='file')], NoneType] = None,\tweights_priority_order: Optional[Sequence[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]] = None) -> Annotated[pathlib.Path, PathType(path_type='file')]:", "funcdef": "def"}, "bioimageio.core.save_bioimageio_yaml_only": {"fullname": "bioimageio.core.save_bioimageio_yaml_only", "modulename": "bioimageio.core", "qualname": "save_bioimageio_yaml_only", "kind": "function", "doc": "path to zipped bioimageio package
\n
write the metadata of a resource description (rd
) to file
\nwithout writing any of the referenced files in it.
Note: To save a resource description with its associated files as a package,\nuse save_bioimageio_package
or save_bioimageio_package_as_folder
.
A wrapper around an xr.DataArray for better integration with bioimageio.spec\nand improved type annotations.
\n", "bases": "bioimageio.core._magic_tensor_ops.MagicTensorOpsMixin"}, "bioimageio.core.Tensor.__init__": {"fullname": "bioimageio.core.Tensor.__init__", "modulename": "bioimageio.core", "qualname": "Tensor.__init__", "kind": "function", "doc": "\n", "signature": "(\tarray: numpy.ndarray[typing.Any, numpy.dtype[typing.Any]],\tdims: Sequence[Union[bioimageio.spec.model.v0_5.AxisId, Literal['b', 'i', 't', 'c', 'z', 'y', 'x'], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexInputAxis, bioimageio.spec.model.v0_5.TimeInputAxis, bioimageio.spec.model.v0_5.SpaceInputAxis], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexOutputAxis, Annotated[Union[Annotated[bioimageio.spec.model.v0_5.TimeOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.core.axis.Axis]])"}, "bioimageio.core.Tensor.from_xarray": {"fullname": "bioimageio.core.Tensor.from_xarray", "modulename": "bioimageio.core", "qualname": "Tensor.from_xarray", "kind": "function", "doc": "create a Tensor
from an xarray data array
note for internal use: this factory method is round-trip save\n for any Tensor
's data
property (an xarray.DataArray).
create a Tensor
from a numpy array
axes
is None and axes guessing fails.Tuple of dimension names associated with this tensor.
\n"}, "bioimageio.core.Tensor.tagged_shape": {"fullname": "bioimageio.core.Tensor.tagged_shape", "modulename": "bioimageio.core", "qualname": "Tensor.tagged_shape", "kind": "variable", "doc": "(alias for sizes
) Ordered, immutable mapping from axis ids to lengths.
Tuple of tensor axes lengths
\n"}, "bioimageio.core.Tensor.size": {"fullname": "bioimageio.core.Tensor.size", "modulename": "bioimageio.core", "qualname": "Tensor.size", "kind": "variable", "doc": "Number of elements in the tensor.
\n\nEqual to math.prod(tensor.shape), i.e., the product of the tensors\u2019 dimensions.
\n"}, "bioimageio.core.Tensor.sum": {"fullname": "bioimageio.core.Tensor.sum", "modulename": "bioimageio.core", "qualname": "Tensor.sum", "kind": "function", "doc": "Reduce this Tensor's data by applying sum along some dimension(s).
\n", "signature": "(\tself,\tdim: Union[bioimageio.spec.model.v0_5.AxisId, Sequence[bioimageio.spec.model.v0_5.AxisId], NoneType] = None) -> Self:", "funcdef": "def"}, "bioimageio.core.Tensor.ndim": {"fullname": "bioimageio.core.Tensor.ndim", "modulename": "bioimageio.core", "qualname": "Tensor.ndim", "kind": "variable", "doc": "Number of tensor dimensions.
\n"}, "bioimageio.core.Tensor.dtype": {"fullname": "bioimageio.core.Tensor.dtype", "modulename": "bioimageio.core", "qualname": "Tensor.dtype", "kind": "variable", "doc": "\n", "annotation": ": Literal['bool', 'float32', 'float64', 'int8', 'int16', 'int32', 'int64', 'uint8', 'uint16', 'uint32', 'uint64']"}, "bioimageio.core.Tensor.sizes": {"fullname": "bioimageio.core.Tensor.sizes", "modulename": "bioimageio.core", "qualname": "Tensor.sizes", "kind": "variable", "doc": "Ordered, immutable mapping from axis ids to axis lengths.
\n"}, "bioimageio.core.Tensor.astype": {"fullname": "bioimageio.core.Tensor.astype", "modulename": "bioimageio.core", "qualname": "Tensor.astype", "kind": "function", "doc": "Return tensor cast to dtype
note: if dtype is already satisfied copy if copy
Return a tensor whose values are limited to [min, max].\nAt least one of max or min must be given.
\n", "signature": "(self, min: Optional[float] = None, max: Optional[float] = None):", "funcdef": "def"}, "bioimageio.core.Tensor.crop_to": {"fullname": "bioimageio.core.Tensor.crop_to", "modulename": "bioimageio.core", "qualname": "Tensor.crop_to", "kind": "function", "doc": "crop to match sizes
pad tensor
to match sizes
return cropped/padded tensor with sizes
return a transposed tensor
\n\nTest a bioimage.io resource dynamically, e.g. prediction of test tensors for models
\n", "signature": "(\tsource: Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], Dict[str, YamlValue]],\t*,\tformat_version: Union[Literal['discover', 'latest'], str] = 'discover',\tweight_format: Optional[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']] = None,\tdevices: Optional[Sequence[str]] = None,\tabsolute_tolerance: float = 0.00015,\trelative_tolerance: float = 0.0001,\tdecimal: Optional[int] = None,\tdeterminism: Literal['seed_only', 'full'] = 'seed_only',\texpected_type: Optional[str] = None) -> bioimageio.spec.summary.ValidationSummary:", "funcdef": "def"}, "bioimageio.core.test_model": {"fullname": "bioimageio.core.test_model", "modulename": "bioimageio.core", "qualname": "test_model", "kind": "function", "doc": "Test model inference
\n", "signature": "(\tsource: Union[bioimageio.spec.model.v0_5.ModelDescr, Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)]],\tweight_format: Optional[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']] = None,\tdevices: Optional[List[str]] = None,\tabsolute_tolerance: float = 0.00015,\trelative_tolerance: float = 0.0001,\tdecimal: Optional[int] = None,\t*,\tdeterminism: Literal['seed_only', 'full'] = 'seed_only') -> bioimageio.spec.summary.ValidationSummary:", "funcdef": "def"}, "bioimageio.core.test_resource": {"fullname": "bioimageio.core.test_resource", "modulename": "bioimageio.core", "qualname": "test_resource", "kind": "function", "doc": "alias of test_description
validate a bioimageio.yaml file (RDF)
\n", "signature": "(\tdata: Dict[str, YamlValue],\t/,\t*,\tformat_version: Union[Literal['latest', 'discover'], str] = 'discover',\tcontext: Optional[bioimageio.spec._internal.validation_context.ValidationContext] = None) -> bioimageio.spec.summary.ValidationSummary:", "funcdef": "def"}, "bioimageio.core.axis": {"fullname": "bioimageio.core.axis", "modulename": "bioimageio.core.axis", "kind": "module", "doc": "\n"}, "bioimageio.core.axis.AxisId": {"fullname": "bioimageio.core.axis.AxisId", "modulename": "bioimageio.core.axis", "qualname": "AxisId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec._internal.types.LowerCaseIdentifier"}, "bioimageio.core.axis.AxisId.root_model": {"fullname": "bioimageio.core.axis.AxisId.root_model", "modulename": "bioimageio.core.axis", "qualname": "AxisId.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[str, MinLen, AfterValidator, AfterValidator, Annotated[TypeVar, Predicate], MaxLen]]'>"}, "bioimageio.core.axis.PerAxis": {"fullname": "bioimageio.core.axis.PerAxis", "modulename": "bioimageio.core.axis", "qualname": "PerAxis", "kind": "variable", "doc": "\n", "default_value": "typing.Mapping[bioimageio.spec.model.v0_5.AxisId, ~T]"}, "bioimageio.core.axis.BatchSize": {"fullname": "bioimageio.core.axis.BatchSize", "modulename": "bioimageio.core.axis", "qualname": "BatchSize", "kind": "variable", "doc": "\n", "default_value": "<class 'int'>"}, "bioimageio.core.axis.AxisLetter": {"fullname": "bioimageio.core.axis.AxisLetter", "modulename": "bioimageio.core.axis", "qualname": "AxisLetter", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['b', 'i', 't', 'c', 'z', 'y', 'x']"}, "bioimageio.core.axis.AxisLike": {"fullname": "bioimageio.core.axis.AxisLike", "modulename": "bioimageio.core.axis", "qualname": "AxisLike", "kind": "variable", "doc": "\n", "default_value": "typing.Union[bioimageio.spec.model.v0_5.AxisId, typing.Literal['b', 'i', 't', 'c', 'z', 'y', 'x'], typing.Annotated[typing.Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexInputAxis, bioimageio.spec.model.v0_5.TimeInputAxis, bioimageio.spec.model.v0_5.SpaceInputAxis], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexOutputAxis, typing.Annotated[typing.Union[typing.Annotated[bioimageio.spec.model.v0_5.TimeOutputAxis, Tag(tag='wo_halo')], typing.Annotated[bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[typing.Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxis, Tag(tag='wo_halo')], typing.Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], ForwardRef('Axis')]"}, "bioimageio.core.axis.Axis": {"fullname": "bioimageio.core.axis.Axis", "modulename": "bioimageio.core.axis", "qualname": "Axis", "kind": "class", "doc": "\n"}, "bioimageio.core.axis.Axis.__init__": {"fullname": "bioimageio.core.axis.Axis.__init__", "modulename": "bioimageio.core.axis", "qualname": "Axis.__init__", "kind": "function", "doc": "\n", "signature": "(\tid: bioimageio.spec.model.v0_5.AxisId,\ttype: Literal['batch', 'channel', 'index', 'space', 'time'])"}, "bioimageio.core.axis.Axis.id": {"fullname": "bioimageio.core.axis.Axis.id", "modulename": "bioimageio.core.axis", "qualname": "Axis.id", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_5.AxisId"}, "bioimageio.core.axis.Axis.type": {"fullname": "bioimageio.core.axis.Axis.type", "modulename": "bioimageio.core.axis", "qualname": "Axis.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['batch', 'channel', 'index', 'space', 'time']"}, "bioimageio.core.axis.Axis.create": {"fullname": "bioimageio.core.axis.Axis.create", "modulename": "bioimageio.core.axis", "qualname": "Axis.create", "kind": "function", "doc": "\n", "signature": "(\tcls,\taxis: Union[bioimageio.spec.model.v0_5.AxisId, Literal['b', 'i', 't', 'c', 'z', 'y', 'x'], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexInputAxis, bioimageio.spec.model.v0_5.TimeInputAxis, bioimageio.spec.model.v0_5.SpaceInputAxis], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexOutputAxis, Annotated[Union[Annotated[bioimageio.spec.model.v0_5.TimeOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.core.axis.Axis]) -> bioimageio.core.axis.Axis:", "funcdef": "def"}, "bioimageio.core.axis.AxisInfo": {"fullname": "bioimageio.core.axis.AxisInfo", "modulename": "bioimageio.core.axis", "qualname": "AxisInfo", "kind": "class", "doc": "\n", "bases": "Axis"}, "bioimageio.core.axis.AxisInfo.__init__": {"fullname": "bioimageio.core.axis.AxisInfo.__init__", "modulename": "bioimageio.core.axis", "qualname": "AxisInfo.__init__", "kind": "function", "doc": "\n", "signature": "(\tid: bioimageio.spec.model.v0_5.AxisId,\ttype: Literal['batch', 'channel', 'index', 'space', 'time'],\tmaybe_singleton: bool)"}, "bioimageio.core.axis.AxisInfo.maybe_singleton": {"fullname": "bioimageio.core.axis.AxisInfo.maybe_singleton", "modulename": "bioimageio.core.axis", "qualname": "AxisInfo.maybe_singleton", "kind": "variable", "doc": "\n", "annotation": ": bool"}, "bioimageio.core.axis.AxisInfo.create": {"fullname": "bioimageio.core.axis.AxisInfo.create", "modulename": "bioimageio.core.axis", "qualname": "AxisInfo.create", "kind": "function", "doc": "\n", "signature": "(\tcls,\taxis: Union[bioimageio.spec.model.v0_5.AxisId, Literal['b', 'i', 't', 'c', 'z', 'y', 'x'], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexInputAxis, bioimageio.spec.model.v0_5.TimeInputAxis, bioimageio.spec.model.v0_5.SpaceInputAxis], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexOutputAxis, Annotated[Union[Annotated[bioimageio.spec.model.v0_5.TimeOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.core.axis.Axis],\tmaybe_singleton: Optional[bool] = None) -> bioimageio.core.axis.AxisInfo:", "funcdef": "def"}, "bioimageio.core.block_meta": {"fullname": "bioimageio.core.block_meta", "modulename": "bioimageio.core.block_meta", "kind": "module", "doc": "\n"}, "bioimageio.core.block_meta.LinearAxisTransform": {"fullname": "bioimageio.core.block_meta.LinearAxisTransform", "modulename": "bioimageio.core.block_meta", "qualname": "LinearAxisTransform", "kind": "class", "doc": "\n"}, "bioimageio.core.block_meta.LinearAxisTransform.__init__": {"fullname": "bioimageio.core.block_meta.LinearAxisTransform.__init__", "modulename": "bioimageio.core.block_meta", "qualname": "LinearAxisTransform.__init__", "kind": "function", "doc": "\n", "signature": "(axis: bioimageio.spec.model.v0_5.AxisId, scale: float, offset: int)"}, "bioimageio.core.block_meta.LinearAxisTransform.axis": {"fullname": "bioimageio.core.block_meta.LinearAxisTransform.axis", "modulename": "bioimageio.core.block_meta", "qualname": "LinearAxisTransform.axis", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_5.AxisId"}, "bioimageio.core.block_meta.LinearAxisTransform.scale": {"fullname": "bioimageio.core.block_meta.LinearAxisTransform.scale", "modulename": "bioimageio.core.block_meta", "qualname": "LinearAxisTransform.scale", "kind": "variable", "doc": "\n", "annotation": ": float"}, "bioimageio.core.block_meta.LinearAxisTransform.offset": {"fullname": "bioimageio.core.block_meta.LinearAxisTransform.offset", "modulename": "bioimageio.core.block_meta", "qualname": "LinearAxisTransform.offset", "kind": "variable", "doc": "\n", "annotation": ": int"}, "bioimageio.core.block_meta.LinearAxisTransform.compute": {"fullname": "bioimageio.core.block_meta.LinearAxisTransform.compute", "modulename": "bioimageio.core.block_meta", "qualname": "LinearAxisTransform.compute", "kind": "function", "doc": "\n", "signature": "(\tself,\ts: int,\tround: Callable[[float], int] = <built-in function floor>) -> int:", "funcdef": "def"}, "bioimageio.core.block_meta.BlockMeta": {"fullname": "bioimageio.core.block_meta.BlockMeta", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta", "kind": "class", "doc": "Block meta data of a sample member (a tensor in a sample)
\n\nFigure for illustration:\nThe first 2d block (dashed) of a sample member (bold).\nThe inner slice (thin) is expanded by a halo in both dimensions on both sides.\nThe outer slice reaches from the sample member origin (0, 0) to the right halo point.
\n\n\u250c \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2510\n\u2577 halo(left) \u2577\n\u2577 \u2577\n\u2577 (0, 0)\u250f\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u252f\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u252f\u2501\u2501\u2501\u2794\n\u2577 \u2503 \u2502 \u2577 sample member\n\u2577 \u2503 inner \u2502 \u2577\n\u2577 \u2503 (and outer) \u2502 outer \u2577\n\u2577 \u2503 slice \u2502 slice \u2577\n\u2577 \u2503 \u2502 \u2577\n\u2577 \u2523\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518 \u2577\n\u2577 \u2503 outer slice \u2577\n\u2577 \u2503 halo(right) \u2577\n\u2514 \u2500 \u2500 \u2500 \u2500\u2503\u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500 \u2500\u2518\n \u2b07\n
\n\nnote:
\n\nthe axis sizes of the whole (unblocked) sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.block_meta.BlockMeta.inner_slice": {"fullname": "bioimageio.core.block_meta.BlockMeta.inner_slice", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.inner_slice", "kind": "variable", "doc": "inner region (without halo) wrt the sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.SliceInfo]"}, "bioimageio.core.block_meta.BlockMeta.halo": {"fullname": "bioimageio.core.block_meta.BlockMeta.halo", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.halo", "kind": "variable", "doc": "halo enlarging the inner region to the block's sizes
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.Halo]"}, "bioimageio.core.block_meta.BlockMeta.block_index": {"fullname": "bioimageio.core.block_meta.BlockMeta.block_index", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.block_index", "kind": "variable", "doc": "the i-th block of the sample
\n", "annotation": ": int"}, "bioimageio.core.block_meta.BlockMeta.blocks_in_sample": {"fullname": "bioimageio.core.block_meta.BlockMeta.blocks_in_sample", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.blocks_in_sample", "kind": "variable", "doc": "total number of blocks in the sample
\n", "annotation": ": int"}, "bioimageio.core.block_meta.BlockMeta.shape": {"fullname": "bioimageio.core.block_meta.BlockMeta.shape", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.shape", "kind": "variable", "doc": "axis lengths of the block
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.block_meta.BlockMeta.padding": {"fullname": "bioimageio.core.block_meta.BlockMeta.padding", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.padding", "kind": "variable", "doc": "padding to realize the halo at the sample edge\nwhere we cannot simply enlarge the inner slice
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.PadWidth]"}, "bioimageio.core.block_meta.BlockMeta.outer_slice": {"fullname": "bioimageio.core.block_meta.BlockMeta.outer_slice", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.outer_slice", "kind": "variable", "doc": "slice of the outer block (without padding) wrt the sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.SliceInfo]"}, "bioimageio.core.block_meta.BlockMeta.inner_shape": {"fullname": "bioimageio.core.block_meta.BlockMeta.inner_shape", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.inner_shape", "kind": "variable", "doc": "axis lengths of the inner region (without halo)
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.block_meta.BlockMeta.local_slice": {"fullname": "bioimageio.core.block_meta.BlockMeta.local_slice", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.local_slice", "kind": "variable", "doc": "inner slice wrt the block, not the sample
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.SliceInfo]"}, "bioimageio.core.block_meta.BlockMeta.dims": {"fullname": "bioimageio.core.block_meta.BlockMeta.dims", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.dims", "kind": "variable", "doc": "\n", "annotation": ": Collection[bioimageio.spec.model.v0_5.AxisId]"}, "bioimageio.core.block_meta.BlockMeta.tagged_shape": {"fullname": "bioimageio.core.block_meta.BlockMeta.tagged_shape", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.tagged_shape", "kind": "variable", "doc": "alias for shape
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.AxisId, int]"}, "bioimageio.core.block_meta.BlockMeta.inner_slice_wo_overlap": {"fullname": "bioimageio.core.block_meta.BlockMeta.inner_slice_wo_overlap", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.inner_slice_wo_overlap", "kind": "variable", "doc": "subslice of the inner slice, such that all inner_slice_wo_overlap
can be\nstiched together trivially to form the original sample.
This can also be used to calculate statistics\nwithout overrepresenting block edge regions.
\n"}, "bioimageio.core.block_meta.BlockMeta.get_transformed": {"fullname": "bioimageio.core.block_meta.BlockMeta.get_transformed", "modulename": "bioimageio.core.block_meta", "qualname": "BlockMeta.get_transformed", "kind": "function", "doc": "\n", "signature": "(\tself,\tnew_axes: Mapping[bioimageio.spec.model.v0_5.AxisId, Union[bioimageio.core.block_meta.LinearAxisTransform, int]]) -> Self:", "funcdef": "def"}, "bioimageio.core.block_meta.split_shape_into_blocks": {"fullname": "bioimageio.core.block_meta.split_shape_into_blocks", "modulename": "bioimageio.core.block_meta", "qualname": "split_shape_into_blocks", "kind": "function", "doc": "\n", "signature": "(\tshape: Mapping[bioimageio.spec.model.v0_5.AxisId, int],\tblock_shape: Mapping[bioimageio.spec.model.v0_5.AxisId, int],\thalo: Mapping[bioimageio.spec.model.v0_5.AxisId, Union[int, Tuple[int, int], bioimageio.core.common.Halo]],\tstride: Optional[Mapping[bioimageio.spec.model.v0_5.AxisId, int]] = None) -> Tuple[int, Generator[bioimageio.core.block_meta.BlockMeta, Any, NoneType]]:", "funcdef": "def"}, "bioimageio.core.block_meta.split_multiple_shapes_into_blocks": {"fullname": "bioimageio.core.block_meta.split_multiple_shapes_into_blocks", "modulename": "bioimageio.core.block_meta", "qualname": "split_multiple_shapes_into_blocks", "kind": "function", "doc": "\n", "signature": "(\tshapes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\tblock_shapes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\t*,\thalo: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, Union[int, Tuple[int, int], bioimageio.core.common.Halo]]],\tstrides: Optional[Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]] = None,\tbroadcast: bool = False) -> Tuple[int, Iterable[Mapping[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.block_meta.BlockMeta]]]:", "funcdef": "def"}, "bioimageio.core.cli": {"fullname": "bioimageio.core.cli", "modulename": "bioimageio.core.cli", "kind": "module", "doc": "bioimageio CLI
\n\nNote: Some docstrings use a hair space '\u200a'\n to place the added '(default: ...)' on a new line.
\n"}, "bioimageio.core.cli.yaml": {"fullname": "bioimageio.core.cli.yaml", "modulename": "bioimageio.core.cli", "qualname": "yaml", "kind": "variable", "doc": "\n", "default_value": "<ruyaml.main.YAML object>"}, "bioimageio.core.cli.CmdBase": {"fullname": "bioimageio.core.cli.CmdBase", "modulename": "bioimageio.core.cli", "qualname": "CmdBase", "kind": "class", "doc": "Usage docs: https://docs.pydantic.dev/2.9/concepts/models/
\n\nA base class for creating Pydantic models.
\n\n__init__
[Signature
][inspect.Signature] of the model.__init__
function.Model.__validators__
and Model.__root_validators__
from Pydantic V1.RootModel
][pydantic.root_model.RootModel].pydantic-core
SchemaSerializer
used to dump instances of the model.pydantic-core
SchemaValidator
used to validate instances of the model.extra
][pydantic.config.ConfigDict.extra]\nis set to 'allow'
.Usage docs: https://docs.pydantic.dev/2.9/concepts/models/
\n\nA base class for creating Pydantic models.
\n\n__init__
[Signature
][inspect.Signature] of the model.__init__
function.Model.__validators__
and Model.__root_validators__
from Pydantic V1.RootModel
][pydantic.root_model.RootModel].pydantic-core
SchemaSerializer
used to dump instances of the model.pydantic-core
SchemaValidator
used to validate instances of the model.extra
][pydantic.config.ConfigDict.extra]\nis set to 'allow'
.Usage docs: https://docs.pydantic.dev/2.9/concepts/models/
\n\nA base class for creating Pydantic models.
\n\n__init__
[Signature
][inspect.Signature] of the model.__init__
function.Model.__validators__
and Model.__root_validators__
from Pydantic V1.RootModel
][pydantic.root_model.RootModel].pydantic-core
SchemaSerializer
used to dump instances of the model.pydantic-core
SchemaValidator
used to validate instances of the model.extra
][pydantic.config.ConfigDict.extra]\nis set to 'allow'
.Url/path to a bioimageio.yaml/rdf.yaml file\nor a bioimage.io resource identifier, e.g. 'affable-shark'
\n", "annotation": ": Annotated[str, <class 'pydantic_settings.sources._CliPositionalArg'>]"}, "bioimageio.core.cli.WithSource.descr": {"fullname": "bioimageio.core.cli.WithSource.descr", "modulename": "bioimageio.core.cli", "qualname": "WithSource.descr", "kind": "variable", "doc": "\n"}, "bioimageio.core.cli.WithSource.descr_id": {"fullname": "bioimageio.core.cli.WithSource.descr_id", "modulename": "bioimageio.core.cli", "qualname": "WithSource.descr_id", "kind": "variable", "doc": "a more user-friendly description id\n(replacing legacy ids with their nicknames)
\n", "annotation": ": str"}, "bioimageio.core.cli.ValidateFormatCmd": {"fullname": "bioimageio.core.cli.ValidateFormatCmd", "modulename": "bioimageio.core.cli", "qualname": "ValidateFormatCmd", "kind": "class", "doc": "validate the meta data format of a bioimageio resource.
\n", "bases": "CmdBase, WithSource"}, "bioimageio.core.cli.ValidateFormatCmd.run": {"fullname": "bioimageio.core.cli.ValidateFormatCmd.run", "modulename": "bioimageio.core.cli", "qualname": "ValidateFormatCmd.run", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.cli.TestCmd": {"fullname": "bioimageio.core.cli.TestCmd", "modulename": "bioimageio.core.cli", "qualname": "TestCmd", "kind": "class", "doc": "Test a bioimageio resource (beyond meta data formatting)
\n", "bases": "CmdBase, WithSource"}, "bioimageio.core.cli.TestCmd.weight_format": {"fullname": "bioimageio.core.cli.TestCmd.weight_format", "modulename": "bioimageio.core.cli", "qualname": "TestCmd.weight_format", "kind": "variable", "doc": "The weight format to limit testing to.
\n\n(only relevant for model resources)
\n", "annotation": ": Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript', 'all']"}, "bioimageio.core.cli.TestCmd.devices": {"fullname": "bioimageio.core.cli.TestCmd.devices", "modulename": "bioimageio.core.cli", "qualname": "TestCmd.devices", "kind": "variable", "doc": "Device(s) to use for testing
\n", "annotation": ": Union[str, Sequence[str], NoneType]"}, "bioimageio.core.cli.TestCmd.decimal": {"fullname": "bioimageio.core.cli.TestCmd.decimal", "modulename": "bioimageio.core.cli", "qualname": "TestCmd.decimal", "kind": "variable", "doc": "Precision for numerical comparisons
\n", "annotation": ": int"}, "bioimageio.core.cli.TestCmd.run": {"fullname": "bioimageio.core.cli.TestCmd.run", "modulename": "bioimageio.core.cli", "qualname": "TestCmd.run", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.cli.PackageCmd": {"fullname": "bioimageio.core.cli.PackageCmd", "modulename": "bioimageio.core.cli", "qualname": "PackageCmd", "kind": "class", "doc": "save a resource's metadata with its associated files.
\n", "bases": "CmdBase, WithSource"}, "bioimageio.core.cli.PackageCmd.path": {"fullname": "bioimageio.core.cli.PackageCmd.path", "modulename": "bioimageio.core.cli", "qualname": "PackageCmd.path", "kind": "variable", "doc": "The path to write the (zipped) package to.\nIf it does not have a .zip
suffix\nthis command will save the package as an unzipped folder instead.
The weight format to include in the package (for model descriptions only).
\n", "annotation": ": Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript', 'all']"}, "bioimageio.core.cli.PackageCmd.run": {"fullname": "bioimageio.core.cli.PackageCmd.run", "modulename": "bioimageio.core.cli", "qualname": "PackageCmd.run", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.cli.PredictCmd": {"fullname": "bioimageio.core.cli.PredictCmd", "modulename": "bioimageio.core.cli", "qualname": "PredictCmd", "kind": "class", "doc": "Run inference on your data with a bioimage.io model.
\n", "bases": "CmdBase, WithSource"}, "bioimageio.core.cli.PredictCmd.inputs": {"fullname": "bioimageio.core.cli.PredictCmd.inputs", "modulename": "bioimageio.core.cli", "qualname": "PredictCmd.inputs", "kind": "variable", "doc": "Model input sample paths (for each input tensor)
\n\nThe input paths are expected to have shape...
\n\nAll substrings that are replaced by metadata from the model description:
\n\nExample inputs to process sample 'a' and 'b'\nfor a model expecting a 'raw' and a 'mask' input tensor:\n--inputs=\"[[\"a_raw.tif\",\"a_mask.tif\"],[\"b_raw.tif\",\"b_mask.tif\"]]\"\n(Note that JSON double quotes need to be escaped.)
\n\nAlternatively a bioimageio-cli.yaml
(or bioimageio-cli.json
) file\nmay provide the arguments, e.g.:
inputs:\n- [a_raw.tif, a_mask.tif]\n- [b_raw.tif, b_mask.tif]\n
\n.npy
and any file extension supported by imageio are supported.\n Aavailable formats are listed at\nhttps://imageio.readthedocs.io/en/stable/formats/index.html#all-formats.\nSome formats have additional dependencies.
Model output path pattern (per output tensor)
\n\nAll substrings that are replaced:
\n\nallow overwriting existing output files
\n", "annotation": ": bool"}, "bioimageio.core.cli.PredictCmd.blockwise": {"fullname": "bioimageio.core.cli.PredictCmd.blockwise", "modulename": "bioimageio.core.cli", "qualname": "PredictCmd.blockwise", "kind": "variable", "doc": "process inputs blockwise
\n", "annotation": ": bool"}, "bioimageio.core.cli.PredictCmd.stats": {"fullname": "bioimageio.core.cli.PredictCmd.stats", "modulename": "bioimageio.core.cli", "qualname": "PredictCmd.stats", "kind": "variable", "doc": "path to dataset statistics\n(will be written if it does not exist,\nbut the model requires statistical dataset measures)
\n", "annotation": ": pathlib.Path"}, "bioimageio.core.cli.PredictCmd.preview": {"fullname": "bioimageio.core.cli.PredictCmd.preview", "modulename": "bioimageio.core.cli", "qualname": "PredictCmd.preview", "kind": "variable", "doc": "preview which files would be processed\nand what outputs would be generated.
\n", "annotation": ": bool"}, "bioimageio.core.cli.PredictCmd.weight_format": {"fullname": "bioimageio.core.cli.PredictCmd.weight_format", "modulename": "bioimageio.core.cli", "qualname": "PredictCmd.weight_format", "kind": "variable", "doc": "The weight format to use.
\n", "annotation": ": Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript', 'any']"}, "bioimageio.core.cli.PredictCmd.example": {"fullname": "bioimageio.core.cli.PredictCmd.example", "modulename": "bioimageio.core.cli", "qualname": "PredictCmd.example", "kind": "variable", "doc": "generate and run an example
\n\n{model_id}_example
folder{model_id}_example/bioimageio-cli.yaml
bioimageio - CLI for bioimage.io resources \ud83e\udd92
\n\nlibrary versions:\n bioimageio.core 0.7.0\n bioimageio.spec 0.7.0
\n\nspec format versions:\n model RDF 0.5.3\n dataset RDF 0.3.0\n notebook RDF 0.3.0
\n", "bases": "pydantic_settings.main.BaseSettings"}, "bioimageio.core.cli.Bioimageio.validate_format": {"fullname": "bioimageio.core.cli.Bioimageio.validate_format", "modulename": "bioimageio.core.cli", "qualname": "Bioimageio.validate_format", "kind": "variable", "doc": "Check a resource's metadata format
\n", "annotation": ": Annotated[Optional[bioimageio.core.cli.ValidateFormatCmd], <class 'pydantic_settings.sources._CliSubCommand'>]"}, "bioimageio.core.cli.Bioimageio.test": {"fullname": "bioimageio.core.cli.Bioimageio.test", "modulename": "bioimageio.core.cli", "qualname": "Bioimageio.test", "kind": "variable", "doc": "Test a bioimageio resource (beyond meta data formatting)
\n", "annotation": ": Annotated[Optional[bioimageio.core.cli.TestCmd], <class 'pydantic_settings.sources._CliSubCommand'>]"}, "bioimageio.core.cli.Bioimageio.package": {"fullname": "bioimageio.core.cli.Bioimageio.package", "modulename": "bioimageio.core.cli", "qualname": "Bioimageio.package", "kind": "variable", "doc": "Package a resource
\n", "annotation": ": Annotated[Optional[bioimageio.core.cli.PackageCmd], <class 'pydantic_settings.sources._CliSubCommand'>]"}, "bioimageio.core.cli.Bioimageio.predict": {"fullname": "bioimageio.core.cli.Bioimageio.predict", "modulename": "bioimageio.core.cli", "qualname": "Bioimageio.predict", "kind": "variable", "doc": "Predict with a model resource
\n", "annotation": ": Annotated[Optional[bioimageio.core.cli.PredictCmd], <class 'pydantic_settings.sources._CliSubCommand'>]"}, "bioimageio.core.cli.Bioimageio.settings_customise_sources": {"fullname": "bioimageio.core.cli.Bioimageio.settings_customise_sources", "modulename": "bioimageio.core.cli", "qualname": "Bioimageio.settings_customise_sources", "kind": "function", "doc": "Define the sources and their order for loading the settings values.
\n\nInitSettingsSource
instance.EnvSettingsSource
instance.DotEnvSettingsSource
instance.SecretsSettingsSource
instance.\n\n", "signature": "(\tcls,\tsettings_cls: Type[pydantic_settings.main.BaseSettings],\tinit_settings: pydantic_settings.sources.PydanticBaseSettingsSource,\tenv_settings: pydantic_settings.sources.PydanticBaseSettingsSource,\tdotenv_settings: pydantic_settings.sources.PydanticBaseSettingsSource,\tfile_secret_settings: pydantic_settings.sources.PydanticBaseSettingsSource) -> Tuple[pydantic_settings.sources.PydanticBaseSettingsSource, ...]:", "funcdef": "def"}, "bioimageio.core.cli.Bioimageio.run": {"fullname": "bioimageio.core.cli.Bioimageio.run", "modulename": "bioimageio.core.cli", "qualname": "Bioimageio.run", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.commands": {"fullname": "bioimageio.core.commands", "modulename": "bioimageio.core.commands", "kind": "module", "doc": "A tuple containing the sources and their order for loading the settings values.
\n
These functions implement the logic of the bioimageio command line interface\ndefined in bioimageio.core.cli
.
test a bioimageio resource
\n\nvalidate the meta data format of a bioimageio resource
\n\nSave a resource's metadata with its associated files.
\n\nNote: If path
does not have a .zip
suffix this command will save the\n package as an unzipped folder instead.
_LeftRight(left, right)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.common.CropWidth.__init__": {"fullname": "bioimageio.core.common.CropWidth.__init__", "modulename": "bioimageio.core.common", "qualname": "CropWidth.__init__", "kind": "function", "doc": "Create new instance of _LeftRight(left, right)
\n", "signature": "(left: int, right: int)"}, "bioimageio.core.common.CropWidthLike": {"fullname": "bioimageio.core.common.CropWidthLike", "modulename": "bioimageio.core.common", "qualname": "CropWidthLike", "kind": "variable", "doc": "\n", "default_value": "typing.Union[int, typing.Tuple[int, int], bioimageio.core.common.CropWidth]"}, "bioimageio.core.common.CropWhere": {"fullname": "bioimageio.core.common.CropWhere", "modulename": "bioimageio.core.common", "qualname": "CropWhere", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['left', 'right', 'left_and_right']"}, "bioimageio.core.common.Halo": {"fullname": "bioimageio.core.common.Halo", "modulename": "bioimageio.core.common", "qualname": "Halo", "kind": "class", "doc": "_LeftRight(left, right)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.common.Halo.__init__": {"fullname": "bioimageio.core.common.Halo.__init__", "modulename": "bioimageio.core.common", "qualname": "Halo.__init__", "kind": "function", "doc": "Create new instance of _LeftRight(left, right)
\n", "signature": "(left: int, right: int)"}, "bioimageio.core.common.HaloLike": {"fullname": "bioimageio.core.common.HaloLike", "modulename": "bioimageio.core.common", "qualname": "HaloLike", "kind": "variable", "doc": "\n", "default_value": "typing.Union[int, typing.Tuple[int, int], bioimageio.core.common.Halo]"}, "bioimageio.core.common.OverlapWidth": {"fullname": "bioimageio.core.common.OverlapWidth", "modulename": "bioimageio.core.common", "qualname": "OverlapWidth", "kind": "class", "doc": "_LeftRight(left, right)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.common.OverlapWidth.__init__": {"fullname": "bioimageio.core.common.OverlapWidth.__init__", "modulename": "bioimageio.core.common", "qualname": "OverlapWidth.__init__", "kind": "function", "doc": "Create new instance of _LeftRight(left, right)
\n", "signature": "(left: int, right: int)"}, "bioimageio.core.common.PadWidth": {"fullname": "bioimageio.core.common.PadWidth", "modulename": "bioimageio.core.common", "qualname": "PadWidth", "kind": "class", "doc": "_LeftRight(left, right)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.common.PadWidth.__init__": {"fullname": "bioimageio.core.common.PadWidth.__init__", "modulename": "bioimageio.core.common", "qualname": "PadWidth.__init__", "kind": "function", "doc": "Create new instance of _LeftRight(left, right)
\n", "signature": "(left: int, right: int)"}, "bioimageio.core.common.PadWidthLike": {"fullname": "bioimageio.core.common.PadWidthLike", "modulename": "bioimageio.core.common", "qualname": "PadWidthLike", "kind": "variable", "doc": "\n", "default_value": "typing.Union[int, typing.Tuple[int, int], bioimageio.core.common.PadWidth]"}, "bioimageio.core.common.PadMode": {"fullname": "bioimageio.core.common.PadMode", "modulename": "bioimageio.core.common", "qualname": "PadMode", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['edge', 'reflect', 'symmetric']"}, "bioimageio.core.common.PadWhere": {"fullname": "bioimageio.core.common.PadWhere", "modulename": "bioimageio.core.common", "qualname": "PadWhere", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['left', 'right', 'left_and_right']"}, "bioimageio.core.common.SliceInfo": {"fullname": "bioimageio.core.common.SliceInfo", "modulename": "bioimageio.core.common", "qualname": "SliceInfo", "kind": "class", "doc": "SliceInfo(start, stop)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.common.SliceInfo.__init__": {"fullname": "bioimageio.core.common.SliceInfo.__init__", "modulename": "bioimageio.core.common", "qualname": "SliceInfo.__init__", "kind": "function", "doc": "Create new instance of SliceInfo(start, stop)
\n", "signature": "(start: int, stop: int)"}, "bioimageio.core.common.SliceInfo.start": {"fullname": "bioimageio.core.common.SliceInfo.start", "modulename": "bioimageio.core.common", "qualname": "SliceInfo.start", "kind": "variable", "doc": "Alias for field number 0
\n", "annotation": ": int"}, "bioimageio.core.common.SliceInfo.stop": {"fullname": "bioimageio.core.common.SliceInfo.stop", "modulename": "bioimageio.core.common", "qualname": "SliceInfo.stop", "kind": "variable", "doc": "Alias for field number 1
\n", "annotation": ": int"}, "bioimageio.core.common.SampleId": {"fullname": "bioimageio.core.common.SampleId", "modulename": "bioimageio.core.common", "qualname": "SampleId", "kind": "variable", "doc": "\n", "default_value": "typing.Hashable"}, "bioimageio.core.common.MemberId": {"fullname": "bioimageio.core.common.MemberId", "modulename": "bioimageio.core.common", "qualname": "MemberId", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.model.v0_5.TensorId'>"}, "bioimageio.core.common.PerMember": {"fullname": "bioimageio.core.common.PerMember", "modulename": "bioimageio.core.common", "qualname": "PerMember", "kind": "variable", "doc": "\n", "default_value": "typing.Mapping[bioimageio.spec.model.v0_5.TensorId, ~T]"}, "bioimageio.core.common.BlockIndex": {"fullname": "bioimageio.core.common.BlockIndex", "modulename": "bioimageio.core.common", "qualname": "BlockIndex", "kind": "variable", "doc": "\n", "default_value": "<class 'int'>"}, "bioimageio.core.common.TotalNumberOfBlocks": {"fullname": "bioimageio.core.common.TotalNumberOfBlocks", "modulename": "bioimageio.core.common", "qualname": "TotalNumberOfBlocks", "kind": "variable", "doc": "\n", "default_value": "<class 'int'>"}, "bioimageio.core.common.Frozen": {"fullname": "bioimageio.core.common.Frozen", "modulename": "bioimageio.core.common", "qualname": "Frozen", "kind": "variable", "doc": "\n", "default_value": "<class 'mappingproxy'>"}, "bioimageio.core.digest_spec": {"fullname": "bioimageio.core.digest_spec", "modulename": "bioimageio.core.digest_spec", "kind": "module", "doc": "\n"}, "bioimageio.core.digest_spec.import_callable": {"fullname": "bioimageio.core.digest_spec.import_callable", "modulename": "bioimageio.core.digest_spec", "qualname": "import_callable", "kind": "function", "doc": "import a callable (e.g. a torch.nn.Module) from a spec node describing it
\n", "signature": "(\tnode: Union[bioimageio.spec.model.v0_4.CallableFromDepencency, bioimageio.spec.model.v0_5.ArchitectureFromLibraryDescr],\t/,\t**kwargs: Unpack[bioimageio.spec._internal.io.HashKwargs]) -> Callable[..., Any]:", "funcdef": "def"}, "bioimageio.core.digest_spec.get_axes_infos": {"fullname": "bioimageio.core.digest_spec.get_axes_infos", "modulename": "bioimageio.core.digest_spec", "qualname": "get_axes_infos", "kind": "function", "doc": "get a unified, simplified axis representation from spec axes
\n", "signature": "(\tio_descr: Union[bioimageio.spec.model.v0_4.InputTensorDescr, bioimageio.spec.model.v0_4.OutputTensorDescr, bioimageio.spec.model.v0_5.InputTensorDescr, bioimageio.spec.model.v0_5.OutputTensorDescr]) -> List[bioimageio.core.axis.AxisInfo]:", "funcdef": "def"}, "bioimageio.core.digest_spec.get_member_id": {"fullname": "bioimageio.core.digest_spec.get_member_id", "modulename": "bioimageio.core.digest_spec", "qualname": "get_member_id", "kind": "function", "doc": "get the normalized tensor ID, usable as a sample member ID
\n", "signature": "(\ttensor_description: Union[bioimageio.spec.model.v0_4.InputTensorDescr, bioimageio.spec.model.v0_4.OutputTensorDescr, bioimageio.spec.model.v0_5.InputTensorDescr, bioimageio.spec.model.v0_5.OutputTensorDescr]) -> bioimageio.spec.model.v0_5.TensorId:", "funcdef": "def"}, "bioimageio.core.digest_spec.get_member_ids": {"fullname": "bioimageio.core.digest_spec.get_member_ids", "modulename": "bioimageio.core.digest_spec", "qualname": "get_member_ids", "kind": "function", "doc": "get normalized tensor IDs to be used as sample member IDs
\n", "signature": "(\ttensor_descriptions: Sequence[Union[bioimageio.spec.model.v0_4.InputTensorDescr, bioimageio.spec.model.v0_4.OutputTensorDescr, bioimageio.spec.model.v0_5.InputTensorDescr, bioimageio.spec.model.v0_5.OutputTensorDescr]]) -> List[bioimageio.spec.model.v0_5.TensorId]:", "funcdef": "def"}, "bioimageio.core.digest_spec.get_test_inputs": {"fullname": "bioimageio.core.digest_spec.get_test_inputs", "modulename": "bioimageio.core.digest_spec", "qualname": "get_test_inputs", "kind": "function", "doc": "returns a model's test input sample
\n", "signature": "(\tmodel: Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]) -> bioimageio.core.sample.Sample:", "funcdef": "def"}, "bioimageio.core.digest_spec.get_test_outputs": {"fullname": "bioimageio.core.digest_spec.get_test_outputs", "modulename": "bioimageio.core.digest_spec", "qualname": "get_test_outputs", "kind": "function", "doc": "returns a model's test output sample
\n", "signature": "(\tmodel: Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]) -> bioimageio.core.sample.Sample:", "funcdef": "def"}, "bioimageio.core.digest_spec.IO_SampleBlockMeta": {"fullname": "bioimageio.core.digest_spec.IO_SampleBlockMeta", "modulename": "bioimageio.core.digest_spec", "qualname": "IO_SampleBlockMeta", "kind": "class", "doc": "IO_SampleBlockMeta(input, output)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.digest_spec.IO_SampleBlockMeta.__init__": {"fullname": "bioimageio.core.digest_spec.IO_SampleBlockMeta.__init__", "modulename": "bioimageio.core.digest_spec", "qualname": "IO_SampleBlockMeta.__init__", "kind": "function", "doc": "Create new instance of IO_SampleBlockMeta(input, output)
\n", "signature": "(\tinput: ForwardRef('SampleBlockMeta'),\toutput: ForwardRef('SampleBlockMeta'))"}, "bioimageio.core.digest_spec.IO_SampleBlockMeta.input": {"fullname": "bioimageio.core.digest_spec.IO_SampleBlockMeta.input", "modulename": "bioimageio.core.digest_spec", "qualname": "IO_SampleBlockMeta.input", "kind": "variable", "doc": "Alias for field number 0
\n", "annotation": ": bioimageio.core.sample.SampleBlockMeta"}, "bioimageio.core.digest_spec.IO_SampleBlockMeta.output": {"fullname": "bioimageio.core.digest_spec.IO_SampleBlockMeta.output", "modulename": "bioimageio.core.digest_spec", "qualname": "IO_SampleBlockMeta.output", "kind": "variable", "doc": "Alias for field number 1
\n", "annotation": ": bioimageio.core.sample.SampleBlockMeta"}, "bioimageio.core.digest_spec.get_input_halo": {"fullname": "bioimageio.core.digest_spec.get_input_halo", "modulename": "bioimageio.core.digest_spec", "qualname": "get_input_halo", "kind": "function", "doc": "returns which halo input tensors need to be divided into blocks with, such that\noutput_halo
can be cropped from their outputs without introducing gaps.
returns how a model's output tensor shapes relates to its input shapes
\n", "signature": "(\tmodel: bioimageio.spec.model.v0_5.ModelDescr) -> Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, Union[bioimageio.core.sample.LinearSampleAxisTransform, int]]]:", "funcdef": "def"}, "bioimageio.core.digest_spec.get_io_sample_block_metas": {"fullname": "bioimageio.core.digest_spec.get_io_sample_block_metas", "modulename": "bioimageio.core.digest_spec", "qualname": "get_io_sample_block_metas", "kind": "function", "doc": "returns an iterable yielding meta data for corresponding input and output samples
\n", "signature": "(\tmodel: bioimageio.spec.model.v0_5.ModelDescr,\tinput_sample_shape: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\tns: Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int],\tbatch_size: int = 1) -> Tuple[int, Iterable[bioimageio.core.digest_spec.IO_SampleBlockMeta]]:", "funcdef": "def"}, "bioimageio.core.digest_spec.get_tensor": {"fullname": "bioimageio.core.digest_spec.get_tensor", "modulename": "bioimageio.core.digest_spec", "qualname": "get_tensor", "kind": "function", "doc": "helper to cast/load various tensor sources
\n", "signature": "(\tsrc: Union[bioimageio.core.tensor.Tensor, xarray.core.dataarray.DataArray, numpy.ndarray[Any, numpy.dtype[Any]], pathlib.Path],\tipt: Union[bioimageio.spec.model.v0_4.InputTensorDescr, bioimageio.spec.model.v0_5.InputTensorDescr]):", "funcdef": "def"}, "bioimageio.core.digest_spec.create_sample_for_model": {"fullname": "bioimageio.core.digest_spec.create_sample_for_model", "modulename": "bioimageio.core.digest_spec", "qualname": "create_sample_for_model", "kind": "function", "doc": "Create a sample from a single set of input(s) for a specific bioimage.io model
\n\nload a single sample from paths
that can be processed by model
load a single image as numpy array
\n\nsave a sample to path
\n\nIf path
is a pathlib.Path or a string it must contain {member_id}
and may contain {sample_id}
,\nwhich are resolved with the sample
object.
