diff --git a/.gitignore b/.gitignore index ddf2a27..4e42fbb 100644 --- a/.gitignore +++ b/.gitignore @@ -39,3 +39,7 @@ htmlcov /logs/ /src/morphoclass/version.py /venv/ + +# pyenv file +.python-version + diff --git a/AUTHORS.md b/AUTHORS.md new file mode 100644 index 0000000..ad68efc --- /dev/null +++ b/AUTHORS.md @@ -0,0 +1,3 @@ +- [Jelena Banjac](https://github.com/JelenaBanjac) @ Blue Brain Project, EPFL +- [Francesco Casalegno](https://github.com/FrancescoCasalegno) @ Blue Brain Project, EPFL +- [Stanislav Schmidt](https://github.com/Stannislav) @ Blue Brain Project, EPFL diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..69377f1 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,77 @@ +# Contributing +Thank you for your interest in contributing to MorphoClass! + +Before you open an issue or start working on a pull request, please make sure +to read the following guidelines. + +1. [Creating Issues](#creating-issues) +1. [Creating Pull Requests](#creating-pull-requests) + 1. [Refer to an issue](#refer-to-an-issue) + 1. [Add unit test](#add-unit-tests) + 1. [Add type annotations](#add-type-annotations) + 1. [Update dependencies](#update-dependencies) + 1. [Ensure all CI tests pass](#ensure-all-ci-tests-pass) + 1. [Get reviews and approval](#get-reviews-and-approval) + + +## Creating Issues +Before you submit an issue, please search our [issue +tracker](https://github.com/BlueBrain/morphoclass/issues) to verify if any +similar issue was raised in the past. Even if you cannot find a direct answer +to your question, this can allow you to collect a list of related issues that +you can link in your new issue. + +Once you have verified that no similar issues exist yet, feel free to open a +new issue. + + +## Creating Pull Requests +If you wish to contribute to the code base, opening a pull request on GitHub is +the right thing to do! + +Please read the following paragraphs to make sure that your work can be +considered for a potential integration in our source code. + +### Refer to an issue +In general, every pull request should refer to a specific issue. If you would +like to provide your contribution on a untracked issue, please create first an +issue as explained [here](#CreatingIssues) so that we can discuss the value of +the proposed contribution and its implementation. + +### Add unit tests +Concerning CI tests, we are running various checks on linting, unit tests, +docs, and packaging. If you are adding or modifying a functionality in the +code, you are also expected to provide a unit test demonstrating and checking +the new behavior. + +### Add type annotations +We are gradually introducing type annotations to our code, and our CI performs +type checking with [mypy](https://mypy.readthedocs.io/en/stable/index.html). If +your PR introduces a new function or heavily modifies an existing function, you +should also add type annotations for such function. + +### Update dependencies +If your PR introduces a dependency on a new python package, this should be +added to both the `setup.py` and the `requirements.txt` files. + +### Ensure all CI tests pass +We use GitHub Actions to run [our CI +tests](https://github.com/BlueBrain/morphoclass/actions?query=workflow%3A%22ci+testing%22). +Once you open a PR, the workflow that runs all CI tests is automatically +triggered. This workflow is also triggered every time a new commit is pushed to +that PR branch. If you want to push a commit without triggering the CI tests +(e.g. if a feature is still work in progress and you want to save time), your +commit message should include an appropriate label like `[skip ci]`, `[ci +skip]`, `[no ci]` etc. (see +[here](https://github.blog/changelog/2021-02-08-github-actions-skip-pull-request-and-push-workflows-with-skip-ci/) +for the complete list). + +All CI tests must pass before the pull request can be considered for review. + +### Get reviews and approval +Once you have satisfied all the previous points, feel free to open your pull +request! + +We will get back to you as soon as possible with comments and feedback in the +format of pull request reviews. A positive review from one of the maintainers +is required for the pull request to be merged into the master. diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..1a9c178 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright 2022 Blue Brain Project / EPFL + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README.md b/README.md index 00c3364..a508d1b 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ # Morphology-Classification -Classify neuron morphologies using deep learning. +MorphoClass is a toolbox for neuronal morphologies processing and +classification using machine learning. ## Installation Clone the repository and set up the virtual environment @@ -16,28 +17,6 @@ Install `morphoclass` ./install.sh ``` -## Installation on the BB5 -Allocate a node -```sh -ssh bbpv1 -salloc -N1 -A -t 2:00:00 -``` - -Clone the repository and set up the virtual environment -```sh -git clone git@github.com:BlueBrain/morphoclass.git -cd morphoclass -module load unstable -module load python -python --version # should be 3.8 -python -m venv venv -. venv/bin/activate -``` - -Install `morphoclass` -```sh -./install.sh -``` ## Known Installation Issues In some cases the installation might fail because either `cmake` or `hdf5` are @@ -74,13 +53,17 @@ Open the file `docs/build/html/index.html` to view the documentation. We provide a docker file that allows you to run `morphoclass` on a docker container. To build the docker image run the following command: ```sh -docker build -f docker/morphoclass.Dockerfile -t morphoclass --build-arg MORPHOCLASS_USERS . +docker build \ + -f docker/morphoclass.Dockerfile \ + -t morphoclass \ + --build-arg MORPHOCLASS_USERS \ + . ``` Notice the `MORPHOCLASS_USERS` build argument, it allows you to add custom users to the container operating system. This way you'll be able to run your container as a given user, which can be useful when writing files to a -bind-mounted volume. In this case you probably want to specify your own username -and user ID and you should set +bind-mounted volume. In this case you probably want to specify your own +username and user ID and you should set ```sh export MORPHOCLASS_USERS="$(whoami)/$(id -u)" ``` @@ -119,5 +102,85 @@ You might want to pass additional flags to `docker run`: Just for reference, the `docker run` command with all flags included, the external port set to `35353`, and the container name to `my-container`: ```sh -docker run -v $PWD:/workdir -p 35353:8888 --rm -it --gpus=all -u $USER --name my-container morphoclass +docker run + -v $PWD:/workdir \ + -p 35353:8888 \ + --rm \ + -it \ + --gpus=all \ + -u $USER \ + --name my-container \ + morphoclass +``` + +# Examples + +MorphoClass functionalities can be accessed using either a command line +interface or by importing `morphoclass` as a Python module and using it as a +library. + +## Command line interface + +By installing MorphoClass, we get access to a command line interface with a +main entrypoint `morphoclass` and various sub-commands. +```shell +$ morphoclass --help +Usage: morphoclass [OPTIONS] COMMAND [ARGS]... + + Welcome to the command line application for morphoclass. + + All functionality is provided through respective sub-commands. To learn more + about their functionality call the corresponding sub-command with the --help + flag to see a detailed