Rename all the things. #12
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## tonytung-rename-base #12 +/- ##
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Coverage ? 71.27%
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Files ? 18
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Hits ? 330
Misses ? 133
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| class Collection(object): | ||
| def __init__(self, extras=None): | ||
| self.extras = extras | ||
| self._partitions = dict() |
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self._tilesets? in general, we shouldn't have the word partition anymore in the codebase right?
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arg. i get it. this could either be a collection or a tileset. i'd just leave a comment about that here and move on until we can come up with a better word than partition
slicedimage/_typeformatting.py
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| @@ -17,7 +17,7 @@ def format_tile_dimensions(tile_dimensions): | |||
| return result | |||
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| def format_imagepartition_dimensions(imagepartition_dimensions): | |||
| def format_tileset_dimensions(imagepartition_dimensions): | |||
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arg should be named tileset_dimensions? or partition_dimensions?
| @@ -5,12 +5,12 @@ Sliced imaging data | |||
| Background | |||
| ========== | |||
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| If we want to store imaging data on the cloud and allow scientists to experiment with this data with interactive local tools (e.g., Jupyter notebooks), we should provide an easy interface to retrieve this data. We should future-proof this model for extremely large images with multiple dimensions, where users may want to pull slices of this data without having to download the entire image. | |||
| If we want to store imaging data on the cloud and allow scientists to experiment with this data with interactive local tools (e.g., Jupyter notebooks), we should provide an easy interface to retrieve this data. We should future-proof this model for extremely large image sets with multiple dimensions, where users may want to pull slices of this data without having to download the entire image set. | |||
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Looking back at #11 the nouns we landed on are: collection (e.g., hybridization.json), tilesets(e.g., hybridization-fov_001.json), and tiles. What is an image set? By this do you mean tileset? What is an image partition? By this do you mean the format for a tile?
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oh i see -- by image sets, you mean i have a sample (some volume, like a brain) and i'm looking at multiple FOVs of this sample. these FOVs are comprised of tensors (high dimensional image stacks). as such, an 'image set' is all of the tensors for all of the FOVs that are used to grok the the sample. is that right? if so i like image sets.
Another pass at this could be something like "... future-proof this model for large sample volumes that are being imaged with multiple high dimensional measurements. We anticipate that users will want to access slices of this data (within and across measurements) without having to download all possible images"
But if you do this, you lose the word image set :(
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It's the logical top-level element, which can either be a collection or a tileset. There's a subtle difference between this and what I'm temporarily (?) calling a partition.
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| Design | ||
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| Images will be stored in a tiled format such that ranged requests can be used to efficiently fetch slices of the data. The tiles of the image is described by a manifest, which is itself broken up into multiple files for easy consumption. | ||
| An image set will be stored in a tiled format such that ranged requests can be used to efficiently fetch slices of the data. The tiles of the image set is described by a manifest, which is itself broken up into multiple files for easy consumption. |
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what do you mean by manifest? Is it a collection?
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Manifest is the entire tree of collection and tilesets.
slicedimage/io.py
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| @@ -94,29 +94,29 @@ def parse(self, json_doc, baseurl): | |||
| class Writer(object): | |||
| @staticmethod | |||
| def write_to_path(imagestack, path, pretty=False, *args, **kwargs): | |||
| document = v0_0_0.Writer().generate_toc(imagestack, path, pretty, *args, **kwargs) | |||
| document = v0_0_0.Writer().generate_partition_document(imagestack, path, pretty, *args, **kwargs) | |||
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what's an imagestack? a tileset? a partition?
Incorporate the renaming in spacetx/slicedimage#12
Incorporate the renaming in spacetx/slicedimage#12
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