Represents model without any preprocessing or postprocessing.
\n\nfrom bioimageio.core import load_description\n\nmodel = load_description(...)\n\n# option 1:\nadapter = ModelAdapter.create(model)\nadapter.forward(...)\nadapter.unload()\n\n# option 2:\nwith ModelAdapter.create(model) as adapter:\n adapter.forward(...)\n
\n", "bases": "abc.ABC"}, "bioimageio.core.model_adapters.ModelAdapter.create": {"fullname": "bioimageio.core.model_adapters.ModelAdapter.create", "modulename": "bioimageio.core.model_adapters", "qualname": "ModelAdapter.create", "kind": "function", "doc": "Creates model adapter based on the passed spec\nNote: All specific adapters should happen inside this function to prevent different framework\ninitializations interfering with each other
\n", "signature": "(\tcls,\tmodel_description: Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr],\t*,\tdevices: Optional[Sequence[str]] = None,\tweight_format_priority_order: Optional[Sequence[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]] = None):", "funcdef": "def"}, "bioimageio.core.model_adapters.ModelAdapter.load": {"fullname": "bioimageio.core.model_adapters.ModelAdapter.load", "modulename": "bioimageio.core.model_adapters", "qualname": "ModelAdapter.load", "kind": "function", "doc": "\n", "signature": "(self, *, devices: Optional[Sequence[str]] = None) -> None:", "funcdef": "def"}, "bioimageio.core.model_adapters.ModelAdapter.forward": {"fullname": "bioimageio.core.model_adapters.ModelAdapter.forward", "modulename": "bioimageio.core.model_adapters", "qualname": "ModelAdapter.forward", "kind": "function", "doc": "Run forward pass of model to get model predictions
\n", "signature": "(\tself,\t*input_tensors: Optional[bioimageio.core.tensor.Tensor]) -> List[Optional[bioimageio.core.tensor.Tensor]]:", "funcdef": "def"}, "bioimageio.core.model_adapters.ModelAdapter.unload": {"fullname": "bioimageio.core.model_adapters.ModelAdapter.unload", "modulename": "bioimageio.core.model_adapters", "qualname": "ModelAdapter.unload", "kind": "function", "doc": "Unload model from any devices, freeing their memory.\nThe moder adapter should be considered unusable afterwards.
\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.model_adapters.create_model_adapter": {"fullname": "bioimageio.core.model_adapters.create_model_adapter", "modulename": "bioimageio.core.model_adapters", "qualname": "create_model_adapter", "kind": "function", "doc": "Creates model adapter based on the passed spec\nNote: All specific adapters should happen inside this function to prevent different framework\ninitializations interfering with each other
\n", "signature": "(\tmodel_description: Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr],\t*,\tdevices: Optional[Sequence[str]] = None,\tweight_format_priority_order: Optional[Sequence[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]] = None):", "funcdef": "def"}, "bioimageio.core.model_adapters.get_weight_formats": {"fullname": "bioimageio.core.model_adapters.get_weight_formats", "modulename": "bioimageio.core.model_adapters", "qualname": "get_weight_formats", "kind": "function", "doc": "Return list of supported weight types
\n", "signature": "() -> List[str]:", "funcdef": "def"}, "bioimageio.core.prediction": {"fullname": "bioimageio.core.prediction", "modulename": "bioimageio.core.prediction", "kind": "module", "doc": "\n"}, "bioimageio.core.prediction.predict": {"fullname": "bioimageio.core.prediction.predict", "modulename": "bioimageio.core.prediction", "qualname": "predict", "kind": "function", "doc": "Run prediction for a single set of input(s) with a bioimage.io model
\n\ninput_block_shape
blocksize_parameter
.{member_id}
{sample_id}
in it\nto save the output to.Run prediction for a multiple sets of inputs with a bioimage.io model
\n\n{i}
will be formatted as the i-th sample.\nIf {i}
(or {i:
) is not present and inputs
is an iterable {i:03}
is appended.{member_id}
{sample_id}
in it\nto save the output to.Calculates sample and/or dataset measures
\n", "bases": "bioimageio.core._op_base.Operator"}, "bioimageio.core.proc_ops.UpdateStats.__init__": {"fullname": "bioimageio.core.proc_ops.UpdateStats.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "UpdateStats.__init__", "kind": "function", "doc": "\n", "signature": "(\tstats_calculator: bioimageio.core.stat_calculators.StatsCalculator,\tkeep_updating_initial_dataset_stats: bool = False)"}, "bioimageio.core.proc_ops.UpdateStats.stats_calculator": {"fullname": "bioimageio.core.proc_ops.UpdateStats.stats_calculator", "modulename": "bioimageio.core.proc_ops", "qualname": "UpdateStats.stats_calculator", "kind": "variable", "doc": "StatsCalculator
to be used by this operator.
indicates if operator calls should keep updating initial dataset statistics or not;\nif the stats_calculator
was not provided with any initial dataset statistics,\nthese are always updated with every new sample.
'output = tensor > threshold'.
\n", "bases": "_SimpleOperator"}, "bioimageio.core.proc_ops.Binarize.__init__": {"fullname": "bioimageio.core.proc_ops.Binarize.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "Binarize.__init__", "kind": "function", "doc": "\n", "signature": "(\tinput: bioimageio.spec.model.v0_5.TensorId,\toutput: bioimageio.spec.model.v0_5.TensorId,\tthreshold: Union[float, Sequence[float]],\taxis: Optional[bioimageio.spec.model.v0_5.AxisId] = None)"}, "bioimageio.core.proc_ops.Binarize.threshold": {"fullname": "bioimageio.core.proc_ops.Binarize.threshold", "modulename": "bioimageio.core.proc_ops", "qualname": "Binarize.threshold", "kind": "variable", "doc": "\n", "annotation": ": Union[float, Sequence[float]]"}, "bioimageio.core.proc_ops.Binarize.axis": {"fullname": "bioimageio.core.proc_ops.Binarize.axis", "modulename": "bioimageio.core.proc_ops", "qualname": "Binarize.axis", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.AxisId]", "default_value": "None"}, "bioimageio.core.proc_ops.Binarize.get_output_shape": {"fullname": "bioimageio.core.proc_ops.Binarize.get_output_shape", "modulename": "bioimageio.core.proc_ops", "qualname": "Binarize.get_output_shape", "kind": "function", "doc": "\n", "signature": "(\tself,\tinput_shape: Mapping[bioimageio.spec.model.v0_5.AxisId, int]) -> Mapping[bioimageio.spec.model.v0_5.AxisId, int]:", "funcdef": "def"}, "bioimageio.core.proc_ops.Binarize.from_proc_descr": {"fullname": "bioimageio.core.proc_ops.Binarize.from_proc_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "Binarize.from_proc_descr", "kind": "function", "doc": "\n", "signature": "(\tcls,\tdescr: Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_5.BinarizeDescr],\tmember_id: bioimageio.spec.model.v0_5.TensorId) -> Self:", "funcdef": "def"}, "bioimageio.core.proc_ops.Clip": {"fullname": "bioimageio.core.proc_ops.Clip", "modulename": "bioimageio.core.proc_ops", "qualname": "Clip", "kind": "class", "doc": "\n", "bases": "_SimpleOperator"}, "bioimageio.core.proc_ops.Clip.__init__": {"fullname": "bioimageio.core.proc_ops.Clip.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "Clip.__init__", "kind": "function", "doc": "\n", "signature": "(\tinput: bioimageio.spec.model.v0_5.TensorId,\toutput: bioimageio.spec.model.v0_5.TensorId,\tmin: Optional[float] = None,\tmax: Optional[float] = None)"}, "bioimageio.core.proc_ops.Clip.min": {"fullname": "bioimageio.core.proc_ops.Clip.min", "modulename": "bioimageio.core.proc_ops", "qualname": "Clip.min", "kind": "variable", "doc": "minimum value for clipping
\n", "annotation": ": Optional[float]", "default_value": "None"}, "bioimageio.core.proc_ops.Clip.max": {"fullname": "bioimageio.core.proc_ops.Clip.max", "modulename": "bioimageio.core.proc_ops", "qualname": "Clip.max", "kind": "variable", "doc": "maximum value for clipping
\n", "annotation": ": Optional[float]", "default_value": "None"}, "bioimageio.core.proc_ops.Clip.get_output_shape": {"fullname": "bioimageio.core.proc_ops.Clip.get_output_shape", "modulename": "bioimageio.core.proc_ops", "qualname": "Clip.get_output_shape", "kind": "function", "doc": "\n", "signature": "(\tself,\tinput_shape: Mapping[bioimageio.spec.model.v0_5.AxisId, int]) -> Mapping[bioimageio.spec.model.v0_5.AxisId, int]:", "funcdef": "def"}, "bioimageio.core.proc_ops.Clip.from_proc_descr": {"fullname": "bioimageio.core.proc_ops.Clip.from_proc_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "Clip.from_proc_descr", "kind": "function", "doc": "\n", "signature": "(\tcls,\tdescr: Union[bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_5.ClipDescr],\tmember_id: bioimageio.spec.model.v0_5.TensorId) -> Self:", "funcdef": "def"}, "bioimageio.core.proc_ops.EnsureDtype": {"fullname": "bioimageio.core.proc_ops.EnsureDtype", "modulename": "bioimageio.core.proc_ops", "qualname": "EnsureDtype", "kind": "class", "doc": "\n", "bases": "_SimpleOperator"}, "bioimageio.core.proc_ops.EnsureDtype.__init__": {"fullname": "bioimageio.core.proc_ops.EnsureDtype.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "EnsureDtype.__init__", "kind": "function", "doc": "\n", "signature": "(\tinput: bioimageio.spec.model.v0_5.TensorId,\toutput: bioimageio.spec.model.v0_5.TensorId,\tdtype: Literal['bool', 'float32', 'float64', 'int8', 'int16', 'int32', 'int64', 'uint8', 'uint16', 'uint32', 'uint64'])"}, "bioimageio.core.proc_ops.EnsureDtype.dtype": {"fullname": "bioimageio.core.proc_ops.EnsureDtype.dtype", "modulename": "bioimageio.core.proc_ops", "qualname": "EnsureDtype.dtype", "kind": "variable", "doc": "\n", "annotation": ": Literal['bool', 'float32', 'float64', 'int8', 'int16', 'int32', 'int64', 'uint8', 'uint16', 'uint32', 'uint64']"}, "bioimageio.core.proc_ops.EnsureDtype.from_proc_descr": {"fullname": "bioimageio.core.proc_ops.EnsureDtype.from_proc_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "EnsureDtype.from_proc_descr", "kind": "function", "doc": "\n", "signature": "(\tcls,\tdescr: bioimageio.spec.model.v0_5.EnsureDtypeDescr,\tmember_id: bioimageio.spec.model.v0_5.TensorId):", "funcdef": "def"}, "bioimageio.core.proc_ops.EnsureDtype.get_descr": {"fullname": "bioimageio.core.proc_ops.EnsureDtype.get_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "EnsureDtype.get_descr", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.proc_ops.EnsureDtype.get_output_shape": {"fullname": "bioimageio.core.proc_ops.EnsureDtype.get_output_shape", "modulename": "bioimageio.core.proc_ops", "qualname": "EnsureDtype.get_output_shape", "kind": "function", "doc": "\n", "signature": "(\tself,\tinput_shape: Mapping[bioimageio.spec.model.v0_5.AxisId, int]) -> Mapping[bioimageio.spec.model.v0_5.AxisId, int]:", "funcdef": "def"}, "bioimageio.core.proc_ops.ScaleLinear": {"fullname": "bioimageio.core.proc_ops.ScaleLinear", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleLinear", "kind": "class", "doc": "\n", "bases": "_SimpleOperator"}, "bioimageio.core.proc_ops.ScaleLinear.__init__": {"fullname": "bioimageio.core.proc_ops.ScaleLinear.__init__", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleLinear.__init__", "kind": "function", "doc": "\n", "signature": "(\tinput: bioimageio.spec.model.v0_5.TensorId,\toutput: bioimageio.spec.model.v0_5.TensorId,\tgain: Union[float, xarray.core.dataarray.DataArray] = 1.0,\toffset: Union[float, xarray.core.dataarray.DataArray] = 0.0)"}, "bioimageio.core.proc_ops.ScaleLinear.gain": {"fullname": "bioimageio.core.proc_ops.ScaleLinear.gain", "modulename": "bioimageio.core.proc_ops", "qualname": "ScaleLinear.gain", "kind": "variable", "doc": "multiplicative factor
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{"fullname": "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.from_proc_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "FixedZeroMeanUnitVariance.from_proc_descr", "kind": "function", "doc": "\n", "signature": "(\tcls,\tdescr: bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceDescr,\tmember_id: bioimageio.spec.model.v0_5.TensorId) -> Self:", "funcdef": "def"}, "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.get_descr": {"fullname": "bioimageio.core.proc_ops.FixedZeroMeanUnitVariance.get_descr", "modulename": "bioimageio.core.proc_ops", "qualname": "FixedZeroMeanUnitVariance.get_descr", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.core.proc_ops.ProcDescr": {"fullname": "bioimageio.core.proc_ops.ProcDescr", "modulename": "bioimageio.core.proc_ops", "qualname": "ProcDescr", "kind": "variable", "doc": "\n", "default_value": "typing.Union[typing.Annotated[typing.Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr, bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.model.v0_5.BinarizeDescr, bioimageio.spec.model.v0_5.ClipDescr, bioimageio.spec.model.v0_5.EnsureDtypeDescr, bioimageio.spec.model.v0_5.ScaleLinearDescr, bioimageio.spec.model.v0_5.SigmoidDescr, bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ScaleRangeDescr], Discriminator(discriminator='id', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.model.v0_5.BinarizeDescr, bioimageio.spec.model.v0_5.ClipDescr, bioimageio.spec.model.v0_5.EnsureDtypeDescr, bioimageio.spec.model.v0_5.ScaleLinearDescr, bioimageio.spec.model.v0_5.SigmoidDescr, bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ScaleRangeDescr, bioimageio.spec.model.v0_5.ScaleMeanVarianceDescr], Discriminator(discriminator='id', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.core.proc_ops.Processing": {"fullname": "bioimageio.core.proc_ops.Processing", "modulename": "bioimageio.core.proc_ops", "qualname": "Processing", "kind": "variable", "doc": "\n", "default_value": "typing.Union[bioimageio.core.proc_ops.AddKnownDatasetStats, bioimageio.core.proc_ops.Binarize, bioimageio.core.proc_ops.Clip, bioimageio.core.proc_ops.EnsureDtype, bioimageio.core.proc_ops.FixedZeroMeanUnitVariance, bioimageio.core.proc_ops.ScaleLinear, bioimageio.core.proc_ops.ScaleMeanVariance, bioimageio.core.proc_ops.ScaleRange, bioimageio.core.proc_ops.Sigmoid, bioimageio.core.proc_ops.UpdateStats, bioimageio.core.proc_ops.ZeroMeanUnitVariance]"}, "bioimageio.core.proc_ops.get_proc_class": {"fullname": "bioimageio.core.proc_ops.get_proc_class", "modulename": "bioimageio.core.proc_ops", "qualname": "get_proc_class", "kind": "function", "doc": "\n", "signature": "(\tproc_spec: Union[Annotated[Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr, bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_5.BinarizeDescr, bioimageio.spec.model.v0_5.ClipDescr, bioimageio.spec.model.v0_5.EnsureDtypeDescr, bioimageio.spec.model.v0_5.ScaleLinearDescr, bioimageio.spec.model.v0_5.SigmoidDescr, bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ScaleRangeDescr], Discriminator(discriminator='id', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_5.BinarizeDescr, bioimageio.spec.model.v0_5.ClipDescr, bioimageio.spec.model.v0_5.EnsureDtypeDescr, bioimageio.spec.model.v0_5.ScaleLinearDescr, bioimageio.spec.model.v0_5.SigmoidDescr, bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_5.ScaleRangeDescr, bioimageio.spec.model.v0_5.ScaleMeanVarianceDescr], Discriminator(discriminator='id', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]):", "funcdef": "def"}, "bioimageio.core.proc_setup": {"fullname": "bioimageio.core.proc_setup", "modulename": "bioimageio.core.proc_setup", "kind": "module", "doc": "\n"}, "bioimageio.core.proc_setup.TensorDescr": {"fullname": "bioimageio.core.proc_setup.TensorDescr", "modulename": "bioimageio.core.proc_setup", "qualname": "TensorDescr", "kind": "variable", "doc": "\n", "default_value": "typing.Union[bioimageio.spec.model.v0_4.InputTensorDescr, bioimageio.spec.model.v0_4.OutputTensorDescr, bioimageio.spec.model.v0_5.InputTensorDescr, bioimageio.spec.model.v0_5.OutputTensorDescr]"}, "bioimageio.core.proc_setup.PreAndPostprocessing": {"fullname": "bioimageio.core.proc_setup.PreAndPostprocessing", "modulename": "bioimageio.core.proc_setup", "qualname": "PreAndPostprocessing", "kind": "class", "doc": "PreAndPostprocessing(pre, post)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.proc_setup.PreAndPostprocessing.__init__": {"fullname": "bioimageio.core.proc_setup.PreAndPostprocessing.__init__", "modulename": "bioimageio.core.proc_setup", "qualname": "PreAndPostprocessing.__init__", "kind": "function", "doc": "Create new instance of PreAndPostprocessing(pre, post)
\n", "signature": "(\tpre: List[Union[bioimageio.core.proc_ops.AddKnownDatasetStats, bioimageio.core.proc_ops.Binarize, bioimageio.core.proc_ops.Clip, bioimageio.core.proc_ops.EnsureDtype, bioimageio.core.proc_ops.FixedZeroMeanUnitVariance, bioimageio.core.proc_ops.ScaleLinear, bioimageio.core.proc_ops.ScaleMeanVariance, bioimageio.core.proc_ops.ScaleRange, bioimageio.core.proc_ops.Sigmoid, bioimageio.core.proc_ops.UpdateStats, bioimageio.core.proc_ops.ZeroMeanUnitVariance]],\tpost: List[Union[bioimageio.core.proc_ops.AddKnownDatasetStats, bioimageio.core.proc_ops.Binarize, bioimageio.core.proc_ops.Clip, bioimageio.core.proc_ops.EnsureDtype, bioimageio.core.proc_ops.FixedZeroMeanUnitVariance, bioimageio.core.proc_ops.ScaleLinear, bioimageio.core.proc_ops.ScaleMeanVariance, bioimageio.core.proc_ops.ScaleRange, bioimageio.core.proc_ops.Sigmoid, bioimageio.core.proc_ops.UpdateStats, bioimageio.core.proc_ops.ZeroMeanUnitVariance]])"}, "bioimageio.core.proc_setup.PreAndPostprocessing.pre": {"fullname": "bioimageio.core.proc_setup.PreAndPostprocessing.pre", "modulename": "bioimageio.core.proc_setup", "qualname": "PreAndPostprocessing.pre", "kind": "variable", "doc": "Alias for field number 0
\n", "annotation": ": List[Union[bioimageio.core.proc_ops.AddKnownDatasetStats, bioimageio.core.proc_ops.Binarize, bioimageio.core.proc_ops.Clip, bioimageio.core.proc_ops.EnsureDtype, bioimageio.core.proc_ops.FixedZeroMeanUnitVariance, bioimageio.core.proc_ops.ScaleLinear, bioimageio.core.proc_ops.ScaleMeanVariance, bioimageio.core.proc_ops.ScaleRange, bioimageio.core.proc_ops.Sigmoid, bioimageio.core.proc_ops.UpdateStats, bioimageio.core.proc_ops.ZeroMeanUnitVariance]]"}, "bioimageio.core.proc_setup.PreAndPostprocessing.post": {"fullname": "bioimageio.core.proc_setup.PreAndPostprocessing.post", "modulename": "bioimageio.core.proc_setup", "qualname": "PreAndPostprocessing.post", "kind": "variable", "doc": "Alias for field number 1
\n", "annotation": ": List[Union[bioimageio.core.proc_ops.AddKnownDatasetStats, bioimageio.core.proc_ops.Binarize, bioimageio.core.proc_ops.Clip, bioimageio.core.proc_ops.EnsureDtype, bioimageio.core.proc_ops.FixedZeroMeanUnitVariance, bioimageio.core.proc_ops.ScaleLinear, bioimageio.core.proc_ops.ScaleMeanVariance, bioimageio.core.proc_ops.ScaleRange, bioimageio.core.proc_ops.Sigmoid, bioimageio.core.proc_ops.UpdateStats, bioimageio.core.proc_ops.ZeroMeanUnitVariance]]"}, "bioimageio.core.proc_setup.setup_pre_and_postprocessing": {"fullname": "bioimageio.core.proc_setup.setup_pre_and_postprocessing", "modulename": "bioimageio.core.proc_setup", "qualname": "setup_pre_and_postprocessing", "kind": "function", "doc": "Get pre- and postprocessing operators for a model
description.\nuserd in `bioimageio.core.create_prediction_pipeline
RequiredMeasures(pre, post)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.proc_setup.RequiredMeasures.__init__": {"fullname": "bioimageio.core.proc_setup.RequiredMeasures.__init__", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredMeasures.__init__", "kind": "function", "doc": "Create new instance of RequiredMeasures(pre, post)
\n", "signature": "(\tpre: Set[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\tpost: Set[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)]])"}, "bioimageio.core.proc_setup.RequiredMeasures.pre": {"fullname": "bioimageio.core.proc_setup.RequiredMeasures.pre", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredMeasures.pre", "kind": "variable", "doc": "Alias for field number 0
\n", "annotation": ": Set[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.core.proc_setup.RequiredMeasures.post": {"fullname": "bioimageio.core.proc_setup.RequiredMeasures.post", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredMeasures.post", "kind": "variable", "doc": "Alias for field number 1
\n", "annotation": ": Set[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.core.proc_setup.RequiredDatasetMeasures": {"fullname": "bioimageio.core.proc_setup.RequiredDatasetMeasures", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredDatasetMeasures", "kind": "class", "doc": "RequiredDatasetMeasures(pre, post)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.proc_setup.RequiredDatasetMeasures.__init__": {"fullname": "bioimageio.core.proc_setup.RequiredDatasetMeasures.__init__", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredDatasetMeasures.__init__", "kind": "function", "doc": "Create new instance of RequiredDatasetMeasures(pre, post)
\n", "signature": "(\tpre: Set[Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\tpost: Set[Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]])"}, "bioimageio.core.proc_setup.RequiredDatasetMeasures.pre": {"fullname": "bioimageio.core.proc_setup.RequiredDatasetMeasures.pre", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredDatasetMeasures.pre", "kind": "variable", "doc": "Alias for field number 0
\n", "annotation": ": Set[Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.core.proc_setup.RequiredDatasetMeasures.post": {"fullname": "bioimageio.core.proc_setup.RequiredDatasetMeasures.post", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredDatasetMeasures.post", "kind": "variable", "doc": "Alias for field number 1
\n", "annotation": ": Set[Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.core.proc_setup.RequiredSampleMeasures": {"fullname": "bioimageio.core.proc_setup.RequiredSampleMeasures", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredSampleMeasures", "kind": "class", "doc": "RequiredSampleMeasures(pre, post)
\n", "bases": "typing.NamedTuple"}, "bioimageio.core.proc_setup.RequiredSampleMeasures.__init__": {"fullname": "bioimageio.core.proc_setup.RequiredSampleMeasures.__init__", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredSampleMeasures.__init__", "kind": "function", "doc": "Create new instance of RequiredSampleMeasures(pre, post)
\n", "signature": "(\tpre: Set[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\tpost: Set[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]])"}, "bioimageio.core.proc_setup.RequiredSampleMeasures.pre": {"fullname": "bioimageio.core.proc_setup.RequiredSampleMeasures.pre", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredSampleMeasures.pre", "kind": "variable", "doc": "Alias for field number 0
\n", "annotation": ": Set[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.core.proc_setup.RequiredSampleMeasures.post": {"fullname": "bioimageio.core.proc_setup.RequiredSampleMeasures.post", "modulename": "bioimageio.core.proc_setup", "qualname": "RequiredSampleMeasures.post", "kind": "variable", "doc": "Alias for field number 1
\n", "annotation": ": Set[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.core.proc_setup.get_requried_measures": {"fullname": "bioimageio.core.proc_setup.get_requried_measures", "modulename": "bioimageio.core.proc_setup", "qualname": "get_requried_measures", "kind": "function", "doc": "\n", "signature": "(\tmodel: Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]) -> bioimageio.core.proc_setup.RequiredMeasures:", "funcdef": "def"}, "bioimageio.core.proc_setup.get_required_dataset_measures": {"fullname": "bioimageio.core.proc_setup.get_required_dataset_measures", "modulename": "bioimageio.core.proc_setup", "qualname": "get_required_dataset_measures", "kind": "function", "doc": "\n", "signature": "(\tmodel: Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]) -> bioimageio.core.proc_setup.RequiredDatasetMeasures:", "funcdef": "def"}, "bioimageio.core.proc_setup.get_requried_sample_measures": {"fullname": "bioimageio.core.proc_setup.get_requried_sample_measures", "modulename": "bioimageio.core.proc_setup", "qualname": "get_requried_sample_measures", "kind": "function", "doc": "\n", "signature": "(\tmodel: Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]) -> bioimageio.core.proc_setup.RequiredSampleMeasures:", "funcdef": "def"}, "bioimageio.core.sample": {"fullname": "bioimageio.core.sample", "modulename": "bioimageio.core.sample", "kind": "module", "doc": "\n"}, "bioimageio.core.sample.Sample": {"fullname": "bioimageio.core.sample.Sample", "modulename": "bioimageio.core.sample", "qualname": "Sample", "kind": "class", "doc": "A dataset sample
\n"}, "bioimageio.core.sample.Sample.__init__": {"fullname": "bioimageio.core.sample.Sample.__init__", "modulename": "bioimageio.core.sample", "qualname": "Sample.__init__", "kind": "function", "doc": "\n", "signature": "(\tmembers: Dict[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.tensor.Tensor],\tstat: Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer>, return_type=PydanticUndefined, when_used='always')]]],\tid: Hashable)"}, "bioimageio.core.sample.Sample.members": {"fullname": "bioimageio.core.sample.Sample.members", "modulename": "bioimageio.core.sample", "qualname": "Sample.members", "kind": "variable", "doc": "the sample's tensors
\n", "annotation": ": Dict[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.tensor.Tensor]"}, "bioimageio.core.sample.Sample.stat": {"fullname": "bioimageio.core.sample.Sample.stat", "modulename": "bioimageio.core.sample", "qualname": "Sample.stat", "kind": "variable", "doc": "sample and dataset statistics
\n", "annotation": ": Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]"}, "bioimageio.core.sample.Sample.id": {"fullname": "bioimageio.core.sample.Sample.id", "modulename": "bioimageio.core.sample", "qualname": "Sample.id", "kind": "variable", "doc": "identifier within the sample's dataset
\n", "annotation": ": Hashable"}, "bioimageio.core.sample.Sample.shape": {"fullname": "bioimageio.core.sample.Sample.shape", "modulename": "bioimageio.core.sample", "qualname": "Sample.shape", "kind": "variable", "doc": "\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]"}, "bioimageio.core.sample.Sample.split_into_blocks": {"fullname": "bioimageio.core.sample.Sample.split_into_blocks", "modulename": "bioimageio.core.sample", "qualname": "Sample.split_into_blocks", "kind": "function", "doc": "\n", "signature": "(\tself,\tblock_shapes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\thalo: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, Union[int, Tuple[int, int], bioimageio.core.common.Halo]]],\tpad_mode: Literal['edge', 'reflect', 'symmetric'],\tbroadcast: bool = False) -> Tuple[int, Iterable[bioimageio.core.sample.SampleBlockWithOrigin]]:", "funcdef": "def"}, "bioimageio.core.sample.Sample.as_single_block": {"fullname": "bioimageio.core.sample.Sample.as_single_block", "modulename": "bioimageio.core.sample", "qualname": "Sample.as_single_block", "kind": "function", "doc": "\n", "signature": "(\tself,\thalo: Optional[Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, bioimageio.core.common.Halo]]] = None):", "funcdef": "def"}, "bioimageio.core.sample.Sample.from_blocks": {"fullname": "bioimageio.core.sample.Sample.from_blocks", "modulename": "bioimageio.core.sample", "qualname": "Sample.from_blocks", "kind": "function", "doc": "\n", "signature": "(\tcls,\tsample_blocks: Iterable[bioimageio.core.sample.SampleBlock],\t*,\tfill_value: float = nan) -> Self:", "funcdef": "def"}, "bioimageio.core.sample.SampleBlockBase": {"fullname": "bioimageio.core.sample.SampleBlockBase", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockBase", "kind": "class", "doc": "base class for SampleBlockMeta
and SampleBlock
the sample shape this block represents a part of
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]"}, "bioimageio.core.sample.SampleBlockBase.sample_id": {"fullname": "bioimageio.core.sample.SampleBlockBase.sample_id", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockBase.sample_id", "kind": "variable", "doc": "identifier for the sample within its dataset
\n", "annotation": ": Hashable"}, "bioimageio.core.sample.SampleBlockBase.blocks": {"fullname": "bioimageio.core.sample.SampleBlockBase.blocks", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockBase.blocks", "kind": "variable", "doc": "Individual tensor blocks comprising this sample block
\n", "annotation": ": Dict[bioimageio.spec.model.v0_5.TensorId, ~BlockT]"}, "bioimageio.core.sample.SampleBlockBase.block_index": {"fullname": "bioimageio.core.sample.SampleBlockBase.block_index", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockBase.block_index", "kind": "variable", "doc": "the n-th block of the sample
\n", "annotation": ": int"}, "bioimageio.core.sample.SampleBlockBase.blocks_in_sample": {"fullname": "bioimageio.core.sample.SampleBlockBase.blocks_in_sample", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockBase.blocks_in_sample", "kind": "variable", "doc": "total number of blocks in the sample
\n", "annotation": ": int"}, "bioimageio.core.sample.SampleBlockBase.shape": {"fullname": "bioimageio.core.sample.SampleBlockBase.shape", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockBase.shape", "kind": "variable", "doc": "\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]"}, "bioimageio.core.sample.SampleBlockBase.inner_shape": {"fullname": "bioimageio.core.sample.SampleBlockBase.inner_shape", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockBase.inner_shape", "kind": "variable", "doc": "\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]"}, "bioimageio.core.sample.LinearSampleAxisTransform": {"fullname": "bioimageio.core.sample.LinearSampleAxisTransform", "modulename": "bioimageio.core.sample", "qualname": "LinearSampleAxisTransform", "kind": "class", "doc": "\n", "bases": "bioimageio.core.block_meta.LinearAxisTransform"}, "bioimageio.core.sample.LinearSampleAxisTransform.__init__": {"fullname": "bioimageio.core.sample.LinearSampleAxisTransform.__init__", "modulename": "bioimageio.core.sample", "qualname": "LinearSampleAxisTransform.__init__", "kind": "function", "doc": "\n", "signature": "(\taxis: bioimageio.spec.model.v0_5.AxisId,\tscale: float,\toffset: int,\tmember: bioimageio.spec.model.v0_5.TensorId)"}, "bioimageio.core.sample.LinearSampleAxisTransform.member": {"fullname": "bioimageio.core.sample.LinearSampleAxisTransform.member", "modulename": "bioimageio.core.sample", "qualname": "LinearSampleAxisTransform.member", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_5.TensorId"}, "bioimageio.core.sample.SampleBlockMeta": {"fullname": "bioimageio.core.sample.SampleBlockMeta", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockMeta", "kind": "class", "doc": "Meta data of a dataset sample block
\n", "bases": "bioimageio.core.sample.SampleBlockBase[bioimageio.core.block_meta.BlockMeta]"}, "bioimageio.core.sample.SampleBlockMeta.__init__": {"fullname": "bioimageio.core.sample.SampleBlockMeta.__init__", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockMeta.__init__", "kind": "function", "doc": "\n", "signature": "(\tsample_shape: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\tsample_id: Hashable,\tblocks: Dict[bioimageio.spec.model.v0_5.TensorId, ~BlockT],\tblock_index: int,\tblocks_in_sample: int)"}, "bioimageio.core.sample.SampleBlockMeta.get_transformed": {"fullname": "bioimageio.core.sample.SampleBlockMeta.get_transformed", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockMeta.get_transformed", "kind": "function", "doc": "\n", "signature": "(\tself,\tnew_axes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, Union[bioimageio.core.sample.LinearSampleAxisTransform, int]]]) -> Self:", "funcdef": "def"}, "bioimageio.core.sample.SampleBlockMeta.with_data": {"fullname": "bioimageio.core.sample.SampleBlockMeta.with_data", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockMeta.with_data", "kind": "function", "doc": "\n", "signature": "(\tself,\tdata: Mapping[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.tensor.Tensor],\t*,\tstat: Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer>, return_type=PydanticUndefined, when_used='always')]]]) -> bioimageio.core.sample.SampleBlock:", "funcdef": "def"}, "bioimageio.core.sample.SampleBlock": {"fullname": "bioimageio.core.sample.SampleBlock", "modulename": "bioimageio.core.sample", "qualname": "SampleBlock", "kind": "class", "doc": "A block of a dataset sample
\n", "bases": "bioimageio.core.sample.SampleBlockBase[bioimageio.core.block.Block]"}, "bioimageio.core.sample.SampleBlock.__init__": {"fullname": "bioimageio.core.sample.SampleBlock.__init__", "modulename": "bioimageio.core.sample", "qualname": "SampleBlock.__init__", "kind": "function", "doc": "\n", "signature": "(\tsample_shape: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\tsample_id: Hashable,\tblocks: Dict[bioimageio.spec.model.v0_5.TensorId, ~BlockT],\tblock_index: int,\tblocks_in_sample: int,\tstat: Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer>, return_type=PydanticUndefined, when_used='always')]]])"}, "bioimageio.core.sample.SampleBlock.stat": {"fullname": "bioimageio.core.sample.SampleBlock.stat", "modulename": "bioimageio.core.sample", "qualname": "SampleBlock.stat", "kind": "variable", "doc": "computed statistics
\n", "annotation": ": Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]"}, "bioimageio.core.sample.SampleBlock.members": {"fullname": "bioimageio.core.sample.SampleBlock.members", "modulename": "bioimageio.core.sample", "qualname": "SampleBlock.members", "kind": "variable", "doc": "the sample block's tensors
\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.tensor.Tensor]"}, "bioimageio.core.sample.SampleBlock.get_transformed_meta": {"fullname": "bioimageio.core.sample.SampleBlock.get_transformed_meta", "modulename": "bioimageio.core.sample", "qualname": "SampleBlock.get_transformed_meta", "kind": "function", "doc": "\n", "signature": "(\tself,\tnew_axes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, Union[bioimageio.core.sample.LinearSampleAxisTransform, int]]]) -> bioimageio.core.sample.SampleBlockMeta:", "funcdef": "def"}, "bioimageio.core.sample.SampleBlockWithOrigin": {"fullname": "bioimageio.core.sample.SampleBlockWithOrigin", "modulename": "bioimageio.core.sample", "qualname": "SampleBlockWithOrigin", "kind": "class", "doc": "A SampleBlock
with a reference (origin
) to the whole Sample
the sample this sample block was taken from
\n", "annotation": ": bioimageio.core.sample.Sample"}, "bioimageio.core.sample.sample_block_meta_generator": {"fullname": "bioimageio.core.sample.sample_block_meta_generator", "modulename": "bioimageio.core.sample", "qualname": "sample_block_meta_generator", "kind": "function", "doc": "\n", "signature": "(\tblocks: Iterable[Mapping[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.block_meta.BlockMeta]],\t*,\tsample_shape: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]],\tsample_id: Hashable):", "funcdef": "def"}, "bioimageio.core.sample.sample_block_generator": {"fullname": "bioimageio.core.sample.sample_block_generator", "modulename": "bioimageio.core.sample", "qualname": "sample_block_generator", "kind": "function", "doc": "\n", "signature": "(\tblocks: Iterable[Mapping[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.block_meta.BlockMeta]],\t*,\torigin: bioimageio.core.sample.Sample,\tpad_mode: Literal['edge', 'reflect', 'symmetric']) -> Iterable[bioimageio.core.sample.SampleBlockWithOrigin]:", "funcdef": "def"}, "bioimageio.core.stat_calculators": {"fullname": "bioimageio.core.stat_calculators", "modulename": "bioimageio.core.stat_calculators", "kind": "module", "doc": "\n"}, "bioimageio.core.stat_calculators.MeanCalculator": {"fullname": "bioimageio.core.stat_calculators.MeanCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanCalculator", "kind": "class", "doc": "to calculate sample and dataset mean for in-memory samples
\n"}, "bioimageio.core.stat_calculators.MeanCalculator.__init__": {"fullname": "bioimageio.core.stat_calculators.MeanCalculator.__init__", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanCalculator.__init__", "kind": "function", "doc": "\n", "signature": "(\tmember_id: bioimageio.spec.model.v0_5.TensorId,\taxes: Optional[Sequence[bioimageio.spec.model.v0_5.AxisId]])"}, "bioimageio.core.stat_calculators.MeanCalculator.compute": {"fullname": "bioimageio.core.stat_calculators.MeanCalculator.compute", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanCalculator.compute", "kind": "function", "doc": "\n", "signature": "(\tself,\tsample: bioimageio.core.sample.Sample) -> Dict[bioimageio.core.stat_measures.SampleMean, Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanCalculator.update": {"fullname": "bioimageio.core.stat_calculators.MeanCalculator.update", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanCalculator.update", "kind": "function", "doc": "\n", "signature": "(self, sample: bioimageio.core.sample.Sample) -> None:", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanCalculator.compute_and_update": {"fullname": "bioimageio.core.stat_calculators.MeanCalculator.compute_and_update", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanCalculator.compute_and_update", "kind": "function", "doc": "\n", "signature": "(\tself,\tsample: bioimageio.core.sample.Sample) -> Dict[bioimageio.core.stat_measures.SampleMean, Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanCalculator.finalize": {"fullname": "bioimageio.core.stat_calculators.MeanCalculator.finalize", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanCalculator.finalize", "kind": "function", "doc": "\n", "signature": "(\tself) -> Dict[bioimageio.core.stat_measures.DatasetMean, Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanVarStdCalculator": {"fullname": "bioimageio.core.stat_calculators.MeanVarStdCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanVarStdCalculator", "kind": "class", "doc": "to calculate sample and dataset mean, variance or standard deviation
\n"}, "bioimageio.core.stat_calculators.MeanVarStdCalculator.__init__": {"fullname": "bioimageio.core.stat_calculators.MeanVarStdCalculator.__init__", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanVarStdCalculator.__init__", "kind": "function", "doc": "\n", "signature": "(\tmember_id: bioimageio.spec.model.v0_5.TensorId,\taxes: Optional[Sequence[bioimageio.spec.model.v0_5.AxisId]])"}, "bioimageio.core.stat_calculators.MeanVarStdCalculator.compute": {"fullname": "bioimageio.core.stat_calculators.MeanVarStdCalculator.compute", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanVarStdCalculator.compute", "kind": "function", "doc": "\n", "signature": "(\tself,\tsample: bioimageio.core.sample.Sample) -> Dict[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleStd], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanVarStdCalculator.update": {"fullname": "bioimageio.core.stat_calculators.MeanVarStdCalculator.update", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanVarStdCalculator.update", "kind": "function", "doc": "\n", "signature": "(self, sample: bioimageio.core.sample.Sample):", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanVarStdCalculator.finalize": {"fullname": "bioimageio.core.stat_calculators.MeanVarStdCalculator.finalize", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanVarStdCalculator.finalize", "kind": "function", "doc": "\n", "signature": "(\tself) -> Dict[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetStd], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.SamplePercentilesCalculator": {"fullname": "bioimageio.core.stat_calculators.SamplePercentilesCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "SamplePercentilesCalculator", "kind": "class", "doc": "to calculate sample percentiles