description. + +Options: + ... + +Commands: + ... +``` +For instance, to train a model for classifying neuronal morphologies, we can +check the help of the corresponding sub-command. +```shell +$ morphoclass train --help +Usage: morphoclass train [OPTIONS] + + Train a morphology classification model. + +Options: + ... ``` + +## Python interface + +MorphoClass is a pure Python package, and can be used as any other module once +it is installed. + +For instance, we can load a PersLay-based model for morphology classification +and check its documentation as follows. +```python +>>> from morphoclass.models.coriander_net import CorianderNet +>>> help(CorianderNet) + +Help on class CorianderNet in module morphoclass.models.coriander_net: + +class CorianderNet(torch.nn.modules.module.Module) + | CorianderNet(n_classes=4, n_features=64, dropout=False) + | + | A PersLay-based neural network for neuron m-type classification. + | + | Parameters + | ---------- + ... +``` + + +# Funding & Acknowledgment + +The development of this software was supported by funding to the Blue Brain +Project, a research center of the École polytechnique fédérale de Lausanne +(EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes +of Technology. + +Copyright © 2022 Blue Brain Project/EPFL + diff --git a/setup.cfg b/setup.cfg index 7ba5ec3..52cac81 100644 --- a/setup.cfg +++ b/setup.cfg @@ -3,8 +3,7 @@ name = morphoclass description = Package for classifying neuron morphologies long_description = file: README.md long_description_content_type = text/markdown -author = Stanislav Schmidt -author_email = stanislav.schmidt@epfl.ch +author = Blue Brain Project, EPFL maintainer = bbp-ou-machinelearning maintainer_email = bbp-ou-machinelearning@groupes.epfl.ch license = BBP-internal-confidential diff --git a/src/morphoclass/__init__.py b/src/morphoclass/__init__.py index 150e4c0..35c3b03 100644 --- a/src/morphoclass/__init__.py +++ b/src/morphoclass/__init__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """MorphoClass - a package for neuron m-type classification using ML.""" from __future__ import annotations diff --git a/src/morphoclass/__main__.py b/src/morphoclass/__main__.py index e18bf86..b7e3f9f 100644 --- a/src/morphoclass/__main__.py +++ b/src/morphoclass/__main__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """The main entry point for the morphoclass module. This allows to run the morphoclass module via ``python -m morphoclass`` and diff --git a/src/morphoclass/augmentation.py b/src/morphoclass/augmentation.py index 6fea198..a8d6e06 100644 --- a/src/morphoclass/augmentation.py +++ b/src/morphoclass/augmentation.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Utilities for morphology data augmentation (deprecated). The functionality in this module has been superseded by the transforms in diff --git a/src/morphoclass/cleanlab.py b/src/morphoclass/cleanlab.py index 71e4c11..a5d7d9d 100644 --- a/src/morphoclass/cleanlab.py +++ b/src/morphoclass/cleanlab.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """CleanLab analysis of labeled data.""" from __future__ import annotations diff --git a/src/morphoclass/console/__init__.py b/src/morphoclass/console/__init__.py index 474e71f..1d6402d 100644 --- a/src/morphoclass/console/__init__.py +++ b/src/morphoclass/console/__init__.py @@ -1,2 +1,15 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """The morphoclass CLI application.""" from __future__ import annotations diff --git a/src/morphoclass/console/cmd_evaluate.py b/src/morphoclass/console/cmd_evaluate.py index 58c0365..a8d1e02 100644 --- a/src/morphoclass/console/cmd_evaluate.py +++ b/src/morphoclass/console/cmd_evaluate.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `morphoclass evaluate` CLI command.""" from __future__ import annotations diff --git a/src/morphoclass/console/cmd_extract_features.py b/src/morphoclass/console/cmd_extract_features.py index bd2c3eb..382d26a 100644 --- a/src/morphoclass/console/cmd_extract_features.py +++ b/src/morphoclass/console/cmd_extract_features.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `morphoclass extract-features` CLI command.""" from __future__ import annotations diff --git a/src/morphoclass/console/cmd_organise_dataset.py b/src/morphoclass/console/cmd_organise_dataset.py index ec2a4da..55372d6 100644 --- a/src/morphoclass/console/cmd_organise_dataset.py +++ b/src/morphoclass/console/cmd_organise_dataset.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Default data preparation script shared across different datasets.""" from __future__ import annotations diff --git a/src/morphoclass/console/cmd_performance_report.py b/src/morphoclass/console/cmd_performance_report.py index acfd51e..3881f28 100644 --- a/src/morphoclass/console/cmd_performance_report.py +++ b/src/morphoclass/console/cmd_performance_report.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Script to collect all models' performances.""" from __future__ import annotations diff --git a/src/morphoclass/console/cmd_performance_table.py b/src/morphoclass/console/cmd_performance_table.py index 5d50d08..d13b4e7 100644 --- a/src/morphoclass/console/cmd_performance_table.py +++ b/src/morphoclass/console/cmd_performance_table.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Script to collect all models' performances.""" from __future__ import annotations diff --git a/src/morphoclass/console/cmd_plot_dataset_stats.py b/src/morphoclass/console/cmd_plot_dataset_stats.py index bc847a5..90a11a2 100644 --- a/src/morphoclass/console/cmd_plot_dataset_stats.py +++ b/src/morphoclass/console/cmd_plot_dataset_stats.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Default data preparation script shared across different datasets.""" from __future__ import annotations diff --git a/src/morphoclass/console/cmd_preprocess_dataset.py b/src/morphoclass/console/cmd_preprocess_dataset.py index 79386de..f7480e5 100644 --- a/src/morphoclass/console/cmd_preprocess_dataset.py +++ b/src/morphoclass/console/cmd_preprocess_dataset.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """The preprocess-dataset subcommand.""" from __future__ import annotations diff --git a/src/morphoclass/console/cmd_train.py b/src/morphoclass/console/cmd_train.py index 135df45..00f34b6 100644 --- a/src/morphoclass/console/cmd_train.py +++ b/src/morphoclass/console/cmd_train.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `morphoclass train` CLI command.""" from __future__ import annotations diff --git a/src/morphoclass/console/dataset_preprocessor.py b/src/morphoclass/console/dataset_preprocessor.py index e788e03..f0d7fec 100644 --- a/src/morphoclass/console/dataset_preprocessor.py +++ b/src/morphoclass/console/dataset_preprocessor.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the data preprocessor.""" from __future__ import annotations diff --git a/src/morphoclass/console/evaluate.py b/src/morphoclass/console/evaluate.py index 9601ca6..49ca0b1 100644 --- a/src/morphoclass/console/evaluate.py +++ b/src/morphoclass/console/evaluate.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Utilities for the morphoclass evaluate command.""" from __future__ import annotations diff --git a/src/morphoclass/console/explain.py b/src/morphoclass/console/explain.py index 09992ca..f4e3cc0 100644 --- a/src/morphoclass/console/explain.py +++ b/src/morphoclass/console/explain.