\n"}, "bioimageio.core.stat_calculators.SamplePercentilesCalculator.__init__": {"fullname": "bioimageio.core.stat_calculators.SamplePercentilesCalculator.__init__", "modulename": "bioimageio.core.stat_calculators", "qualname": "SamplePercentilesCalculator.__init__", "kind": "function", "doc": "\n", "signature": "(\tmember_id: bioimageio.spec.model.v0_5.TensorId,\taxes: Optional[Sequence[bioimageio.spec.model.v0_5.AxisId]],\tqs: Collection[float])"}, "bioimageio.core.stat_calculators.SamplePercentilesCalculator.compute": {"fullname": "bioimageio.core.stat_calculators.SamplePercentilesCalculator.compute", "modulename": "bioimageio.core.stat_calculators", "qualname": "SamplePercentilesCalculator.compute", "kind": "function", "doc": "\n", "signature": "(\tself,\tsample: bioimageio.core.sample.Sample) -> Dict[bioimageio.core.stat_measures.SampleQuantile, Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanPercentilesCalculator": {"fullname": "bioimageio.core.stat_calculators.MeanPercentilesCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanPercentilesCalculator", "kind": "class", "doc": "to calculate dataset percentiles heuristically by averaging across samples\nnote: the returned dataset percentiles are an estiamte and not mathematically correct
\n"}, "bioimageio.core.stat_calculators.MeanPercentilesCalculator.__init__": {"fullname": "bioimageio.core.stat_calculators.MeanPercentilesCalculator.__init__", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanPercentilesCalculator.__init__", "kind": "function", "doc": "\n", "signature": "(\tmember_id: bioimageio.spec.model.v0_5.TensorId,\taxes: Optional[Sequence[bioimageio.spec.model.v0_5.AxisId]],\tqs: Collection[float])"}, "bioimageio.core.stat_calculators.MeanPercentilesCalculator.update": {"fullname": "bioimageio.core.stat_calculators.MeanPercentilesCalculator.update", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanPercentilesCalculator.update", "kind": "function", "doc": "\n", "signature": "(self, sample: bioimageio.core.sample.Sample):", "funcdef": "def"}, "bioimageio.core.stat_calculators.MeanPercentilesCalculator.finalize": {"fullname": "bioimageio.core.stat_calculators.MeanPercentilesCalculator.finalize", "modulename": "bioimageio.core.stat_calculators", "qualname": "MeanPercentilesCalculator.finalize", "kind": "function", "doc": "\n", "signature": "(\tself) -> Dict[bioimageio.core.stat_measures.DatasetPercentile, Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.CrickPercentilesCalculator": {"fullname": "bioimageio.core.stat_calculators.CrickPercentilesCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "CrickPercentilesCalculator", "kind": "class", "doc": "to calculate dataset percentiles with the experimental crick libray
\n"}, "bioimageio.core.stat_calculators.CrickPercentilesCalculator.__init__": {"fullname": "bioimageio.core.stat_calculators.CrickPercentilesCalculator.__init__", "modulename": "bioimageio.core.stat_calculators", "qualname": "CrickPercentilesCalculator.__init__", "kind": "function", "doc": "\n", "signature": "(\tmember_id: bioimageio.spec.model.v0_5.TensorId,\taxes: Optional[Sequence[bioimageio.spec.model.v0_5.AxisId]],\tqs: Collection[float])"}, "bioimageio.core.stat_calculators.CrickPercentilesCalculator.update": {"fullname": "bioimageio.core.stat_calculators.CrickPercentilesCalculator.update", "modulename": "bioimageio.core.stat_calculators", "qualname": "CrickPercentilesCalculator.update", "kind": "function", "doc": "\n", "signature": "(self, part: bioimageio.core.sample.Sample):", "funcdef": "def"}, "bioimageio.core.stat_calculators.CrickPercentilesCalculator.finalize": {"fullname": "bioimageio.core.stat_calculators.CrickPercentilesCalculator.finalize", "modulename": "bioimageio.core.stat_calculators", "qualname": "CrickPercentilesCalculator.finalize", "kind": "function", "doc": "\n", "signature": "(\tself) -> Dict[bioimageio.core.stat_measures.DatasetPercentile, Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator": {"fullname": "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "NaiveSampleMeasureCalculator", "kind": "class", "doc": "wrapper for measures to match interface of other sample measure calculators
\n"}, "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.__init__": {"fullname": "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.__init__", "modulename": "bioimageio.core.stat_calculators", "qualname": "NaiveSampleMeasureCalculator.__init__", "kind": "function", "doc": "\n", "signature": "(\tmember_id: bioimageio.spec.model.v0_5.TensorId,\tmeasure: Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)])"}, "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.tensor_name": {"fullname": "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.tensor_name", "modulename": "bioimageio.core.stat_calculators", "qualname": "NaiveSampleMeasureCalculator.tensor_name", "kind": "variable", "doc": "\n"}, "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.measure": {"fullname": "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.measure", "modulename": "bioimageio.core.stat_calculators", "qualname": "NaiveSampleMeasureCalculator.measure", "kind": "variable", "doc": "\n"}, "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.compute": {"fullname": "bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator.compute", "modulename": "bioimageio.core.stat_calculators", "qualname": "NaiveSampleMeasureCalculator.compute", "kind": "function", "doc": "\n", "signature": "(\tself,\tsample: bioimageio.core.sample.Sample) -> Dict[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.SampleMeasureCalculator": {"fullname": "bioimageio.core.stat_calculators.SampleMeasureCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "SampleMeasureCalculator", "kind": "variable", "doc": "\n", "default_value": "typing.Union[bioimageio.core.stat_calculators.MeanCalculator, bioimageio.core.stat_calculators.MeanVarStdCalculator, bioimageio.core.stat_calculators.SamplePercentilesCalculator, bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator]"}, "bioimageio.core.stat_calculators.DatasetMeasureCalculator": {"fullname": "bioimageio.core.stat_calculators.DatasetMeasureCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "DatasetMeasureCalculator", "kind": "variable", "doc": "\n", "default_value": "typing.Union[bioimageio.core.stat_calculators.MeanCalculator, bioimageio.core.stat_calculators.MeanVarStdCalculator, bioimageio.core.stat_calculators.MeanPercentilesCalculator]"}, "bioimageio.core.stat_calculators.StatsCalculator": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator", "kind": "class", "doc": "Estimates dataset statistics and computes sample statistics efficiently
\n"}, "bioimageio.core.stat_calculators.StatsCalculator.__init__": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator.__init__", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator.__init__", "kind": "function", "doc": "\n", "signature": "(\tmeasures: Collection[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\tinitial_dataset_measures: Optional[Mapping[Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer>, return_type=PydanticUndefined, when_used='always')]]]] = None)"}, "bioimageio.core.stat_calculators.StatsCalculator.sample_count": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator.sample_count", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator.sample_count", "kind": "variable", "doc": "\n"}, "bioimageio.core.stat_calculators.StatsCalculator.has_dataset_measures": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator.has_dataset_measures", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator.has_dataset_measures", "kind": "variable", "doc": "\n"}, "bioimageio.core.stat_calculators.StatsCalculator.update": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator.update", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator.update", "kind": "function", "doc": "\n", "signature": "(\tself,\tsample: Union[bioimageio.core.sample.Sample, Iterable[bioimageio.core.sample.Sample]]) -> None:", "funcdef": "def"}, "bioimageio.core.stat_calculators.StatsCalculator.finalize": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator.finalize", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator.finalize", "kind": "function", "doc": "returns aggregated dataset statistics
\n", "signature": "(\tself) -> Dict[Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.StatsCalculator.update_and_get_all": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator.update_and_get_all", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator.update_and_get_all", "kind": "function", "doc": "Returns sample as well as updated dataset statistics
\n", "signature": "(\tself,\tsample: Union[bioimageio.core.sample.Sample, Iterable[bioimageio.core.sample.Sample]]) -> Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.StatsCalculator.skip_update_and_get_all": {"fullname": "bioimageio.core.stat_calculators.StatsCalculator.skip_update_and_get_all", "modulename": "bioimageio.core.stat_calculators", "qualname": "StatsCalculator.skip_update_and_get_all", "kind": "function", "doc": "Returns sample as well as previously computed dataset statistics
\n", "signature": "(\tself,\tsample: bioimageio.core.sample.Sample) -> Dict[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.get_measure_calculators": {"fullname": "bioimageio.core.stat_calculators.get_measure_calculators", "modulename": "bioimageio.core.stat_calculators", "qualname": "get_measure_calculators", "kind": "function", "doc": "determines which calculators are needed to compute the required measures efficiently
\n", "signature": "(\trequired_measures: Iterable[Annotated[Union[Annotated[Union[bioimageio.core.stat_measures.SampleMean, bioimageio.core.stat_measures.SampleStd, bioimageio.core.stat_measures.SampleVar, bioimageio.core.stat_measures.SampleQuantile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.core.stat_measures.DatasetMean, bioimageio.core.stat_measures.DatasetStd, bioimageio.core.stat_measures.DatasetVar, bioimageio.core.stat_measures.DatasetPercentile], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='scope', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]) -> Tuple[List[Union[bioimageio.core.stat_calculators.MeanCalculator, bioimageio.core.stat_calculators.MeanVarStdCalculator, bioimageio.core.stat_calculators.SamplePercentilesCalculator, bioimageio.core.stat_calculators.NaiveSampleMeasureCalculator]], List[Union[bioimageio.core.stat_calculators.MeanCalculator, bioimageio.core.stat_calculators.MeanVarStdCalculator, bioimageio.core.stat_calculators.MeanPercentilesCalculator]]]:", "funcdef": "def"}, "bioimageio.core.stat_calculators.compute_dataset_measures": {"fullname": "bioimageio.core.stat_calculators.compute_dataset_measures", "modulename": "bioimageio.core.stat_calculators", "qualname": "compute_dataset_measures", "kind": "function", "doc": "compute all dataset measures
for the given dataset
compute all sample measures
for the given sample
compute all measures
for the given dataset
\nsample measures are computed for the last sample in dataset
Base class for protocol classes.
\n\nProtocol classes are defined as::
\n\nclass Proto(Protocol):\n def meth(self) -> int:\n ...\n
\n\nSuch classes are primarily used with static type checkers that recognize\nstructural subtyping (static duck-typing).
\n\nFor example::
\n\nclass C:\n def meth(self) -> int:\n return 0\n\ndef func(x: Proto) -> int:\n return x.meth()\n\nfunc(C()) # Passes static type check\n
\n\nSee PEP 544 for details. Protocol classes decorated with\n@typing.runtime_checkable act as simple-minded runtime protocols that check\nonly the presence of given attributes, ignoring their type signatures.\nProtocol classes can be generic, they are defined as::
\n\nclass GenProto[T](Protocol):\n def meth(self) -> T:\n ...\n
\n", "bases": "typing.Protocol"}, "bioimageio.core.stat_measures.SampleLike.__init__": {"fullname": "bioimageio.core.stat_measures.SampleLike.__init__", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleLike.__init__", "kind": "function", "doc": "\n", "signature": "(*args, **kwargs)"}, "bioimageio.core.stat_measures.SampleLike.members": {"fullname": "bioimageio.core.stat_measures.SampleLike.members", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleLike.members", "kind": "variable", "doc": "\n", "annotation": ": Mapping[bioimageio.spec.model.v0_5.TensorId, bioimageio.core.tensor.Tensor]"}, "bioimageio.core.stat_measures.MeasureBase": {"fullname": "bioimageio.core.stat_measures.MeasureBase", "modulename": "bioimageio.core.stat_measures", "qualname": "MeasureBase", "kind": "class", "doc": "Usage docs: https://docs.pydantic.dev/2.9/concepts/models/
\n\nA base class for creating Pydantic models.
\n\n__init__
[Signature
][inspect.Signature] of the model.__init__
function.Model.__validators__
and Model.__root_validators__
from Pydantic V1.RootModel
][pydantic.root_model.RootModel].pydantic-core
SchemaSerializer
used to dump instances of the model.pydantic-core
SchemaValidator
used to validate instances of the model.extra
][pydantic.config.ConfigDict.extra]\nis set to 'allow'
.Usage docs: https://docs.pydantic.dev/2.9/concepts/models/
\n\nA base class for creating Pydantic models.
\n\n__init__
[Signature
][inspect.Signature] of the model.__init__
function.Model.__validators__
and Model.__root_validators__
from Pydantic V1.RootModel
][pydantic.root_model.RootModel].pydantic-core
SchemaSerializer
used to dump instances of the model.pydantic-core
SchemaValidator
used to validate instances of the model.extra
][pydantic.config.ConfigDict.extra]\nis set to 'allow'
.compute the measure
\n", "signature": "(\tself,\tsample: bioimageio.core.stat_measures.SampleLike) -> Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]:", "funcdef": "def"}, "bioimageio.core.stat_measures.DatasetMeasureBase": {"fullname": "bioimageio.core.stat_measures.DatasetMeasureBase", "modulename": "bioimageio.core.stat_measures", "qualname": "DatasetMeasureBase", "kind": "class", "doc": "Usage docs: https://docs.pydantic.dev/2.9/concepts/models/
\n\nA base class for creating Pydantic models.
\n\n__init__
[Signature
][inspect.Signature] of the model.__init__
function.Model.__validators__
and Model.__root_validators__
from Pydantic V1.RootModel
][pydantic.root_model.RootModel].pydantic-core
SchemaSerializer
used to dump instances of the model.pydantic-core
SchemaValidator
used to validate instances of the model.extra
][pydantic.config.ConfigDict.extra]\nis set to 'allow'
.The mean value of a single tensor
\n", "bases": "_Mean, SampleMeasureBase"}, "bioimageio.core.stat_measures.SampleMean.compute": {"fullname": "bioimageio.core.stat_measures.SampleMean.compute", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleMean.compute", "kind": "function", "doc": "compute the measure
\n", "signature": "(\tself,\tsample: bioimageio.core.stat_measures.SampleLike) -> Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]:", "funcdef": "def"}, "bioimageio.core.stat_measures.SampleMean.model_post_init": {"fullname": "bioimageio.core.stat_measures.SampleMean.model_post_init", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleMean.model_post_init", "kind": "function", "doc": "Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
The mean value across multiple samples
\n", "bases": "_Mean, DatasetMeasureBase"}, "bioimageio.core.stat_measures.DatasetMean.model_post_init": {"fullname": "bioimageio.core.stat_measures.DatasetMean.model_post_init", "modulename": "bioimageio.core.stat_measures", "qualname": "DatasetMean.model_post_init", "kind": "function", "doc": "Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
The standard deviation of a single tensor
\n", "bases": "_Std, SampleMeasureBase"}, "bioimageio.core.stat_measures.SampleStd.compute": {"fullname": "bioimageio.core.stat_measures.SampleStd.compute", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleStd.compute", "kind": "function", "doc": "compute the measure
\n", "signature": "(\tself,\tsample: bioimageio.core.stat_measures.SampleLike) -> Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]:", "funcdef": "def"}, "bioimageio.core.stat_measures.SampleStd.model_post_init": {"fullname": "bioimageio.core.stat_measures.SampleStd.model_post_init", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleStd.model_post_init", "kind": "function", "doc": "Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
The standard deviation across multiple samples
\n", "bases": "_Std, DatasetMeasureBase"}, "bioimageio.core.stat_measures.DatasetStd.model_post_init": {"fullname": "bioimageio.core.stat_measures.DatasetStd.model_post_init", "modulename": "bioimageio.core.stat_measures", "qualname": "DatasetStd.model_post_init", "kind": "function", "doc": "Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
The variance of a single tensor
\n", "bases": "_Var, SampleMeasureBase"}, "bioimageio.core.stat_measures.SampleVar.compute": {"fullname": "bioimageio.core.stat_measures.SampleVar.compute", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleVar.compute", "kind": "function", "doc": "compute the measure
\n", "signature": "(\tself,\tsample: bioimageio.core.stat_measures.SampleLike) -> Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]:", "funcdef": "def"}, "bioimageio.core.stat_measures.SampleVar.model_post_init": {"fullname": "bioimageio.core.stat_measures.SampleVar.model_post_init", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleVar.model_post_init", "kind": "function", "doc": "Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
The variance across multiple samples
\n", "bases": "_Var, DatasetMeasureBase"}, "bioimageio.core.stat_measures.DatasetVar.model_post_init": {"fullname": "bioimageio.core.stat_measures.DatasetVar.model_post_init", "modulename": "bioimageio.core.stat_measures", "qualname": "DatasetVar.model_post_init", "kind": "function", "doc": "Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
The n
th percentile of a single tensor
compute the measure
\n", "signature": "(\tself,\tsample: bioimageio.core.stat_measures.SampleLike) -> Union[float, Annotated[bioimageio.core.tensor.Tensor, BeforeValidator(func=<function tensor_custom_before_validator at 0x7f1c4fafe840>, json_schema_input_type=PydanticUndefined), PlainSerializer(func=<function tensor_custom_serializer at 0x7f1c4fafea20>, return_type=PydanticUndefined, when_used='always')]]:", "funcdef": "def"}, "bioimageio.core.stat_measures.SampleQuantile.model_post_init": {"fullname": "bioimageio.core.stat_measures.SampleQuantile.model_post_init", "modulename": "bioimageio.core.stat_measures", "qualname": "SampleQuantile.model_post_init", "kind": "function", "doc": "Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
The n
th percentile across multiple samples
Override this method to perform additional initialization after __init__
and model_construct
.\nThis is useful if you want to do some validation that requires the entire model to be initialized.
A wrapper around an xr.DataArray for better integration with bioimageio.spec\nand improved type annotations.
\n", "bases": "bioimageio.core._magic_tensor_ops.MagicTensorOpsMixin"}, "bioimageio.core.tensor.Tensor.__init__": {"fullname": "bioimageio.core.tensor.Tensor.__init__", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.__init__", "kind": "function", "doc": "\n", "signature": "(\tarray: numpy.ndarray[typing.Any, numpy.dtype[typing.Any]],\tdims: Sequence[Union[bioimageio.spec.model.v0_5.AxisId, Literal['b', 'i', 't', 'c', 'z', 'y', 'x'], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexInputAxis, bioimageio.spec.model.v0_5.TimeInputAxis, bioimageio.spec.model.v0_5.SpaceInputAxis], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexOutputAxis, Annotated[Union[Annotated[bioimageio.spec.model.v0_5.TimeOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxis, Tag(tag='wo_halo')], Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.core.axis.Axis]])"}, "bioimageio.core.tensor.Tensor.from_xarray": {"fullname": "bioimageio.core.tensor.Tensor.from_xarray", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.from_xarray", "kind": "function", "doc": "create a Tensor
from an xarray data array
note for internal use: this factory method is round-trip save\n for any Tensor
's data
property (an xarray.DataArray).
create a Tensor
from a numpy array
axes
is None and axes guessing fails.Tuple of dimension names associated with this tensor.
\n"}, "bioimageio.core.tensor.Tensor.tagged_shape": {"fullname": "bioimageio.core.tensor.Tensor.tagged_shape", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.tagged_shape", "kind": "variable", "doc": "(alias for sizes
) Ordered, immutable mapping from axis ids to lengths.
Tuple of tensor axes lengths
\n"}, "bioimageio.core.tensor.Tensor.size": {"fullname": "bioimageio.core.tensor.Tensor.size", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.size", "kind": "variable", "doc": "Number of elements in the tensor.
\n\nEqual to math.prod(tensor.shape), i.e., the product of the tensors\u2019 dimensions.
\n"}, "bioimageio.core.tensor.Tensor.sum": {"fullname": "bioimageio.core.tensor.Tensor.sum", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.sum", "kind": "function", "doc": "Reduce this Tensor's data by applying sum along some dimension(s).
\n", "signature": "(\tself,\tdim: Union[bioimageio.spec.model.v0_5.AxisId, Sequence[bioimageio.spec.model.v0_5.AxisId], NoneType] = None) -> Self:", "funcdef": "def"}, "bioimageio.core.tensor.Tensor.ndim": {"fullname": "bioimageio.core.tensor.Tensor.ndim", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.ndim", "kind": "variable", "doc": "Number of tensor dimensions.
\n"}, "bioimageio.core.tensor.Tensor.dtype": {"fullname": "bioimageio.core.tensor.Tensor.dtype", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.dtype", "kind": "variable", "doc": "\n", "annotation": ": Literal['bool', 'float32', 'float64', 'int8', 'int16', 'int32', 'int64', 'uint8', 'uint16', 'uint32', 'uint64']"}, "bioimageio.core.tensor.Tensor.sizes": {"fullname": "bioimageio.core.tensor.Tensor.sizes", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.sizes", "kind": "variable", "doc": "Ordered, immutable mapping from axis ids to axis lengths.
\n"}, "bioimageio.core.tensor.Tensor.astype": {"fullname": "bioimageio.core.tensor.Tensor.astype", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.astype", "kind": "function", "doc": "Return tensor cast to dtype
note: if dtype is already satisfied copy if copy
Return a tensor whose values are limited to [min, max].\nAt least one of max or min must be given.
\n", "signature": "(self, min: Optional[float] = None, max: Optional[float] = None):", "funcdef": "def"}, "bioimageio.core.tensor.Tensor.crop_to": {"fullname": "bioimageio.core.tensor.Tensor.crop_to", "modulename": "bioimageio.core.tensor", "qualname": "Tensor.crop_to", "kind": "function", "doc": "crop to match sizes
pad tensor
to match sizes
return cropped/padded tensor with sizes
return a transposed tensor
\n\nBioimage.io description of an application.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.ApplicationDescr.type": {"fullname": "bioimageio.spec.ApplicationDescr.type", "modulename": "bioimageio.spec", "qualname": "ApplicationDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['application']"}, "bioimageio.spec.ApplicationDescr.id": {"fullname": "bioimageio.spec.ApplicationDescr.id", "modulename": "bioimageio.spec", "qualname": "ApplicationDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.application.v0_3.ApplicationId]"}, "bioimageio.spec.ApplicationDescr.parent": {"fullname": "bioimageio.spec.ApplicationDescr.parent", "modulename": "bioimageio.spec", "qualname": "ApplicationDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.application.v0_3.ApplicationId]"}, "bioimageio.spec.ApplicationDescr.source": {"fullname": "bioimageio.spec.ApplicationDescr.source", "modulename": "bioimageio.spec", "qualname": "ApplicationDescr.source", "kind": "variable", "doc": "The primary source of the application
\n", "annotation": ": Annotated[Optional[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')]], FieldInfo(annotation=NoneType, required=True, description='URL or path to the source of the application')]"}, "bioimageio.spec.ApplicationDescr.implemented_format_version": {"fullname": "bioimageio.spec.ApplicationDescr.implemented_format_version", "modulename": "bioimageio.spec", "qualname": "ApplicationDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.ApplicationDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.ApplicationDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec", "qualname": "ApplicationDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.ApplicationDescr.model_post_init": {"fullname": "bioimageio.spec.ApplicationDescr.model_post_init", "modulename": "bioimageio.spec", "qualname": "ApplicationDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.build_description": {"fullname": "bioimageio.spec.build_description", "modulename": "bioimageio.spec", "qualname": "build_description", "kind": "function", "doc": "build a bioimage.io resource description from an RDF's content.
\n\nUse load_description
if you want to build a resource description from an rdf.yaml\nor bioimage.io zip-package.
\n\n", "signature": "(\tcontent: Dict[str, YamlValue],\t/,\t*,\tcontext: Optional[bioimageio.spec._internal.validation_context.ValidationContext] = None,\tformat_version: Union[Literal['latest', 'discover'], str] = 'discover') -> Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec._internal.common_nodes.InvalidDescr]:", "funcdef": "def"}, "bioimageio.spec.DatasetDescr": {"fullname": "bioimageio.spec.DatasetDescr", "modulename": "bioimageio.spec", "qualname": "DatasetDescr", "kind": "class", "doc": "An object holding all metadata of the bioimage.io resource
\n
A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage\nprocessing.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.DatasetDescr.type": {"fullname": "bioimageio.spec.DatasetDescr.type", "modulename": "bioimageio.spec", "qualname": "DatasetDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['dataset']"}, "bioimageio.spec.DatasetDescr.id": {"fullname": "bioimageio.spec.DatasetDescr.id", "modulename": "bioimageio.spec", "qualname": "DatasetDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.dataset.v0_3.DatasetId]"}, "bioimageio.spec.DatasetDescr.parent": {"fullname": "bioimageio.spec.DatasetDescr.parent", "modulename": "bioimageio.spec", "qualname": "DatasetDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.dataset.v0_3.DatasetId]"}, "bioimageio.spec.DatasetDescr.source": {"fullname": "bioimageio.spec.DatasetDescr.source", "modulename": "bioimageio.spec", "qualname": "DatasetDescr.source", "kind": "variable", "doc": "\"URL to the source of the dataset.
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.DatasetDescr.implemented_format_version": {"fullname": "bioimageio.spec.DatasetDescr.implemented_format_version", "modulename": "bioimageio.spec", "qualname": "DatasetDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.DatasetDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.DatasetDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec", "qualname": "DatasetDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.DatasetDescr.model_post_init": {"fullname": "bioimageio.spec.DatasetDescr.model_post_init", "modulename": "bioimageio.spec", "qualname": "DatasetDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.dump_description": {"fullname": "bioimageio.spec.dump_description", "modulename": "bioimageio.spec", "qualname": "dump_description", "kind": "function", "doc": "Converts a resource to a dictionary containing only simple types that can directly be serialzed to YAML.
\n", "signature": "(\trd: Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec._internal.common_nodes.InvalidDescr],\texclude_unset: bool = True) -> Dict[str, YamlValue]:", "funcdef": "def"}, "bioimageio.spec.enable_pretty_validation_errors_in_ipynb": {"fullname": "bioimageio.spec.enable_pretty_validation_errors_in_ipynb", "modulename": "bioimageio.spec", "qualname": "enable_pretty_validation_errors_in_ipynb", "kind": "function", "doc": "A modestly hacky way to display prettified validaiton error messages and traceback\nin interactive Python notebooks
\n", "signature": "():", "funcdef": "def"}, "bioimageio.spec.GenericDescr": {"fullname": "bioimageio.spec.GenericDescr", "modulename": "bioimageio.spec", "qualname": "GenericDescr", "kind": "class", "doc": "Specification of the fields used in a generic bioimage.io-compliant resource description file (RDF).
\n\nAn RDF is a YAML file that describes a resource such as a model, a dataset, or a notebook.\nNote that those resources are described with a type-specific RDF.\nUse this generic resource description, if none of the known specific types matches your resource.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.GenericDescr.type": {"fullname": "bioimageio.spec.GenericDescr.type", "modulename": "bioimageio.spec", "qualname": "GenericDescr.type", "kind": "variable", "doc": "The resource type assigns a broad category to the resource.
\n", "annotation": ": Annotated[str, Annotated[~_StrType, Predicate(str.islower)]]"}, "bioimageio.spec.GenericDescr.id": {"fullname": "bioimageio.spec.GenericDescr.id", "modulename": "bioimageio.spec", "qualname": "GenericDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_3.ResourceId]"}, "bioimageio.spec.GenericDescr.parent": {"fullname": "bioimageio.spec.GenericDescr.parent", "modulename": "bioimageio.spec", "qualname": "GenericDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_3.ResourceId]"}, "bioimageio.spec.GenericDescr.source": {"fullname": "bioimageio.spec.GenericDescr.source", "modulename": "bioimageio.spec", "qualname": "GenericDescr.source", "kind": "variable", "doc": "The primary source of the resource
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.GenericDescr.check_specific_types": {"fullname": "bioimageio.spec.GenericDescr.check_specific_types", "modulename": "bioimageio.spec", "qualname": "GenericDescr.check_specific_types", "kind": "function", "doc": "\n", "signature": "(cls, value: str) -> str:", "funcdef": "def"}, "bioimageio.spec.GenericDescr.implemented_format_version": {"fullname": "bioimageio.spec.GenericDescr.implemented_format_version", "modulename": "bioimageio.spec", "qualname": "GenericDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.GenericDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.GenericDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec", "qualname": "GenericDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.GenericDescr.model_post_init": {"fullname": "bioimageio.spec.GenericDescr.model_post_init", "modulename": "bioimageio.spec", "qualname": "GenericDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.get_resource_package_content": {"fullname": "bioimageio.spec.get_resource_package_content", "modulename": "bioimageio.spec", "qualname": "get_resource_package_content", "kind": "function", "doc": "A representation of an invalid resource description
\n", "bases": "bioimageio.spec._internal.common_nodes.ResourceDescrBase"}, "bioimageio.spec.InvalidDescr.type": {"fullname": "bioimageio.spec.InvalidDescr.type", "modulename": "bioimageio.spec", "qualname": "InvalidDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Any"}, "bioimageio.spec.InvalidDescr.format_version": {"fullname": "bioimageio.spec.InvalidDescr.format_version", "modulename": "bioimageio.spec", "qualname": "InvalidDescr.format_version", "kind": "variable", "doc": "\n", "annotation": ": Any"}, "bioimageio.spec.InvalidDescr.fields_to_set_explicitly": {"fullname": "bioimageio.spec.InvalidDescr.fields_to_set_explicitly", "modulename": "bioimageio.spec", "qualname": "InvalidDescr.fields_to_set_explicitly", "kind": "variable", "doc": "set set these fields explicitly with their default value if they are not set,\nsuch that they are always included even when dumping with 'exlude_unset'
\n", "annotation": ": ClassVar[FrozenSet[LiteralString]]", "default_value": "frozenset()"}, "bioimageio.spec.InvalidDescr.implemented_format_version": {"fullname": "bioimageio.spec.InvalidDescr.implemented_format_version", "modulename": "bioimageio.spec", "qualname": "InvalidDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'unknown'"}, "bioimageio.spec.InvalidDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.InvalidDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec", "qualname": "InvalidDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 0, 0)"}, "bioimageio.spec.InvalidDescr.model_post_init": {"fullname": "bioimageio.spec.InvalidDescr.model_post_init", "modulename": "bioimageio.spec", "qualname": "InvalidDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.LatestResourceDescr": {"fullname": "bioimageio.spec.LatestResourceDescr", "modulename": "bioimageio.spec", "qualname": "LatestResourceDescr", "kind": "variable", "doc": "\n", "default_value": "typing.Union[typing.Annotated[typing.Union[bioimageio.spec.application.v0_3.ApplicationDescr, bioimageio.spec.dataset.v0_3.DatasetDescr, bioimageio.spec.model.v0_5.ModelDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec.generic.v0_3.GenericDescr]"}, "bioimageio.spec.load_dataset_description": {"fullname": "bioimageio.spec.load_dataset_description", "modulename": "bioimageio.spec", "qualname": "load_dataset_description", "kind": "function", "doc": "same as load_description
, but addtionally ensures that the loaded\ndescription is valid and of type 'dataset'.
load a bioimage.io resource description
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], zipfile.ZipFile],\t/,\t*,\tformat_version: Union[Literal['discover'], Literal['latest'], str] = 'discover',\tperform_io_checks: bool = True,\tknown_files: Optional[Dict[str, bioimageio.spec._internal.io_basics.Sha256]] = None) -> bioimageio.spec.summary.ValidationSummary:", "funcdef": "def"}, "bioimageio.spec.load_description": {"fullname": "bioimageio.spec.load_description", "modulename": "bioimageio.spec", "qualname": "load_description", "kind": "function", "doc": "Validation summary of the bioimage.io resource found at
\nsource
.
load a bioimage.io resource description
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], zipfile.ZipFile],\t/,\t*,\tformat_version: Union[Literal['discover'], Literal['latest'], str] = 'discover',\tperform_io_checks: bool = True,\tknown_files: Optional[Dict[str, bioimageio.spec._internal.io_basics.Sha256]] = None) -> Union[Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], bioimageio.spec._internal.common_nodes.InvalidDescr]:", "funcdef": "def"}, "bioimageio.spec.load_model_description": {"fullname": "bioimageio.spec.load_model_description", "modulename": "bioimageio.spec", "qualname": "load_model_description", "kind": "function", "doc": "An object holding all metadata of the bioimage.io resource
\n
same as load_description
, but addtionally ensures that the loaded\ndescription is valid and of type 'model'.
Specification of the fields used in a bioimage.io-compliant RDF to describe AI models with pretrained weights.\nThese fields are typically stored in a YAML file which we call a model resource description file (model RDF).
\n", "bases": "bioimageio.spec.generic.v0_3.GenericModelDescrBase"}, "bioimageio.spec.ModelDescr.format_version": {"fullname": "bioimageio.spec.ModelDescr.format_version", "modulename": "bioimageio.spec", "qualname": "ModelDescr.format_version", "kind": "variable", "doc": "Version of the bioimage.io model description specification used.\nWhen creating a new model always use the latest micro/patch version described here.\nThe format_version
is important for any consumer software to understand how to parse the fields.
Specialized resource type 'model'
\n", "annotation": ": Literal['model']"}, "bioimageio.spec.ModelDescr.id": {"fullname": "bioimageio.spec.ModelDescr.id", "modulename": "bioimageio.spec", "qualname": "ModelDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.ModelId]"}, "bioimageio.spec.ModelDescr.authors": {"fullname": "bioimageio.spec.ModelDescr.authors", "modulename": "bioimageio.spec", "qualname": "ModelDescr.authors", "kind": "variable", "doc": "The authors are the creators of the model RDF and the primary points of contact.
\n", "annotation": ": Annotated[List[bioimageio.spec.generic.v0_3.Author], MinLen(min_length=1)]"}, "bioimageio.spec.ModelDescr.documentation": {"fullname": "bioimageio.spec.ModelDescr.documentation", "modulename": "bioimageio.spec", "qualname": "ModelDescr.documentation", "kind": "variable", "doc": "\u2208\ud83d\udce6 URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is README.md
. An .md
suffix is mandatory.\nThe documentation should include a '#[#] Validation' (sub)section\nwith details on how to quantitatively validate the model on unseen data.
Describes the input tensors expected by this model.
\n", "annotation": ": Annotated[Sequence[bioimageio.spec.model.v0_5.InputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.ModelDescr.name": {"fullname": "bioimageio.spec.ModelDescr.name", "modulename": "bioimageio.spec", "qualname": "ModelDescr.name", "kind": "variable", "doc": "A human-readable name of this model.\nIt should be no longer than 64 characters\nand may only contain letter, number, underscore, minus, parentheses and spaces.\nWe recommend to chose a name that refers to the model's task and image modality.
\n", "annotation": ": Annotated[str, RestrictCharacters(alphabet='abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_- ()'), MinLen(min_length=5), MaxLen(max_length=128), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f1c4d1a20c0>, severity=20, msg='Name longer than 64 characters.', context={'typ': Annotated[Any, MaxLen(max_length=64)]})]"}, "bioimageio.spec.ModelDescr.outputs": {"fullname": "bioimageio.spec.ModelDescr.outputs", "modulename": "bioimageio.spec", "qualname": "ModelDescr.outputs", "kind": "variable", "doc": "Describes the output tensors.
\n", "annotation": ": Annotated[Sequence[bioimageio.spec.model.v0_5.OutputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.ModelDescr.packaged_by": {"fullname": "bioimageio.spec.ModelDescr.packaged_by", "modulename": "bioimageio.spec", "qualname": "ModelDescr.packaged_by", "kind": "variable", "doc": "The persons that have packaged and uploaded this model.\nOnly required if those persons differ from the authors
.
The model from which this model is derived, e.g. by fine-tuning the weights.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.LinkedModel]"}, "bioimageio.spec.ModelDescr.run_mode": {"fullname": "bioimageio.spec.ModelDescr.run_mode", "modulename": "bioimageio.spec", "qualname": "ModelDescr.run_mode", "kind": "variable", "doc": "Custom run mode for this model: for more complex prediction procedures like test time\ndata augmentation that currently cannot be expressed in the specification.\nNo standard run modes are defined yet.
\n", "annotation": ": Annotated[Optional[bioimageio.spec.model.v0_4.RunMode], AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f1c4d1a2520>, severity=30, msg="Run mode '{value}' has limited support across consumer softwares.", context={'typ': None})]"}, "bioimageio.spec.ModelDescr.timestamp": {"fullname": "bioimageio.spec.ModelDescr.timestamp", "modulename": "bioimageio.spec", "qualname": "ModelDescr.timestamp", "kind": "variable", "doc": "Timestamp in ISO 8601 format\nwith a few restrictions listed here.\n(In Python a datetime object is valid, too).