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation fo the `morphoclass explain` CLI command.""" from __future__ import annotations diff --git a/src/morphoclass/console/explain_models.py b/src/morphoclass/console/explain_models.py index 7454853..bc02b5d 100644 --- a/src/morphoclass/console/explain_models.py +++ b/src/morphoclass/console/explain_models.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """XAI subcommands.""" from __future__ import annotations diff --git a/src/morphoclass/console/helpers.py b/src/morphoclass/console/helpers.py index a6b9c12..c7c24be 100644 --- a/src/morphoclass/console/helpers.py +++ b/src/morphoclass/console/helpers.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Helper functions for morphoclass checkpoints.""" from __future__ import annotations diff --git a/src/morphoclass/console/main.py b/src/morphoclass/console/main.py index 20f5964..096d71a 100644 --- a/src/morphoclass/console/main.py +++ b/src/morphoclass/console/main.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """The main morphoclass CLI entrypoint.""" from __future__ import annotations diff --git a/src/morphoclass/console/outlier_detection.py b/src/morphoclass/console/outlier_detection.py index 8974634..1f0af00 100644 --- a/src/morphoclass/console/outlier_detection.py +++ b/src/morphoclass/console/outlier_detection.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `morphoclass outlier-detection` CLI command.""" from __future__ import annotations diff --git a/src/morphoclass/console/performance_report.py b/src/morphoclass/console/performance_report.py index a92cfef..b9406b8 100644 --- a/src/morphoclass/console/performance_report.py +++ b/src/morphoclass/console/performance_report.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Utilities for the morphoclass performance-report command.""" from __future__ import annotations diff --git a/src/morphoclass/console/performance_table.py b/src/morphoclass/console/performance_table.py index 17a57a2..d2c54b8 100644 --- a/src/morphoclass/console/performance_table.py +++ b/src/morphoclass/console/performance_table.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Utilities for the morphoclass performance-table command.""" from __future__ import annotations diff --git a/src/morphoclass/console/stats_plotter.py b/src/morphoclass/console/stats_plotter.py index 0c47511..7436868 100644 --- a/src/morphoclass/console/stats_plotter.py +++ b/src/morphoclass/console/stats_plotter.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Default data preparation script shared across different datasets.""" from __future__ import annotations diff --git a/src/morphoclass/console/transfer_learning.py b/src/morphoclass/console/transfer_learning.py index c0fd94e..4ff91dc 100644 --- a/src/morphoclass/console/transfer_learning.py +++ b/src/morphoclass/console/transfer_learning.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `morphoclass train_and_eval` CLI command.""" from __future__ import annotations diff --git a/src/morphoclass/constants.py b/src/morphoclass/constants.py index 52b193b..07e77a7 100644 --- a/src/morphoclass/constants.py +++ b/src/morphoclass/constants.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Various constants and definitions.""" from __future__ import annotations diff --git a/src/morphoclass/data/__init__.py b/src/morphoclass/data/__init__.py index 8fcc9e0..e8e82f7 100644 --- a/src/morphoclass/data/__init__.py +++ b/src/morphoclass/data/__init__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Dataset abstractions and data helper functions.""" from __future__ import annotations diff --git a/src/morphoclass/data/_helper.py b/src/morphoclass/data/_helper.py index 156d2b5..cf19ad9 100644 --- a/src/morphoclass/data/_helper.py +++ b/src/morphoclass/data/_helper.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. from __future__ import annotations import logging diff --git a/src/morphoclass/data/filters.py b/src/morphoclass/data/filters.py index e125050..f28bc3e 100644 --- a/src/morphoclass/data/filters.py +++ b/src/morphoclass/data/filters.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Various filters used for morphology data loading. A typical use of filter is in constructing instances of the diff --git a/src/morphoclass/data/morphology_data.py b/src/morphoclass/data/morphology_data.py index 1b6b3fe..c1f4bf1 100644 --- a/src/morphoclass/data/morphology_data.py +++ b/src/morphoclass/data/morphology_data.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the MorphologyData class.""" from __future__ import annotations diff --git a/src/morphoclass/data/morphology_data_loader.py b/src/morphoclass/data/morphology_data_loader.py index b5e5de4..c42ece3 100644 --- a/src/morphoclass/data/morphology_data_loader.py +++ b/src/morphoclass/data/morphology_data_loader.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Morphology data loader.""" from __future__ import annotations diff --git a/src/morphoclass/data/morphology_dataset.py b/src/morphoclass/data/morphology_dataset.py index 5e17143..b6cb703 100644 --- a/src/morphoclass/data/morphology_dataset.py +++ b/src/morphoclass/data/morphology_dataset.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the MorphologyDataset class.""" from __future__ import annotations diff --git a/src/morphoclass/data/morphology_embedding_data_loader.py b/src/morphoclass/data/morphology_embedding_data_loader.py index dd8a9a0..995bb86 100644 --- a/src/morphoclass/data/morphology_embedding_data_loader.py +++ b/src/morphoclass/data/morphology_embedding_data_loader.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Morphology embedding data loader.""" from __future__ import annotations diff --git a/src/morphoclass/data/morphology_embedding_dataset.py b/src/morphoclass/data/morphology_embedding_dataset.py index 89d94fe..3fc8288 100644 --- a/src/morphoclass/data/morphology_embedding_dataset.py +++ b/src/morphoclass/data/morphology_embedding_dataset.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the MorphologyEmbedding class.""" from __future__ import annotations diff --git a/src/morphoclass/data/tns_dataset.py b/src/morphoclass/data/tns_dataset.py index 68df3e3..aa2ad96 100644 --- a/src/morphoclass/data/tns_dataset.py +++ b/src/morphoclass/data/tns_dataset.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Dataset of synthetic morphologies generated by TNS.""" from __future__ import annotations diff --git a/src/morphoclass/deepwalk.py b/src/morphoclass/deepwalk.py index 2f989d8..8274dd9 100644 --- a/src/morphoclass/deepwalk.py +++ b/src/morphoclass/deepwalk.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Portal to DeepWalk methods from morphoclass.""" from __future__ import annotations diff --git a/src/morphoclass/feature_extractors/__init__.py b/src/morphoclass/feature_extractors/__init__.py index fedad49..a1e4543 100644 --- a/src/morphoclass/feature_extractors/__init__.py +++ b/src/morphoclass/feature_extractors/__init__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Feature extractors.""" from __future__ import annotations diff --git a/src/morphoclass/feature_extractors/feature_extraction.py b/src/morphoclass/feature_extractors/feature_extraction.py index 110394a..058c989 100644 --- a/src/morphoclass/feature_extractors/feature_extraction.py +++ b/src/morphoclass/feature_extractors/feature_extraction.