\n", "annotation": ": bioimageio.spec._internal.types.Datetime"}, "bioimageio.spec.ModelDescr.training_data": {"fullname": "bioimageio.spec.ModelDescr.training_data", "modulename": "bioimageio.spec", "qualname": "ModelDescr.training_data", "kind": "variable", "doc": "The dataset used to train this model
\n", "annotation": ": Annotated[Union[NoneType, bioimageio.spec.dataset.v0_3.LinkedDataset, bioimageio.spec.dataset.v0_3.DatasetDescr, bioimageio.spec.dataset.v0_2.DatasetDescr], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]"}, "bioimageio.spec.ModelDescr.weights": {"fullname": "bioimageio.spec.ModelDescr.weights", "modulename": "bioimageio.spec", "qualname": "ModelDescr.weights", "kind": "variable", "doc": "The weights for this model.\nWeights can be given for different formats, but should otherwise be equivalent.\nThe available weight formats determine which consumers can use this model.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.WeightsDescr, WrapSerializer(func=<function package_weights at 0x7f1c5bd54360>, return_type=PydanticUndefined, when_used='always')]"}, "bioimageio.spec.ModelDescr.get_input_test_arrays": {"fullname": "bioimageio.spec.ModelDescr.get_input_test_arrays", "modulename": "bioimageio.spec", "qualname": "ModelDescr.get_input_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.ModelDescr.get_output_test_arrays": {"fullname": "bioimageio.spec.ModelDescr.get_output_test_arrays", "modulename": "bioimageio.spec", "qualname": "ModelDescr.get_output_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.ModelDescr.get_batch_size": {"fullname": "bioimageio.spec.ModelDescr.get_batch_size", "modulename": "bioimageio.spec", "qualname": "ModelDescr.get_batch_size", "kind": "function", "doc": "\n", "signature": "(\ttensor_sizes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]) -> int:", "funcdef": "def"}, "bioimageio.spec.ModelDescr.get_output_tensor_sizes": {"fullname": "bioimageio.spec.ModelDescr.get_output_tensor_sizes", "modulename": "bioimageio.spec", "qualname": "ModelDescr.get_output_tensor_sizes", "kind": "function", "doc": "Returns the tensor output sizes for given input_sizes.\nOnly if input_sizes has a valid input shape, the tensor output size is exact.\nOtherwise it might be larger than the actual (valid) output
\n", "signature": "(\tself,\tinput_sizes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]) -> Dict[bioimageio.spec.model.v0_5.TensorId, Dict[bioimageio.spec.model.v0_5.AxisId, Union[int, bioimageio.spec.model.v0_5._DataDepSize]]]:", "funcdef": "def"}, "bioimageio.spec.ModelDescr.get_ns": {"fullname": "bioimageio.spec.ModelDescr.get_ns", "modulename": "bioimageio.spec", "qualname": "ModelDescr.get_ns", "kind": "function", "doc": "get parameter n
for each parameterized axis\nsuch that the valid input size is >= the given input size
Determine input and output block shape for scale factors ns\nof parameterized input sizes.
\n\nn
for each axis (keyed by (tensor_id, axis_id))\nthat is parameterized as size = min + n * step
.n
, is larger\nthan max_input_shape is set to the minimal value n_min
for which\nthis is still true.\nUse this for small input samples or large values of ns.\nOr simply whenever you know the full input shape.\n\n", "signature": "(\tself,\tns: Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int],\tbatch_size: Optional[int] = None,\t*,\tmax_input_shape: Optional[Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int]] = None) -> bioimageio.spec.model.v0_5._AxisSizes:", "funcdef": "def"}, "bioimageio.spec.ModelDescr.implemented_format_version": {"fullname": "bioimageio.spec.ModelDescr.implemented_format_version", "modulename": "bioimageio.spec", "qualname": "ModelDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.5.3'"}, "bioimageio.spec.ModelDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.ModelDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec", "qualname": "ModelDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 5, 3)"}, "bioimageio.spec.ModelDescr.model_post_init": {"fullname": "bioimageio.spec.ModelDescr.model_post_init", "modulename": "bioimageio.spec", "qualname": "ModelDescr.model_post_init", "kind": "function", "doc": "Resolved axis sizes for model inputs and outputs.
\n
We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.NotebookDescr": {"fullname": "bioimageio.spec.NotebookDescr", "modulename": "bioimageio.spec", "qualname": "NotebookDescr", "kind": "class", "doc": "Bioimage.io description of a Jupyter notebook.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.NotebookDescr.type": {"fullname": "bioimageio.spec.NotebookDescr.type", "modulename": "bioimageio.spec", "qualname": "NotebookDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['notebook']"}, "bioimageio.spec.NotebookDescr.id": {"fullname": "bioimageio.spec.NotebookDescr.id", "modulename": "bioimageio.spec", "qualname": "NotebookDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.notebook.v0_3.NotebookId]"}, "bioimageio.spec.NotebookDescr.parent": {"fullname": "bioimageio.spec.NotebookDescr.parent", "modulename": "bioimageio.spec", "qualname": "NotebookDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.notebook.v0_3.NotebookId]"}, "bioimageio.spec.NotebookDescr.source": {"fullname": "bioimageio.spec.NotebookDescr.source", "modulename": "bioimageio.spec", "qualname": "NotebookDescr.source", "kind": "variable", "doc": "The Jupyter notebook
\n", "annotation": ": Union[Annotated[bioimageio.spec._internal.url.HttpUrl, WithSuffix(suffix='.ipynb', case_sensitive=True)], Annotated[pathlib.Path, PathType(path_type='file'), Predicate(is_absolute), WithSuffix(suffix='.ipynb', case_sensitive=True)], Annotated[bioimageio.spec._internal.io.RelativeFilePath, WithSuffix(suffix='.ipynb', case_sensitive=True)]]"}, "bioimageio.spec.NotebookDescr.implemented_format_version": {"fullname": "bioimageio.spec.NotebookDescr.implemented_format_version", "modulename": "bioimageio.spec", "qualname": "NotebookDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.NotebookDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.NotebookDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec", "qualname": "NotebookDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.NotebookDescr.model_post_init": {"fullname": "bioimageio.spec.NotebookDescr.model_post_init", "modulename": "bioimageio.spec", "qualname": "NotebookDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.ResourceDescr": {"fullname": "bioimageio.spec.ResourceDescr", "modulename": "bioimageio.spec", "qualname": "ResourceDescr", "kind": "variable", "doc": "\n", "default_value": "typing.Union[typing.Annotated[typing.Union[typing.Annotated[typing.Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.spec.save_bioimageio_package_as_folder": {"fullname": "bioimageio.spec.save_bioimageio_package_as_folder", "modulename": "bioimageio.spec", "qualname": "save_bioimageio_package_as_folder", "kind": "function", "doc": "Write the content of a bioimage.io resource package to a folder.
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], Dict[str, YamlValue], Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\t/,\t*,\toutput_path: Union[Annotated[pathlib.Path, PathType(path_type='new')], Annotated[pathlib.Path, PathType(path_type='dir')], NoneType] = None,\tweights_priority_order: Optional[Sequence[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]] = None) -> Annotated[pathlib.Path, PathType(path_type='dir')]:", "funcdef": "def"}, "bioimageio.spec.save_bioimageio_package_to_stream": {"fullname": "bioimageio.spec.save_bioimageio_package_to_stream", "modulename": "bioimageio.spec", "qualname": "save_bioimageio_package_to_stream", "kind": "function", "doc": "directory path to bioimageio package folder
\n
Package a bioimageio resource into a stream.
\n\nNote: this function bypasses safety checks and does not load/validate the model after writing.
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], Dict[str, YamlValue], Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\t/,\t*,\tcompression: int = 8,\tcompression_level: int = 1,\toutput_stream: Optional[IO[bytes]] = None,\tweights_priority_order: Optional[Sequence[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]] = None) -> IO[bytes]:", "funcdef": "def"}, "bioimageio.spec.save_bioimageio_package": {"fullname": "bioimageio.spec.save_bioimageio_package", "modulename": "bioimageio.spec", "qualname": "save_bioimageio_package", "kind": "function", "doc": "stream of zipped bioimageio package
\n
Package a bioimageio resource as a zip file.
\n\n\n\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], Dict[str, YamlValue], Annotated[Union[Annotated[Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.notebook.v0_2.NotebookDescr, bioimageio.spec.notebook.v0_3.NotebookDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], Annotated[Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]],\t/,\t*,\tcompression: int = 8,\tcompression_level: int = 1,\toutput_path: Union[Annotated[pathlib.Path, PathType(path_type='new')], Annotated[pathlib.Path, PathType(path_type='file')], NoneType] = None,\tweights_priority_order: Optional[Sequence[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]] = None) -> Annotated[pathlib.Path, PathType(path_type='file')]:", "funcdef": "def"}, "bioimageio.spec.save_bioimageio_yaml_only": {"fullname": "bioimageio.spec.save_bioimageio_yaml_only", "modulename": "bioimageio.spec", "qualname": "save_bioimageio_yaml_only", "kind": "function", "doc": "path to zipped bioimageio package
\n
write the metadata of a resource description (rd
) to file
\nwithout writing any of the referenced files in it.
Note: To save a resource description with its associated files as a package,\nuse save_bioimageio_package
or save_bioimageio_package_as_folder
.
validate a bioimageio.yaml file (RDF)
\n", "signature": "(\tdata: Dict[str, YamlValue],\t/,\t*,\tformat_version: Union[Literal['latest', 'discover'], str] = 'discover',\tcontext: Optional[bioimageio.spec._internal.validation_context.ValidationContext] = None) -> bioimageio.spec.summary.ValidationSummary:", "funcdef": "def"}, "bioimageio.spec.ValidationContext": {"fullname": "bioimageio.spec.ValidationContext", "modulename": "bioimageio.spec", "qualname": "ValidationContext", "kind": "class", "doc": "\n"}, "bioimageio.spec.ValidationContext.__init__": {"fullname": "bioimageio.spec.ValidationContext.__init__", "modulename": "bioimageio.spec", "qualname": "ValidationContext.__init__", "kind": "function", "doc": "\n", "signature": "(\troot: Union[bioimageio.spec._internal.root_url.RootHttpUrl, Annotated[pathlib.Path, PathType(path_type='dir'), Predicate(is_absolute)], zipfile.ZipFile] = PosixPath('.'),\twarning_level: Literal[20, 30, 35, 50] = 50,\tlog_warnings: bool = True,\tfile_name: Optional[str] = None,\tperform_io_checks: bool = True,\tknown_files: Dict[str, bioimageio.spec._internal.io_basics.Sha256] = <factory>)"}, "bioimageio.spec.ValidationContext.root": {"fullname": "bioimageio.spec.ValidationContext.root", "modulename": "bioimageio.spec", "qualname": "ValidationContext.root", "kind": "variable", "doc": "url/directory serving as base to resolve any relative file paths
\n", "annotation": ": Union[bioimageio.spec._internal.root_url.RootHttpUrl, Annotated[pathlib.Path, PathType(path_type='dir'), Predicate(is_absolute)], zipfile.ZipFile]", "default_value": "PosixPath('.')"}, "bioimageio.spec.ValidationContext.warning_level": {"fullname": "bioimageio.spec.ValidationContext.warning_level", "modulename": "bioimageio.spec", "qualname": "ValidationContext.warning_level", "kind": "variable", "doc": "raise warnings of severity s
as validation errors if s >= warning_level
if True
log warnings that are not raised to the console
file name of the bioimageio Yaml file
\n", "annotation": ": Optional[str]", "default_value": "None"}, "bioimageio.spec.ValidationContext.perform_io_checks": {"fullname": "bioimageio.spec.ValidationContext.perform_io_checks", "modulename": "bioimageio.spec", "qualname": "ValidationContext.perform_io_checks", "kind": "variable", "doc": "wether or not to perform validation that requires file io,\ne.g. downloading a remote files.
\n\nExistence of local absolute file paths is still being checked.
\n", "annotation": ": bool", "default_value": "True"}, "bioimageio.spec.ValidationContext.known_files": {"fullname": "bioimageio.spec.ValidationContext.known_files", "modulename": "bioimageio.spec", "qualname": "ValidationContext.known_files", "kind": "variable", "doc": "allows to bypass download and hashing of referenced files
\n", "annotation": ": Dict[str, bioimageio.spec._internal.io_basics.Sha256]"}, "bioimageio.spec.ValidationContext.replace": {"fullname": "bioimageio.spec.ValidationContext.replace", "modulename": "bioimageio.spec", "qualname": "ValidationContext.replace", "kind": "function", "doc": "\n", "signature": "(\tself,\troot: Union[bioimageio.spec._internal.root_url.RootHttpUrl, Annotated[pathlib.Path, PathType(path_type='dir')], zipfile.ZipFile, NoneType] = None,\twarning_level: Optional[Literal[20, 30, 35, 50]] = None,\tlog_warnings: Optional[bool] = None,\tfile_name: Optional[str] = None,\tperform_io_checks: Optional[bool] = None,\tknown_files: Optional[Dict[str, bioimageio.spec._internal.io_basics.Sha256]] = None) -> bioimageio.spec._internal.validation_context.ValidationContext:", "funcdef": "def"}, "bioimageio.spec.ValidationContext.source_name": {"fullname": "bioimageio.spec.ValidationContext.source_name", "modulename": "bioimageio.spec", "qualname": "ValidationContext.source_name", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.ValidationSummary": {"fullname": "bioimageio.spec.ValidationSummary", "modulename": "bioimageio.spec", "qualname": "ValidationSummary", "kind": "class", "doc": "Summarizes output of all bioimageio validations and tests\nfor one specific ResourceDescr
instance.
list of selected, relevant package versions
\n", "annotation": ": Set[bioimageio.spec.summary.InstalledPackage]"}, "bioimageio.spec.ValidationSummary.conda_list": {"fullname": "bioimageio.spec.ValidationSummary.conda_list", "modulename": "bioimageio.spec", "qualname": "ValidationSummary.conda_list", "kind": "variable", "doc": "parsed output of conda list
\n", "annotation": ": Optional[Sequence[bioimageio.spec.summary.InstalledPackage]]"}, "bioimageio.spec.ValidationSummary.status_icon": {"fullname": "bioimageio.spec.ValidationSummary.status_icon", "modulename": "bioimageio.spec", "qualname": "ValidationSummary.status_icon", "kind": "variable", "doc": "\n"}, "bioimageio.spec.ValidationSummary.errors": {"fullname": "bioimageio.spec.ValidationSummary.errors", "modulename": "bioimageio.spec", "qualname": "ValidationSummary.errors", "kind": "variable", "doc": "\n", "annotation": ": List[bioimageio.spec.summary.ErrorEntry]"}, "bioimageio.spec.ValidationSummary.warnings": {"fullname": "bioimageio.spec.ValidationSummary.warnings", "modulename": "bioimageio.spec", "qualname": "ValidationSummary.warnings", "kind": "variable", "doc": "\n", "annotation": ": List[bioimageio.spec.summary.WarningEntry]"}, "bioimageio.spec.ValidationSummary.format": {"fullname": "bioimageio.spec.ValidationSummary.format", "modulename": "bioimageio.spec", "qualname": "ValidationSummary.format", "kind": "function", "doc": "Format summary as Markdown string
\n\n Suitable to embed in HTML using '<br>' instead of '\n
\n\n'.
\n", "signature": "(\tself,\thide_tracebacks: bool = False,\thide_source: bool = False,\thide_env: bool = False,\troot_loc: Tuple[Union[int, str], ...] = ()) -> str:", "funcdef": "def"}, "bioimageio.spec.ValidationSummary.display": {"fullname": "bioimageio.spec.ValidationSummary.display", "modulename": "bioimageio.spec", "qualname": "ValidationSummary.display", "kind": "function", "doc": "\n", "signature": "(self) -> None:", "funcdef": "def"}, "bioimageio.spec.ValidationSummary.add_detail": {"fullname": "bioimageio.spec.ValidationSummary.add_detail", "modulename": "bioimageio.spec", "qualname": "ValidationSummary.add_detail", "kind": "function", "doc": "\n", "signature": "(self, detail: bioimageio.spec.summary.ValidationDetail):", "funcdef": "def"}, "bioimageio.spec.application": {"fullname": "bioimageio.spec.application", "modulename": "bioimageio.spec.application", "kind": "module", "doc": "implementaions of all released minor versions are available in submodules:
\n\nbioimageio.spec.application.v0_2.ApplicationDescr
bioimageio.spec.application.v0_3.ApplicationDescr
Bioimage.io description of an application.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.application.ApplicationDescr.type": {"fullname": "bioimageio.spec.application.ApplicationDescr.type", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['application']"}, "bioimageio.spec.application.ApplicationDescr.id": {"fullname": "bioimageio.spec.application.ApplicationDescr.id", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.application.v0_3.ApplicationId]"}, "bioimageio.spec.application.ApplicationDescr.parent": {"fullname": "bioimageio.spec.application.ApplicationDescr.parent", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.application.v0_3.ApplicationId]"}, "bioimageio.spec.application.ApplicationDescr.source": {"fullname": "bioimageio.spec.application.ApplicationDescr.source", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr.source", "kind": "variable", "doc": "The primary source of the application
\n", "annotation": ": Annotated[Optional[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')]], FieldInfo(annotation=NoneType, required=True, description='URL or path to the source of the application')]"}, "bioimageio.spec.application.ApplicationDescr.implemented_format_version": {"fullname": "bioimageio.spec.application.ApplicationDescr.implemented_format_version", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.application.ApplicationDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.application.ApplicationDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.application.ApplicationDescr.model_post_init": {"fullname": "bioimageio.spec.application.ApplicationDescr.model_post_init", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.application.ApplicationDescr_v0_2": {"fullname": "bioimageio.spec.application.ApplicationDescr_v0_2", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr_v0_2", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.application.v0_2.ApplicationDescr'>"}, "bioimageio.spec.application.ApplicationDescr_v0_3": {"fullname": "bioimageio.spec.application.ApplicationDescr_v0_3", "modulename": "bioimageio.spec.application", "qualname": "ApplicationDescr_v0_3", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.application.v0_3.ApplicationDescr'>"}, "bioimageio.spec.application.AnyApplicationDescr": {"fullname": "bioimageio.spec.application.AnyApplicationDescr", "modulename": "bioimageio.spec.application", "qualname": "AnyApplicationDescr", "kind": "variable", "doc": "Union of any released application desription
\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.application.v0_2.ApplicationDescr, bioimageio.spec.application.v0_3.ApplicationDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]"}, "bioimageio.spec.application.v0_2": {"fullname": "bioimageio.spec.application.v0_2", "modulename": "bioimageio.spec.application.v0_2", "kind": "module", "doc": "\n"}, "bioimageio.spec.application.v0_2.ApplicationId": {"fullname": "bioimageio.spec.application.v0_2.ApplicationId", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec.generic.v0_2.ResourceId"}, "bioimageio.spec.application.v0_2.ApplicationDescr": {"fullname": "bioimageio.spec.application.v0_2.ApplicationDescr", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationDescr", "kind": "class", "doc": "Bioimage.io description of an application.
\n", "bases": "bioimageio.spec.generic.v0_2.GenericDescrBase"}, "bioimageio.spec.application.v0_2.ApplicationDescr.type": {"fullname": "bioimageio.spec.application.v0_2.ApplicationDescr.type", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['application']"}, "bioimageio.spec.application.v0_2.ApplicationDescr.id": {"fullname": "bioimageio.spec.application.v0_2.ApplicationDescr.id", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.application.v0_2.ApplicationId]"}, "bioimageio.spec.application.v0_2.ApplicationDescr.source": {"fullname": "bioimageio.spec.application.v0_2.ApplicationDescr.source", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationDescr.source", "kind": "variable", "doc": "The primary source of the application
\n", "annotation": ": Annotated[Optional[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')]], FieldInfo(annotation=NoneType, required=True, description='URL or path to the source of the application')]"}, "bioimageio.spec.application.v0_2.ApplicationDescr.implemented_format_version": {"fullname": "bioimageio.spec.application.v0_2.ApplicationDescr.implemented_format_version", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.2.4'"}, "bioimageio.spec.application.v0_2.ApplicationDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.application.v0_2.ApplicationDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 2, 4)"}, "bioimageio.spec.application.v0_2.ApplicationDescr.model_post_init": {"fullname": "bioimageio.spec.application.v0_2.ApplicationDescr.model_post_init", "modulename": "bioimageio.spec.application.v0_2", "qualname": "ApplicationDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.application.v0_2.LinkedApplication": {"fullname": "bioimageio.spec.application.v0_2.LinkedApplication", "modulename": "bioimageio.spec.application.v0_2", "qualname": "LinkedApplication", "kind": "class", "doc": "Reference to a bioimage.io application.
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.application.v0_2.LinkedApplication.id": {"fullname": "bioimageio.spec.application.v0_2.LinkedApplication.id", "modulename": "bioimageio.spec.application.v0_2", "qualname": "LinkedApplication.id", "kind": "variable", "doc": "A valid application id
from the bioimage.io collection.
version number (n-th published version, not the semantic version) of linked application
\n", "annotation": ": Optional[int]"}, "bioimageio.spec.application.v0_3": {"fullname": "bioimageio.spec.application.v0_3", "modulename": "bioimageio.spec.application.v0_3", "kind": "module", "doc": "\n"}, "bioimageio.spec.application.v0_3.ApplicationId": {"fullname": "bioimageio.spec.application.v0_3.ApplicationId", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec.generic.v0_3.ResourceId"}, "bioimageio.spec.application.v0_3.ApplicationDescr": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr", "kind": "class", "doc": "Bioimage.io description of an application.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.application.v0_3.ApplicationDescr.type": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr.type", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['application']"}, "bioimageio.spec.application.v0_3.ApplicationDescr.id": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr.id", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.application.v0_3.ApplicationId]"}, "bioimageio.spec.application.v0_3.ApplicationDescr.parent": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr.parent", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.application.v0_3.ApplicationId]"}, "bioimageio.spec.application.v0_3.ApplicationDescr.source": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr.source", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr.source", "kind": "variable", "doc": "The primary source of the application
\n", "annotation": ": Annotated[Optional[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')]], FieldInfo(annotation=NoneType, required=True, description='URL or path to the source of the application')]"}, "bioimageio.spec.application.v0_3.ApplicationDescr.implemented_format_version": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr.implemented_format_version", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.application.v0_3.ApplicationDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.application.v0_3.ApplicationDescr.model_post_init": {"fullname": "bioimageio.spec.application.v0_3.ApplicationDescr.model_post_init", "modulename": "bioimageio.spec.application.v0_3", "qualname": "ApplicationDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.application.v0_3.LinkedApplication": {"fullname": "bioimageio.spec.application.v0_3.LinkedApplication", "modulename": "bioimageio.spec.application.v0_3", "qualname": "LinkedApplication", "kind": "class", "doc": "Reference to a bioimage.io application.
\n", "bases": "bioimageio.spec.generic.v0_3.LinkedResourceNode"}, "bioimageio.spec.application.v0_3.LinkedApplication.id": {"fullname": "bioimageio.spec.application.v0_3.LinkedApplication.id", "modulename": "bioimageio.spec.application.v0_3", "qualname": "LinkedApplication.id", "kind": "variable", "doc": "A valid application id
from the bioimage.io collection.
Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.common.FileDescr.source": {"fullname": "bioimageio.spec.common.FileDescr.source", "modulename": "bioimageio.spec.common", "qualname": "FileDescr.source", "kind": "variable", "doc": "\u2208\ud83d\udce6 file source
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.common.FileDescr.sha256": {"fullname": "bioimageio.spec.common.FileDescr.sha256", "modulename": "bioimageio.spec.common", "qualname": "FileDescr.sha256", "kind": "variable", "doc": "SHA256 checksum of the source file
\n", "annotation": ": Optional[bioimageio.spec._internal.io_basics.Sha256]"}, "bioimageio.spec.common.FileDescr.validate_sha256": {"fullname": "bioimageio.spec.common.FileDescr.validate_sha256", "modulename": "bioimageio.spec.common", "qualname": "FileDescr.validate_sha256", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.common.FileDescr.download": {"fullname": "bioimageio.spec.common.FileDescr.download", "modulename": "bioimageio.spec.common", "qualname": "FileDescr.download", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.spec.common.FileName": {"fullname": "bioimageio.spec.common.FileName", "modulename": "bioimageio.spec.common", "qualname": "FileName", "kind": "variable", "doc": "\n", "default_value": "<class 'str'>"}, "bioimageio.spec.common.FileSource": {"fullname": "bioimageio.spec.common.FileSource", "modulename": "bioimageio.spec.common", "qualname": "FileSource", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, typing.Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]"}, "bioimageio.spec.common.HttpUrl": {"fullname": "bioimageio.spec.common.HttpUrl", "modulename": "bioimageio.spec.common", "qualname": "HttpUrl", "kind": "class", "doc": "A 'URL folder', possibly an invalid http URL
\n", "bases": "bioimageio.spec._internal.root_url.RootHttpUrl"}, "bioimageio.spec.common.HttpUrl.root_model": {"fullname": "bioimageio.spec.common.HttpUrl.root_model", "modulename": "bioimageio.spec.common", "qualname": "HttpUrl.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)]]'>"}, "bioimageio.spec.common.HttpUrl.exists": {"fullname": "bioimageio.spec.common.HttpUrl.exists", "modulename": "bioimageio.spec.common", "qualname": "HttpUrl.exists", "kind": "function", "doc": "True if URL is available
\n", "signature": "(self):", "funcdef": "def"}, "bioimageio.spec.common.InvalidDescr": {"fullname": "bioimageio.spec.common.InvalidDescr", "modulename": "bioimageio.spec.common", "qualname": "InvalidDescr", "kind": "class", "doc": "A representation of an invalid resource description
\n", "bases": "bioimageio.spec._internal.common_nodes.ResourceDescrBase"}, "bioimageio.spec.common.InvalidDescr.type": {"fullname": "bioimageio.spec.common.InvalidDescr.type", "modulename": "bioimageio.spec.common", "qualname": "InvalidDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Any"}, "bioimageio.spec.common.InvalidDescr.format_version": {"fullname": "bioimageio.spec.common.InvalidDescr.format_version", "modulename": "bioimageio.spec.common", "qualname": "InvalidDescr.format_version", "kind": "variable", "doc": "\n", "annotation": ": Any"}, "bioimageio.spec.common.InvalidDescr.fields_to_set_explicitly": {"fullname": "bioimageio.spec.common.InvalidDescr.fields_to_set_explicitly", "modulename": "bioimageio.spec.common", "qualname": "InvalidDescr.fields_to_set_explicitly", "kind": "variable", "doc": "set set these fields explicitly with their default value if they are not set,\nsuch that they are always included even when dumping with 'exlude_unset'
\n", "annotation": ": ClassVar[FrozenSet[LiteralString]]", "default_value": "frozenset()"}, "bioimageio.spec.common.InvalidDescr.implemented_format_version": {"fullname": "bioimageio.spec.common.InvalidDescr.implemented_format_version", "modulename": "bioimageio.spec.common", "qualname": "InvalidDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'unknown'"}, "bioimageio.spec.common.InvalidDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.common.InvalidDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.common", "qualname": "InvalidDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 0, 0)"}, "bioimageio.spec.common.InvalidDescr.model_post_init": {"fullname": "bioimageio.spec.common.InvalidDescr.model_post_init", "modulename": "bioimageio.spec.common", "qualname": "InvalidDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.common.PermissiveFileSource": {"fullname": "bioimageio.spec.common.PermissiveFileSource", "modulename": "bioimageio.spec.common", "qualname": "PermissiveFileSource", "kind": "variable", "doc": "\n", "default_value": "typing.Union[typing.Annotated[typing.Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, typing.Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], str, typing.Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)]]"}, "bioimageio.spec.common.RelativeFilePath": {"fullname": "bioimageio.spec.common.RelativeFilePath", "modulename": "bioimageio.spec.common", "qualname": "RelativeFilePath", "kind": "class", "doc": "A path relative to the rdf.yaml
file (also if the RDF source is a URL).
We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.common.RelativeFilePath.get_absolute": {"fullname": "bioimageio.spec.common.RelativeFilePath.get_absolute", "modulename": "bioimageio.spec.common", "qualname": "RelativeFilePath.get_absolute", "kind": "function", "doc": "\n", "signature": "(\tself,\troot: bioimageio.spec._internal.root_url.RootHttpUrl | pathlib.Path | pydantic_core._pydantic_core.Url | zipfile.ZipFile) -> Union[Annotated[pathlib.Path, PathType(path_type='file'), Predicate(is_absolute)], bioimageio.spec._internal.url.HttpUrl, zipp.Path]:", "funcdef": "def"}, "bioimageio.spec.common.RootHttpUrl": {"fullname": "bioimageio.spec.common.RootHttpUrl", "modulename": "bioimageio.spec.common", "qualname": "RootHttpUrl", "kind": "class", "doc": "A 'URL folder', possibly an invalid http URL
\n", "bases": "bioimageio.spec._internal.validated_string.ValidatedString"}, "bioimageio.spec.common.RootHttpUrl.root_model": {"fullname": "bioimageio.spec.common.RootHttpUrl.root_model", "modulename": "bioimageio.spec.common", "qualname": "RootHttpUrl.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)]]'>"}, "bioimageio.spec.common.RootHttpUrl.absolute": {"fullname": "bioimageio.spec.common.RootHttpUrl.absolute", "modulename": "bioimageio.spec.common", "qualname": "RootHttpUrl.absolute", "kind": "function", "doc": "analog to absolute
method of pathlib.
SHA-256 hash value
\n", "bases": "bioimageio.spec._internal.validated_string.ValidatedString"}, "bioimageio.spec.common.Sha256.root_model": {"fullname": "bioimageio.spec.common.Sha256.root_model", "modulename": "bioimageio.spec.common", "qualname": "Sha256.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[str, StringConstraints]]'>"}, "bioimageio.spec.common.ValidationError": {"fullname": "bioimageio.spec.common.ValidationError", "modulename": "bioimageio.spec.common", "qualname": "ValidationError", "kind": "class", "doc": "Inappropriate argument value (of correct type).
\n", "bases": "builtins.ValueError"}, "bioimageio.spec.common.ValidationError.from_exception_data": {"fullname": "bioimageio.spec.common.ValidationError.from_exception_data", "modulename": "bioimageio.spec.common", "qualname": "ValidationError.from_exception_data", "kind": "function", "doc": "\n", "signature": "(title, line_errors, input_type='python', hide_input=False):", "funcdef": "def"}, "bioimageio.spec.common.ValidationError.error_count": {"fullname": "bioimageio.spec.common.ValidationError.error_count", "modulename": "bioimageio.spec.common", "qualname": "ValidationError.error_count", "kind": "function", "doc": "\n", "signature": "(self, /):", "funcdef": "def"}, "bioimageio.spec.common.ValidationError.errors": {"fullname": "bioimageio.spec.common.ValidationError.errors", "modulename": "bioimageio.spec.common", "qualname": "ValidationError.errors", "kind": "function", "doc": "\n", "signature": "(\tself,\t/,\t*,\tinclude_url=True,\tinclude_context=True,\tinclude_input=True):", "funcdef": "def"}, "bioimageio.spec.common.ValidationError.json": {"fullname": "bioimageio.spec.common.ValidationError.json", "modulename": "bioimageio.spec.common", "qualname": "ValidationError.json", "kind": "function", "doc": "\n", "signature": "(\tself,\t/,\t*,\tindent=None,\tinclude_url=True,\tinclude_context=True,\tinclude_input=True):", "funcdef": "def"}, "bioimageio.spec.common.ValidationError.title": {"fullname": "bioimageio.spec.common.ValidationError.title", "modulename": "bioimageio.spec.common", "qualname": "ValidationError.title", "kind": "variable", "doc": "\n"}, "bioimageio.spec.common.YamlValue": {"fullname": "bioimageio.spec.common.YamlValue", "modulename": "bioimageio.spec.common", "qualname": "YamlValue", "kind": "variable", "doc": "\n", "default_value": "Union[bool, datetime.date, datetime.datetime, int, float, str, NoneType, List[ForwardRef('YamlValue')], Dict[Union[bool, datetime.date, datetime.datetime, int, float, str, NoneType, Tuple[Union[bool, datetime.date, datetime.datetime, int, float, str, NoneType], ...]], ForwardRef('YamlValue')]]"}, "bioimageio.spec.conda_env": {"fullname": "bioimageio.spec.conda_env", "modulename": "bioimageio.spec.conda_env", "kind": "module", "doc": "\n"}, "bioimageio.spec.conda_env.PipDeps": {"fullname": "bioimageio.spec.conda_env.PipDeps", "modulename": "bioimageio.spec.conda_env", "qualname": "PipDeps", "kind": "class", "doc": "Pip dependencies to include in conda dependecies
\n", "bases": "pydantic.main.BaseModel"}, "bioimageio.spec.conda_env.PipDeps.pip": {"fullname": "bioimageio.spec.conda_env.PipDeps.pip", "modulename": "bioimageio.spec.conda_env", "qualname": "PipDeps.pip", "kind": "variable", "doc": "\n", "annotation": ": List[str]"}, "bioimageio.spec.conda_env.CondaEnv": {"fullname": "bioimageio.spec.conda_env.CondaEnv", "modulename": "bioimageio.spec.conda_env", "qualname": "CondaEnv", "kind": "class", "doc": "Represenation of the content of a conda environment.yaml file
\n", "bases": "pydantic.main.BaseModel"}, "bioimageio.spec.conda_env.CondaEnv.name": {"fullname": "bioimageio.spec.conda_env.CondaEnv.name", "modulename": "bioimageio.spec.conda_env", "qualname": "CondaEnv.name", "kind": "variable", "doc": "\n", "annotation": ": Optional[str]"}, "bioimageio.spec.conda_env.CondaEnv.channels": {"fullname": "bioimageio.spec.conda_env.CondaEnv.channels", "modulename": "bioimageio.spec.conda_env", "qualname": "CondaEnv.channels", "kind": "variable", "doc": "\n", "annotation": ": List[str]"}, "bioimageio.spec.conda_env.CondaEnv.dependencies": {"fullname": "bioimageio.spec.conda_env.CondaEnv.dependencies", "modulename": "bioimageio.spec.conda_env", "qualname": "CondaEnv.dependencies", "kind": "variable", "doc": "\n", "annotation": ": List[Union[str, bioimageio.spec.conda_env.PipDeps]]"}, "bioimageio.spec.conda_env.CondaEnv.wo_name": {"fullname": "bioimageio.spec.conda_env.CondaEnv.wo_name", "modulename": "bioimageio.spec.conda_env", "qualname": "CondaEnv.wo_name", "kind": "variable", "doc": "\n"}, "bioimageio.spec.conda_env.BioimageioCondaEnv": {"fullname": "bioimageio.spec.conda_env.BioimageioCondaEnv", "modulename": "bioimageio.spec.conda_env", "qualname": "BioimageioCondaEnv", "kind": "class", "doc": "A special CondaEnv
that
implementaions of all released minor versions are available in submodules:
\n\nbioimageio.spec.dataset.v0_2.DatasetDescr
bioimageio.spec.dataset.v0_3.DatasetDescr
A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage\nprocessing.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.dataset.DatasetDescr.type": {"fullname": "bioimageio.spec.dataset.DatasetDescr.type", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['dataset']"}, "bioimageio.spec.dataset.DatasetDescr.id": {"fullname": "bioimageio.spec.dataset.DatasetDescr.id", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.dataset.v0_3.DatasetId]"}, "bioimageio.spec.dataset.DatasetDescr.parent": {"fullname": "bioimageio.spec.dataset.DatasetDescr.parent", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.dataset.v0_3.DatasetId]"}, "bioimageio.spec.dataset.DatasetDescr.source": {"fullname": "bioimageio.spec.dataset.DatasetDescr.source", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr.source", "kind": "variable", "doc": "\"URL to the source of the dataset.
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.dataset.DatasetDescr.implemented_format_version": {"fullname": "bioimageio.spec.dataset.DatasetDescr.implemented_format_version", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.dataset.DatasetDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.dataset.DatasetDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.dataset.DatasetDescr.model_post_init": {"fullname": "bioimageio.spec.dataset.DatasetDescr.model_post_init", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.dataset.DatasetDescr_v0_2": {"fullname": "bioimageio.spec.dataset.DatasetDescr_v0_2", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr_v0_2", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.dataset.v0_2.DatasetDescr'>"}, "bioimageio.spec.dataset.DatasetDescr_v0_3": {"fullname": "bioimageio.spec.dataset.DatasetDescr_v0_3", "modulename": "bioimageio.spec.dataset", "qualname": "DatasetDescr_v0_3", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.dataset.v0_3.DatasetDescr'>"}, "bioimageio.spec.dataset.AnyDatasetDescr": {"fullname": "bioimageio.spec.dataset.AnyDatasetDescr", "modulename": "bioimageio.spec.dataset", "qualname": "AnyDatasetDescr", "kind": "variable", "doc": "Union of any released dataset desription
\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.dataset.v0_2.DatasetDescr, bioimageio.spec.dataset.v0_3.DatasetDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]"}, "bioimageio.spec.dataset.v0_2": {"fullname": "bioimageio.spec.dataset.v0_2", "modulename": "bioimageio.spec.dataset.v0_2", "kind": "module", "doc": "\n"}, "bioimageio.spec.dataset.v0_2.DatasetId": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetId", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec.generic.v0_2.ResourceId"}, "bioimageio.spec.dataset.v0_2.DatasetDescr": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetDescr", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetDescr", "kind": "class", "doc": "A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage\nprocessing.
\n", "bases": "bioimageio.spec.generic.v0_2.GenericDescrBase"}, "bioimageio.spec.dataset.v0_2.DatasetDescr.type": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetDescr.type", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['dataset']"}, "bioimageio.spec.dataset.v0_2.DatasetDescr.id": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetDescr.id", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.dataset.v0_2.DatasetId]"}, "bioimageio.spec.dataset.v0_2.DatasetDescr.source": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetDescr.source", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetDescr.source", "kind": "variable", "doc": "\"URL to the source of the dataset.
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.dataset.v0_2.DatasetDescr.implemented_format_version": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetDescr.implemented_format_version", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.2.4'"}, "bioimageio.spec.dataset.v0_2.DatasetDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 2, 4)"}, "bioimageio.spec.dataset.v0_2.DatasetDescr.model_post_init": {"fullname": "bioimageio.spec.dataset.v0_2.DatasetDescr.model_post_init", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "DatasetDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.dataset.v0_2.LinkedDataset": {"fullname": "bioimageio.spec.dataset.v0_2.LinkedDataset", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "LinkedDataset", "kind": "class", "doc": "Reference to a bioimage.io dataset.
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.dataset.v0_2.LinkedDataset.id": {"fullname": "bioimageio.spec.dataset.v0_2.LinkedDataset.id", "modulename": "bioimageio.spec.dataset.v0_2", "qualname": "LinkedDataset.id", "kind": "variable", "doc": "A valid dataset id
from the bioimage.io collection.
version number (n-th published version, not the semantic version) of linked dataset
\n", "annotation": ": Optional[int]"}, "bioimageio.spec.dataset.v0_3": {"fullname": "bioimageio.spec.dataset.v0_3", "modulename": "bioimageio.spec.dataset.v0_3", "kind": "module", "doc": "\n"}, "bioimageio.spec.dataset.v0_3.DatasetId": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetId", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec.generic.v0_3.ResourceId"}, "bioimageio.spec.dataset.v0_3.DatasetDescr": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr", "kind": "class", "doc": "A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage\nprocessing.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.dataset.v0_3.DatasetDescr.type": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr.type", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['dataset']"}, "bioimageio.spec.dataset.v0_3.DatasetDescr.id": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr.id", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.dataset.v0_3.DatasetId]"}, "bioimageio.spec.dataset.v0_3.DatasetDescr.parent": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr.parent", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.dataset.v0_3.DatasetId]"}, "bioimageio.spec.dataset.v0_3.DatasetDescr.source": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr.source", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr.source", "kind": "variable", "doc": "\"URL to the source of the dataset.
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.dataset.v0_3.DatasetDescr.implemented_format_version": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr.implemented_format_version", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.dataset.v0_3.DatasetDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.dataset.v0_3.DatasetDescr.model_post_init": {"fullname": "bioimageio.spec.dataset.v0_3.DatasetDescr.model_post_init", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "DatasetDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.dataset.v0_3.LinkedDataset": {"fullname": "bioimageio.spec.dataset.v0_3.LinkedDataset", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "LinkedDataset", "kind": "class", "doc": "Reference to a bioimage.io dataset.
\n", "bases": "bioimageio.spec.generic.v0_3.LinkedResourceNode"}, "bioimageio.spec.dataset.v0_3.LinkedDataset.id": {"fullname": "bioimageio.spec.dataset.v0_3.LinkedDataset.id", "modulename": "bioimageio.spec.dataset.v0_3", "qualname": "LinkedDataset.id", "kind": "variable", "doc": "A valid dataset id
from the bioimage.io collection.
implementaions of all released minor versions are available in submodules:
\n\nbioimageio.spec.generic.v0_2.GenericDescr
bioimageio.spec.generic.v0_3.GenericDescr
Specification of the fields used in a generic bioimage.io-compliant resource description file (RDF).
\n\nAn RDF is a YAML file that describes a resource such as a model, a dataset, or a notebook.\nNote that those resources are described with a type-specific RDF.\nUse this generic resource description, if none of the known specific types matches your resource.
\n", "bases": "bioimageio.spec.generic.v0_3.GenericDescrBase"}, "bioimageio.spec.generic.GenericDescr.type": {"fullname": "bioimageio.spec.generic.GenericDescr.type", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.type", "kind": "variable", "doc": "The resource type assigns a broad category to the resource.
\n", "annotation": ": Annotated[str, Annotated[~_StrType, Predicate(str.islower)]]"}, "bioimageio.spec.generic.GenericDescr.id": {"fullname": "bioimageio.spec.generic.GenericDescr.id", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_3.ResourceId]"}, "bioimageio.spec.generic.GenericDescr.parent": {"fullname": "bioimageio.spec.generic.GenericDescr.parent", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_3.ResourceId]"}, "bioimageio.spec.generic.GenericDescr.source": {"fullname": "bioimageio.spec.generic.GenericDescr.source", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.source", "kind": "variable", "doc": "The primary source of the resource
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.generic.GenericDescr.check_specific_types": {"fullname": "bioimageio.spec.generic.GenericDescr.check_specific_types", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.check_specific_types", "kind": "function", "doc": "\n", "signature": "(cls, value: str) -> str:", "funcdef": "def"}, "bioimageio.spec.generic.GenericDescr.implemented_format_version": {"fullname": "bioimageio.spec.generic.GenericDescr.implemented_format_version", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.generic.GenericDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.generic.GenericDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.generic.GenericDescr.model_post_init": {"fullname": "bioimageio.spec.generic.GenericDescr.model_post_init", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.generic.GenericDescr_v0_2": {"fullname": "bioimageio.spec.generic.GenericDescr_v0_2", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr_v0_2", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.generic.v0_2.GenericDescr'>"}, "bioimageio.spec.generic.GenericDescr_v0_3": {"fullname": "bioimageio.spec.generic.GenericDescr_v0_3", "modulename": "bioimageio.spec.generic", "qualname": "GenericDescr_v0_3", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.generic.v0_3.GenericDescr'>"}, "bioimageio.spec.generic.AnyGenericDescr": {"fullname": "bioimageio.spec.generic.AnyGenericDescr", "modulename": "bioimageio.spec.generic", "qualname": "AnyGenericDescr", "kind": "variable", "doc": "Union of any released generic desription
\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.generic.v0_2.GenericDescr, bioimageio.spec.generic.v0_3.GenericDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]"}, "bioimageio.spec.generic.v0_2": {"fullname": "bioimageio.spec.generic.v0_2", "modulename": "bioimageio.spec.generic.v0_2", "kind": "module", "doc": "\n"}, "bioimageio.spec.generic.v0_2.ResourceId": {"fullname": "bioimageio.spec.generic.v0_2.ResourceId", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "ResourceId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec._internal.validated_string.ValidatedString"}, "bioimageio.spec.generic.v0_2.ResourceId.root_model": {"fullname": "bioimageio.spec.generic.v0_2.ResourceId.root_model", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "ResourceId.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[str, MinLen, AfterValidator, RestrictCharacters, Predicate]]'>"}, "bioimageio.spec.generic.v0_2.KNOWN_SPECIFIC_RESOURCE_TYPES": {"fullname": "bioimageio.spec.generic.v0_2.KNOWN_SPECIFIC_RESOURCE_TYPES", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "KNOWN_SPECIFIC_RESOURCE_TYPES", "kind": "variable", "doc": "\n", "default_value": "('application', 'collection', 'dataset', 'model', 'notebook')"}, "bioimageio.spec.generic.v0_2.VALID_COVER_IMAGE_EXTENSIONS": {"fullname": "bioimageio.spec.generic.v0_2.VALID_COVER_IMAGE_EXTENSIONS", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "VALID_COVER_IMAGE_EXTENSIONS", "kind": "variable", "doc": "\n", "default_value": "('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')"}, "bioimageio.spec.generic.v0_2.CoverImageSource": {"fullname": "bioimageio.spec.generic.v0_2.CoverImageSource", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "CoverImageSource", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[typing.Union[typing.Annotated[pathlib.Path, PathType(path_type='file'), Predicate(is_absolute)], bioimageio.spec._internal.io.RelativeFilePath, bioimageio.spec._internal.url.HttpUrl], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), WithSuffix(suffix=('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff'), case_sensitive=False), PlainSerializer(func=<function _package>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.generic.v0_2.AttachmentsDescr": {"fullname": "bioimageio.spec.generic.v0_2.AttachmentsDescr", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "AttachmentsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_2.AttachmentsDescr.model_config": {"fullname": "bioimageio.spec.generic.v0_2.AttachmentsDescr.model_config", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "AttachmentsDescr.model_config", "kind": "variable", "doc": "update pydantic model config to allow additional unknown keys
\n", "default_value": "{'extra': 'allow', 'frozen': False, 'populate_by_name': True, 'revalidate_instances': 'never', 'validate_assignment': True, 'validate_default': False, 'validate_return': True, 'use_attribute_docstrings': True}"}, "bioimageio.spec.generic.v0_2.AttachmentsDescr.files": {"fullname": "bioimageio.spec.generic.v0_2.AttachmentsDescr.files", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "AttachmentsDescr.files", "kind": "variable", "doc": "\u2208\ud83d\udce6 File attachments
\n", "annotation": ": List[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')]]"}, "bioimageio.spec.generic.v0_2.Uploader": {"fullname": "bioimageio.spec.generic.v0_2.Uploader", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Uploader", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_2.Uploader.email": {"fullname": "bioimageio.spec.generic.v0_2.Uploader.email", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Uploader.email", "kind": "variable", "doc": "name
\n", "annotation": ": Optional[Annotated[str, AfterValidator(func=<function _remove_slashes at 0x7f1c5bd54680>)]]"}, "bioimageio.spec.generic.v0_2.Author": {"fullname": "bioimageio.spec.generic.v0_2.Author", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Author", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "_Person"}, "bioimageio.spec.generic.v0_2.Author.name": {"fullname": "bioimageio.spec.generic.v0_2.Author.name", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Author.name", "kind": "variable", "doc": "\n", "annotation": ": Annotated[str, AfterValidator(func=<function _remove_slashes at 0x7f1c5bd54680>)]"}, "bioimageio.spec.generic.v0_2.Author.github_user": {"fullname": "bioimageio.spec.generic.v0_2.Author.github_user", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Author.github_user", "kind": "variable", "doc": "\n", "annotation": ": Optional[str]"}, "bioimageio.spec.generic.v0_2.Maintainer": {"fullname": "bioimageio.spec.generic.v0_2.Maintainer", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Maintainer", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "_Person"}, "bioimageio.spec.generic.v0_2.Maintainer.name": {"fullname": "bioimageio.spec.generic.v0_2.Maintainer.name", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Maintainer.name", "kind": "variable", "doc": "\n", "annotation": ": Optional[Annotated[str, AfterValidator(func=<function _remove_slashes at 0x7f1c5bd54680>)]]"}, "bioimageio.spec.generic.v0_2.Maintainer.github_user": {"fullname": "bioimageio.spec.generic.v0_2.Maintainer.github_user", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "Maintainer.github_user", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.generic.v0_2.BadgeDescr": {"fullname": "bioimageio.spec.generic.v0_2.BadgeDescr", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "BadgeDescr", "kind": "class", "doc": "A custom badge
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_2.BadgeDescr.label": {"fullname": "bioimageio.spec.generic.v0_2.BadgeDescr.label", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "BadgeDescr.label", "kind": "variable", "doc": "badge label to display on hover
\n", "annotation": ": Annotated[str, FieldInfo(annotation=NoneType, required=True, examples=['Open in Colab'])]"}, "bioimageio.spec.generic.v0_2.BadgeDescr.icon": {"fullname": "bioimageio.spec.generic.v0_2.BadgeDescr.icon", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "BadgeDescr.icon", "kind": "variable", "doc": "badge icon
\n", "annotation": ": Annotated[Union[Annotated[Union[Annotated[pathlib.Path, PathType(path_type='file')], bioimageio.spec._internal.io.RelativeFilePath], AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')], bioimageio.spec._internal.url.HttpUrl, Annotated[pydantic_core._pydantic_core.Url, UrlConstraints(max_length=2083, allowed_schemes=['http', 'https'], host_required=None, default_host=None, default_port=None, default_path=None)], NoneType], FieldInfo(annotation=NoneType, required=True, examples=['https://colab.research.google.com/assets/colab-badge.svg'])]"}, "bioimageio.spec.generic.v0_2.BadgeDescr.url": {"fullname": "bioimageio.spec.generic.v0_2.BadgeDescr.url", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "BadgeDescr.url", "kind": "variable", "doc": "target URL
\n", "annotation": ": Annotated[bioimageio.spec._internal.url.HttpUrl, FieldInfo(annotation=NoneType, required=True, examples=['https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb'])]"}, "bioimageio.spec.generic.v0_2.CiteEntry": {"fullname": "bioimageio.spec.generic.v0_2.CiteEntry", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "CiteEntry", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_2.CiteEntry.text": {"fullname": "bioimageio.spec.generic.v0_2.CiteEntry.text", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "CiteEntry.text", "kind": "variable", "doc": "free text description
\n", "annotation": ": str"}, "bioimageio.spec.generic.v0_2.CiteEntry.doi": {"fullname": "bioimageio.spec.generic.v0_2.CiteEntry.doi", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "CiteEntry.doi", "kind": "variable", "doc": "A digital object identifier (DOI) is the prefered citation reference.\nSee https://www.doi.org/ for details. (alternatively specify url
)
URL to cite (preferably specify a doi
instead)
Reference to a bioimage.io resource
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_2.LinkedResource.id": {"fullname": "bioimageio.spec.generic.v0_2.LinkedResource.id", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "LinkedResource.id", "kind": "variable", "doc": "A valid resource id
from the bioimage.io collection.
version number (n-th published version, not the semantic version) of linked resource
\n", "annotation": ": Optional[int]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase", "kind": "class", "doc": "Base for all resource descriptions including of model descriptions
\n", "bases": "bioimageio.spec._internal.common_nodes.ResourceDescrBase"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.name": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.name", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.name", "kind": "variable", "doc": "A human-friendly name of the resource description
\n", "annotation": ": Annotated[str, MinLen(min_length=1), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f1c5bd3b380>, severity=30, msg='Longer than 128 characters.', context={'typ': Annotated[Any, MaxLen(max_length=128)]})]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.description": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.description", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.description", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.covers": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.covers", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.covers", "kind": "variable", "doc": "\u2208\ud83d\udce6 Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.
\n", "annotation": ": Annotated[List[Annotated[Union[Annotated[pathlib.Path, PathType(path_type='file'), Predicate(is_absolute)], bioimageio.spec._internal.io.RelativeFilePath, bioimageio.spec._internal.url.HttpUrl], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), WithSuffix(suffix=('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff'), case_sensitive=False), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')]], FieldInfo(annotation=NoneType, required=True, description="Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.\\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')", examples=['cover.png'])]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.id_emoji": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.id_emoji", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.id_emoji", "kind": "variable", "doc": "UTF-8 emoji for display alongside the id
.
The authors are the creators of the RDF and the primary points of contact.
\n", "annotation": ": List[bioimageio.spec.generic.v0_2.Author]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.accept_author_strings": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.accept_author_strings", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.accept_author_strings", "kind": "function", "doc": "we unofficially accept strings as author entries
\n", "signature": "(cls, authors: Union[Any, Sequence[Any]]) -> Any:", "funcdef": "def"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.attachments": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.attachments", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.attachments", "kind": "variable", "doc": "file and other attachments
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_2.AttachmentsDescr]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.cite": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.cite", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.cite", "kind": "variable", "doc": "citations
\n", "annotation": ": List[bioimageio.spec.generic.v0_2.CiteEntry]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.config": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.config", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.config", "kind": "variable", "doc": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a github repo URL in config
since we already have the\ngit_repo
field defined in the spec.\nKeys in config
may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:
config:\n bioimageio: # here is the domain name\n my_custom_key: 3837283\n another_key:\n nested: value\n imagej: # config specific to ImageJ\n macro_dir: path/to/macro/file\n
\nIf possible, please use snake_case
for keys in config
.\nYou may want to list linked files additionally under attachments
to include them when packaging a resource\n(packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files)
URL to download the resource from (deprecated)
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.git_repo": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.git_repo", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.git_repo", "kind": "variable", "doc": "A URL to the Git repository where the resource is being developed.
\n", "annotation": ": Annotated[Optional[str], FieldInfo(annotation=NoneType, required=True, examples=['https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad'])]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.icon": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.icon", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.icon", "kind": "variable", "doc": "An icon for illustration
\n", "annotation": ": Union[Annotated[str, Len(min_length=1, max_length=2)], Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')], NoneType]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.links": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.links", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.links", "kind": "variable", "doc": "IDs of other bioimage.io resources
\n", "annotation": ": Annotated[List[str], FieldInfo(annotation=NoneType, required=True, examples=[('ilastik/ilastik', 'deepimagej/deepimagej', 'zero/notebook_u-net_3d_zerocostdl4mic')])]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.uploader": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.uploader", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.uploader", "kind": "variable", "doc": "The person who uploaded the model (e.g. to bioimage.io)
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_2.Uploader]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.maintainers": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.maintainers", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.maintainers", "kind": "variable", "doc": "Maintainers of this resource.\nIf not specified authors
are maintainers and at least some of them should specify their github_user
name
Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from.\nDo not set this field in a YAML file.
\n", "annotation": ": Optional[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.tags": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.tags", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.tags", "kind": "variable", "doc": "Associated tags
\n", "annotation": ": Annotated[List[str], FieldInfo(annotation=NoneType, required=True, examples=[('unet2d', 'pytorch', 'nucleus', 'segmentation', 'dsb2018')])]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.warn_about_tag_categories": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.warn_about_tag_categories", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.warn_about_tag_categories", "kind": "function", "doc": "\n", "signature": "(value: Any, info: pydantic_core.core_schema.ValidationInfo) -> Any:", "funcdef": "def"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.version": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.version", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.version", "kind": "variable", "doc": "The version of the resource following SemVer 2.0.
\n", "annotation": ": Optional[bioimageio.spec._internal.version_type.Version]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.version_number": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.version_number", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.version_number", "kind": "variable", "doc": "version number (n-th published version, not the semantic version)
\n", "annotation": ": Optional[int]"}, "bioimageio.spec.generic.v0_2.GenericModelDescrBase.model_post_init": {"fullname": "bioimageio.spec.generic.v0_2.GenericModelDescrBase.model_post_init", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericModelDescrBase.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.generic.v0_2.GenericDescrBase": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescrBase", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescrBase", "kind": "class", "doc": "Base for all resource descriptions except for the model descriptions
\n", "bases": "GenericModelDescrBase"}, "bioimageio.spec.generic.v0_2.GenericDescrBase.format_version": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescrBase.format_version", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescrBase.format_version", "kind": "variable", "doc": "The format version of this resource specification\n(not the version
of the resource description)\nWhen creating a new resource always use the latest micro/patch version described here.\nThe format_version
is important for any consumer software to understand how to parse the fields.
badges associated with this resource
\n", "annotation": ": List[bioimageio.spec.generic.v0_2.BadgeDescr]"}, "bioimageio.spec.generic.v0_2.GenericDescrBase.documentation": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescrBase.documentation", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescrBase.documentation", "kind": "variable", "doc": "\u2208\ud83d\udce6 URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is README.md
. An .md
suffix is mandatory.
A SPDX license identifier.\nWe do not support custom license beyond the SPDX license list, if you need that please\nopen a GitHub issue to discuss your intentions with the community.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.license_id.LicenseId, bioimageio.spec._internal.license_id.DeprecatedLicenseId, str, NoneType], FieldInfo(annotation=NoneType, required=True, examples=['CC0-1.0', 'MIT', 'BSD-2-Clause'], metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]"}, "bioimageio.spec.generic.v0_2.GenericDescrBase.deprecated_spdx_license": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescrBase.deprecated_spdx_license", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescrBase.deprecated_spdx_license", "kind": "function", "doc": "\n", "signature": "(\tcls,\tvalue: Union[bioimageio.spec._internal.license_id.LicenseId, bioimageio.spec._internal.license_id.DeprecatedLicenseId, str, NoneType]):", "funcdef": "def"}, "bioimageio.spec.generic.v0_2.GenericDescrBase.implemented_format_version": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescrBase.implemented_format_version", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescrBase.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.2.4'"}, "bioimageio.spec.generic.v0_2.GenericDescrBase.implemented_format_version_tuple": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescrBase.implemented_format_version_tuple", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescrBase.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 2, 4)"}, "bioimageio.spec.generic.v0_2.GenericDescrBase.model_post_init": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescrBase.model_post_init", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescrBase.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.generic.v0_2.GenericDescr": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr", "kind": "class", "doc": "Specification of the fields used in a generic bioimage.io-compliant resource description file (RDF).
\n\nAn RDF is a YAML file that describes a resource such as a model, a dataset, or a notebook.\nNote that those resources are described with a type-specific RDF.\nUse this generic resource description, if none of the known specific types matches your resource.
\n", "bases": "GenericDescrBase"}, "bioimageio.spec.generic.v0_2.GenericDescr.type": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr.type", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr.type", "kind": "variable", "doc": "The resource type assigns a broad category to the resource.
\n", "annotation": ": Annotated[str, Annotated[~_StrType, Predicate(str.islower)], FieldInfo(annotation=NoneType, required=True, frozen=True)]"}, "bioimageio.spec.generic.v0_2.GenericDescr.id": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr.id", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_2.ResourceId]"}, "bioimageio.spec.generic.v0_2.GenericDescr.source": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr.source", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr.source", "kind": "variable", "doc": "The primary source of the resource
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.generic.v0_2.GenericDescr.check_specific_types": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr.check_specific_types", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr.check_specific_types", "kind": "function", "doc": "\n", "signature": "(cls, value: str) -> str:", "funcdef": "def"}, "bioimageio.spec.generic.v0_2.GenericDescr.implemented_format_version": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr.implemented_format_version", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.2.4'"}, "bioimageio.spec.generic.v0_2.GenericDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 2, 4)"}, "bioimageio.spec.generic.v0_2.GenericDescr.model_post_init": {"fullname": "bioimageio.spec.generic.v0_2.GenericDescr.model_post_init", "modulename": "bioimageio.spec.generic.v0_2", "qualname": "GenericDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.generic.v0_3": {"fullname": "bioimageio.spec.generic.v0_3", "modulename": "bioimageio.spec.generic.v0_3", "kind": "module", "doc": "\n"}, "bioimageio.spec.generic.v0_3.KNOWN_SPECIFIC_RESOURCE_TYPES": {"fullname": "bioimageio.spec.generic.v0_3.KNOWN_SPECIFIC_RESOURCE_TYPES", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "KNOWN_SPECIFIC_RESOURCE_TYPES", "kind": "variable", "doc": "\n", "default_value": "('application', 'collection', 'dataset', 'model', 'notebook')"}, "bioimageio.spec.generic.v0_3.VALID_COVER_IMAGE_EXTENSIONS": {"fullname": "bioimageio.spec.generic.v0_3.VALID_COVER_IMAGE_EXTENSIONS", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "VALID_COVER_IMAGE_EXTENSIONS", "kind": "variable", "doc": "\n", "default_value": "('.gif', '.jpeg', '.jpg', '.png', '.svg')"}, "bioimageio.spec.generic.v0_3.ResourceId": {"fullname": "bioimageio.spec.generic.v0_3.ResourceId", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "ResourceId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec._internal.validated_string.ValidatedString"}, "bioimageio.spec.generic.v0_3.ResourceId.root_model": {"fullname": "bioimageio.spec.generic.v0_3.ResourceId.root_model", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "ResourceId.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[str, MinLen, RestrictCharacters, Predicate]]'>"}, "bioimageio.spec.generic.v0_3.DocumentationSource": {"fullname": "bioimageio.spec.generic.v0_3.DocumentationSource", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "DocumentationSource", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[typing.Union[typing.Annotated[pathlib.Path, PathType(path_type='file'), Predicate(is_absolute)], bioimageio.spec._internal.io.RelativeFilePath, bioimageio.spec._internal.url.HttpUrl], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function _validate_md_suffix>), PlainSerializer(func=<function _package>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.generic.v0_3.Author": {"fullname": "bioimageio.spec.generic.v0_3.Author", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "Author", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec.generic.v0_2.Author"}, "bioimageio.spec.generic.v0_3.Author.name": {"fullname": "bioimageio.spec.generic.v0_3.Author.name", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "Author.name", "kind": "variable", "doc": "\n", "annotation": ": Annotated[str, Predicate(func=<function _has_no_slash at 0x7f1c529a8040>)]"}, "bioimageio.spec.generic.v0_3.Author.github_user": {"fullname": "bioimageio.spec.generic.v0_3.Author.github_user", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "Author.github_user", "kind": "variable", "doc": "\n", "annotation": ": Optional[str]"}, "bioimageio.spec.generic.v0_3.Maintainer": {"fullname": "bioimageio.spec.generic.v0_3.Maintainer", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "Maintainer", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec.generic.v0_2.Maintainer"}, "bioimageio.spec.generic.v0_3.Maintainer.name": {"fullname": "bioimageio.spec.generic.v0_3.Maintainer.name", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "Maintainer.name", "kind": "variable", "doc": "\n", "annotation": ": Optional[Annotated[str, Predicate(func=<function _has_no_slash at 0x7f1c529a8040>)]]"}, "bioimageio.spec.generic.v0_3.Maintainer.github_user": {"fullname": "bioimageio.spec.generic.v0_3.Maintainer.github_user", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "Maintainer.github_user", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.generic.v0_3.Maintainer.validate_gh_user": {"fullname": "bioimageio.spec.generic.v0_3.Maintainer.validate_gh_user", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "Maintainer.validate_gh_user", "kind": "function", "doc": "\n", "signature": "(cls, value: str):", "funcdef": "def"}, "bioimageio.spec.generic.v0_3.CiteEntry": {"fullname": "bioimageio.spec.generic.v0_3.CiteEntry", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "CiteEntry", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_3.CiteEntry.text": {"fullname": "bioimageio.spec.generic.v0_3.CiteEntry.text", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "CiteEntry.text", "kind": "variable", "doc": "free text description
\n", "annotation": ": str"}, "bioimageio.spec.generic.v0_3.CiteEntry.doi": {"fullname": "bioimageio.spec.generic.v0_3.CiteEntry.doi", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "CiteEntry.doi", "kind": "variable", "doc": "A digital object identifier (DOI) is the prefered citation reference.\nSee https://www.doi.org/ for details. (alternatively specify url
)
URL to cite (preferably specify a doi
instead)
Reference to a bioimage.io resource
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_3.LinkedResource.id": {"fullname": "bioimageio.spec.generic.v0_3.LinkedResource.id", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "LinkedResource.id", "kind": "variable", "doc": "A valid resource id
from the official bioimage.io collection.
Base for all resource descriptions including of model descriptions
\n", "bases": "bioimageio.spec._internal.common_nodes.ResourceDescrBase"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.name": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.name", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.name", "kind": "variable", "doc": "A human-friendly name of the resource description.\nMay only contains letters, digits, underscore, minus, parentheses and spaces.
\n", "annotation": ": Annotated[str, MinLen(min_length=1), MaxLen(max_length=128)]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.description": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.description", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.description", "kind": "variable", "doc": "A string containing a brief description.
\n", "annotation": ": Annotated[str, MaxLen(max_length=1024), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f1c4df31800>, severity=30, msg='Description longer than 512 characters.', context={'typ': Annotated[Any, MaxLen(max_length=512)]})]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.covers": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.covers", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.covers", "kind": "variable", "doc": "\u2208\ud83d\udce6 Cover images.
\n", "annotation": ": Annotated[List[Annotated[Union[Annotated[pathlib.Path, PathType(path_type='file'), Predicate(is_absolute)], bioimageio.spec._internal.io.RelativeFilePath, bioimageio.spec._internal.url.HttpUrl], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), WithSuffix(suffix=('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff'), case_sensitive=False), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')]], FieldInfo(annotation=NoneType, required=True, description="Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1 or 1:1.\\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg')", examples=[])]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.id_emoji": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.id_emoji", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.id_emoji", "kind": "variable", "doc": "UTF-8 emoji for display alongside the id
.
The authors are the creators of this resource description and the primary points of contact.
\n", "annotation": ": Annotated[List[bioimageio.spec.generic.v0_3.Author], MinLen(min_length=1)]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.attachments": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.attachments", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.attachments", "kind": "variable", "doc": "file attachments
\n", "annotation": ": List[bioimageio.spec._internal.io.FileDescr]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.cite": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.cite", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.cite", "kind": "variable", "doc": "citations
\n", "annotation": ": Annotated[List[bioimageio.spec.generic.v0_3.CiteEntry], MinLen(min_length=1)]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.license": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.license", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.license", "kind": "variable", "doc": "A SPDX license identifier.\nWe do not support custom license beyond the SPDX license list, if you need that please\nopen a GitHub issue\nto discuss your intentions with the community.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.license_id.LicenseId, bioimageio.spec._internal.license_id.DeprecatedLicenseId], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f1c4df320c0>, severity=30, msg='{value} is deprecated, see https://spdx.org/licenses/{value}.html', context={'typ': <class 'bioimageio.spec._internal.license_id.LicenseId'>}), FieldInfo(annotation=NoneType, required=True, examples=['CC0-1.0', 'MIT', 'BSD-2-Clause'])]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.config": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.config", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.config", "kind": "variable", "doc": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a GitHub repo URL in config
since there is a git_repo
field.\nKeys in config
may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:
config:\n bioimageio: # here is the domain name\n my_custom_key: 3837283\n another_key:\n nested: value\n imagej: # config specific to ImageJ\n macro_dir: path/to/macro/file\n
\nIf possible, please use snake_case
for keys in config
.\nYou may want to list linked files additionally under attachments
to include them when packaging a resource.\n(Packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files.)
A URL to the Git repository where the resource is being developed.
\n", "annotation": ": Annotated[Optional[bioimageio.spec._internal.url.HttpUrl], FieldInfo(annotation=NoneType, required=True, examples=['https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad'])]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.icon": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.icon", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.icon", "kind": "variable", "doc": "An icon for illustration, e.g. on bioimage.io
\n", "annotation": ": Union[Annotated[str, Len(min_length=1, max_length=2)], Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')], NoneType]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.links": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.links", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.links", "kind": "variable", "doc": "IDs of other bioimage.io resources
\n", "annotation": ": Annotated[List[str], FieldInfo(annotation=NoneType, required=True, examples=[('ilastik/ilastik', 'deepimagej/deepimagej', 'zero/notebook_u-net_3d_zerocostdl4mic')])]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.uploader": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.uploader", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.uploader", "kind": "variable", "doc": "The person who uploaded the model (e.g. to bioimage.io)
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_2.Uploader]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.maintainers": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.maintainers", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.maintainers", "kind": "variable", "doc": "Maintainers of this resource.\nIf not specified, authors
are maintainers and at least some of them has to specify their github_user
name
Associated tags
\n", "annotation": ": Annotated[List[str], FieldInfo(annotation=NoneType, required=True, examples=[('unet2d', 'pytorch', 'nucleus', 'segmentation', 'dsb2018')])]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.warn_about_tag_categories": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.warn_about_tag_categories", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.warn_about_tag_categories", "kind": "function", "doc": "\n", "signature": "(value: Any, info: pydantic_core.core_schema.ValidationInfo) -> Any:", "funcdef": "def"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.version": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.version", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.version", "kind": "variable", "doc": "The version of the resource following SemVer 2.0.
\n", "annotation": ": Optional[bioimageio.spec._internal.version_type.Version]"}, "bioimageio.spec.generic.v0_3.GenericModelDescrBase.model_post_init": {"fullname": "bioimageio.spec.generic.v0_3.GenericModelDescrBase.model_post_init", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericModelDescrBase.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.generic.v0_3.GenericDescrBase": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescrBase", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescrBase", "kind": "class", "doc": "Base for all resource descriptions except for the model descriptions
\n", "bases": "GenericModelDescrBase"}, "bioimageio.spec.generic.v0_3.GenericDescrBase.format_version": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescrBase.format_version", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescrBase.format_version", "kind": "variable", "doc": "The format version of this resource specification
\n", "annotation": ": Literal['0.3.0']"}, "bioimageio.spec.generic.v0_3.GenericDescrBase.documentation": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescrBase.documentation", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescrBase.documentation", "kind": "variable", "doc": "\u2208\ud83d\udce6 URL or relative path to a markdown file encoded in UTF-8 with additional documentation.\nThe recommended documentation file name is README.md
. An .md
suffix is mandatory.
badges associated with this resource
\n", "annotation": ": List[bioimageio.spec.generic.v0_2.BadgeDescr]"}, "bioimageio.spec.generic.v0_3.GenericDescrBase.implemented_format_version": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescrBase.implemented_format_version", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescrBase.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.generic.v0_3.GenericDescrBase.implemented_format_version_tuple": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescrBase.implemented_format_version_tuple", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescrBase.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.generic.v0_3.GenericDescrBase.model_post_init": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescrBase.model_post_init", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescrBase.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.generic.v0_3.GenericDescr": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr", "kind": "class", "doc": "Specification of the fields used in a generic bioimage.io-compliant resource description file (RDF).
\n\nAn RDF is a YAML file that describes a resource such as a model, a dataset, or a notebook.\nNote that those resources are described with a type-specific RDF.\nUse this generic resource description, if none of the known specific types matches your resource.
\n", "bases": "GenericDescrBase"}, "bioimageio.spec.generic.v0_3.GenericDescr.type": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.type", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.type", "kind": "variable", "doc": "The resource type assigns a broad category to the resource.
\n", "annotation": ": Annotated[str, Annotated[~_StrType, Predicate(str.islower)]]"}, "bioimageio.spec.generic.v0_3.GenericDescr.id": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.id", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_3.ResourceId]"}, "bioimageio.spec.generic.v0_3.GenericDescr.parent": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.parent", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.parent", "kind": "variable", "doc": "The description from which this one is derived
\n", "annotation": ": Optional[bioimageio.spec.generic.v0_3.ResourceId]"}, "bioimageio.spec.generic.v0_3.GenericDescr.source": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.source", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.source", "kind": "variable", "doc": "The primary source of the resource
\n", "annotation": ": Optional[bioimageio.spec._internal.url.HttpUrl]"}, "bioimageio.spec.generic.v0_3.GenericDescr.check_specific_types": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.check_specific_types", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.check_specific_types", "kind": "function", "doc": "\n", "signature": "(cls, value: str) -> str:", "funcdef": "def"}, "bioimageio.spec.generic.v0_3.GenericDescr.implemented_format_version": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.implemented_format_version", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.3.0'"}, "bioimageio.spec.generic.v0_3.GenericDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 3, 0)"}, "bioimageio.spec.generic.v0_3.GenericDescr.model_post_init": {"fullname": "bioimageio.spec.generic.v0_3.GenericDescr.model_post_init", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "GenericDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.generic.v0_3.LinkedResourceNode": {"fullname": "bioimageio.spec.generic.v0_3.LinkedResourceNode", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "LinkedResourceNode", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.generic.v0_3.LinkedResourceNode.version": {"fullname": "bioimageio.spec.generic.v0_3.LinkedResourceNode.version", "modulename": "bioimageio.spec.generic.v0_3", "qualname": "LinkedResourceNode.version", "kind": "variable", "doc": "The version of the linked resource following SemVer 2.0.
\n", "annotation": ": Optional[bioimageio.spec._internal.version_type.Version]"}, "bioimageio.spec.model": {"fullname": "bioimageio.spec.model", "modulename": "bioimageio.spec.model", "kind": "module", "doc": "implementaions of all released minor versions are available in submodules:
\n\nbioimageio.spec.model.v0_4.ModelDescr
bioimageio.spec.model.v0_5.ModelDescr
Specification of the fields used in a bioimage.io-compliant RDF to describe AI models with pretrained weights.\nThese fields are typically stored in a YAML file which we call a model resource description file (model RDF).
\n", "bases": "bioimageio.spec.generic.v0_3.GenericModelDescrBase"}, "bioimageio.spec.model.ModelDescr.format_version": {"fullname": "bioimageio.spec.model.ModelDescr.format_version", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.format_version", "kind": "variable", "doc": "Version of the bioimage.io model description specification used.\nWhen creating a new model always use the latest micro/patch version described here.\nThe format_version
is important for any consumer software to understand how to parse the fields.
Specialized resource type 'model'
\n", "annotation": ": Literal['model']"}, "bioimageio.spec.model.ModelDescr.id": {"fullname": "bioimageio.spec.model.ModelDescr.id", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.ModelId]"}, "bioimageio.spec.model.ModelDescr.authors": {"fullname": "bioimageio.spec.model.ModelDescr.authors", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.authors", "kind": "variable", "doc": "The authors are the creators of the model RDF and the primary points of contact.
\n", "annotation": ": Annotated[List[bioimageio.spec.generic.v0_3.Author], MinLen(min_length=1)]"}, "bioimageio.spec.model.ModelDescr.documentation": {"fullname": "bioimageio.spec.model.ModelDescr.documentation", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.documentation", "kind": "variable", "doc": "\u2208\ud83d\udce6 URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is README.md
. An .md
suffix is mandatory.\nThe documentation should include a '#[#] Validation' (sub)section\nwith details on how to quantitatively validate the model on unseen data.
Describes the input tensors expected by this model.
\n", "annotation": ": Annotated[Sequence[bioimageio.spec.model.v0_5.InputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.model.ModelDescr.name": {"fullname": "bioimageio.spec.model.ModelDescr.name", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.name", "kind": "variable", "doc": "A human-readable name of this model.\nIt should be no longer than 64 characters\nand may only contain letter, number, underscore, minus, parentheses and spaces.\nWe recommend to chose a name that refers to the model's task and image modality.
\n", "annotation": ": Annotated[str, RestrictCharacters(alphabet='abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_- ()'), MinLen(min_length=5), MaxLen(max_length=128), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f1c4c7b5c60>, severity=20, msg='Name longer than 64 characters.', context={'typ': Annotated[Any, MaxLen(max_length=64)]})]"}, "bioimageio.spec.model.ModelDescr.outputs": {"fullname": "bioimageio.spec.model.ModelDescr.outputs", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.outputs", "kind": "variable", "doc": "Describes the output tensors.
\n", "annotation": ": Annotated[Sequence[bioimageio.spec.model.v0_5.OutputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.model.ModelDescr.packaged_by": {"fullname": "bioimageio.spec.model.ModelDescr.packaged_by", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.packaged_by", "kind": "variable", "doc": "The persons that have packaged and uploaded this model.\nOnly required if those persons differ from the authors
.
The model from which this model is derived, e.g. by fine-tuning the weights.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.LinkedModel]"}, "bioimageio.spec.model.ModelDescr.run_mode": {"fullname": "bioimageio.spec.model.ModelDescr.run_mode", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.run_mode", "kind": "variable", "doc": "Custom run mode for this model: for more complex prediction procedures like test time\ndata augmentation that currently cannot be expressed in the specification.\nNo standard run modes are defined yet.
\n", "annotation": ": Annotated[Optional[bioimageio.spec.model.v0_4.RunMode], AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f1c4c7b4e00>, severity=30, msg="Run mode '{value}' has limited support across consumer softwares.", context={'typ': None})]"}, "bioimageio.spec.model.ModelDescr.timestamp": {"fullname": "bioimageio.spec.model.ModelDescr.timestamp", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.timestamp", "kind": "variable", "doc": "Timestamp in ISO 8601 format\nwith a few restrictions listed here.\n(In Python a datetime object is valid, too).
\n", "annotation": ": bioimageio.spec._internal.types.Datetime"}, "bioimageio.spec.model.ModelDescr.training_data": {"fullname": "bioimageio.spec.model.ModelDescr.training_data", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.training_data", "kind": "variable", "doc": "The dataset used to train this model
\n", "annotation": ": Annotated[Union[NoneType, bioimageio.spec.dataset.v0_3.LinkedDataset, bioimageio.spec.dataset.v0_3.DatasetDescr, bioimageio.spec.dataset.v0_2.DatasetDescr], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]"}, "bioimageio.spec.model.ModelDescr.weights": {"fullname": "bioimageio.spec.model.ModelDescr.weights", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.weights", "kind": "variable", "doc": "The weights for this model.\nWeights can be given for different formats, but should otherwise be equivalent.\nThe available weight formats determine which consumers can use this model.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.WeightsDescr, WrapSerializer(func=<function package_weights at 0x7f1c5bd54360>, return_type=PydanticUndefined, when_used='always')]"}, "bioimageio.spec.model.ModelDescr.get_input_test_arrays": {"fullname": "bioimageio.spec.model.ModelDescr.get_input_test_arrays", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.get_input_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.model.ModelDescr.get_output_test_arrays": {"fullname": "bioimageio.spec.model.ModelDescr.get_output_test_arrays", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.get_output_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.model.ModelDescr.get_batch_size": {"fullname": "bioimageio.spec.model.ModelDescr.get_batch_size", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.get_batch_size", "kind": "function", "doc": "\n", "signature": "(\ttensor_sizes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]) -> int:", "funcdef": "def"}, "bioimageio.spec.model.ModelDescr.get_output_tensor_sizes": {"fullname": "bioimageio.spec.model.ModelDescr.get_output_tensor_sizes", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.get_output_tensor_sizes", "kind": "function", "doc": "Returns the tensor output sizes for given input_sizes.\nOnly if input_sizes has a valid input shape, the tensor output size is exact.\nOtherwise it might be larger than the actual (valid) output
\n", "signature": "(\tself,\tinput_sizes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]) -> Dict[bioimageio.spec.model.v0_5.TensorId, Dict[bioimageio.spec.model.v0_5.AxisId, Union[int, bioimageio.spec.model.v0_5._DataDepSize]]]:", "funcdef": "def"}, "bioimageio.spec.model.ModelDescr.get_ns": {"fullname": "bioimageio.spec.model.ModelDescr.get_ns", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.get_ns", "kind": "function", "doc": "get parameter n
for each parameterized axis\nsuch that the valid input size is >= the given input size
Determine input and output block shape for scale factors ns\nof parameterized input sizes.
\n\nn
for each axis (keyed by (tensor_id, axis_id))\nthat is parameterized as size = min + n * step
.n
, is larger\nthan max_input_shape is set to the minimal value n_min
for which\nthis is still true.\nUse this for small input samples or large values of ns.\nOr simply whenever you know the full input shape.\n\n", "signature": "(\tself,\tns: Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int],\tbatch_size: Optional[int] = None,\t*,\tmax_input_shape: Optional[Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int]] = None) -> bioimageio.spec.model.v0_5._AxisSizes:", "funcdef": "def"}, "bioimageio.spec.model.ModelDescr.implemented_format_version": {"fullname": "bioimageio.spec.model.ModelDescr.implemented_format_version", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.5.3'"}, "bioimageio.spec.model.ModelDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.model.ModelDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 5, 3)"}, "bioimageio.spec.model.ModelDescr.model_post_init": {"fullname": "bioimageio.spec.model.ModelDescr.model_post_init", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr.model_post_init", "kind": "function", "doc": "Resolved axis sizes for model inputs and outputs.
\n
We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.model.ModelDescr_v0_4": {"fullname": "bioimageio.spec.model.ModelDescr_v0_4", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr_v0_4", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.model.v0_4.ModelDescr'>"}, "bioimageio.spec.model.ModelDescr_v0_5": {"fullname": "bioimageio.spec.model.ModelDescr_v0_5", "modulename": "bioimageio.spec.model", "qualname": "ModelDescr_v0_5", "kind": "variable", "doc": "\n", "default_value": "<class 'bioimageio.spec.model.v0_5.ModelDescr'>"}, "bioimageio.spec.model.AnyModelDescr": {"fullname": "bioimageio.spec.model.AnyModelDescr", "modulename": "bioimageio.spec.model", "qualname": "AnyModelDescr", "kind": "variable", "doc": "Union of any released model desription
\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.model.v0_4.ModelDescr, bioimageio.spec.model.v0_5.ModelDescr], Discriminator(discriminator='format_version', custom_error_type=None, custom_error_message=None, custom_error_context=None)]"}, "bioimageio.spec.model.v0_4": {"fullname": "bioimageio.spec.model.v0_4", "modulename": "bioimageio.spec.model.v0_4", "kind": "module", "doc": "\n"}, "bioimageio.spec.model.v0_4.ModelId": {"fullname": "bioimageio.spec.model.v0_4.ModelId", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec.generic.v0_2.ResourceId"}, "bioimageio.spec.model.v0_4.AxesStr": {"fullname": "bioimageio.spec.model.v0_4.AxesStr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "AxesStr", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[str, RestrictCharacters(alphabet='bitczyx'), AfterValidator(func=<function validate_unique_entries>)]"}, "bioimageio.spec.model.v0_4.AxesInCZYX": {"fullname": "bioimageio.spec.model.v0_4.AxesInCZYX", "modulename": "bioimageio.spec.model.v0_4", "qualname": "AxesInCZYX", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[str, RestrictCharacters(alphabet='czyx'), AfterValidator(func=<function validate_unique_entries>)]"}, "bioimageio.spec.model.v0_4.PostprocessingName": {"fullname": "bioimageio.spec.model.v0_4.PostprocessingName", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PostprocessingName", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['binarize', 'clip', 'scale_linear', 'sigmoid', 'zero_mean_unit_variance', 'scale_range', 'scale_mean_variance']"}, "bioimageio.spec.model.v0_4.PreprocessingName": {"fullname": "bioimageio.spec.model.v0_4.PreprocessingName", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PreprocessingName", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['binarize', 'clip', 'scale_linear', 'sigmoid', 'zero_mean_unit_variance', 'scale_range']"}, "bioimageio.spec.model.v0_4.TensorName": {"fullname": "bioimageio.spec.model.v0_4.TensorName", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorName", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec._internal.types.LowerCaseIdentifier"}, "bioimageio.spec.model.v0_4.CallableFromDepencency": {"fullname": "bioimageio.spec.model.v0_4.CallableFromDepencency", "modulename": "bioimageio.spec.model.v0_4", "qualname": "CallableFromDepencency", "kind": "class", "doc": "deprecated! don't use for new spec fields!