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `morphoclass feature-extraction` CLI command.""" from __future__ import annotations diff --git a/src/morphoclass/feature_extractors/interneurons.py b/src/morphoclass/feature_extractors/interneurons.py index 4d8b660..609f517 100644 --- a/src/morphoclass/feature_extractors/interneurons.py +++ b/src/morphoclass/feature_extractors/interneurons.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Morphology preprocessing and feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/feature_extractors/non_graph.py b/src/morphoclass/feature_extractors/non_graph.py index 02d7c1c..1a186b9 100644 --- a/src/morphoclass/feature_extractors/non_graph.py +++ b/src/morphoclass/feature_extractors/non_graph.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Non-graph feature extraction such as persistence diagrams and images.""" from __future__ import annotations diff --git a/src/morphoclass/feature_extractors/pyramidal_cells.py b/src/morphoclass/feature_extractors/pyramidal_cells.py index 2eae651..6946edf 100644 --- a/src/morphoclass/feature_extractors/pyramidal_cells.py +++ b/src/morphoclass/feature_extractors/pyramidal_cells.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Morphology preprocessing and feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/layers/__init__.py b/src/morphoclass/layers/__init__.py index 61ceea4..3952268 100644 --- a/src/morphoclass/layers/__init__.py +++ b/src/morphoclass/layers/__init__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Various layers used in neural networks in this package.""" from __future__ import annotations diff --git a/src/morphoclass/layers/attention_global_pool.py b/src/morphoclass/layers/attention_global_pool.py index c19f7e9..5527769 100644 --- a/src/morphoclass/layers/attention_global_pool.py +++ b/src/morphoclass/layers/attention_global_pool.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the AttentionGlobalPool layer.""" from __future__ import annotations diff --git a/src/morphoclass/layers/bidirectional_block.py b/src/morphoclass/layers/bidirectional_block.py index 6074ce1..4fcfa26 100644 --- a/src/morphoclass/layers/bidirectional_block.py +++ b/src/morphoclass/layers/bidirectional_block.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the BidirectionalBlock layer.""" from __future__ import annotations diff --git a/src/morphoclass/layers/bidirectional_res_block.py b/src/morphoclass/layers/bidirectional_res_block.py index 2fc58ab..7978026 100644 --- a/src/morphoclass/layers/bidirectional_res_block.py +++ b/src/morphoclass/layers/bidirectional_res_block.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the BidirectionalResBlock layer.""" from __future__ import annotations diff --git a/src/morphoclass/layers/cat.py b/src/morphoclass/layers/cat.py index d5d38cf..ca98b9a 100644 --- a/src/morphoclass/layers/cat.py +++ b/src/morphoclass/layers/cat.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the Cat layer.""" from __future__ import annotations diff --git a/src/morphoclass/layers/cheb_conv.py b/src/morphoclass/layers/cheb_conv.py index 8844650..82bc62a 100644 --- a/src/morphoclass/layers/cheb_conv.py +++ b/src/morphoclass/layers/cheb_conv.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the ChebConv layer.""" from __future__ import annotations diff --git a/src/morphoclass/layers/cheb_conv_separable.py b/src/morphoclass/layers/cheb_conv_separable.py index c57ce23..131b5d9 100644 --- a/src/morphoclass/layers/cheb_conv_separable.py +++ b/src/morphoclass/layers/cheb_conv_separable.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the ChebConvSeparable layer.""" from __future__ import annotations diff --git a/src/morphoclass/layers/perslay.py b/src/morphoclass/layers/perslay.py index d5582b6..2e822af 100644 --- a/src/morphoclass/layers/perslay.py +++ b/src/morphoclass/layers/perslay.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the PersLay layer.""" from __future__ import annotations diff --git a/src/morphoclass/layers/running_std.py b/src/morphoclass/layers/running_std.py index 9125a51..3e50f49 100644 --- a/src/morphoclass/layers/running_std.py +++ b/src/morphoclass/layers/running_std.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Layer for normalization by the standard deviation.""" from __future__ import annotations diff --git a/src/morphoclass/layers/tree_lstm_pool.py b/src/morphoclass/layers/tree_lstm_pool.py index 5ae86f4..bb49002 100644 --- a/src/morphoclass/layers/tree_lstm_pool.py +++ b/src/morphoclass/layers/tree_lstm_pool.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the tree-LSTM pooling layer.""" from __future__ import annotations diff --git a/src/morphoclass/metrics.py b/src/morphoclass/metrics.py index eb9bd89..1c46af7 100644 --- a/src/morphoclass/metrics.py +++ b/src/morphoclass/metrics.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of various metric functions.""" from __future__ import annotations diff --git a/src/morphoclass/model_utils.py b/src/morphoclass/model_utils.py index fb4b008..d398291 100644 --- a/src/morphoclass/model_utils.py +++ b/src/morphoclass/model_utils.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Utilities for GNN models. Currently, only the hierarchical labels.""" from __future__ import annotations diff --git a/src/morphoclass/models/__init__.py b/src/morphoclass/models/__init__.py index 7c8f3a0..5c52e0b 100644 --- a/src/morphoclass/models/__init__.py +++ b/src/morphoclass/models/__init__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Various models for morphology type classification of neurons.""" from __future__ import annotations diff --git a/src/morphoclass/models/bidirectional_net.py b/src/morphoclass/models/bidirectional_net.py index 23c9c5b..c3b9da2 100644 --- a/src/morphoclass/models/bidirectional_net.py +++ b/src/morphoclass/models/bidirectional_net.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the BidirectionalNet classifier.""" from __future__ import annotations diff --git a/src/morphoclass/models/cnnet.py b/src/morphoclass/models/cnnet.py index 7cd3b0c..92628fd 100644 --- a/src/morphoclass/models/cnnet.py +++ b/src/morphoclass/models/cnnet.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Classification of persistence images using a CNN. This module includes a convolutional model and a corresponding diff --git a/src/morphoclass/models/concatecnnet.py b/src/morphoclass/models/concatecnnet.py index 2911add..b62d264 100644 --- a/src/morphoclass/models/concatecnnet.py +++ b/src/morphoclass/models/concatecnnet.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the ConcateCNNet classifier.""" from __future__ import annotations diff --git a/src/morphoclass/models/concatenet.py b/src/morphoclass/models/concatenet.py index 5e29811..b645411 100644 --- a/src/morphoclass/models/concatenet.py +++ b/src/morphoclass/models/concatenet.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the ConcateNet classifier.""" from __future__ import annotations diff --git a/src/morphoclass/models/coriander_net.py b/src/morphoclass/models/coriander_net.py index b37ebf7..2f8e175 100644 --- a/src/morphoclass/models/coriander_net.py +++ b/src/morphoclass/models/coriander_net.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the PersLay-based CorianderNet network.""" from __future__ import annotations diff --git a/src/morphoclass/models/hbnet.py b/src/morphoclass/models/hbnet.py index 4694e70..64b8ee7 100644 --- a/src/morphoclass/models/hbnet.py +++ b/src/morphoclass/models/hbnet.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the hierarchical, bidirectional net (HBNet).""" from __future__ import annotations diff --git a/src/morphoclass/models/man_net.py b/src/morphoclass/models/man_net.py index 3841a18..63421a9 100644 --- a/src/morphoclass/models/man_net.py +++ b/src/morphoclass/models/man_net.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """The `ManNet` model and trainer classes.""" from __future__ import annotations diff --git a/src/morphoclass/models/man_res_nets.py b/src/morphoclass/models/man_res_nets.py index cbac8e3..9f0235d 100644 --- a/src/morphoclass/models/man_res_nets.py +++ b/src/morphoclass/models/man_res_nets.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `ManResNet1`, `ManResNet2`, and `ManResNet3` models.""" from __future__ import annotations diff --git a/src/morphoclass/models/multi_adj_net.py b/src/morphoclass/models/multi_adj_net.py index d711b1a..7c8ad36 100644 --- a/src/morphoclass/models/multi_adj_net.py +++ b/src/morphoclass/models/multi_adj_net.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the MultiAdjNet classifier.""" from __future__ import annotations diff --git a/src/morphoclass/orientation.py b/src/morphoclass/orientation.py index cbe1480..708ad2e 100644 --- a/src/morphoclass/orientation.py +++ b/src/morphoclass/orientation.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Tools for orienting neurons in their 3D embedding vector space.""" from __future__ import annotations diff --git a/src/morphoclass/report.py b/src/morphoclass/report.py index a87365d..31aa73a 100644 --- a/src/morphoclass/report.py +++ b/src/morphoclass/report.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Module for creating Jinja reports.""" from __future__ import annotations diff --git a/src/morphoclass/serialization.py b/src/morphoclass/serialization.py index 7c5fb8d..c8df8ca 100644 --- a/src/morphoclass/serialization.py +++ b/src/morphoclass/serialization.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Module with tools and utilities for data and model serialization.""" from __future__ import annotations diff --git a/src/morphoclass/training/__init__.py b/src/morphoclass/training/__init__.py index e01187d..971bae6 100644 --- a/src/morphoclass/training/__init__.py +++ b/src/morphoclass/training/__init__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Utilities for setting up and running model training.""" from __future__ import annotations diff --git a/src/morphoclass/training/_helpers.py b/src/morphoclass/training/_helpers.py index 8006aea..7c44e15 100644 --- a/src/morphoclass/training/_helpers.py +++ b/src/morphoclass/training/_helpers.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. from __future__ import annotations import numpy as np diff --git a/src/morphoclass/training/cli.py b/src/morphoclass/training/cli.py index ef27af5..20fa1ad 100644 --- a/src/morphoclass/training/cli.py +++ b/src/morphoclass/training/cli.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Utilities for the morphoclass train command.""" from __future__ import annotations diff --git a/src/morphoclass/training/rd_dataset_prep.py b/src/morphoclass/training/rd_dataset_prep.py index 5d5d04d..6fecf37 100644 --- a/src/morphoclass/training/rd_dataset_prep.py +++ b/src/morphoclass/training/rd_dataset_prep.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Helper functions for preparation of morphology dataset splits.""" from __future__ import annotations diff --git a/src/morphoclass/training/reports/__init__.py b/src/morphoclass/training/reports/__init__.py index 82968ce..a5231d0 100644 --- a/src/morphoclass/training/reports/__init__.py +++ b/src/morphoclass/training/reports/__init__.py @@ -1,2 +1,15 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Training reports.""" from __future__ import annotations diff --git a/src/morphoclass/training/reports/transfer_learning_report.py b/src/morphoclass/training/reports/transfer_learning_report.py index 057af9f..d52b892 100644 --- a/src/morphoclass/training/reports/transfer_learning_report.py +++ b/src/morphoclass/training/reports/transfer_learning_report.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Collect plots from different pretraining datasets and compile a report.""" from __future__ import annotations diff --git a/src/morphoclass/training/tns_utils.py b/src/morphoclass/training/tns_utils.py index 88c1040..cbcd012 100644 --- a/src/morphoclass/training/tns_utils.py +++ b/src/morphoclass/training/tns_utils.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Utilities for working with the TNS package.""" from __future__ import annotations diff --git a/src/morphoclass/training/trainers.py b/src/morphoclass/training/trainers.py index 8589436..61c70c5 100644 --- a/src/morphoclass/training/trainers.py +++ b/src/morphoclass/training/trainers.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """A collection of model trainers.""" from __future__ import annotations diff --git a/src/morphoclass/training/training_config.py b/src/morphoclass/training/training_config.py index d1e7b03..5823ebb 100644 --- a/src/morphoclass/training/training_config.py +++ b/src/morphoclass/training/training_config.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the training config.""" from __future__ import annotations diff --git a/src/morphoclass/training/training_log.py b/src/morphoclass/training/training_log.py index 3ad6b56..8c5aa41 100644 --- a/src/morphoclass/training/training_log.py +++ b/src/morphoclass/training/training_log.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the training log.""" from __future__ import annotations diff --git a/src/morphoclass/training/training_loop_cv.py b/src/morphoclass/training/training_loop_cv.py index 33d8a96..6a86f93 100644 --- a/src/morphoclass/training/training_loop_cv.py +++ b/src/morphoclass/training/training_loop_cv.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Functions for model training with cross-validation.""" from __future__ import annotations diff --git a/src/morphoclass/training/training_loop_loo.py b/src/morphoclass/training/training_loop_loo.py index 7c18004..a406227 100644 --- a/src/morphoclass/training/training_loop_loo.py +++ b/src/morphoclass/training/training_loop_loo.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Functions for model training with the leave-one-out strategy.""" from __future__ import annotations diff --git a/src/morphoclass/training/training_loop_regression.py b/src/morphoclass/training/training_loop_regression.py index 9f065ea..b28656b 100644 --- a/src/morphoclass/training/training_loop_regression.py +++ b/src/morphoclass/training/training_loop_regression.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Functions for running training of a regression model.""" from __future__ import annotations diff --git a/src/morphoclass/training/training_loop_simple.py b/src/morphoclass/training/training_loop_simple.py index 37bd965..84fe0a7 100644 --- a/src/morphoclass/training/training_loop_simple.py +++ b/src/morphoclass/training/training_loop_simple.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Functions for simple model training without cross-validation.""" from __future__ import annotations diff --git a/src/morphoclass/training/transfer_learning.py b/src/morphoclass/training/transfer_learning.py index c928bae..7c0ad2e 100644 --- a/src/morphoclass/training/transfer_learning.py +++ b/src/morphoclass/training/transfer_learning.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the transfer learning curves command.