\n", "bases": "bioimageio.spec._internal.common_nodes.StringNode"}, "bioimageio.spec.model.v0_4.CallableFromDepencency.module_name": {"fullname": "bioimageio.spec.model.v0_4.CallableFromDepencency.module_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "CallableFromDepencency.module_name", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.model.v0_4.CallableFromDepencency.check_submodules": {"fullname": "bioimageio.spec.model.v0_4.CallableFromDepencency.check_submodules", "modulename": "bioimageio.spec.model.v0_4", "qualname": "CallableFromDepencency.check_submodules", "kind": "function", "doc": "\n", "signature": "(cls, module_name: str) -> str:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.CallableFromDepencency.callable_name": {"fullname": "bioimageio.spec.model.v0_4.CallableFromDepencency.callable_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "CallableFromDepencency.callable_name", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec._internal.types.Identifier"}, "bioimageio.spec.model.v0_4.CallableFromFile": {"fullname": "bioimageio.spec.model.v0_4.CallableFromFile", "modulename": "bioimageio.spec.model.v0_4", "qualname": "CallableFromFile", "kind": "class", "doc": "deprecated! don't use for new spec fields!
\n", "bases": "bioimageio.spec._internal.common_nodes.StringNode"}, "bioimageio.spec.model.v0_4.CallableFromFile.source_file": {"fullname": "bioimageio.spec.model.v0_4.CallableFromFile.source_file", "modulename": "bioimageio.spec.model.v0_4", "qualname": "CallableFromFile.source_file", "kind": "variable", "doc": "\u2208\ud83d\udce6 Python module that implements callable_name
The Python identifier of
\n", "annotation": ": bioimageio.spec._internal.types.Identifier"}, "bioimageio.spec.model.v0_4.CustomCallable": {"fullname": "bioimageio.spec.model.v0_4.CustomCallable", "modulename": "bioimageio.spec.model.v0_4", "qualname": "CustomCallable", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.model.v0_4.CallableFromFile, bioimageio.spec.model.v0_4.CallableFromDepencency], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]"}, "bioimageio.spec.model.v0_4.Dependencies": {"fullname": "bioimageio.spec.model.v0_4.Dependencies", "modulename": "bioimageio.spec.model.v0_4", "qualname": "Dependencies", "kind": "class", "doc": "deprecated! don't use for new spec fields!
\n", "bases": "bioimageio.spec._internal.common_nodes.StringNode"}, "bioimageio.spec.model.v0_4.Dependencies.manager": {"fullname": "bioimageio.spec.model.v0_4.Dependencies.manager", "modulename": "bioimageio.spec.model.v0_4", "qualname": "Dependencies.manager", "kind": "variable", "doc": "Dependency manager
\n", "annotation": ": Annotated[str, MinLen(min_length=1), FieldInfo(annotation=NoneType, required=True, examples=['conda', 'maven', 'pip'])]"}, "bioimageio.spec.model.v0_4.Dependencies.file": {"fullname": "bioimageio.spec.model.v0_4.Dependencies.file", "modulename": "bioimageio.spec.model.v0_4", "qualname": "Dependencies.file", "kind": "variable", "doc": "\u2208\ud83d\udce6 Dependency file
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none'), FieldInfo(annotation=NoneType, required=True, examples=['environment.yaml', 'pom.xml', 'requirements.txt'])]"}, "bioimageio.spec.model.v0_4.WeightsFormat": {"fullname": "bioimageio.spec.model.v0_4.WeightsFormat", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsFormat", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']"}, "bioimageio.spec.model.v0_4.WeightsDescr": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_4.WeightsDescr.keras_hdf5": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr.keras_hdf5", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr.keras_hdf5", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.KerasHdf5WeightsDescr]"}, "bioimageio.spec.model.v0_4.WeightsDescr.onnx": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr.onnx", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr.onnx", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.OnnxWeightsDescr]"}, "bioimageio.spec.model.v0_4.WeightsDescr.pytorch_state_dict": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr.pytorch_state_dict", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr.pytorch_state_dict", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr]"}, "bioimageio.spec.model.v0_4.WeightsDescr.tensorflow_js": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr.tensorflow_js", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr.tensorflow_js", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr]"}, "bioimageio.spec.model.v0_4.WeightsDescr.tensorflow_saved_model_bundle": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr.tensorflow_saved_model_bundle", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr.tensorflow_saved_model_bundle", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr]"}, "bioimageio.spec.model.v0_4.WeightsDescr.torchscript": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr.torchscript", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr.torchscript", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.TorchscriptWeightsDescr]"}, "bioimageio.spec.model.v0_4.WeightsDescr.check_one_entry": {"fullname": "bioimageio.spec.model.v0_4.WeightsDescr.check_one_entry", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsDescr.check_one_entry", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.WeightsEntryDescrBase": {"fullname": "bioimageio.spec.model.v0_4.WeightsEntryDescrBase", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsEntryDescrBase", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.io.FileDescr"}, "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.type": {"fullname": "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsEntryDescrBase.type", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]"}, "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.weights_format_name": {"fullname": "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.weights_format_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsEntryDescrBase.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]"}, "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.source": {"fullname": "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.source", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsEntryDescrBase.source", "kind": "variable", "doc": "\u2208\ud83d\udce6 The weights file.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.attachments": {"fullname": "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.attachments", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsEntryDescrBase.attachments", "kind": "variable", "doc": "Attachments that are specific to this weights entry.
\n", "annotation": ": Annotated[Optional[bioimageio.spec.generic.v0_2.AttachmentsDescr], AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f1c4d1a0360>, severity=35, msg='Weights entry depends on additional attachments.', context={'typ': None})]"}, "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.authors": {"fullname": "bioimageio.spec.model.v0_4.WeightsEntryDescrBase.authors", "modulename": "bioimageio.spec.model.v0_4", "qualname": "WeightsEntryDescrBase.authors", "kind": "variable", "doc": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a parent
)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a parent
field)
Dependency manager and dependency file, specified as <dependency manager>:<relative file path>
.
The source weights these weights were converted from.\nFor example, if a model's weights were converted from the pytorch_state_dict
format to torchscript
,\nThe pytorch_state_dict
weights entry has no parent
and is the parent of the torchscript
weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.
Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_4.KerasHdf5WeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_4.KerasHdf5WeightsDescr.type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "KerasHdf5WeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'keras_hdf5'"}, "bioimageio.spec.model.v0_4.KerasHdf5WeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_4.KerasHdf5WeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "KerasHdf5WeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Keras HDF5'"}, "bioimageio.spec.model.v0_4.KerasHdf5WeightsDescr.tensorflow_version": {"fullname": "bioimageio.spec.model.v0_4.KerasHdf5WeightsDescr.tensorflow_version", "modulename": "bioimageio.spec.model.v0_4", "qualname": "KerasHdf5WeightsDescr.tensorflow_version", "kind": "variable", "doc": "TensorFlow version used to create these weights
\n", "annotation": ": Optional[bioimageio.spec._internal.version_type.Version]"}, "bioimageio.spec.model.v0_4.OnnxWeightsDescr": {"fullname": "bioimageio.spec.model.v0_4.OnnxWeightsDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OnnxWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_4.OnnxWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_4.OnnxWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OnnxWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'onnx'"}, "bioimageio.spec.model.v0_4.OnnxWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_4.OnnxWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OnnxWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'ONNX'"}, "bioimageio.spec.model.v0_4.OnnxWeightsDescr.opset_version": {"fullname": "bioimageio.spec.model.v0_4.OnnxWeightsDescr.opset_version", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OnnxWeightsDescr.opset_version", "kind": "variable", "doc": "ONNX opset version
\n", "annotation": ": Optional[Annotated[int, Ge(ge=7)]]"}, "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr": {"fullname": "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PytorchStateDictWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PytorchStateDictWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'pytorch_state_dict'"}, "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PytorchStateDictWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Pytorch State Dict'"}, "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr.architecture": {"fullname": "bioimageio.spec.model.v0_4.PytorchStateDictWeightsDescr.architecture", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PytorchStateDictWeightsDescr.architecture", "kind": "variable", "doc": "callable returning a torch.nn.Module instance.\nLocal implementation: <relative path to file>:<identifier of implementation within the file>
.\nImplementation in a dependency: <dependency-package>.<[dependency-module]>.<identifier>
.
The SHA256 of the architecture source file,\nif the architecture is not defined in a module listed in dependencies
key word arguments for the architecture
callable
Version of the PyTorch library used.\nIf depencencies
is specified it should include pytorch and the verison has to match.\n(dependencies
overrules pytorch_version
)
Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_4.TorchscriptWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_4.TorchscriptWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TorchscriptWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'torchscript'"}, "bioimageio.spec.model.v0_4.TorchscriptWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_4.TorchscriptWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TorchscriptWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'TorchScript'"}, "bioimageio.spec.model.v0_4.TorchscriptWeightsDescr.pytorch_version": {"fullname": "bioimageio.spec.model.v0_4.TorchscriptWeightsDescr.pytorch_version", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TorchscriptWeightsDescr.pytorch_version", "kind": "variable", "doc": "Version of the PyTorch library used.
\n", "annotation": ": Optional[bioimageio.spec._internal.version_type.Version]"}, "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr": {"fullname": "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowJsWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowJsWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'tensorflow_js'"}, "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowJsWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Tensorflow.js'"}, "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.tensorflow_version": {"fullname": "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.tensorflow_version", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowJsWeightsDescr.tensorflow_version", "kind": "variable", "doc": "Version of the TensorFlow library used.
\n", "annotation": ": Optional[bioimageio.spec._internal.version_type.Version]"}, "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.source": {"fullname": "bioimageio.spec.model.v0_4.TensorflowJsWeightsDescr.source", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowJsWeightsDescr.source", "kind": "variable", "doc": "\u2208\ud83d\udce6 The multi-file weights.\nAll required files/folders should be a zip archive.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr": {"fullname": "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowSavedModelBundleWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowSavedModelBundleWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'tensorflow_saved_model_bundle'"}, "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowSavedModelBundleWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Tensorflow Saved Model'"}, "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr.tensorflow_version": {"fullname": "bioimageio.spec.model.v0_4.TensorflowSavedModelBundleWeightsDescr.tensorflow_version", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorflowSavedModelBundleWeightsDescr.tensorflow_version", "kind": "variable", "doc": "Version of the TensorFlow library used.
\n", "annotation": ": Optional[bioimageio.spec._internal.version_type.Version]"}, "bioimageio.spec.model.v0_4.ParameterizedInputShape": {"fullname": "bioimageio.spec.model.v0_4.ParameterizedInputShape", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ParameterizedInputShape", "kind": "class", "doc": "A sequence of valid shapes given by shape_k = min + k * step for k in {0, 1, ...}
.
The minimum input shape
\n", "annotation": ": Annotated[List[int], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_4.ParameterizedInputShape.step": {"fullname": "bioimageio.spec.model.v0_4.ParameterizedInputShape.step", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ParameterizedInputShape.step", "kind": "variable", "doc": "The minimum shape change
\n", "annotation": ": Annotated[List[int], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_4.ParameterizedInputShape.matching_lengths": {"fullname": "bioimageio.spec.model.v0_4.ParameterizedInputShape.matching_lengths", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ParameterizedInputShape.matching_lengths", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ImplicitOutputShape": {"fullname": "bioimageio.spec.model.v0_4.ImplicitOutputShape", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ImplicitOutputShape", "kind": "class", "doc": "Output tensor shape depending on an input tensor shape.\nshape(output_tensor) = shape(input_tensor) * scale + 2 * offset
Name of the reference tensor.
\n", "annotation": ": bioimageio.spec.model.v0_4.TensorName"}, "bioimageio.spec.model.v0_4.ImplicitOutputShape.scale": {"fullname": "bioimageio.spec.model.v0_4.ImplicitOutputShape.scale", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ImplicitOutputShape.scale", "kind": "variable", "doc": "output_pix/input_pix for each dimension.\n'null' values indicate new dimensions, whose length is defined by 2*offset
Position of origin wrt to input.
\n", "annotation": ": Annotated[List[Union[int, Annotated[float, MultipleOf(multiple_of=0.5)]]], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_4.ImplicitOutputShape.matching_lengths": {"fullname": "bioimageio.spec.model.v0_4.ImplicitOutputShape.matching_lengths", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ImplicitOutputShape.matching_lengths", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.TensorDescrBase": {"fullname": "bioimageio.spec.model.v0_4.TensorDescrBase", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorDescrBase", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_4.TensorDescrBase.name": {"fullname": "bioimageio.spec.model.v0_4.TensorDescrBase.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorDescrBase.name", "kind": "variable", "doc": "Tensor name. No duplicates are allowed.
\n", "annotation": ": bioimageio.spec.model.v0_4.TensorName"}, "bioimageio.spec.model.v0_4.TensorDescrBase.description": {"fullname": "bioimageio.spec.model.v0_4.TensorDescrBase.description", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorDescrBase.description", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.model.v0_4.TensorDescrBase.axes": {"fullname": "bioimageio.spec.model.v0_4.TensorDescrBase.axes", "modulename": "bioimageio.spec.model.v0_4", "qualname": "TensorDescrBase.axes", "kind": "variable", "doc": "Axes identifying characters. Same length and order as the axes in shape
.
axis | \ndescription | \n
---|---|
b | \nbatch (groups multiple samples) | \n
i | \ninstance/index/element | \n
t | \ntime | \n
c | \nchannel | \n
z | \nspatial dimension z | \n
y | \nspatial dimension y | \n
x | \nspatial dimension x | \n
Tuple (minimum, maximum)
specifying the allowed range of the data in this tensor.\nIf not specified, the full data range that can be expressed in data_type
is allowed.
base class for pre-/postprocessing key word arguments
\n", "bases": "bioimageio.spec._internal.common_nodes.KwargsNode"}, "bioimageio.spec.model.v0_4.ProcessingDescrBase": {"fullname": "bioimageio.spec.model.v0_4.ProcessingDescrBase", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ProcessingDescrBase", "kind": "class", "doc": "processing base class
\n", "bases": "bioimageio.spec._internal.common_nodes.NodeWithExplicitlySetFields"}, "bioimageio.spec.model.v0_4.ProcessingDescrBase.fields_to_set_explicitly": {"fullname": "bioimageio.spec.model.v0_4.ProcessingDescrBase.fields_to_set_explicitly", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ProcessingDescrBase.fields_to_set_explicitly", "kind": "variable", "doc": "set set these fields explicitly with their default value if they are not set,\nsuch that they are always included even when dumping with 'exlude_unset'
\n", "annotation": ": ClassVar[FrozenSet[LiteralString]]", "default_value": "frozenset({'name'})"}, "bioimageio.spec.model.v0_4.BinarizeKwargs": {"fullname": "bioimageio.spec.model.v0_4.BinarizeKwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "BinarizeKwargs", "kind": "class", "doc": "key word arguments for BinarizeDescr
The fixed threshold
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_4.BinarizeDescr": {"fullname": "bioimageio.spec.model.v0_4.BinarizeDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "BinarizeDescr", "kind": "class", "doc": "BinarizeDescr the tensor with a fixed BinarizeKwargs.threshold
.\nValues above the threshold will be set to one, values below the threshold to zero.
key word arguments for ClipDescr
minimum value for clipping
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_4.ClipKwargs.max": {"fullname": "bioimageio.spec.model.v0_4.ClipKwargs.max", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ClipKwargs.max", "kind": "variable", "doc": "maximum value for clipping
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_4.ClipDescr": {"fullname": "bioimageio.spec.model.v0_4.ClipDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ClipDescr", "kind": "class", "doc": "Clip tensor values to a range.
\n\nSet tensor values below ClipKwargs.min
to ClipKwargs.min
\nand above ClipKwargs.max
to ClipKwargs.max
.
key word arguments for ScaleLinearDescr
The subset of axes to scale jointly.\nFor example xy to scale the two image axes for 2d data jointly.
\n", "annotation": ": Annotated[Optional[Annotated[str, RestrictCharacters(alphabet='czyx'), AfterValidator(func=<function validate_unique_entries at 0x7f1c60346ac0>)]], FieldInfo(annotation=NoneType, required=True, examples=['xy'])]"}, "bioimageio.spec.model.v0_4.ScaleLinearKwargs.gain": {"fullname": "bioimageio.spec.model.v0_4.ScaleLinearKwargs.gain", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleLinearKwargs.gain", "kind": "variable", "doc": "multiplicative factor
\n", "annotation": ": Union[float, List[float]]"}, "bioimageio.spec.model.v0_4.ScaleLinearKwargs.offset": {"fullname": "bioimageio.spec.model.v0_4.ScaleLinearKwargs.offset", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleLinearKwargs.offset", "kind": "variable", "doc": "additive term
\n", "annotation": ": Union[float, List[float]]"}, "bioimageio.spec.model.v0_4.ScaleLinearKwargs.either_gain_or_offset": {"fullname": "bioimageio.spec.model.v0_4.ScaleLinearKwargs.either_gain_or_offset", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleLinearKwargs.either_gain_or_offset", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ScaleLinearDescr": {"fullname": "bioimageio.spec.model.v0_4.ScaleLinearDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleLinearDescr", "kind": "class", "doc": "Fixed linear scaling.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_4.ScaleLinearDescr.name": {"fullname": "bioimageio.spec.model.v0_4.ScaleLinearDescr.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleLinearDescr.name", "kind": "variable", "doc": "\n", "annotation": ": Literal['scale_linear']"}, "bioimageio.spec.model.v0_4.ScaleLinearDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_4.ScaleLinearDescr.kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleLinearDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_4.ScaleLinearKwargs"}, "bioimageio.spec.model.v0_4.SigmoidDescr": {"fullname": "bioimageio.spec.model.v0_4.SigmoidDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "SigmoidDescr", "kind": "class", "doc": "The logistic sigmoid funciton, a.k.a. expit function.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_4.SigmoidDescr.name": {"fullname": "bioimageio.spec.model.v0_4.SigmoidDescr.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "SigmoidDescr.name", "kind": "variable", "doc": "\n", "annotation": ": Literal['sigmoid']"}, "bioimageio.spec.model.v0_4.SigmoidDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_4.SigmoidDescr.kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "SigmoidDescr.kwargs", "kind": "variable", "doc": "empty kwargs
\n", "annotation": ": bioimageio.spec.model.v0_4.ProcessingKwargs"}, "bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceKwargs": {"fullname": "bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceKwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ZeroMeanUnitVarianceKwargs", "kind": "class", "doc": "key word arguments for ZeroMeanUnitVarianceDescr
Mode for computing mean and variance.
\n\nmode | \ndescription | \n
---|---|
fixed | \nFixed values for mean and variance | \n
per_dataset | \nCompute for the entire dataset | \n
per_sample | \nCompute for each sample individually | \n
The subset of axes to normalize jointly.\nFor example xy
to normalize the two image axes for 2d data jointly.
The mean value(s) to use for mode: fixed
.\nFor example [1.1, 2.2, 3.3]
in the case of a 3 channel image with axes: xy
.
The standard deviation values to use for mode: fixed
. Analogous to mean.
epsilon for numeric stability: out = (tensor - mean) / (std + eps)
.
Subtract mean and divide by variance.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr.name": {"fullname": "bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ZeroMeanUnitVarianceDescr.name", "kind": "variable", "doc": "\n", "annotation": ": Literal['zero_mean_unit_variance']"}, "bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr.kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ZeroMeanUnitVarianceDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceKwargs"}, "bioimageio.spec.model.v0_4.ScaleRangeKwargs": {"fullname": "bioimageio.spec.model.v0_4.ScaleRangeKwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleRangeKwargs", "kind": "class", "doc": "key word arguments for ScaleRangeDescr
For min_percentile
=0.0 (the default) and max_percentile
=100 (the default)\nthis processing step normalizes data to the [0, 1] intervall.\nFor other percentiles the normalized values will partially be outside the [0, 1]\nintervall. Use ScaleRange
followed by ClipDescr
if you want to limit the\nnormalized values to a range.
Mode for computing percentiles.
\n\nmode | \ndescription | \n
---|---|
per_dataset | \ncompute for the entire dataset | \n
per_sample | \ncompute for each sample individually | \n
The subset of axes to normalize jointly.\nFor example xy to normalize the two image axes for 2d data jointly.
\n", "annotation": ": Annotated[str, RestrictCharacters(alphabet='czyx'), AfterValidator(func=<function validate_unique_entries at 0x7f1c60346ac0>), FieldInfo(annotation=NoneType, required=True, examples=['xy'])]"}, "bioimageio.spec.model.v0_4.ScaleRangeKwargs.min_percentile": {"fullname": "bioimageio.spec.model.v0_4.ScaleRangeKwargs.min_percentile", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleRangeKwargs.min_percentile", "kind": "variable", "doc": "The lower percentile used to determine the value to align with zero.
\n", "annotation": ": Annotated[Union[int, float], Interval(gt=None, ge=0, lt=100, le=None)]"}, "bioimageio.spec.model.v0_4.ScaleRangeKwargs.max_percentile": {"fullname": "bioimageio.spec.model.v0_4.ScaleRangeKwargs.max_percentile", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleRangeKwargs.max_percentile", "kind": "variable", "doc": "The upper percentile used to determine the value to align with one.\nHas to be bigger than min_percentile
.\nThe range is 1 to 100 instead of 0 to 100 to avoid mistakenly\naccepting percentiles specified in the range 0.0 to 1.0.
Epsilon for numeric stability.\nout = (tensor - v_lower) / (v_upper - v_lower + eps)
;\nwith v_lower,v_upper
values at the respective percentiles.
Tensor name to compute the percentiles from. Default: The tensor itself.\nFor any tensor in inputs
only input tensor references are allowed.\nFor a tensor in outputs
only input tensor refereences are allowed if mode: per_dataset
Scale with percentiles.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_4.ScaleRangeDescr.name": {"fullname": "bioimageio.spec.model.v0_4.ScaleRangeDescr.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleRangeDescr.name", "kind": "variable", "doc": "\n", "annotation": ": Literal['scale_range']"}, "bioimageio.spec.model.v0_4.ScaleRangeDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_4.ScaleRangeDescr.kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleRangeDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_4.ScaleRangeKwargs"}, "bioimageio.spec.model.v0_4.ScaleMeanVarianceKwargs": {"fullname": "bioimageio.spec.model.v0_4.ScaleMeanVarianceKwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleMeanVarianceKwargs", "kind": "class", "doc": "key word arguments for ScaleMeanVarianceDescr
Mode for computing mean and variance.
\n\nmode | \ndescription | \n
---|---|
per_dataset | \nCompute for the entire dataset | \n
per_sample | \nCompute for each sample individually | \n
Name of tensor to match.
\n", "annotation": ": bioimageio.spec.model.v0_4.TensorName"}, "bioimageio.spec.model.v0_4.ScaleMeanVarianceKwargs.axes": {"fullname": "bioimageio.spec.model.v0_4.ScaleMeanVarianceKwargs.axes", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleMeanVarianceKwargs.axes", "kind": "variable", "doc": "The subset of axes to scale jointly.\nFor example xy to normalize the two image axes for 2d data jointly.\nDefault: scale all non-batch axes jointly.
\n", "annotation": ": Annotated[Optional[Annotated[str, RestrictCharacters(alphabet='czyx'), AfterValidator(func=<function validate_unique_entries at 0x7f1c60346ac0>)]], FieldInfo(annotation=NoneType, required=True, examples=['xy'])]"}, "bioimageio.spec.model.v0_4.ScaleMeanVarianceKwargs.eps": {"fullname": "bioimageio.spec.model.v0_4.ScaleMeanVarianceKwargs.eps", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleMeanVarianceKwargs.eps", "kind": "variable", "doc": "Epsilon for numeric stability:\n\"`out = (tensor - mean) / (std + eps) * (ref_std + eps) + ref_mean.
\n", "annotation": ": Annotated[float, Interval(gt=0, ge=None, lt=None, le=0.1)]"}, "bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr": {"fullname": "bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleMeanVarianceDescr", "kind": "class", "doc": "Scale the tensor s.t. its mean and variance match a reference tensor.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr.name": {"fullname": "bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleMeanVarianceDescr.name", "kind": "variable", "doc": "\n", "annotation": ": Literal['scale_mean_variance']"}, "bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr.kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ScaleMeanVarianceDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_4.ScaleMeanVarianceKwargs"}, "bioimageio.spec.model.v0_4.PreprocessingDescr": {"fullname": "bioimageio.spec.model.v0_4.PreprocessingDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PreprocessingDescr", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]"}, "bioimageio.spec.model.v0_4.PostprocessingDescr": {"fullname": "bioimageio.spec.model.v0_4.PostprocessingDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "PostprocessingDescr", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr, bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]"}, "bioimageio.spec.model.v0_4.InputTensorDescr": {"fullname": "bioimageio.spec.model.v0_4.InputTensorDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "InputTensorDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "TensorDescrBase"}, "bioimageio.spec.model.v0_4.InputTensorDescr.data_type": {"fullname": "bioimageio.spec.model.v0_4.InputTensorDescr.data_type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "InputTensorDescr.data_type", "kind": "variable", "doc": "For now an input tensor is expected to be given as float32
.\nThe data flow in bioimage.io models is explained\nin this diagram..
Specification of input tensor shape.
\n", "annotation": ": Annotated[Union[Sequence[int], bioimageio.spec.model.v0_4.ParameterizedInputShape], FieldInfo(annotation=NoneType, required=True, examples=[(1, 512, 512, 1), {'min': (1, 64, 64, 1), 'step': (0, 32, 32, 0)}])]"}, "bioimageio.spec.model.v0_4.InputTensorDescr.preprocessing": {"fullname": "bioimageio.spec.model.v0_4.InputTensorDescr.preprocessing", "modulename": "bioimageio.spec.model.v0_4", "qualname": "InputTensorDescr.preprocessing", "kind": "variable", "doc": "Description of how this input should be preprocessed.
\n", "annotation": ": List[Annotated[Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.spec.model.v0_4.InputTensorDescr.zero_batch_step_and_one_batch_size": {"fullname": "bioimageio.spec.model.v0_4.InputTensorDescr.zero_batch_step_and_one_batch_size", "modulename": "bioimageio.spec.model.v0_4", "qualname": "InputTensorDescr.zero_batch_step_and_one_batch_size", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.InputTensorDescr.validate_preprocessing_kwargs": {"fullname": "bioimageio.spec.model.v0_4.InputTensorDescr.validate_preprocessing_kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "InputTensorDescr.validate_preprocessing_kwargs", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.OutputTensorDescr": {"fullname": "bioimageio.spec.model.v0_4.OutputTensorDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OutputTensorDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "TensorDescrBase"}, "bioimageio.spec.model.v0_4.OutputTensorDescr.data_type": {"fullname": "bioimageio.spec.model.v0_4.OutputTensorDescr.data_type", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OutputTensorDescr.data_type", "kind": "variable", "doc": "Data type.\nThe data flow in bioimage.io models is explained\nin this diagram..
\n", "annotation": ": Literal['float32', 'float64', 'uint8', 'int8', 'uint16', 'int16', 'uint32', 'int32', 'uint64', 'int64', 'bool']"}, "bioimageio.spec.model.v0_4.OutputTensorDescr.shape": {"fullname": "bioimageio.spec.model.v0_4.OutputTensorDescr.shape", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OutputTensorDescr.shape", "kind": "variable", "doc": "Output tensor shape.
\n", "annotation": ": Union[Sequence[int], bioimageio.spec.model.v0_4.ImplicitOutputShape]"}, "bioimageio.spec.model.v0_4.OutputTensorDescr.halo": {"fullname": "bioimageio.spec.model.v0_4.OutputTensorDescr.halo", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OutputTensorDescr.halo", "kind": "variable", "doc": "The halo
that should be cropped from the output tensor to avoid boundary effects.\nThe halo
is to be cropped from both sides, i.e. shape_after_crop = shape - 2 * halo
.\nTo document a halo
that is already cropped by the model shape.offset
has to be used instead.
Description of how this output should be postprocessed.
\n", "annotation": ": List[Annotated[Union[bioimageio.spec.model.v0_4.BinarizeDescr, bioimageio.spec.model.v0_4.ClipDescr, bioimageio.spec.model.v0_4.ScaleLinearDescr, bioimageio.spec.model.v0_4.SigmoidDescr, bioimageio.spec.model.v0_4.ZeroMeanUnitVarianceDescr, bioimageio.spec.model.v0_4.ScaleRangeDescr, bioimageio.spec.model.v0_4.ScaleMeanVarianceDescr], Discriminator(discriminator='name', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.spec.model.v0_4.OutputTensorDescr.matching_halo_length": {"fullname": "bioimageio.spec.model.v0_4.OutputTensorDescr.matching_halo_length", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OutputTensorDescr.matching_halo_length", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.OutputTensorDescr.validate_postprocessing_kwargs": {"fullname": "bioimageio.spec.model.v0_4.OutputTensorDescr.validate_postprocessing_kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "OutputTensorDescr.validate_postprocessing_kwargs", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.KnownRunMode": {"fullname": "bioimageio.spec.model.v0_4.KnownRunMode", "modulename": "bioimageio.spec.model.v0_4", "qualname": "KnownRunMode", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['deepimagej']"}, "bioimageio.spec.model.v0_4.RunMode": {"fullname": "bioimageio.spec.model.v0_4.RunMode", "modulename": "bioimageio.spec.model.v0_4", "qualname": "RunMode", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_4.RunMode.name": {"fullname": "bioimageio.spec.model.v0_4.RunMode.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "RunMode.name", "kind": "variable", "doc": "Run mode name
\n", "annotation": ": Annotated[Union[Literal['deepimagej'], str], AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f1c4c5c6ca0>, severity=30, msg="Unknown run mode '{value}'.", context={'typ': Literal['deepimagej']})]"}, "bioimageio.spec.model.v0_4.RunMode.kwargs": {"fullname": "bioimageio.spec.model.v0_4.RunMode.kwargs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "RunMode.kwargs", "kind": "variable", "doc": "Run mode specific key word arguments
\n", "annotation": ": Dict[str, Any]"}, "bioimageio.spec.model.v0_4.LinkedModel": {"fullname": "bioimageio.spec.model.v0_4.LinkedModel", "modulename": "bioimageio.spec.model.v0_4", "qualname": "LinkedModel", "kind": "class", "doc": "Reference to a bioimage.io model.
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_4.LinkedModel.id": {"fullname": "bioimageio.spec.model.v0_4.LinkedModel.id", "modulename": "bioimageio.spec.model.v0_4", "qualname": "LinkedModel.id", "kind": "variable", "doc": "A valid model id
from the bioimage.io collection.
version number (n-th published version, not the semantic version) of linked model
\n", "annotation": ": Optional[int]"}, "bioimageio.spec.model.v0_4.package_weights": {"fullname": "bioimageio.spec.model.v0_4.package_weights", "modulename": "bioimageio.spec.model.v0_4", "qualname": "package_weights", "kind": "function", "doc": "\n", "signature": "(\tvalue: bioimageio.spec._internal.node.Node,\thandler: pydantic_core.core_schema.SerializerFunctionWrapHandler,\tinfo: pydantic_core.core_schema.SerializationInfo):", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr", "kind": "class", "doc": "Specification of the fields used in a bioimage.io-compliant RDF that describes AI models with pretrained weights.
\n\nThese fields are typically stored in a YAML file which we call a model resource description file (model RDF).
\n", "bases": "bioimageio.spec.generic.v0_2.GenericModelDescrBase"}, "bioimageio.spec.model.v0_4.ModelDescr.format_version": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.format_version", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.format_version", "kind": "variable", "doc": "Version of the bioimage.io model description specification used.\nWhen creating a new model always use the latest micro/patch version described here.\nThe format_version
is important for any consumer software to understand how to parse the fields.
Specialized resource type 'model'
\n", "annotation": ": Literal['model']"}, "bioimageio.spec.model.v0_4.ModelDescr.id": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.id", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.ModelId]"}, "bioimageio.spec.model.v0_4.ModelDescr.authors": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.authors", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.authors", "kind": "variable", "doc": "The authors are the creators of the model RDF and the primary points of contact.
\n", "annotation": ": Annotated[List[bioimageio.spec.generic.v0_2.Author], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_4.ModelDescr.documentation": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.documentation", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.documentation", "kind": "variable", "doc": "\u2208\ud83d\udce6 URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is README.md
. An .md
suffix is mandatory.\nThe documentation should include a '[#[#]]# Validation' (sub)section\nwith details on how to quantitatively validate the model on unseen data.
Describes the input tensors expected by this model.
\n", "annotation": ": Annotated[List[bioimageio.spec.model.v0_4.InputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_4.ModelDescr.license": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.license", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.license", "kind": "variable", "doc": "A SPDX license identifier.\nWe do notsupport custom license beyond the SPDX license list, if you need that please\nopen a GitHub issue to discuss your intentions with the community.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.license_id.LicenseId, str], AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f1c4c5c5da0>, severity=30, msg="Unknown license id '{value}'.", context={'typ': <class 'bioimageio.spec._internal.license_id.LicenseId'>}), FieldInfo(annotation=NoneType, required=True, examples=['CC0-1.0', 'MIT', 'BSD-2-Clause'])]"}, "bioimageio.spec.model.v0_4.ModelDescr.name": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.name", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.name", "kind": "variable", "doc": "A human-readable name of this model.\nIt should be no longer than 64 characters and only contain letter, number, underscore, minus or space characters.
\n", "annotation": ": Annotated[str, MinLen(min_length=1), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f1c4c5c67a0>, severity=20, msg='Name shorter than 5 characters.', context={'typ': Annotated[Any, MinLen(min_length=5)]}), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f1c4c5c4540>, severity=20, msg='Name longer than 64 characters.', context={'typ': Annotated[Any, MaxLen(max_length=64)]})]"}, "bioimageio.spec.model.v0_4.ModelDescr.outputs": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.outputs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.outputs", "kind": "variable", "doc": "Describes the output tensors.
\n", "annotation": ": Annotated[List[bioimageio.spec.model.v0_4.OutputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_4.ModelDescr.unique_tensor_descr_names": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.unique_tensor_descr_names", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.unique_tensor_descr_names", "kind": "function", "doc": "\n", "signature": "(\tcls,\tvalue: Sequence[Union[bioimageio.spec.model.v0_4.InputTensorDescr, bioimageio.spec.model.v0_4.OutputTensorDescr]]) -> Sequence[Union[bioimageio.spec.model.v0_4.InputTensorDescr, bioimageio.spec.model.v0_4.OutputTensorDescr]]:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.unique_io_names": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.unique_io_names", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.unique_io_names", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.minimum_shape2valid_output": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.minimum_shape2valid_output", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.minimum_shape2valid_output", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.validate_tensor_references_in_inputs": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.validate_tensor_references_in_inputs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.validate_tensor_references_in_inputs", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.validate_tensor_references_in_outputs": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.validate_tensor_references_in_outputs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.validate_tensor_references_in_outputs", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.packaged_by": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.packaged_by", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.packaged_by", "kind": "variable", "doc": "The persons that have packaged and uploaded this model.\nOnly required if those persons differ from the authors
.
The model from which this model is derived, e.g. by fine-tuning the weights.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.LinkedModel]"}, "bioimageio.spec.model.v0_4.ModelDescr.ignore_url_parent": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.ignore_url_parent", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.ignore_url_parent", "kind": "function", "doc": "\n", "signature": "(cls, parent: Any):", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.run_mode": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.run_mode", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.run_mode", "kind": "variable", "doc": "Custom run mode for this model: for more complex prediction procedures like test time\ndata augmentation that currently cannot be expressed in the specification.\nNo standard run modes are defined yet.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_4.RunMode]"}, "bioimageio.spec.model.v0_4.ModelDescr.sample_inputs": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.sample_inputs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.sample_inputs", "kind": "variable", "doc": "\u2208\ud83d\udce6 URLs/relative paths to sample inputs to illustrate possible inputs for the model,\nfor example stored as PNG or TIFF images.\nThe sample files primarily serve to inform a human user about an example use case
\n", "annotation": ": List[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')]]"}, "bioimageio.spec.model.v0_4.ModelDescr.sample_outputs": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.sample_outputs", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.sample_outputs", "kind": "variable", "doc": "\u2208\ud83d\udce6 URLs/relative paths to sample outputs corresponding to the sample_inputs
.
\u2208\ud83d\udce6 Test input tensors compatible with the inputs
description for a single test case.\nThis means if your model has more than one input, you should provide one URL/relative path for each input.\nEach test input should be a file with an ndarray in\nnumpy.lib file format.\nThe extension must be '.npy'.
\u2208\ud83d\udce6 Analog to test_inputs
.
Timestamp in ISO 8601 format\nwith a few restrictions listed here.
\n", "annotation": ": bioimageio.spec._internal.types.Datetime"}, "bioimageio.spec.model.v0_4.ModelDescr.training_data": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.training_data", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.training_data", "kind": "variable", "doc": "The dataset used to train this model
\n", "annotation": ": Union[bioimageio.spec.dataset.v0_2.LinkedDataset, bioimageio.spec.dataset.v0_2.DatasetDescr, NoneType]"}, "bioimageio.spec.model.v0_4.ModelDescr.weights": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.weights", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.weights", "kind": "variable", "doc": "The weights for this model.\nWeights can be given for different formats, but should otherwise be equivalent.\nThe available weight formats determine which consumers can use this model.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_4.WeightsDescr, WrapSerializer(func=<function package_weights at 0x7f1c5bd54360>, return_type=PydanticUndefined, when_used='always')]"}, "bioimageio.spec.model.v0_4.ModelDescr.get_input_test_arrays": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.get_input_test_arrays", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.get_input_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.get_output_test_arrays": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.get_output_test_arrays", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.get_output_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.model.v0_4.ModelDescr.implemented_format_version": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.implemented_format_version", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.4.10'"}, "bioimageio.spec.model.v0_4.ModelDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 4, 10)"}, "bioimageio.spec.model.v0_4.ModelDescr.model_post_init": {"fullname": "bioimageio.spec.model.v0_4.ModelDescr.model_post_init", "modulename": "bioimageio.spec.model.v0_4", "qualname": "ModelDescr.model_post_init", "kind": "function", "doc": "We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.model.v0_5": {"fullname": "bioimageio.spec.model.v0_5", "modulename": "bioimageio.spec.model.v0_5", "kind": "module", "doc": "\n"}, "bioimageio.spec.model.v0_5.SpaceUnit": {"fullname": "bioimageio.spec.model.v0_5.SpaceUnit", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceUnit", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['attometer', 'angstrom', 'centimeter', 'decimeter', 'exameter', 'femtometer', 'foot', 'gigameter', 'hectometer', 'inch', 'kilometer', 'megameter', 'meter', 'micrometer', 'mile', 'millimeter', 'nanometer', 'parsec', 'petameter', 'picometer', 'terameter', 'yard', 'yoctometer', 'yottameter', 'zeptometer', 'zettameter']"}, "bioimageio.spec.model.v0_5.TimeUnit": {"fullname": "bioimageio.spec.model.v0_5.TimeUnit", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeUnit", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['attosecond', 'centisecond', 'day', 'decisecond', 'exasecond', 'femtosecond', 'gigasecond', 'hectosecond', 'hour', 'kilosecond', 'megasecond', 'microsecond', 'millisecond', 'minute', 'nanosecond', 'petasecond', 'picosecond', 'second', 'terasecond', 'yoctosecond', 'yottasecond', 'zeptosecond', 'zettasecond']"}, "bioimageio.spec.model.v0_5.AxisType": {"fullname": "bioimageio.spec.model.v0_5.AxisType", "modulename": "bioimageio.spec.model.v0_5", "qualname": "AxisType", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['batch', 'channel', 'index', 'time', 'space']"}, "bioimageio.spec.model.v0_5.TensorId": {"fullname": "bioimageio.spec.model.v0_5.TensorId", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec._internal.types.LowerCaseIdentifier"}, "bioimageio.spec.model.v0_5.TensorId.root_model": {"fullname": "bioimageio.spec.model.v0_5.TensorId.root_model", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorId.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[str, MinLen, AfterValidator, AfterValidator, Annotated[TypeVar, Predicate], MaxLen]]'>"}, "bioimageio.spec.model.v0_5.AxisId": {"fullname": "bioimageio.spec.model.v0_5.AxisId", "modulename": "bioimageio.spec.model.v0_5", "qualname": "AxisId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec._internal.types.LowerCaseIdentifier"}, "bioimageio.spec.model.v0_5.AxisId.root_model": {"fullname": "bioimageio.spec.model.v0_5.AxisId.root_model", "modulename": "bioimageio.spec.model.v0_5", "qualname": "AxisId.root_model", "kind": "variable", "doc": "the pydantic root model to validate the string
\n", "annotation": ": ClassVar[Type[pydantic.root_model.RootModel[Any]]]", "default_value": "<class 'pydantic.root_model.RootModel[Annotated[str, MinLen, AfterValidator, AfterValidator, Annotated[TypeVar, Predicate], MaxLen]]'>"}, "bioimageio.spec.model.v0_5.NonBatchAxisId": {"fullname": "bioimageio.spec.model.v0_5.NonBatchAxisId", "modulename": "bioimageio.spec.model.v0_5", "qualname": "NonBatchAxisId", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_not_batch)]"}, "bioimageio.spec.model.v0_5.PostprocessingId": {"fullname": "bioimageio.spec.model.v0_5.PostprocessingId", "modulename": "bioimageio.spec.model.v0_5", "qualname": "PostprocessingId", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['binarize', 'clip', 'ensure_dtype', 'fixed_zero_mean_unit_variance', 'scale_linear', 'scale_mean_variance', 'scale_range', 'sigmoid', 'zero_mean_unit_variance']"}, "bioimageio.spec.model.v0_5.PreprocessingId": {"fullname": "bioimageio.spec.model.v0_5.PreprocessingId", "modulename": "bioimageio.spec.model.v0_5", "qualname": "PreprocessingId", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['binarize', 'clip', 'ensure_dtype', 'scale_linear', 'sigmoid', 'zero_mean_unit_variance', 'scale_range']"}, "bioimageio.spec.model.v0_5.SAME_AS_TYPE": {"fullname": "bioimageio.spec.model.v0_5.SAME_AS_TYPE", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SAME_AS_TYPE", "kind": "variable", "doc": "\n", "default_value": "'<same as type>'"}, "bioimageio.spec.model.v0_5.ParameterizedSize_N": {"fullname": "bioimageio.spec.model.v0_5.ParameterizedSize_N", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ParameterizedSize_N", "kind": "variable", "doc": "\n", "default_value": "<class 'int'>"}, "bioimageio.spec.model.v0_5.ParameterizedSize": {"fullname": "bioimageio.spec.model.v0_5.ParameterizedSize", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ParameterizedSize", "kind": "class", "doc": "Describes a range of valid tensor axis sizes as size = min + n*step
.
integer to parameterize this axis
\n", "annotation": ": ClassVar[Type[int]]", "default_value": "<class 'int'>"}, "bioimageio.spec.model.v0_5.ParameterizedSize.min": {"fullname": "bioimageio.spec.model.v0_5.ParameterizedSize.min", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ParameterizedSize.min", "kind": "variable", "doc": "\n", "annotation": ": Annotated[int, Gt(gt=0)]"}, "bioimageio.spec.model.v0_5.ParameterizedSize.step": {"fullname": "bioimageio.spec.model.v0_5.ParameterizedSize.step", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ParameterizedSize.step", "kind": "variable", "doc": "\n", "annotation": ": Annotated[int, Gt(gt=0)]"}, "bioimageio.spec.model.v0_5.ParameterizedSize.validate_size": {"fullname": "bioimageio.spec.model.v0_5.ParameterizedSize.validate_size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ParameterizedSize.validate_size", "kind": "function", "doc": "\n", "signature": "(self, size: int) -> int:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ParameterizedSize.get_size": {"fullname": "bioimageio.spec.model.v0_5.ParameterizedSize.get_size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ParameterizedSize.get_size", "kind": "function", "doc": "\n", "signature": "(self, n: int) -> int:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ParameterizedSize.get_n": {"fullname": "bioimageio.spec.model.v0_5.ParameterizedSize.get_n", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ParameterizedSize.get_n", "kind": "function", "doc": "return smallest n parameterizing a size greater or equal than s
Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_5.DataDependentSize.min": {"fullname": "bioimageio.spec.model.v0_5.DataDependentSize.min", "modulename": "bioimageio.spec.model.v0_5", "qualname": "DataDependentSize.min", "kind": "variable", "doc": "\n", "annotation": ": Annotated[int, Gt(gt=0)]"}, "bioimageio.spec.model.v0_5.DataDependentSize.max": {"fullname": "bioimageio.spec.model.v0_5.DataDependentSize.max", "modulename": "bioimageio.spec.model.v0_5", "qualname": "DataDependentSize.max", "kind": "variable", "doc": "\n", "annotation": ": Annotated[Optional[int], Gt(gt=1)]"}, "bioimageio.spec.model.v0_5.DataDependentSize.validate_size": {"fullname": "bioimageio.spec.model.v0_5.DataDependentSize.validate_size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "DataDependentSize.validate_size", "kind": "function", "doc": "\n", "signature": "(self, size: int) -> int:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.SizeReference": {"fullname": "bioimageio.spec.model.v0_5.SizeReference", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SizeReference", "kind": "class", "doc": "A tensor axis size (extent in pixels/frames) defined in relation to a reference axis.