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/__init__.py b/src/morphoclass/transforms/__init__.py index abd1ba8..4563f48 100644 --- a/src/morphoclass/transforms/__init__.py +++ b/src/morphoclass/transforms/__init__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Transformations of `Data` objects. Some of these transformations return a copy of the `Data` object, others diff --git a/src/morphoclass/transforms/add_one_hot_labels.py b/src/morphoclass/transforms/add_one_hot_labels.py index ec531a6..b14866e 100644 --- a/src/morphoclass/transforms/add_one_hot_labels.py +++ b/src/morphoclass/transforms/add_one_hot_labels.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `AddOneHotLabels` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/augmentors/__init__.py b/src/morphoclass/transforms/augmentors/__init__.py index 3b8f214..cf6b9d2 100644 --- a/src/morphoclass/transforms/augmentors/__init__.py +++ b/src/morphoclass/transforms/augmentors/__init__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Transforms that generate morphology data augmentations. This implies that the transforms in this module will modify the actual diff --git a/src/morphoclass/transforms/augmentors/add_nodes_at_intervals.py b/src/morphoclass/transforms/augmentors/add_nodes_at_intervals.py index dd0026e..364e206 100644 --- a/src/morphoclass/transforms/augmentors/add_nodes_at_intervals.py +++ b/src/morphoclass/transforms/augmentors/add_nodes_at_intervals.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `AddNodesAtIntervals` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/augmentors/add_random_points_to_reduction_mask.py b/src/morphoclass/transforms/augmentors/add_random_points_to_reduction_mask.py index ec929f7..66d6977 100644 --- a/src/morphoclass/transforms/augmentors/add_random_points_to_reduction_mask.py +++ b/src/morphoclass/transforms/augmentors/add_random_points_to_reduction_mask.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `AddRandomPointsToReductionMask` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/augmentors/add_section_middle_points.py b/src/morphoclass/transforms/augmentors/add_section_middle_points.py index 06177a5..b040406 100644 --- a/src/morphoclass/transforms/augmentors/add_section_middle_points.py +++ b/src/morphoclass/transforms/augmentors/add_section_middle_points.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `AddSectionMiddlePoints` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/augmentors/apply_node_reduction_masks.py b/src/morphoclass/transforms/augmentors/apply_node_reduction_masks.py index 3ccade3..738dcc6 100644 --- a/src/morphoclass/transforms/augmentors/apply_node_reduction_masks.py +++ b/src/morphoclass/transforms/augmentors/apply_node_reduction_masks.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `ApplyNodeReductionMasks` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/augmentors/branching_only_neurites.py b/src/morphoclass/transforms/augmentors/branching_only_neurites.py index 2447aa5..4cf5c5a 100644 --- a/src/morphoclass/transforms/augmentors/branching_only_neurites.py +++ b/src/morphoclass/transforms/augmentors/branching_only_neurites.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Branching only using the neurites.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/augmentors/branching_only_neuron.py b/src/morphoclass/transforms/augmentors/branching_only_neuron.py index 32731b7..be10609 100644 --- a/src/morphoclass/transforms/augmentors/branching_only_neuron.py +++ b/src/morphoclass/transforms/augmentors/branching_only_neuron.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `BranchingOnlyNeuron` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/augmentors/equalize_node_counts.py b/src/morphoclass/transforms/augmentors/equalize_node_counts.py index 0cc5b06..044e8a8 100644 --- a/src/morphoclass/transforms/augmentors/equalize_node_counts.py +++ b/src/morphoclass/transforms/augmentors/equalize_node_counts.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `EqualizeNodeCounts` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/augmentors/extract_branching_node_reduction_masks.py b/src/morphoclass/transforms/augmentors/extract_branching_node_reduction_masks.py index bba396e..2bb9aeb 100644 --- a/src/morphoclass/transforms/augmentors/extract_branching_node_reduction_masks.py +++ b/src/morphoclass/transforms/augmentors/extract_branching_node_reduction_masks.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `ExtractBranchingNodeReductionMasks` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/augmentors/orient_apicals.py b/src/morphoclass/transforms/augmentors/orient_apicals.py index 7ead5f4..5581c1e 100644 --- a/src/morphoclass/transforms/augmentors/orient_apicals.py +++ b/src/morphoclass/transforms/augmentors/orient_apicals.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `OrientApicals` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/augmentors/orient_neuron.py b/src/morphoclass/transforms/augmentors/orient_neuron.py index 9e7da28..d7e99e9 100644 --- a/src/morphoclass/transforms/augmentors/orient_neuron.py +++ b/src/morphoclass/transforms/augmentors/orient_neuron.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `OrientNeuron` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/augmentors/random_jitter.py b/src/morphoclass/transforms/augmentors/random_jitter.py index 2fa2852..21922b5 100644 --- a/src/morphoclass/transforms/augmentors/random_jitter.py +++ b/src/morphoclass/transforms/augmentors/random_jitter.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `RandomJitter` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/augmentors/random_rotation.py b/src/morphoclass/transforms/augmentors/random_rotation.py index f8bbe69..6be5da8 100644 --- a/src/morphoclass/transforms/augmentors/random_rotation.py +++ b/src/morphoclass/transforms/augmentors/random_rotation.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `RandomRotation` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/augmentors/random_stretching.py b/src/morphoclass/transforms/augmentors/random_stretching.py index e0b9b45..6d96cc5 100644 --- a/src/morphoclass/transforms/augmentors/random_stretching.py +++ b/src/morphoclass/transforms/augmentors/random_stretching.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `RandomStretching` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/compose.py b/src/morphoclass/transforms/compose.py index 0153d5e..0130e5f 100644 --- a/src/morphoclass/transforms/compose.py +++ b/src/morphoclass/transforms/compose.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `Compose` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/edge_features/__init__.py b/src/morphoclass/transforms/edge_features/__init__.py index 00dba18..e746d56 100644 --- a/src/morphoclass/transforms/edge_features/__init__.py +++ b/src/morphoclass/transforms/edge_features/__init__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Transforms for edge feature extraction.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/edge_features/extract_distance_weights.py b/src/morphoclass/transforms/edge_features/extract_distance_weights.py index 0594a8f..ee9e6ef 100644 --- a/src/morphoclass/transforms/edge_features/extract_distance_weights.py +++ b/src/morphoclass/transforms/edge_features/extract_distance_weights.