\n\naxis.size = reference.size * reference.scale / axis.scale + offset
note:
\n\nconcatenable
the referencing axis is assumed to be\nconcatenable
as well with the same block order.example:\nAn unisotropic input image of wh=10049 pixels depicts a phsical space of 200196mm\u00b2.\nLet's assume that we want to express the image height h in relation to its width w\ninstead of only accepting input images of exactly 10049 pixels\n(for example to express a range of valid image shapes by parametrizing w, see ParameterizedSize
).
>>> w = SpaceInputAxis(id=AxisId("w"), size=100, unit="millimeter", scale=2)\n>>> h = SpaceInputAxis(\n... id=AxisId("h"),\n... size=SizeReference(tensor_id=TensorId("input"), axis_id=AxisId("w"), offset=-1),\n... unit="millimeter",\n... scale=4,\n... )\n>>> print(h.size.compute(h, w))\n49\n
\n-> h = w * w.scale / h.scale + offset = 100 * 2mm / 4mm - 1 = 49
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_5.SizeReference.tensor_id": {"fullname": "bioimageio.spec.model.v0_5.SizeReference.tensor_id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SizeReference.tensor_id", "kind": "variable", "doc": "tensor id of the reference axis
\n", "annotation": ": bioimageio.spec.model.v0_5.TensorId"}, "bioimageio.spec.model.v0_5.SizeReference.axis_id": {"fullname": "bioimageio.spec.model.v0_5.SizeReference.axis_id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SizeReference.axis_id", "kind": "variable", "doc": "axis id of the reference axis
\n", "annotation": ": bioimageio.spec.model.v0_5.AxisId"}, "bioimageio.spec.model.v0_5.SizeReference.offset": {"fullname": "bioimageio.spec.model.v0_5.SizeReference.offset", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SizeReference.offset", "kind": "variable", "doc": "\n", "annotation": ": int"}, "bioimageio.spec.model.v0_5.SizeReference.get_size": {"fullname": "bioimageio.spec.model.v0_5.SizeReference.get_size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SizeReference.get_size", "kind": "function", "doc": "Compute the concrete size for a given axis and its reference axis.
\n\nSizeReference
is the size of.ParameterizedSize
)\nand no fixed ref_size is given,\nn is used to compute the size of the parameterized ref_axis.Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.common_nodes.NodeWithExplicitlySetFields"}, "bioimageio.spec.model.v0_5.AxisBase.fields_to_set_explicitly": {"fullname": "bioimageio.spec.model.v0_5.AxisBase.fields_to_set_explicitly", "modulename": "bioimageio.spec.model.v0_5", "qualname": "AxisBase.fields_to_set_explicitly", "kind": "variable", "doc": "set set these fields explicitly with their default value if they are not set,\nsuch that they are always included even when dumping with 'exlude_unset'
\n", "annotation": ": ClassVar[FrozenSet[LiteralString]]", "default_value": "frozenset({'type'})"}, "bioimageio.spec.model.v0_5.AxisBase.id": {"fullname": "bioimageio.spec.model.v0_5.AxisBase.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "AxisBase.id", "kind": "variable", "doc": "An axis id unique across all axes of one tensor.
\n", "annotation": ": bioimageio.spec.model.v0_5.AxisId"}, "bioimageio.spec.model.v0_5.AxisBase.description": {"fullname": "bioimageio.spec.model.v0_5.AxisBase.description", "modulename": "bioimageio.spec.model.v0_5", "qualname": "AxisBase.description", "kind": "variable", "doc": "\n", "annotation": ": Annotated[str, MaxLen(max_length=128)]"}, "bioimageio.spec.model.v0_5.WithHalo": {"fullname": "bioimageio.spec.model.v0_5.WithHalo", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WithHalo", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_5.WithHalo.halo": {"fullname": "bioimageio.spec.model.v0_5.WithHalo.halo", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WithHalo.halo", "kind": "variable", "doc": "The halo should be cropped from the output tensor to avoid boundary effects.\nIt is to be cropped from both sides, i.e. size_after_crop = size - 2 * halo
.\nTo document a halo that is already cropped by the model use size.offset
instead.
reference to another axis with an optional offset (see SizeReference
)
Subpart of a resource description
\n", "bases": "AxisBase"}, "bioimageio.spec.model.v0_5.BatchAxis.type": {"fullname": "bioimageio.spec.model.v0_5.BatchAxis.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BatchAxis.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['batch']"}, "bioimageio.spec.model.v0_5.BatchAxis.id": {"fullname": "bioimageio.spec.model.v0_5.BatchAxis.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BatchAxis.id", "kind": "variable", "doc": "An axis id unique across all axes of one tensor.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_batch)]"}, "bioimageio.spec.model.v0_5.BatchAxis.size": {"fullname": "bioimageio.spec.model.v0_5.BatchAxis.size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BatchAxis.size", "kind": "variable", "doc": "The batch size may be fixed to 1,\notherwise (the default) it may be chosen arbitrarily depending on available memory
\n", "annotation": ": Optional[Literal[1]]"}, "bioimageio.spec.model.v0_5.BatchAxis.scale": {"fullname": "bioimageio.spec.model.v0_5.BatchAxis.scale", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BatchAxis.scale", "kind": "variable", "doc": "\n"}, "bioimageio.spec.model.v0_5.BatchAxis.concatenable": {"fullname": "bioimageio.spec.model.v0_5.BatchAxis.concatenable", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BatchAxis.concatenable", "kind": "variable", "doc": "\n"}, "bioimageio.spec.model.v0_5.BatchAxis.unit": {"fullname": "bioimageio.spec.model.v0_5.BatchAxis.unit", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BatchAxis.unit", "kind": "variable", "doc": "\n"}, "bioimageio.spec.model.v0_5.ChannelAxis": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "AxisBase"}, "bioimageio.spec.model.v0_5.ChannelAxis.type": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['channel']"}, "bioimageio.spec.model.v0_5.ChannelAxis.id": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis.id", "kind": "variable", "doc": "An axis id unique across all axes of one tensor.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_not_batch)]"}, "bioimageio.spec.model.v0_5.ChannelAxis.channel_names": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis.channel_names", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis.channel_names", "kind": "variable", "doc": "\n", "annotation": ": Annotated[List[bioimageio.spec._internal.types.Identifier], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_5.ChannelAxis.size": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis.size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis.size", "kind": "variable", "doc": "\n", "annotation": ": int"}, "bioimageio.spec.model.v0_5.ChannelAxis.concatenable": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis.concatenable", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis.concatenable", "kind": "variable", "doc": "\n"}, "bioimageio.spec.model.v0_5.ChannelAxis.scale": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis.scale", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis.scale", "kind": "variable", "doc": "\n", "annotation": ": float"}, "bioimageio.spec.model.v0_5.ChannelAxis.unit": {"fullname": "bioimageio.spec.model.v0_5.ChannelAxis.unit", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ChannelAxis.unit", "kind": "variable", "doc": "\n"}, "bioimageio.spec.model.v0_5.IndexAxisBase": {"fullname": "bioimageio.spec.model.v0_5.IndexAxisBase", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexAxisBase", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "AxisBase"}, "bioimageio.spec.model.v0_5.IndexAxisBase.type": {"fullname": "bioimageio.spec.model.v0_5.IndexAxisBase.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexAxisBase.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['index']"}, "bioimageio.spec.model.v0_5.IndexAxisBase.id": {"fullname": "bioimageio.spec.model.v0_5.IndexAxisBase.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexAxisBase.id", "kind": "variable", "doc": "An axis id unique across all axes of one tensor.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_not_batch)]"}, "bioimageio.spec.model.v0_5.IndexAxisBase.scale": {"fullname": "bioimageio.spec.model.v0_5.IndexAxisBase.scale", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexAxisBase.scale", "kind": "variable", "doc": "\n", "annotation": ": float"}, "bioimageio.spec.model.v0_5.IndexAxisBase.unit": {"fullname": "bioimageio.spec.model.v0_5.IndexAxisBase.unit", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexAxisBase.unit", "kind": "variable", "doc": "\n"}, "bioimageio.spec.model.v0_5.IndexInputAxis": {"fullname": "bioimageio.spec.model.v0_5.IndexInputAxis", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexInputAxis", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "IndexAxisBase, _WithInputAxisSize"}, "bioimageio.spec.model.v0_5.IndexInputAxis.concatenable": {"fullname": "bioimageio.spec.model.v0_5.IndexInputAxis.concatenable", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexInputAxis.concatenable", "kind": "variable", "doc": "If a model has a concatenable
input axis, it can be processed blockwise,\nsplitting a longer sample axis into blocks matching its input tensor description.\nOutput axes are concatenable if they have a SizeReference
to a concatenable\ninput axis.
Subpart of a resource description
\n", "bases": "IndexAxisBase"}, "bioimageio.spec.model.v0_5.IndexOutputAxis.size": {"fullname": "bioimageio.spec.model.v0_5.IndexOutputAxis.size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IndexOutputAxis.size", "kind": "variable", "doc": "The size/length of this axis can be specified as
\n\nSizeReference
)DataDependentSize
(size is only known after model inference)Subpart of a resource description
\n", "bases": "AxisBase"}, "bioimageio.spec.model.v0_5.TimeAxisBase.type": {"fullname": "bioimageio.spec.model.v0_5.TimeAxisBase.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeAxisBase.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['time']"}, "bioimageio.spec.model.v0_5.TimeAxisBase.id": {"fullname": "bioimageio.spec.model.v0_5.TimeAxisBase.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeAxisBase.id", "kind": "variable", "doc": "An axis id unique across all axes of one tensor.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_not_batch)]"}, "bioimageio.spec.model.v0_5.TimeAxisBase.unit": {"fullname": "bioimageio.spec.model.v0_5.TimeAxisBase.unit", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeAxisBase.unit", "kind": "variable", "doc": "\n", "annotation": ": Optional[Literal['attosecond', 'centisecond', 'day', 'decisecond', 'exasecond', 'femtosecond', 'gigasecond', 'hectosecond', 'hour', 'kilosecond', 'megasecond', 'microsecond', 'millisecond', 'minute', 'nanosecond', 'petasecond', 'picosecond', 'second', 'terasecond', 'yoctosecond', 'yottasecond', 'zeptosecond', 'zettasecond']]"}, "bioimageio.spec.model.v0_5.TimeAxisBase.scale": {"fullname": "bioimageio.spec.model.v0_5.TimeAxisBase.scale", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeAxisBase.scale", "kind": "variable", "doc": "\n", "annotation": ": Annotated[float, Gt(gt=0)]"}, "bioimageio.spec.model.v0_5.TimeInputAxis": {"fullname": "bioimageio.spec.model.v0_5.TimeInputAxis", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeInputAxis", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "TimeAxisBase, _WithInputAxisSize"}, "bioimageio.spec.model.v0_5.TimeInputAxis.concatenable": {"fullname": "bioimageio.spec.model.v0_5.TimeInputAxis.concatenable", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeInputAxis.concatenable", "kind": "variable", "doc": "If a model has a concatenable
input axis, it can be processed blockwise,\nsplitting a longer sample axis into blocks matching its input tensor description.\nOutput axes are concatenable if they have a SizeReference
to a concatenable\ninput axis.
Subpart of a resource description
\n", "bases": "AxisBase"}, "bioimageio.spec.model.v0_5.SpaceAxisBase.type": {"fullname": "bioimageio.spec.model.v0_5.SpaceAxisBase.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceAxisBase.type", "kind": "variable", "doc": "\n", "annotation": ": Literal['space']"}, "bioimageio.spec.model.v0_5.SpaceAxisBase.id": {"fullname": "bioimageio.spec.model.v0_5.SpaceAxisBase.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceAxisBase.id", "kind": "variable", "doc": "An axis id unique across all axes of one tensor.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_not_batch), FieldInfo(annotation=NoneType, required=True, examples=['x', 'y', 'z'])]"}, "bioimageio.spec.model.v0_5.SpaceAxisBase.unit": {"fullname": "bioimageio.spec.model.v0_5.SpaceAxisBase.unit", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceAxisBase.unit", "kind": "variable", "doc": "\n", "annotation": ": Optional[Literal['attometer', 'angstrom', 'centimeter', 'decimeter', 'exameter', 'femtometer', 'foot', 'gigameter', 'hectometer', 'inch', 'kilometer', 'megameter', 'meter', 'micrometer', 'mile', 'millimeter', 'nanometer', 'parsec', 'petameter', 'picometer', 'terameter', 'yard', 'yoctometer', 'yottameter', 'zeptometer', 'zettameter']]"}, "bioimageio.spec.model.v0_5.SpaceAxisBase.scale": {"fullname": "bioimageio.spec.model.v0_5.SpaceAxisBase.scale", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceAxisBase.scale", "kind": "variable", "doc": "\n", "annotation": ": Annotated[float, Gt(gt=0)]"}, "bioimageio.spec.model.v0_5.SpaceInputAxis": {"fullname": "bioimageio.spec.model.v0_5.SpaceInputAxis", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceInputAxis", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "SpaceAxisBase, _WithInputAxisSize"}, "bioimageio.spec.model.v0_5.SpaceInputAxis.concatenable": {"fullname": "bioimageio.spec.model.v0_5.SpaceInputAxis.concatenable", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceInputAxis.concatenable", "kind": "variable", "doc": "If a model has a concatenable
input axis, it can be processed blockwise,\nsplitting a longer sample axis into blocks matching its input tensor description.\nOutput axes are concatenable if they have a SizeReference
to a concatenable\ninput axis.
Subpart of a resource description
\n", "bases": "TimeAxisBase, _WithOutputAxisSize"}, "bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo": {"fullname": "bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TimeOutputAxisWithHalo", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "TimeAxisBase, WithHalo"}, "bioimageio.spec.model.v0_5.SpaceOutputAxis": {"fullname": "bioimageio.spec.model.v0_5.SpaceOutputAxis", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceOutputAxis", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "SpaceAxisBase, _WithOutputAxisSize"}, "bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo": {"fullname": "bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SpaceOutputAxisWithHalo", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "SpaceAxisBase, WithHalo"}, "bioimageio.spec.model.v0_5.OutputAxis": {"fullname": "bioimageio.spec.model.v0_5.OutputAxis", "modulename": "bioimageio.spec.model.v0_5", "qualname": "OutputAxis", "kind": "variable", "doc": "\n", "default_value": "typing.Annotated[typing.Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexOutputAxis, typing.Annotated[typing.Union[typing.Annotated[bioimageio.spec.model.v0_5.TimeOutputAxis, Tag(tag='wo_halo')], typing.Annotated[bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[typing.Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxis, Tag(tag='wo_halo')], typing.Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)]"}, "bioimageio.spec.model.v0_5.AnyAxis": {"fullname": "bioimageio.spec.model.v0_5.AnyAxis", "modulename": "bioimageio.spec.model.v0_5", "qualname": "AnyAxis", "kind": "variable", "doc": "\n", "default_value": "typing.Union[typing.Annotated[typing.Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexInputAxis, bioimageio.spec.model.v0_5.TimeInputAxis, bioimageio.spec.model.v0_5.SpaceInputAxis], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[bioimageio.spec.model.v0_5.BatchAxis, bioimageio.spec.model.v0_5.ChannelAxis, bioimageio.spec.model.v0_5.IndexOutputAxis, typing.Annotated[typing.Union[typing.Annotated[bioimageio.spec.model.v0_5.TimeOutputAxis, Tag(tag='wo_halo')], typing.Annotated[bioimageio.spec.model.v0_5.TimeOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)], typing.Annotated[typing.Union[typing.Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxis, Tag(tag='wo_halo')], typing.Annotated[bioimageio.spec.model.v0_5.SpaceOutputAxisWithHalo, Tag(tag='with_halo')]], Discriminator(discriminator=<function _get_halo_axis_discriminator_value>, custom_error_type=None, custom_error_message=None, custom_error_context=None)]], Discriminator(discriminator='type', custom_error_type=None, custom_error_message=None, custom_error_context=None)]]"}, "bioimageio.spec.model.v0_5.TVs": {"fullname": "bioimageio.spec.model.v0_5.TVs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TVs", "kind": "variable", "doc": "\n", "default_value": "typing.Union[typing.Annotated[typing.List[int], MinLen(min_length=1)], typing.Annotated[typing.List[float], MinLen(min_length=1)], typing.Annotated[typing.List[bool], MinLen(min_length=1)], typing.Annotated[typing.List[str], MinLen(min_length=1)]]"}, "bioimageio.spec.model.v0_5.NominalOrOrdinalDType": {"fullname": "bioimageio.spec.model.v0_5.NominalOrOrdinalDType", "modulename": "bioimageio.spec.model.v0_5", "qualname": "NominalOrOrdinalDType", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['float32', 'float64', 'uint8', 'int8', 'uint16', 'int16', 'uint32', 'int32', 'uint64', 'int64', 'bool']"}, "bioimageio.spec.model.v0_5.NominalOrOrdinalDataDescr": {"fullname": "bioimageio.spec.model.v0_5.NominalOrOrdinalDataDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "NominalOrOrdinalDataDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_5.NominalOrOrdinalDataDescr.values": {"fullname": "bioimageio.spec.model.v0_5.NominalOrOrdinalDataDescr.values", "modulename": "bioimageio.spec.model.v0_5", "qualname": "NominalOrOrdinalDataDescr.values", "kind": "variable", "doc": "A fixed set of nominal or an ascending sequence of ordinal values.\nIn this case data_type
is required to be an unsigend integer type, e.g. 'uint8'.\nString values
are interpreted as labels for tensor values 0, ..., N.\nNote: as YAML 1.2 does not natively support a \"set\" datatype,\nnominal values should be given as a sequence (aka list/array) as well.
Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_5.IntervalOrRatioDataDescr.type": {"fullname": "bioimageio.spec.model.v0_5.IntervalOrRatioDataDescr.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IntervalOrRatioDataDescr.type", "kind": "variable", "doc": "\n", "annotation": ": Annotated[Literal['float32', 'float64', 'uint8', 'int8', 'uint16', 'int16', 'uint32', 'int32', 'uint64', 'int64'], FieldInfo(annotation=NoneType, required=True, examples=['float32', 'float64', 'uint8', 'uint16'])]"}, "bioimageio.spec.model.v0_5.IntervalOrRatioDataDescr.range": {"fullname": "bioimageio.spec.model.v0_5.IntervalOrRatioDataDescr.range", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IntervalOrRatioDataDescr.range", "kind": "variable", "doc": "Tuple (minimum, maximum)
specifying the allowed range of the data in this tensor.\nNone
corresponds to min/max of what can be expressed by data_type
.
Scale for data on an interval (or ratio) scale.
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_5.IntervalOrRatioDataDescr.offset": {"fullname": "bioimageio.spec.model.v0_5.IntervalOrRatioDataDescr.offset", "modulename": "bioimageio.spec.model.v0_5", "qualname": "IntervalOrRatioDataDescr.offset", "kind": "variable", "doc": "Offset for data on a ratio scale.
\n", "annotation": ": Optional[float]"}, "bioimageio.spec.model.v0_5.TensorDataDescr": {"fullname": "bioimageio.spec.model.v0_5.TensorDataDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDataDescr", "kind": "variable", "doc": "\n", "default_value": "typing.Union[bioimageio.spec.model.v0_5.NominalOrOrdinalDataDescr, bioimageio.spec.model.v0_5.IntervalOrRatioDataDescr]"}, "bioimageio.spec.model.v0_5.ProcessingDescrBase": {"fullname": "bioimageio.spec.model.v0_5.ProcessingDescrBase", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ProcessingDescrBase", "kind": "class", "doc": "processing base class
\n", "bases": "bioimageio.spec._internal.common_nodes.NodeWithExplicitlySetFields, abc.ABC"}, "bioimageio.spec.model.v0_5.ProcessingDescrBase.fields_to_set_explicitly": {"fullname": "bioimageio.spec.model.v0_5.ProcessingDescrBase.fields_to_set_explicitly", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ProcessingDescrBase.fields_to_set_explicitly", "kind": "variable", "doc": "set set these fields explicitly with their default value if they are not set,\nsuch that they are always included even when dumping with 'exlude_unset'
\n", "annotation": ": ClassVar[FrozenSet[LiteralString]]", "default_value": "frozenset({'id'})"}, "bioimageio.spec.model.v0_5.BinarizeKwargs": {"fullname": "bioimageio.spec.model.v0_5.BinarizeKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BinarizeKwargs", "kind": "class", "doc": "key word arguments for BinarizeDescr
The fixed threshold
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_5.BinarizeAlongAxisKwargs": {"fullname": "bioimageio.spec.model.v0_5.BinarizeAlongAxisKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "BinarizeAlongAxisKwargs", "kind": "class", "doc": "key word arguments for BinarizeDescr
The fixed threshold values along axis
The threshold
axis
Binarize the tensor with a fixed threshold.
\n\nValues above BinarizeKwargs.threshold
/BinarizeAlongAxisKwargs.threshold
\nwill be set to one, values below the threshold to zero.
Set tensor values below min to min and above max to max.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_5.ClipDescr.id": {"fullname": "bioimageio.spec.model.v0_5.ClipDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ClipDescr.id", "kind": "variable", "doc": "\n", "annotation": ": Literal['clip']"}, "bioimageio.spec.model.v0_5.ClipDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_5.ClipDescr.kwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ClipDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_4.ClipKwargs"}, "bioimageio.spec.model.v0_5.EnsureDtypeKwargs": {"fullname": "bioimageio.spec.model.v0_5.EnsureDtypeKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "EnsureDtypeKwargs", "kind": "class", "doc": "key word arguments for EnsureDtypeDescr
cast the tensor data type to EnsureDtypeKwargs.dtype
(if not matching)
key word arguments for ScaleLinearDescr
multiplicative factor
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_5.ScaleLinearKwargs.offset": {"fullname": "bioimageio.spec.model.v0_5.ScaleLinearKwargs.offset", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleLinearKwargs.offset", "kind": "variable", "doc": "additive term
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_5.ScaleLinearAlongAxisKwargs": {"fullname": "bioimageio.spec.model.v0_5.ScaleLinearAlongAxisKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleLinearAlongAxisKwargs", "kind": "class", "doc": "key word arguments for ScaleLinearDescr
The axis of of gains/offsets values.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_not_batch), FieldInfo(annotation=NoneType, required=True, examples=['channel'])]"}, "bioimageio.spec.model.v0_5.ScaleLinearAlongAxisKwargs.gain": {"fullname": "bioimageio.spec.model.v0_5.ScaleLinearAlongAxisKwargs.gain", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleLinearAlongAxisKwargs.gain", "kind": "variable", "doc": "multiplicative factor
\n", "annotation": ": Union[float, Annotated[List[float], MinLen(min_length=1)]]"}, "bioimageio.spec.model.v0_5.ScaleLinearAlongAxisKwargs.offset": {"fullname": "bioimageio.spec.model.v0_5.ScaleLinearAlongAxisKwargs.offset", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleLinearAlongAxisKwargs.offset", "kind": "variable", "doc": "additive term
\n", "annotation": ": Union[float, Annotated[List[float], MinLen(min_length=1)]]"}, "bioimageio.spec.model.v0_5.ScaleLinearDescr": {"fullname": "bioimageio.spec.model.v0_5.ScaleLinearDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleLinearDescr", "kind": "class", "doc": "Fixed linear scaling.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_5.ScaleLinearDescr.id": {"fullname": "bioimageio.spec.model.v0_5.ScaleLinearDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleLinearDescr.id", "kind": "variable", "doc": "\n", "annotation": ": Literal['scale_linear']"}, "bioimageio.spec.model.v0_5.ScaleLinearDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_5.ScaleLinearDescr.kwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleLinearDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": Union[bioimageio.spec.model.v0_5.ScaleLinearKwargs, bioimageio.spec.model.v0_5.ScaleLinearAlongAxisKwargs]"}, "bioimageio.spec.model.v0_5.SigmoidDescr": {"fullname": "bioimageio.spec.model.v0_5.SigmoidDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SigmoidDescr", "kind": "class", "doc": "The logistic sigmoid funciton, a.k.a. expit function.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_5.SigmoidDescr.id": {"fullname": "bioimageio.spec.model.v0_5.SigmoidDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SigmoidDescr.id", "kind": "variable", "doc": "\n", "annotation": ": Literal['sigmoid']"}, "bioimageio.spec.model.v0_5.SigmoidDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_5.SigmoidDescr.kwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "SigmoidDescr.kwargs", "kind": "variable", "doc": "empty kwargs
\n", "annotation": ": bioimageio.spec.model.v0_4.ProcessingKwargs"}, "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceKwargs": {"fullname": "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "FixedZeroMeanUnitVarianceKwargs", "kind": "class", "doc": "key word arguments for FixedZeroMeanUnitVarianceDescr
The mean value to normalize with.
\n", "annotation": ": float"}, "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceKwargs.std": {"fullname": "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceKwargs.std", "modulename": "bioimageio.spec.model.v0_5", "qualname": "FixedZeroMeanUnitVarianceKwargs.std", "kind": "variable", "doc": "The standard deviation value to normalize with.
\n", "annotation": ": Annotated[float, Ge(ge=1e-06)]"}, "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceAlongAxisKwargs": {"fullname": "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceAlongAxisKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "FixedZeroMeanUnitVarianceAlongAxisKwargs", "kind": "class", "doc": "key word arguments for FixedZeroMeanUnitVarianceDescr
The mean value(s) to normalize with.
\n", "annotation": ": Annotated[List[float], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceAlongAxisKwargs.std": {"fullname": "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceAlongAxisKwargs.std", "modulename": "bioimageio.spec.model.v0_5", "qualname": "FixedZeroMeanUnitVarianceAlongAxisKwargs.std", "kind": "variable", "doc": "The standard deviation value(s) to normalize with.\nSize must match mean
values.
The axis of the mean/std values to normalize each entry along that dimension\nseparately.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.AxisId, Predicate(_is_not_batch), FieldInfo(annotation=NoneType, required=True, examples=['channel', 'index'])]"}, "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceDescr": {"fullname": "bioimageio.spec.model.v0_5.FixedZeroMeanUnitVarianceDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "FixedZeroMeanUnitVarianceDescr", "kind": "class", "doc": "Subtract a given mean and divide by the standard deviation.
\n\nNormalize with fixed, precomputed values for\nFixedZeroMeanUnitVarianceKwargs.mean
and FixedZeroMeanUnitVarianceKwargs.std
\nUse FixedZeroMeanUnitVarianceAlongAxisKwargs
for independent scaling along given\naxes.
key word arguments for ZeroMeanUnitVarianceDescr
The subset of axes to normalize jointly, i.e. axes to reduce to compute mean/std.\nFor example to normalize 'batch', 'x' and 'y' jointly in a tensor ('batch', 'channel', 'y', 'x')\nresulting in a tensor of equal shape normalized per channel, specify axes=('batch', 'x', 'y')
.\nTo normalize each sample independently leave out the 'batch' axis.\nDefault: Scale all axes jointly.
epsilon for numeric stability: out = (tensor - mean) / (std + eps)
.
Subtract mean and divide by variance.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr.id": {"fullname": "bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ZeroMeanUnitVarianceDescr.id", "kind": "variable", "doc": "\n", "annotation": ": Literal['zero_mean_unit_variance']"}, "bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceDescr.kwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ZeroMeanUnitVarianceDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_5.ZeroMeanUnitVarianceKwargs"}, "bioimageio.spec.model.v0_5.ScaleRangeKwargs": {"fullname": "bioimageio.spec.model.v0_5.ScaleRangeKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleRangeKwargs", "kind": "class", "doc": "key word arguments for ScaleRangeDescr
For min_percentile
=0.0 (the default) and max_percentile
=100 (the default)\nthis processing step normalizes data to the [0, 1] intervall.\nFor other percentiles the normalized values will partially be outside the [0, 1]\nintervall. Use ScaleRange
followed by ClipDescr
if you want to limit the\nnormalized values to a range.
The subset of axes to normalize jointly, i.e. axes to reduce to compute the min/max percentile value.\nFor example to normalize 'batch', 'x' and 'y' jointly in a tensor ('batch', 'channel', 'y', 'x')\nresulting in a tensor of equal shape normalized per channel, specify axes=('batch', 'x', 'y')
.\nTo normalize samples indepdencently, leave out the \"batch\" axis.\nDefault: Scale all axes jointly.
The lower percentile used to determine the value to align with zero.
\n", "annotation": ": Annotated[float, Interval(gt=None, ge=0, lt=100, le=None)]"}, "bioimageio.spec.model.v0_5.ScaleRangeKwargs.max_percentile": {"fullname": "bioimageio.spec.model.v0_5.ScaleRangeKwargs.max_percentile", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleRangeKwargs.max_percentile", "kind": "variable", "doc": "The upper percentile used to determine the value to align with one.\nHas to be bigger than min_percentile
.\nThe range is 1 to 100 instead of 0 to 100 to avoid mistakenly\naccepting percentiles specified in the range 0.0 to 1.0.
Epsilon for numeric stability.\nout = (tensor - v_lower) / (v_upper - v_lower + eps)
;\nwith v_lower,v_upper
values at the respective percentiles.
Tensor ID to compute the percentiles from. Default: The tensor itself.\nFor any tensor in inputs
only input tensor references are allowed.
Scale with percentiles.
\n", "bases": "ProcessingDescrBase"}, "bioimageio.spec.model.v0_5.ScaleRangeDescr.id": {"fullname": "bioimageio.spec.model.v0_5.ScaleRangeDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleRangeDescr.id", "kind": "variable", "doc": "\n", "annotation": ": Literal['scale_range']"}, "bioimageio.spec.model.v0_5.ScaleRangeDescr.kwargs": {"fullname": "bioimageio.spec.model.v0_5.ScaleRangeDescr.kwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleRangeDescr.kwargs", "kind": "variable", "doc": "\n", "annotation": ": bioimageio.spec.model.v0_5.ScaleRangeKwargs"}, "bioimageio.spec.model.v0_5.ScaleMeanVarianceKwargs": {"fullname": "bioimageio.spec.model.v0_5.ScaleMeanVarianceKwargs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleMeanVarianceKwargs", "kind": "class", "doc": "key word arguments for ScaleMeanVarianceKwargs
Name of tensor to match.
\n", "annotation": ": bioimageio.spec.model.v0_5.TensorId"}, "bioimageio.spec.model.v0_5.ScaleMeanVarianceKwargs.axes": {"fullname": "bioimageio.spec.model.v0_5.ScaleMeanVarianceKwargs.axes", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ScaleMeanVarianceKwargs.axes", "kind": "variable", "doc": "The subset of axes to normalize jointly, i.e. axes to reduce to compute mean/std.\nFor example to normalize 'batch', 'x' and 'y' jointly in a tensor ('batch', 'channel', 'y', 'x')\nresulting in a tensor of equal shape normalized per channel, specify axes=('batch', 'x', 'y')
.\nTo normalize samples independently, leave out the 'batch' axis.\nDefault: Scale all axes jointly.
Epsilon for numeric stability:\nout = (tensor - mean) / (std + eps) * (ref_std + eps) + ref_mean.
Scale a tensor's data distribution to match another tensor's mean/std.\nout = (tensor - mean) / (std + eps) * (ref_std + eps) + ref_mean.
Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node, typing.Generic[~IO_AxisT]"}, "bioimageio.spec.model.v0_5.TensorDescrBase.id": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase.id", "kind": "variable", "doc": "Tensor id. No duplicates are allowed.
\n", "annotation": ": bioimageio.spec.model.v0_5.TensorId"}, "bioimageio.spec.model.v0_5.TensorDescrBase.description": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase.description", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase.description", "kind": "variable", "doc": "free text description
\n", "annotation": ": Annotated[str, MaxLen(max_length=128)]"}, "bioimageio.spec.model.v0_5.TensorDescrBase.axes": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase.axes", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase.axes", "kind": "variable", "doc": "tensor axes
\n", "annotation": ": Annotated[Sequence[~IO_AxisT], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_5.TensorDescrBase.shape": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase.shape", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase.shape", "kind": "variable", "doc": "\n"}, "bioimageio.spec.model.v0_5.TensorDescrBase.test_tensor": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase.test_tensor", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase.test_tensor", "kind": "variable", "doc": "An example tensor to use for testing.\nUsing the model with the test input tensors is expected to yield the test output tensors.\nEach test tensor has be a an ndarray in the\nnumpy.lib file format.\nThe file extension must be '.npy'.
\n", "annotation": ": bioimageio.spec._internal.io.FileDescr"}, "bioimageio.spec.model.v0_5.TensorDescrBase.sample_tensor": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase.sample_tensor", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase.sample_tensor", "kind": "variable", "doc": "A sample tensor to illustrate a possible input/output for the model,\nThe sample image primarily serves to inform a human user about an example use case\nand is typically stored as .hdf5, .png or .tiff.\nIt has to be readable by the imageio library\n(numpy's .npy
format is not supported).\nThe image dimensionality has to match the number of axes specified in this tensor description.
Description of the tensor's data values, optionally per channel.\nIf specified per channel, the data type
needs to match across channels.
dtype as specified under data.type
or data[i].type
Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node, typing.Generic[~IO_AxisT]"}, "bioimageio.spec.model.v0_5.InputTensorDescr.id": {"fullname": "bioimageio.spec.model.v0_5.InputTensorDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "InputTensorDescr.id", "kind": "variable", "doc": "Input tensor id.\nNo duplicates are allowed across all inputs and outputs.
\n", "annotation": ": bioimageio.spec.model.v0_5.TensorId"}, "bioimageio.spec.model.v0_5.InputTensorDescr.optional": {"fullname": "bioimageio.spec.model.v0_5.InputTensorDescr.optional", "modulename": "bioimageio.spec.model.v0_5", "qualname": "InputTensorDescr.optional", "kind": "variable", "doc": "indicates that this tensor may be None
Description of how this input should be preprocessed.
\n\nnotes:
\n\nSubpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node, typing.Generic[~IO_AxisT]"}, "bioimageio.spec.model.v0_5.OutputTensorDescr.id": {"fullname": "bioimageio.spec.model.v0_5.OutputTensorDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "OutputTensorDescr.id", "kind": "variable", "doc": "Output tensor id.\nNo duplicates are allowed across all inputs and outputs.
\n", "annotation": ": bioimageio.spec.model.v0_5.TensorId"}, "bioimageio.spec.model.v0_5.OutputTensorDescr.postprocessing": {"fullname": "bioimageio.spec.model.v0_5.OutputTensorDescr.postprocessing", "modulename": "bioimageio.spec.model.v0_5", "qualname": "OutputTensorDescr.postprocessing", "kind": "variable", "doc": "Description of how this output should be postprocessed.
\n\nnote: postprocessing
always ends with an 'ensure_dtype' operation.\n If not given this is added to cast to this tensor's data.type
.
Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.io.FileDescr"}, "bioimageio.spec.model.v0_5.EnvironmentFileDescr.source": {"fullname": "bioimageio.spec.model.v0_5.EnvironmentFileDescr.source", "modulename": "bioimageio.spec.model.v0_5", "qualname": "EnvironmentFileDescr.source", "kind": "variable", "doc": "\u2208\ud83d\udce6 Conda environment file.\nAllows to specify custom dependencies, see conda docs:
\n\n\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none'), WithSuffix(suffix=('.yaml', '.yml'), case_sensitive=True), FieldInfo(annotation=NoneType, required=True, examples=['environment.yaml'])]"}, "bioimageio.spec.model.v0_5.ArchitectureFromFileDescr": {"fullname": "bioimageio.spec.model.v0_5.ArchitectureFromFileDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ArchitectureFromFileDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "_ArchitectureCallableDescr, bioimageio.spec._internal.io.FileDescr"}, "bioimageio.spec.model.v0_5.ArchitectureFromLibraryDescr": {"fullname": "bioimageio.spec.model.v0_5.ArchitectureFromLibraryDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ArchitectureFromLibraryDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "_ArchitectureCallableDescr"}, "bioimageio.spec.model.v0_5.ArchitectureFromLibraryDescr.import_from": {"fullname": "bioimageio.spec.model.v0_5.ArchitectureFromLibraryDescr.import_from", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ArchitectureFromLibraryDescr.import_from", "kind": "variable", "doc": "Where to import the callable from, i.e. from <import_from> import <callable>
Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.io.FileDescr"}, "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.type": {"fullname": "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsEntryDescrBase.type", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_js', 'tensorflow_saved_model_bundle', 'torchscript']]"}, "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.weights_format_name": {"fullname": "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.weights_format_name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsEntryDescrBase.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]"}, "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.source": {"fullname": "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.source", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsEntryDescrBase.source", "kind": "variable", "doc": "\u2208\ud83d\udce6 The weights file.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.authors": {"fullname": "bioimageio.spec.model.v0_5.WeightsEntryDescrBase.authors", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsEntryDescrBase.authors", "kind": "variable", "doc": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a parent
)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a parent
field)
The source weights these weights were converted from.\nFor example, if a model's weights were converted from the pytorch_state_dict
format to torchscript
,\nThe pytorch_state_dict
weights entry has no parent
and is the parent of the torchscript
weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.
Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_5.KerasHdf5WeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_5.KerasHdf5WeightsDescr.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "KerasHdf5WeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'keras_hdf5'"}, "bioimageio.spec.model.v0_5.KerasHdf5WeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_5.KerasHdf5WeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "KerasHdf5WeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Keras HDF5'"}, "bioimageio.spec.model.v0_5.KerasHdf5WeightsDescr.tensorflow_version": {"fullname": "bioimageio.spec.model.v0_5.KerasHdf5WeightsDescr.tensorflow_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "KerasHdf5WeightsDescr.tensorflow_version", "kind": "variable", "doc": "TensorFlow version used to create these weights.