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the distance weights edge feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/edge_features/extract_edge_features.py b/src/morphoclass/transforms/edge_features/extract_edge_features.py index bda5d4c..ff363e6 100644 --- a/src/morphoclass/transforms/edge_features/extract_edge_features.py +++ b/src/morphoclass/transforms/edge_features/extract_edge_features.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the base class for edge feature extractors.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/edge_features/extract_edge_index.py b/src/morphoclass/transforms/edge_features/extract_edge_index.py index c2f3cda..9286c39 100644 --- a/src/morphoclass/transforms/edge_features/extract_edge_index.py +++ b/src/morphoclass/transforms/edge_features/extract_edge_index.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the edge index (adjacency matrix) extractor.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/extract_tmd_neurites.py b/src/morphoclass/transforms/extract_tmd_neurites.py index c40bcfc..64e38ca 100644 --- a/src/morphoclass/transforms/extract_tmd_neurites.py +++ b/src/morphoclass/transforms/extract_tmd_neurites.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Extract TMD neurites.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/extract_tmd_neuron.py b/src/morphoclass/transforms/extract_tmd_neuron.py index e1f858c..62553f5 100644 --- a/src/morphoclass/transforms/extract_tmd_neuron.py +++ b/src/morphoclass/transforms/extract_tmd_neuron.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `ExtractTMDNeuron` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/global_feature_to_label.py b/src/morphoclass/transforms/global_feature_to_label.py index 81c9689..6211495 100644 --- a/src/morphoclass/transforms/global_feature_to_label.py +++ b/src/morphoclass/transforms/global_feature_to_label.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `GlobalFeatureToLabel` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/global_features/__init__.py b/src/morphoclass/transforms/global_features/__init__.py index c3fc187..8afc515 100644 --- a/src/morphoclass/transforms/global_features/__init__.py +++ b/src/morphoclass/transforms/global_features/__init__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Global feature extractors. All transforms in this submodule should modify the `data.u` attribute diff --git a/src/morphoclass/transforms/global_features/abstract_global_feature_extractor.py b/src/morphoclass/transforms/global_features/abstract_global_feature_extractor.py index 0679b58..6babf36 100644 --- a/src/morphoclass/transforms/global_features/abstract_global_feature_extractor.py +++ b/src/morphoclass/transforms/global_features/abstract_global_feature_extractor.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the abstract base class for global feature extractors.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/global_features/average_branch_order.py b/src/morphoclass/transforms/global_features/average_branch_order.py index f162127..f5455d4 100644 --- a/src/morphoclass/transforms/global_features/average_branch_order.py +++ b/src/morphoclass/transforms/global_features/average_branch_order.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `AverageBranchOrder` global feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/global_features/average_radius.py b/src/morphoclass/transforms/global_features/average_radius.py index 76f3bbc..d4ed02a 100644 --- a/src/morphoclass/transforms/global_features/average_radius.py +++ b/src/morphoclass/transforms/global_features/average_radius.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `AverageRadius` global feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/global_features/extract_maximal_apical_path_length.py b/src/morphoclass/transforms/global_features/extract_maximal_apical_path_length.py index 0f97e8e..8aeb3d1 100644 --- a/src/morphoclass/transforms/global_features/extract_maximal_apical_path_length.py +++ b/src/morphoclass/transforms/global_features/extract_maximal_apical_path_length.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `ExtractMaximalApicalPathLength` global feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/global_features/extract_number_branch_points.py b/src/morphoclass/transforms/global_features/extract_number_branch_points.py index 92e315b..fb3de45 100644 --- a/src/morphoclass/transforms/global_features/extract_number_branch_points.py +++ b/src/morphoclass/transforms/global_features/extract_number_branch_points.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `ExtractNumberBranchPoints` global feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/global_features/extract_number_leaves.py b/src/morphoclass/transforms/global_features/extract_number_leaves.py index d4e1f84..5ec2bf8 100644 --- a/src/morphoclass/transforms/global_features/extract_number_leaves.py +++ b/src/morphoclass/transforms/global_features/extract_number_leaves.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `ExtractNumberLeaves` global feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/global_features/total_path_length.py b/src/morphoclass/transforms/global_features/total_path_length.py index 8f515c0..e345979 100644 --- a/src/morphoclass/transforms/global_features/total_path_length.py +++ b/src/morphoclass/transforms/global_features/total_path_length.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `TotalPathLength` global feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/helper.py b/src/morphoclass/transforms/helper.py index b2cda8d..4dccb6f 100644 --- a/src/morphoclass/transforms/helper.py +++ b/src/morphoclass/transforms/helper.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Various helper and utility functions used in the data transforms.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/make_copy.py b/src/morphoclass/transforms/make_copy.py index 4749b6d..7e20ec5 100644 --- a/src/morphoclass/transforms/make_copy.py +++ b/src/morphoclass/transforms/make_copy.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `MakeCopy` transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/node_features/__init__.py b/src/morphoclass/transforms/node_features/__init__.py index 033eda1..3e3152d 100644 --- a/src/morphoclass/transforms/node_features/__init__.py +++ b/src/morphoclass/transforms/node_features/__init__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Node feature extractors. All transforms in this submodule should modify the `data.x` attribute diff --git a/src/morphoclass/transforms/node_features/extract_branching_angles.py b/src/morphoclass/transforms/node_features/extract_branching_angles.py index d0cf081..b5ed7be 100644 --- a/src/morphoclass/transforms/node_features/extract_branching_angles.py +++ b/src/morphoclass/transforms/node_features/extract_branching_angles.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the branching angles node feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/node_features/extract_const_feature.py b/src/morphoclass/transforms/node_features/extract_const_feature.py index ee35628..a838e04 100644 --- a/src/morphoclass/transforms/node_features/extract_const_feature.py +++ b/src/morphoclass/transforms/node_features/extract_const_feature.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the node feature extractor for constant node features.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/node_features/extract_coordinates.py b/src/morphoclass/transforms/node_features/extract_coordinates.py index 16b865b..d0e0e6b 100644 --- a/src/morphoclass/transforms/node_features/extract_coordinates.py +++ b/src/morphoclass/transforms/node_features/extract_coordinates.