\n", "annotation": ": bioimageio.spec._internal.version_type.Version"}, "bioimageio.spec.model.v0_5.OnnxWeightsDescr": {"fullname": "bioimageio.spec.model.v0_5.OnnxWeightsDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "OnnxWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_5.OnnxWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_5.OnnxWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "OnnxWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'onnx'"}, "bioimageio.spec.model.v0_5.OnnxWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_5.OnnxWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "OnnxWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'ONNX'"}, "bioimageio.spec.model.v0_5.OnnxWeightsDescr.opset_version": {"fullname": "bioimageio.spec.model.v0_5.OnnxWeightsDescr.opset_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "OnnxWeightsDescr.opset_version", "kind": "variable", "doc": "ONNX opset version
\n", "annotation": ": Annotated[int, Ge(ge=7)]"}, "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr": {"fullname": "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "PytorchStateDictWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "PytorchStateDictWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'pytorch_state_dict'"}, "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "PytorchStateDictWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Pytorch State Dict'"}, "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.architecture": {"fullname": "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.architecture", "modulename": "bioimageio.spec.model.v0_5", "qualname": "PytorchStateDictWeightsDescr.architecture", "kind": "variable", "doc": "\n", "annotation": ": Annotated[Union[bioimageio.spec.model.v0_5.ArchitectureFromFileDescr, bioimageio.spec.model.v0_5.ArchitectureFromLibraryDescr], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]"}, "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.pytorch_version": {"fullname": "bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr.pytorch_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "PytorchStateDictWeightsDescr.pytorch_version", "kind": "variable", "doc": "Version of the PyTorch library used.\nIf architecture.depencencies
is specified it has to include pytorch and any version pinning has to be compatible.
Custom depencies beyond pytorch.\nThe conda environment file should include pytorch and any version pinning has to be compatible with\npytorch_version
.
Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowJsWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'tensorflow_js'"}, "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowJsWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Tensorflow.js'"}, "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.tensorflow_version": {"fullname": "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.tensorflow_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowJsWeightsDescr.tensorflow_version", "kind": "variable", "doc": "Version of the TensorFlow library used.
\n", "annotation": ": bioimageio.spec._internal.version_type.Version"}, "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.source": {"fullname": "bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr.source", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowJsWeightsDescr.source", "kind": "variable", "doc": "\u2208\ud83d\udce6 The multi-file weights.\nAll required files/folders should be a zip archive.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr": {"fullname": "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowSavedModelBundleWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowSavedModelBundleWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'tensorflow_saved_model_bundle'"}, "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowSavedModelBundleWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'Tensorflow Saved Model'"}, "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.tensorflow_version": {"fullname": "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.tensorflow_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowSavedModelBundleWeightsDescr.tensorflow_version", "kind": "variable", "doc": "Version of the TensorFlow library used.
\n", "annotation": ": bioimageio.spec._internal.version_type.Version"}, "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.dependencies": {"fullname": "bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr.dependencies", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorflowSavedModelBundleWeightsDescr.dependencies", "kind": "variable", "doc": "Custom dependencies beyond tensorflow.\nShould include tensorflow and any version pinning has to be compatible with tensorflow_version
.
\u2208\ud83d\udce6 The multi-file weights.\nAll required files/folders should be a zip archive.
\n", "annotation": ": Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')]), AfterValidator(func=<function wo_special_file_name at 0x7f1c5e518ea0>), PlainSerializer(func=<function _package at 0x7f1c5e519620>, return_type=PydanticUndefined, when_used='unless-none')]"}, "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr": {"fullname": "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TorchscriptWeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "WeightsEntryDescrBase"}, "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr.type": {"fullname": "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr.type", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TorchscriptWeightsDescr.type", "kind": "variable", "doc": "\n", "default_value": "'torchscript'"}, "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr.weights_format_name": {"fullname": "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr.weights_format_name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TorchscriptWeightsDescr.weights_format_name", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'TorchScript'"}, "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr.pytorch_version": {"fullname": "bioimageio.spec.model.v0_5.TorchscriptWeightsDescr.pytorch_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TorchscriptWeightsDescr.pytorch_version", "kind": "variable", "doc": "Version of the PyTorch library used.
\n", "annotation": ": bioimageio.spec._internal.version_type.Version"}, "bioimageio.spec.model.v0_5.WeightsDescr": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node"}, "bioimageio.spec.model.v0_5.WeightsDescr.keras_hdf5": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr.keras_hdf5", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr.keras_hdf5", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.KerasHdf5WeightsDescr]"}, "bioimageio.spec.model.v0_5.WeightsDescr.onnx": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr.onnx", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr.onnx", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.OnnxWeightsDescr]"}, "bioimageio.spec.model.v0_5.WeightsDescr.pytorch_state_dict": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr.pytorch_state_dict", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr.pytorch_state_dict", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.PytorchStateDictWeightsDescr]"}, "bioimageio.spec.model.v0_5.WeightsDescr.tensorflow_js": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr.tensorflow_js", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr.tensorflow_js", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.TensorflowJsWeightsDescr]"}, "bioimageio.spec.model.v0_5.WeightsDescr.tensorflow_saved_model_bundle": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr.tensorflow_saved_model_bundle", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr.tensorflow_saved_model_bundle", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.TensorflowSavedModelBundleWeightsDescr]"}, "bioimageio.spec.model.v0_5.WeightsDescr.torchscript": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr.torchscript", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr.torchscript", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.TorchscriptWeightsDescr]"}, "bioimageio.spec.model.v0_5.WeightsDescr.check_entries": {"fullname": "bioimageio.spec.model.v0_5.WeightsDescr.check_entries", "modulename": "bioimageio.spec.model.v0_5", "qualname": "WeightsDescr.check_entries", "kind": "function", "doc": "\n", "signature": "(self) -> Self:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ModelId": {"fullname": "bioimageio.spec.model.v0_5.ModelId", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelId", "kind": "class", "doc": "str(object='') -> str\nstr(bytes_or_buffer[, encoding[, errors]]) -> str
\n\nCreate a new string object from the given object. If encoding or\nerrors is specified, then the object must expose a data buffer\nthat will be decoded using the given encoding and error handler.\nOtherwise, returns the result of object.__str__() (if defined)\nor repr(object).\nencoding defaults to sys.getdefaultencoding().\nerrors defaults to 'strict'.
\n", "bases": "bioimageio.spec.generic.v0_3.ResourceId"}, "bioimageio.spec.model.v0_5.LinkedModel": {"fullname": "bioimageio.spec.model.v0_5.LinkedModel", "modulename": "bioimageio.spec.model.v0_5", "qualname": "LinkedModel", "kind": "class", "doc": "Reference to a bioimage.io model.
\n", "bases": "bioimageio.spec.generic.v0_3.LinkedResourceNode"}, "bioimageio.spec.model.v0_5.LinkedModel.id": {"fullname": "bioimageio.spec.model.v0_5.LinkedModel.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "LinkedModel.id", "kind": "variable", "doc": "A valid model id
from the bioimage.io collection.
Specification of the fields used in a bioimage.io-compliant RDF to describe AI models with pretrained weights.\nThese fields are typically stored in a YAML file which we call a model resource description file (model RDF).
\n", "bases": "bioimageio.spec.generic.v0_3.GenericModelDescrBase"}, "bioimageio.spec.model.v0_5.ModelDescr.format_version": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.format_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.format_version", "kind": "variable", "doc": "Version of the bioimage.io model description specification used.\nWhen creating a new model always use the latest micro/patch version described here.\nThe format_version
is important for any consumer software to understand how to parse the fields.
Specialized resource type 'model'
\n", "annotation": ": Literal['model']"}, "bioimageio.spec.model.v0_5.ModelDescr.id": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.id", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.id", "kind": "variable", "doc": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version unspecific.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.ModelId]"}, "bioimageio.spec.model.v0_5.ModelDescr.authors": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.authors", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.authors", "kind": "variable", "doc": "The authors are the creators of the model RDF and the primary points of contact.
\n", "annotation": ": Annotated[List[bioimageio.spec.generic.v0_3.Author], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_5.ModelDescr.documentation": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.documentation", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.documentation", "kind": "variable", "doc": "\u2208\ud83d\udce6 URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is README.md
. An .md
suffix is mandatory.\nThe documentation should include a '#[#] Validation' (sub)section\nwith details on how to quantitatively validate the model on unseen data.
Describes the input tensors expected by this model.
\n", "annotation": ": Annotated[Sequence[bioimageio.spec.model.v0_5.InputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_5.ModelDescr.name": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.name", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.name", "kind": "variable", "doc": "A human-readable name of this model.\nIt should be no longer than 64 characters\nand may only contain letter, number, underscore, minus, parentheses and spaces.\nWe recommend to chose a name that refers to the model's task and image modality.
\n", "annotation": ": Annotated[str, RestrictCharacters(alphabet='abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_- ()'), MinLen(min_length=5), MaxLen(max_length=128), AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f1c4dc18040>, severity=20, msg='Name longer than 64 characters.', context={'typ': Annotated[Any, MaxLen(max_length=64)]})]"}, "bioimageio.spec.model.v0_5.ModelDescr.outputs": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.outputs", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.outputs", "kind": "variable", "doc": "Describes the output tensors.
\n", "annotation": ": Annotated[Sequence[bioimageio.spec.model.v0_5.OutputTensorDescr], MinLen(min_length=1)]"}, "bioimageio.spec.model.v0_5.ModelDescr.packaged_by": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.packaged_by", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.packaged_by", "kind": "variable", "doc": "The persons that have packaged and uploaded this model.\nOnly required if those persons differ from the authors
.
The model from which this model is derived, e.g. by fine-tuning the weights.
\n", "annotation": ": Optional[bioimageio.spec.model.v0_5.LinkedModel]"}, "bioimageio.spec.model.v0_5.ModelDescr.run_mode": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.run_mode", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.run_mode", "kind": "variable", "doc": "Custom run mode for this model: for more complex prediction procedures like test time\ndata augmentation that currently cannot be expressed in the specification.\nNo standard run modes are defined yet.
\n", "annotation": ": Annotated[Optional[bioimageio.spec.model.v0_4.RunMode], AfterWarner(func=<function as_warning.<locals>.wrapper at 0x7f1c4ef2dee0>, severity=30, msg="Run mode '{value}' has limited support across consumer softwares.", context={'typ': None})]"}, "bioimageio.spec.model.v0_5.ModelDescr.timestamp": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.timestamp", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.timestamp", "kind": "variable", "doc": "Timestamp in ISO 8601 format\nwith a few restrictions listed here.\n(In Python a datetime object is valid, too).
\n", "annotation": ": bioimageio.spec._internal.types.Datetime"}, "bioimageio.spec.model.v0_5.ModelDescr.training_data": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.training_data", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.training_data", "kind": "variable", "doc": "The dataset used to train this model
\n", "annotation": ": Annotated[Union[NoneType, bioimageio.spec.dataset.v0_3.LinkedDataset, bioimageio.spec.dataset.v0_3.DatasetDescr, bioimageio.spec.dataset.v0_2.DatasetDescr], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])]"}, "bioimageio.spec.model.v0_5.ModelDescr.weights": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.weights", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.weights", "kind": "variable", "doc": "The weights for this model.\nWeights can be given for different formats, but should otherwise be equivalent.\nThe available weight formats determine which consumers can use this model.
\n", "annotation": ": Annotated[bioimageio.spec.model.v0_5.WeightsDescr, WrapSerializer(func=<function package_weights at 0x7f1c5bd54360>, return_type=PydanticUndefined, when_used='always')]"}, "bioimageio.spec.model.v0_5.ModelDescr.get_input_test_arrays": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.get_input_test_arrays", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.get_input_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ModelDescr.get_output_test_arrays": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.get_output_test_arrays", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.get_output_test_arrays", "kind": "function", "doc": "\n", "signature": "(self) -> List[numpy.ndarray[Any, numpy.dtype[Any]]]:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ModelDescr.get_batch_size": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.get_batch_size", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.get_batch_size", "kind": "function", "doc": "\n", "signature": "(\ttensor_sizes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]) -> int:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ModelDescr.get_output_tensor_sizes": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.get_output_tensor_sizes", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.get_output_tensor_sizes", "kind": "function", "doc": "Returns the tensor output sizes for given input_sizes.\nOnly if input_sizes has a valid input shape, the tensor output size is exact.\nOtherwise it might be larger than the actual (valid) output
\n", "signature": "(\tself,\tinput_sizes: Mapping[bioimageio.spec.model.v0_5.TensorId, Mapping[bioimageio.spec.model.v0_5.AxisId, int]]) -> Dict[bioimageio.spec.model.v0_5.TensorId, Dict[bioimageio.spec.model.v0_5.AxisId, Union[int, bioimageio.spec.model.v0_5._DataDepSize]]]:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ModelDescr.get_ns": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.get_ns", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.get_ns", "kind": "function", "doc": "get parameter n
for each parameterized axis\nsuch that the valid input size is >= the given input size
Determine input and output block shape for scale factors ns\nof parameterized input sizes.
\n\nn
for each axis (keyed by (tensor_id, axis_id))\nthat is parameterized as size = min + n * step
.n
, is larger\nthan max_input_shape is set to the minimal value n_min
for which\nthis is still true.\nUse this for small input samples or large values of ns.\nOr simply whenever you know the full input shape.\n\n", "signature": "(\tself,\tns: Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int],\tbatch_size: Optional[int] = None,\t*,\tmax_input_shape: Optional[Mapping[Tuple[bioimageio.spec.model.v0_5.TensorId, bioimageio.spec.model.v0_5.AxisId], int]] = None) -> bioimageio.spec.model.v0_5._AxisSizes:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.ModelDescr.implemented_format_version": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.implemented_format_version", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.implemented_format_version", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[str]", "default_value": "'0.5.3'"}, "bioimageio.spec.model.v0_5.ModelDescr.implemented_format_version_tuple": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.implemented_format_version_tuple", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.implemented_format_version_tuple", "kind": "variable", "doc": "\n", "annotation": ": ClassVar[Tuple[int, int, int]]", "default_value": "(0, 5, 3)"}, "bioimageio.spec.model.v0_5.ModelDescr.model_post_init": {"fullname": "bioimageio.spec.model.v0_5.ModelDescr.model_post_init", "modulename": "bioimageio.spec.model.v0_5", "qualname": "ModelDescr.model_post_init", "kind": "function", "doc": "Resolved axis sizes for model inputs and outputs.
\n
We need to both initialize private attributes and call the user-defined model_post_init\nmethod.
\n", "signature": "(self: pydantic.main.BaseModel, context: Any, /) -> None:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.generate_covers": {"fullname": "bioimageio.spec.model.v0_5.generate_covers", "modulename": "bioimageio.spec.model.v0_5", "qualname": "generate_covers", "kind": "function", "doc": "\n", "signature": "(\tinputs: Sequence[Tuple[bioimageio.spec.model.v0_5.InputTensorDescr, numpy.ndarray[Any, numpy.dtype[Any]]]],\toutputs: Sequence[Tuple[bioimageio.spec.model.v0_5.OutputTensorDescr, numpy.ndarray[Any, numpy.dtype[Any]]]]) -> List[pathlib.Path]:", "funcdef": "def"}, "bioimageio.spec.model.v0_5.TensorDescrBase[Annotated[Union[BatchAxis, ChannelAxis, IndexInputAxis, TimeInputAxis, SpaceInputAxis], Discriminator]]": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase[Annotated[Union[BatchAxis, ChannelAxis, IndexInputAxis, TimeInputAxis, SpaceInputAxis], Discriminator]]", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase[Annotated[Union[BatchAxis, ChannelAxis, IndexInputAxis, TimeInputAxis, SpaceInputAxis], Discriminator]]", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node, typing.Generic[~IO_AxisT]"}, "bioimageio.spec.model.v0_5.TensorDescrBase[Annotated[Union[BatchAxis, ChannelAxis, IndexOutputAxis, Annotated[Union[Annotated[TimeOutputAxis, Tag], Annotated[TimeOutputAxisWithHalo, Tag]], Discriminator], Annotated[Union[Annotated[SpaceOutputAxis, Tag], Annotated[SpaceOutputAxisWithHalo, Tag]], Discriminator]], Discriminator]]": {"fullname": "bioimageio.spec.model.v0_5.TensorDescrBase[Annotated[Union[BatchAxis, ChannelAxis, IndexOutputAxis, Annotated[Union[Annotated[TimeOutputAxis, Tag], Annotated[TimeOutputAxisWithHalo, Tag]], Discriminator], Annotated[Union[Annotated[SpaceOutputAxis, Tag], Annotated[SpaceOutputAxisWithHalo, Tag]], Discriminator]], Discriminator]]", "modulename": "bioimageio.spec.model.v0_5", "qualname": "TensorDescrBase[Annotated[Union[BatchAxis, ChannelAxis, IndexOutputAxis, Annotated[Union[Annotated[TimeOutputAxis, Tag], Annotated[TimeOutputAxisWithHalo, Tag]], Discriminator], Annotated[Union[Annotated[SpaceOutputAxis, Tag], Annotated[SpaceOutputAxisWithHalo, Tag]], Discriminator]], Discriminator]]", "kind": "class", "doc": "Subpart of a resource description
\n", "bases": "bioimageio.spec._internal.node.Node, typing.Generic[~IO_AxisT]"}, "bioimageio.spec.pretty_validation_errors": {"fullname": "bioimageio.spec.pretty_validation_errors", "modulename": "bioimageio.spec.pretty_validation_errors", "kind": "module", "doc": "\n"}, "bioimageio.spec.pretty_validation_errors.PrettyValidationError": {"fullname": "bioimageio.spec.pretty_validation_errors.PrettyValidationError", "modulename": "bioimageio.spec.pretty_validation_errors", "qualname": "PrettyValidationError", "kind": "class", "doc": "Wrap a pydantic.ValidationError to custumize formatting.
\n", "bases": "builtins.ValueError"}, "bioimageio.spec.pretty_validation_errors.PrettyValidationError.__init__": {"fullname": "bioimageio.spec.pretty_validation_errors.PrettyValidationError.__init__", "modulename": "bioimageio.spec.pretty_validation_errors", "qualname": "PrettyValidationError.__init__", "kind": "function", "doc": "\n", "signature": "(validation_error: pydantic_core._pydantic_core.ValidationError)"}, "bioimageio.spec.pretty_validation_errors.PrettyValidationError.error": {"fullname": "bioimageio.spec.pretty_validation_errors.PrettyValidationError.error", "modulename": "bioimageio.spec.pretty_validation_errors", "qualname": "PrettyValidationError.error", "kind": "variable", "doc": "\n"}, "bioimageio.spec.pretty_validation_errors.enable_pretty_validation_errors_in_ipynb": {"fullname": "bioimageio.spec.pretty_validation_errors.enable_pretty_validation_errors_in_ipynb", "modulename": "bioimageio.spec.pretty_validation_errors", "qualname": "enable_pretty_validation_errors_in_ipynb", "kind": "function", "doc": "A modestly hacky way to display prettified validaiton error messages and traceback\nin interactive Python notebooks
\n", "signature": "():", "funcdef": "def"}, "bioimageio.spec.summary": {"fullname": "bioimageio.spec.summary", "modulename": "bioimageio.spec.summary", "kind": "module", "doc": "\n"}, "bioimageio.spec.summary.Loc": {"fullname": "bioimageio.spec.summary.Loc", "modulename": "bioimageio.spec.summary", "qualname": "Loc", "kind": "variable", "doc": "location of error/warning in a nested data structure
\n", "default_value": "typing.Tuple[typing.Union[int, str], ...]"}, "bioimageio.spec.summary.WarningSeverityName": {"fullname": "bioimageio.spec.summary.WarningSeverityName", "modulename": "bioimageio.spec.summary", "qualname": "WarningSeverityName", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['info', 'warning', 'alert']"}, "bioimageio.spec.summary.WarningLevelName": {"fullname": "bioimageio.spec.summary.WarningLevelName", "modulename": "bioimageio.spec.summary", "qualname": "WarningLevelName", "kind": "variable", "doc": "\n", "default_value": "typing.Literal['info', 'warning', 'alert', 'error']"}, "bioimageio.spec.summary.WARNING_SEVERITY_TO_NAME": {"fullname": "bioimageio.spec.summary.WARNING_SEVERITY_TO_NAME", "modulename": "bioimageio.spec.summary", "qualname": "WARNING_SEVERITY_TO_NAME", "kind": "variable", "doc": "\n", "annotation": ": Mapping[Literal[20, 30, 35], Literal['info', 'warning', 'alert']]", "default_value": "mappingproxy({20: 'info', 30: 'warning', 35: 'alert'})"}, "bioimageio.spec.summary.WARNING_LEVEL_TO_NAME": {"fullname": "bioimageio.spec.summary.WARNING_LEVEL_TO_NAME", "modulename": "bioimageio.spec.summary", "qualname": "WARNING_LEVEL_TO_NAME", "kind": "variable", "doc": "\n", "annotation": ": Mapping[Literal[20, 30, 35, 50], Literal['info', 'warning', 'alert', 'error']]", "default_value": "mappingproxy({20: 'info', 30: 'warning', 35: 'alert', 50: 'error'})"}, "bioimageio.spec.summary.WARNING_NAME_TO_LEVEL": {"fullname": "bioimageio.spec.summary.WARNING_NAME_TO_LEVEL", "modulename": "bioimageio.spec.summary", "qualname": "WARNING_NAME_TO_LEVEL", "kind": "variable", "doc": "\n", "annotation": ": Mapping[Literal['info', 'warning', 'alert', 'error'], Literal[20, 30, 35, 50]]", "default_value": "mappingproxy({'info': 20, 'warning': 30, 'alert': 35, 'error': 50})"}, "bioimageio.spec.summary.ValidationEntry": {"fullname": "bioimageio.spec.summary.ValidationEntry", "modulename": "bioimageio.spec.summary", "qualname": "ValidationEntry", "kind": "class", "doc": "Base of ErrorEntry
and WarningEntry
An error in a ValidationDetail
A warning in a ValidationDetail
helper to format a location tuple Loc
as Markdown string
InstalledPackage(name, version, build, channel)
\n", "bases": "typing.NamedTuple"}, "bioimageio.spec.summary.InstalledPackage.__init__": {"fullname": "bioimageio.spec.summary.InstalledPackage.__init__", "modulename": "bioimageio.spec.summary", "qualname": "InstalledPackage.__init__", "kind": "function", "doc": "Create new instance of InstalledPackage(name, version, build, channel)
\n", "signature": "(name: str, version: str, build: str = '', channel: str = '')"}, "bioimageio.spec.summary.InstalledPackage.name": {"fullname": "bioimageio.spec.summary.InstalledPackage.name", "modulename": "bioimageio.spec.summary", "qualname": "InstalledPackage.name", "kind": "variable", "doc": "Alias for field number 0
\n", "annotation": ": str"}, "bioimageio.spec.summary.InstalledPackage.version": {"fullname": "bioimageio.spec.summary.InstalledPackage.version", "modulename": "bioimageio.spec.summary", "qualname": "InstalledPackage.version", "kind": "variable", "doc": "Alias for field number 1
\n", "annotation": ": str"}, "bioimageio.spec.summary.InstalledPackage.build": {"fullname": "bioimageio.spec.summary.InstalledPackage.build", "modulename": "bioimageio.spec.summary", "qualname": "InstalledPackage.build", "kind": "variable", "doc": "Alias for field number 2
\n", "annotation": ": str"}, "bioimageio.spec.summary.InstalledPackage.channel": {"fullname": "bioimageio.spec.summary.InstalledPackage.channel", "modulename": "bioimageio.spec.summary", "qualname": "InstalledPackage.channel", "kind": "variable", "doc": "Alias for field number 3
\n", "annotation": ": str"}, "bioimageio.spec.summary.ValidationContextSummary": {"fullname": "bioimageio.spec.summary.ValidationContextSummary", "modulename": "bioimageio.spec.summary", "qualname": "ValidationContextSummary", "kind": "class", "doc": "\n", "bases": "typing_extensions.TypedDict"}, "bioimageio.spec.summary.ValidationContextSummary.perform_io_checks": {"fullname": "bioimageio.spec.summary.ValidationContextSummary.perform_io_checks", "modulename": "bioimageio.spec.summary", "qualname": "ValidationContextSummary.perform_io_checks", "kind": "variable", "doc": "\n", "annotation": ": bool"}, "bioimageio.spec.summary.ValidationContextSummary.known_files": {"fullname": "bioimageio.spec.summary.ValidationContextSummary.known_files", "modulename": "bioimageio.spec.summary", "qualname": "ValidationContextSummary.known_files", "kind": "variable", "doc": "\n", "annotation": ": Mapping[str, str]"}, "bioimageio.spec.summary.ValidationContextSummary.root": {"fullname": "bioimageio.spec.summary.ValidationContextSummary.root", "modulename": "bioimageio.spec.summary", "qualname": "ValidationContextSummary.root", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.summary.ValidationContextSummary.warning_level": {"fullname": "bioimageio.spec.summary.ValidationContextSummary.warning_level", "modulename": "bioimageio.spec.summary", "qualname": "ValidationContextSummary.warning_level", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.summary.ValidationDetail": {"fullname": "bioimageio.spec.summary.ValidationDetail", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail", "kind": "class", "doc": "a detail in a validation summary
\n", "bases": "pydantic.main.BaseModel"}, "bioimageio.spec.summary.ValidationDetail.name": {"fullname": "bioimageio.spec.summary.ValidationDetail.name", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.name", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.summary.ValidationDetail.status": {"fullname": "bioimageio.spec.summary.ValidationDetail.status", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.status", "kind": "variable", "doc": "\n", "annotation": ": Literal['passed', 'failed']"}, "bioimageio.spec.summary.ValidationDetail.loc": {"fullname": "bioimageio.spec.summary.ValidationDetail.loc", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.loc", "kind": "variable", "doc": "location in the RDF that this detail applies to
\n", "annotation": ": Tuple[Union[int, str], ...]"}, "bioimageio.spec.summary.ValidationDetail.errors": {"fullname": "bioimageio.spec.summary.ValidationDetail.errors", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.errors", "kind": "variable", "doc": "\n", "annotation": ": List[bioimageio.spec.summary.ErrorEntry]"}, "bioimageio.spec.summary.ValidationDetail.warnings": {"fullname": "bioimageio.spec.summary.ValidationDetail.warnings", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.warnings", "kind": "variable", "doc": "\n", "annotation": ": List[bioimageio.spec.summary.WarningEntry]"}, "bioimageio.spec.summary.ValidationDetail.context": {"fullname": "bioimageio.spec.summary.ValidationDetail.context", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.context", "kind": "variable", "doc": "\n", "annotation": ": Optional[bioimageio.spec.summary.ValidationContextSummary]"}, "bioimageio.spec.summary.ValidationDetail.recommended_env": {"fullname": "bioimageio.spec.summary.ValidationDetail.recommended_env", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.recommended_env", "kind": "variable", "doc": "recommended conda environemnt for this validation detail
\n", "annotation": ": Optional[bioimageio.spec.conda_env.CondaEnv]"}, "bioimageio.spec.summary.ValidationDetail.conda_compare": {"fullname": "bioimageio.spec.summary.ValidationDetail.conda_compare", "modulename": "bioimageio.spec.summary", "qualname": "ValidationDetail.conda_compare", "kind": "variable", "doc": "output of conda compare <recommended env>
create conda_compare
default value if needed
format as Markdown string
\n", "signature": "(\tself,\thide_tracebacks: bool = False,\troot_loc: Tuple[Union[int, str], ...] = ()) -> str:", "funcdef": "def"}, "bioimageio.spec.summary.ValidationSummary": {"fullname": "bioimageio.spec.summary.ValidationSummary", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary", "kind": "class", "doc": "Summarizes output of all bioimageio validations and tests\nfor one specific ResourceDescr
instance.
list of selected, relevant package versions
\n", "annotation": ": Set[bioimageio.spec.summary.InstalledPackage]"}, "bioimageio.spec.summary.ValidationSummary.conda_list": {"fullname": "bioimageio.spec.summary.ValidationSummary.conda_list", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary.conda_list", "kind": "variable", "doc": "parsed output of conda list
\n", "annotation": ": Optional[Sequence[bioimageio.spec.summary.InstalledPackage]]"}, "bioimageio.spec.summary.ValidationSummary.status_icon": {"fullname": "bioimageio.spec.summary.ValidationSummary.status_icon", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary.status_icon", "kind": "variable", "doc": "\n"}, "bioimageio.spec.summary.ValidationSummary.errors": {"fullname": "bioimageio.spec.summary.ValidationSummary.errors", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary.errors", "kind": "variable", "doc": "\n", "annotation": ": List[bioimageio.spec.summary.ErrorEntry]"}, "bioimageio.spec.summary.ValidationSummary.warnings": {"fullname": "bioimageio.spec.summary.ValidationSummary.warnings", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary.warnings", "kind": "variable", "doc": "\n", "annotation": ": List[bioimageio.spec.summary.WarningEntry]"}, "bioimageio.spec.summary.ValidationSummary.format": {"fullname": "bioimageio.spec.summary.ValidationSummary.format", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary.format", "kind": "function", "doc": "Format summary as Markdown string
\n\n Suitable to embed in HTML using '<br>' instead of '\n
\n\n'.
\n", "signature": "(\tself,\thide_tracebacks: bool = False,\thide_source: bool = False,\thide_env: bool = False,\troot_loc: Tuple[Union[int, str], ...] = ()) -> str:", "funcdef": "def"}, "bioimageio.spec.summary.ValidationSummary.display": {"fullname": "bioimageio.spec.summary.ValidationSummary.display", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary.display", "kind": "function", "doc": "\n", "signature": "(self) -> None:", "funcdef": "def"}, "bioimageio.spec.summary.ValidationSummary.add_detail": {"fullname": "bioimageio.spec.summary.ValidationSummary.add_detail", "modulename": "bioimageio.spec.summary", "qualname": "ValidationSummary.add_detail", "kind": "function", "doc": "\n", "signature": "(self, detail: bioimageio.spec.summary.ValidationDetail):", "funcdef": "def"}, "bioimageio.spec.utils": {"fullname": "bioimageio.spec.utils", "modulename": "bioimageio.spec.utils", "kind": "module", "doc": "\n"}, "bioimageio.spec.utils.download": {"fullname": "bioimageio.spec.utils.download", "modulename": "bioimageio.spec.utils", "qualname": "download", "kind": "function", "doc": "Resolve file source
(download if needed)
from https://stackoverflow.com/a/44873382
\n", "signature": "(\tpath: Union[pathlib.Path, zipp.Path]) -> bioimageio.spec._internal.io_basics.Sha256:", "funcdef": "def"}, "bioimageio.spec.utils.get_spdx_licenses": {"fullname": "bioimageio.spec.utils.get_spdx_licenses", "modulename": "bioimageio.spec.utils", "qualname": "get_spdx_licenses", "kind": "function", "doc": "get details of the SPDX licenses known to bioimageio.spec
\n", "signature": "() -> bioimageio.spec.utils.SpdxLicenses:", "funcdef": "def"}, "bioimageio.spec.utils.identify_bioimageio_yaml_file_name": {"fullname": "bioimageio.spec.utils.identify_bioimageio_yaml_file_name", "modulename": "bioimageio.spec.utils", "qualname": "identify_bioimageio_yaml_file_name", "kind": "function", "doc": "\n", "signature": "(file_names: Iterable[str]) -> str:", "funcdef": "def"}, "bioimageio.spec.utils.is_valid_bioimageio_yaml_name": {"fullname": "bioimageio.spec.utils.is_valid_bioimageio_yaml_name", "modulename": "bioimageio.spec.utils", "qualname": "is_valid_bioimageio_yaml_name", "kind": "function", "doc": "\n", "signature": "(file_name: str) -> bool:", "funcdef": "def"}, "bioimageio.spec.utils.load_array": {"fullname": "bioimageio.spec.utils.load_array", "modulename": "bioimageio.spec.utils", "qualname": "load_array", "kind": "function", "doc": "\n", "signature": "(\tsource: Union[Annotated[Union[bioimageio.spec._internal.url.HttpUrl, bioimageio.spec._internal.io.RelativeFilePath, Annotated[pathlib.Path, PathType(path_type='file')]], FieldInfo(annotation=NoneType, required=True, metadata=[_PydanticGeneralMetadata(union_mode='left_to_right')])], bioimageio.spec._internal.io.FileDescr, zipp.Path]) -> numpy.ndarray[typing.Any, numpy.dtype[typing.Any]]:", "funcdef": "def"}, "bioimageio.spec.utils.save_array": {"fullname": "bioimageio.spec.utils.save_array", "modulename": "bioimageio.spec.utils", "qualname": "save_array", "kind": "function", "doc": "\n", "signature": "(\tpath: Union[pathlib.Path, zipp.Path],\tarray: numpy.ndarray[typing.Any, numpy.dtype[typing.Any]]) -> None:", "funcdef": "def"}, "bioimageio.spec.utils.SpdxLicenseEntry": {"fullname": "bioimageio.spec.utils.SpdxLicenseEntry", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenseEntry", "kind": "class", "doc": "\n", "bases": "typing.TypedDict"}, "bioimageio.spec.utils.SpdxLicenseEntry.isDeprecatedLicenseId": {"fullname": "bioimageio.spec.utils.SpdxLicenseEntry.isDeprecatedLicenseId", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenseEntry.isDeprecatedLicenseId", "kind": "variable", "doc": "\n", "annotation": ": bool"}, "bioimageio.spec.utils.SpdxLicenseEntry.isKnownByZenodo": {"fullname": "bioimageio.spec.utils.SpdxLicenseEntry.isKnownByZenodo", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenseEntry.isKnownByZenodo", "kind": "variable", "doc": "\n", "annotation": ": bool"}, "bioimageio.spec.utils.SpdxLicenseEntry.isOsiApproved": {"fullname": "bioimageio.spec.utils.SpdxLicenseEntry.isOsiApproved", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenseEntry.isOsiApproved", "kind": "variable", "doc": "\n", "annotation": ": bool"}, "bioimageio.spec.utils.SpdxLicenseEntry.licenseId": {"fullname": "bioimageio.spec.utils.SpdxLicenseEntry.licenseId", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenseEntry.licenseId", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.utils.SpdxLicenseEntry.name": {"fullname": "bioimageio.spec.utils.SpdxLicenseEntry.name", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenseEntry.name", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.utils.SpdxLicenseEntry.reference": {"fullname": "bioimageio.spec.utils.SpdxLicenseEntry.reference", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenseEntry.reference", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.utils.SpdxLicenses": {"fullname": "bioimageio.spec.utils.SpdxLicenses", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenses", "kind": "class", "doc": "\n", "bases": "typing.TypedDict"}, "bioimageio.spec.utils.SpdxLicenses.licenseListVersion": {"fullname": "bioimageio.spec.utils.SpdxLicenses.licenseListVersion", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenses.licenseListVersion", "kind": "variable", "doc": "\n", "annotation": ": str"}, "bioimageio.spec.utils.SpdxLicenses.licenses": {"fullname": "bioimageio.spec.utils.SpdxLicenses.licenses", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenses.licenses", "kind": "variable", "doc": "\n", "annotation": ": List[bioimageio.spec.utils.SpdxLicenseEntry]"}, "bioimageio.spec.utils.SpdxLicenses.releaseDate": {"fullname": "bioimageio.spec.utils.SpdxLicenses.releaseDate", "modulename": "bioimageio.spec.utils", "qualname": "SpdxLicenses.releaseDate", "kind": "variable", "doc": "\n", "annotation": ": str"}}, "docInfo": {"bioimageio.core": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 2770}, "bioimageio.core.Axis": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "bioimageio.core.Axis.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 97, "bases": 0, "doc": 3}, "bioimageio.core.Axis.id": {"qualname": 2, "fullname": 4, "annotation": 7, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "bioimageio.core.Axis.type": {"qualname": 2, "fullname": 4, "annotation": 18, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "bioimageio.core.Axis.create": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 881, "bases": 0, "doc": 3}, "bioimageio.core.AxisId": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 5, "doc": 72}, "bioimageio.core.AxisId.root_model": {"qualname": 3, "fullname": 5, "annotation": 5, "default_value": 17, "signature": 0, "bases": 0, "doc": 10}, "bioimageio.core.BlockMeta": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 209}, "bioimageio.core.BlockMeta.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 193, "bases": 0, "doc": 3}, "bioimageio.core.BlockMeta.sample_shape": {"qualname": 3, "fullname": 5, "annotation": 8, "default_value": 0, "signature": 0, "bases": 0, "doc": 10}, "bioimageio.core.BlockMeta.inner_slice": {"qualname": 3, "fullname": 5, "annotation": 11, "default_value": 0, "signature": 0, "bases": 0, "doc": 9}, "bioimageio.core.BlockMeta.halo": {"qualname": 2, "fullname": 4, "annotation": 11, "default_value": 0, "signature": 0, "bases": 0, "doc": 12}, "bioimageio.core.BlockMeta.block_index": {"qualname": 3, "fullname": 5, "annotation": 2, "default_value": 0, "signature": 0, "bases": 0, "doc": 9}, "bioimageio.core.BlockMeta.blocks_in_sample": {"qualname": 4, "fullname": 6, "annotation": 2, "default_value": 0, "signature": 0, "bases": 0, "doc": 9}, "bioimageio.core.BlockMeta.shape": {"qualname": 2, "fullname": 4, "annotation": 8, "default_value": 0, "signature": 0, "bases": 0, "doc": 7}, "bioimageio.core.BlockMeta.padding": {"qualname": 2, "fullname": 4, "annotation": 11, "default_value": 0, "signature": 0, "bases": 0, "doc": 19}, "bioimageio.core.BlockMeta.outer_slice": {"qualname": 3, "fullname": 5, "annotation": 11, "default_value": 0, "signature": 0, "bases": 0, "doc": 12}, "bioimageio.core.BlockMeta.inner_shape": {"qualname": 3, "fullname": 5, "annotation": 8, "default_value": 0, "signature": 0, "bases": 0, "doc": 11}, "bioimageio.core.BlockMeta.local_slice": {"qualname": 3, "fullname": 5, "annotation": 11, "default_value": 0, "signature": 0, "bases": 0, "doc": 12}, "bioimageio.core.BlockMeta.dims": {"qualname": 2, "fullname": 4, "annotation": 7, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "bioimageio.core.BlockMeta.tagged_shape": {"qualname": 3, "fullname": 5, "annotation": 8, "default_value": 0, "signature": 0, "bases": 0, "doc": 5}, "bioimageio.core.BlockMeta.inner_slice_wo_overlap": {"qualname": 5, "fullname": 7, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 43}, "bioimageio.core.BlockMeta.get_transformed": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 86, "bases": 0, "doc": 3}, "bioimageio.core.build_description": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 854, "bases": 0, "doc": 115}, "bioimageio.core.compute_dataset_measures": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 507, "bases": 0, "doc": 14}, "bioimageio.core.create_prediction_pipeline": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 930, "bases": 0, "doc": 33}, "bioimageio.core.dump_description": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 762, "bases": 0, "doc": 20}, "bioimageio.core.enable_determinism": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 37, "bases": 0, "doc": 113}, "bioimageio.core.load_dataset_description": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 578, "bases": 0, "doc": 22}, "bioimageio.core.load_description_and_test": {"qualname": 4, "fullname": 6, "annotation": 0, "default_value": 0, "signature": 2022, "bases": 0, "doc": 12}, "bioimageio.core.load_description_and_validate_format_only": {"qualname": 6, "fullname": 8, "annotation": 0, "default_value": 0, "signature": 474, "bases": 0, "doc": 144}, "bioimageio.core.load_description": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 1170, "bases": 0, "doc": 141}, "bioimageio.core.load_model_description": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 578, "bases": 0, "doc": 40}, "bioimageio.core.load_model": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 578, "bases": 0, "doc": 9}, "bioimageio.core.load_resource": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 1170, "bases": 0, "doc": 8}, "bioimageio.core.MemberId": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 13, "signature": 0, "bases": 0, "doc": 3}, "bioimageio.core.predict_many": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 742, "bases": 0, "doc": 185}, "bioimageio.core.predict": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 841, "bases": 0, "doc": 198}, "bioimageio.core.PredictionPipeline": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 18}, "bioimageio.core.PredictionPipeline.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 814, "bases": 0, "doc": 3}, "bioimageio.core.PredictionPipeline.name": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "bioimageio.core.PredictionPipeline.model_description": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "bioimageio.core.PredictionPipeline.predict_sample_block": {"qualname": 4, "fullname": 6, "annotation": 0, "default_value": 0, "signature": 95, "bases": 0, "doc": 3}, "bioimageio.core.PredictionPipeline.predict_sample_without_blocking": {"qualname": 5, "fullname": 7, "annotation": 0, "default_value": 0, "signature": 94, "bases": 0, "doc": 32}, "bioimageio.core.PredictionPipeline.get_output_sample_id": {"qualname": 5, "fullname": 7, "annotation": 0, "default_value": 0, "signature": 23, "bases": 0, "doc": 3}, "bioimageio.core.PredictionPipeline.predict_sample_with_fixed_blocking": {"qualname": 6, "fullname": 8, "annotation": 0, "default_value": 0, "signature": 177, "bases": 0, "doc": 3}, "bioimageio.core.PredictionPipeline.predict_sample_with_blocking": {"qualname": 5, "fullname": 7, "annotation": 0, "default_value": 0, "signature": 217, "bases": 0, "doc": 20}, "bioimageio.core.PredictionPipeline.apply_preprocessing": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 68, "bases": 0, "doc": 10}, "bioimageio.core.PredictionPipeline.apply_postprocessing": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 89, "bases": 0, "doc": 10}, "bioimageio.core.PredictionPipeline.load": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 11, "bases": 0, "doc": 18}, "bioimageio.core.PredictionPipeline.unload": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 11, "bases": 0, "doc": 8}, "bioimageio.core.Sample": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 5}, "bioimageio.core.Sample.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 596, "bases": 0, "doc": 3}, "bioimageio.core.Sample.members": {"qualname": 2, "fullname": 4, "annotation": 11, "default_value": 0, "signature": 0, "bases": 0, "doc": 6}, "bioimageio.core.Sample.stat": {"qualname": 2, "fullname": 4, 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