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the 3D coordinate node feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/node_features/extract_diameters.py b/src/morphoclass/transforms/node_features/extract_diameters.py index 2264c41..282f6e2 100644 --- a/src/morphoclass/transforms/node_features/extract_diameters.py +++ b/src/morphoclass/transforms/node_features/extract_diameters.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the branch diameter node feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/node_features/extract_distances.py b/src/morphoclass/transforms/node_features/extract_distances.py index 955fe49..3c141d2 100644 --- a/src/morphoclass/transforms/node_features/extract_distances.py +++ b/src/morphoclass/transforms/node_features/extract_distances.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """The base class for node distance feature extractors.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/node_features/extract_node_features.py b/src/morphoclass/transforms/node_features/extract_node_features.py index b7c4cd1..62a28a7 100644 --- a/src/morphoclass/transforms/node_features/extract_node_features.py +++ b/src/morphoclass/transforms/node_features/extract_node_features.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Abstract base class for node feature extractors.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/node_features/extract_node_onehot_properties.py b/src/morphoclass/transforms/node_features/extract_node_onehot_properties.py index 32afd2d..2956a41 100644 --- a/src/morphoclass/transforms/node_features/extract_node_onehot_properties.py +++ b/src/morphoclass/transforms/node_features/extract_node_onehot_properties.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Various one-hot property node-feature extractors. This name is misleading as what the transforms in this module extract are rather diff --git a/src/morphoclass/transforms/node_features/extract_path_distances.py b/src/morphoclass/transforms/node_features/extract_path_distances.py index abe7d08..641990d 100644 --- a/src/morphoclass/transforms/node_features/extract_path_distances.py +++ b/src/morphoclass/transforms/node_features/extract_path_distances.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the path distance node feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/node_features/extract_radial_distances.py b/src/morphoclass/transforms/node_features/extract_radial_distances.py index 8d7545f..76afcc0 100644 --- a/src/morphoclass/transforms/node_features/extract_radial_distances.py +++ b/src/morphoclass/transforms/node_features/extract_radial_distances.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the radial distance node feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/node_features/extract_vertical_distances.py b/src/morphoclass/transforms/node_features/extract_vertical_distances.py index c6e7ccf..b9fe77c 100644 --- a/src/morphoclass/transforms/node_features/extract_vertical_distances.py +++ b/src/morphoclass/transforms/node_features/extract_vertical_distances.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the vertical distance node feature extractor.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/scalers/__init__.py b/src/morphoclass/transforms/scalers/__init__.py index f085c0d..b0b72fd 100644 --- a/src/morphoclass/transforms/scalers/__init__.py +++ b/src/morphoclass/transforms/scalers/__init__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Various feature scalers for morphology node features.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/scalers/abstract_scaler.py b/src/morphoclass/transforms/scalers/abstract_scaler.py index f794003..97b2938 100644 --- a/src/morphoclass/transforms/scalers/abstract_scaler.py +++ b/src/morphoclass/transforms/scalers/abstract_scaler.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """The abstract base class for all feature scalers.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/scalers/manual_scaler.py b/src/morphoclass/transforms/scalers/manual_scaler.py index 696b913..753aad9 100644 --- a/src/morphoclass/transforms/scalers/manual_scaler.py +++ b/src/morphoclass/transforms/scalers/manual_scaler.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the manual scaler transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/scalers/min_max_scaler.py b/src/morphoclass/transforms/scalers/min_max_scaler.py index 346a760..24ff65b 100644 --- a/src/morphoclass/transforms/scalers/min_max_scaler.py +++ b/src/morphoclass/transforms/scalers/min_max_scaler.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the min-max scaler transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/scalers/robust_scaler.py b/src/morphoclass/transforms/scalers/robust_scaler.py index 7836550..e86c070 100644 --- a/src/morphoclass/transforms/scalers/robust_scaler.py +++ b/src/morphoclass/transforms/scalers/robust_scaler.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the robust scaler transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/scalers/standard_scaler.py b/src/morphoclass/transforms/scalers/standard_scaler.py index efc74ab..f4ba9b4 100644 --- a/src/morphoclass/transforms/scalers/standard_scaler.py +++ b/src/morphoclass/transforms/scalers/standard_scaler.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the standard scaler transform.""" from __future__ import annotations diff --git a/src/morphoclass/transforms/zero_out_features.py b/src/morphoclass/transforms/zero_out_features.py index cdc5207..84479d2 100644 --- a/src/morphoclass/transforms/zero_out_features.py +++ b/src/morphoclass/transforms/zero_out_features.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `ZeroOutFeatures` transform.""" from __future__ import annotations diff --git a/src/morphoclass/types.py b/src/morphoclass/types.py index eef4c32..151f70d 100644 --- a/src/morphoclass/types.py +++ b/src/morphoclass/types.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Custom type definitions.""" from __future__ import annotations diff --git a/src/morphoclass/unsupervised/__init__.py b/src/morphoclass/unsupervised/__init__.py index 94cf570..32cf9f9 100644 --- a/src/morphoclass/unsupervised/__init__.py +++ b/src/morphoclass/unsupervised/__init__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Utilities for unsupervised methods for neuron m-type classification.""" from __future__ import annotations diff --git a/src/morphoclass/unsupervised/plotting.py b/src/morphoclass/unsupervised/plotting.py index adcfc7f..4546027 100644 --- a/src/morphoclass/unsupervised/plotting.py +++ b/src/morphoclass/unsupervised/plotting.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Plotting utilities for unsupervised m-type classification tools.""" from __future__ import annotations diff --git a/src/morphoclass/utils.py b/src/morphoclass/utils.py index 2a01128..886470e 100644 --- a/src/morphoclass/utils.py +++ b/src/morphoclass/utils.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Miscellaneous utilities.""" from __future__ import annotations diff --git a/src/morphoclass/vis.py b/src/morphoclass/vis.py index bcdf9d0..62eb826 100644 --- a/src/morphoclass/vis.py +++ b/src/morphoclass/vis.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Functions for visualizing data.""" from __future__ import annotations diff --git a/src/morphoclass/xai/__init__.py b/src/morphoclass/xai/__init__.py index a996daf..793b638 100644 --- a/src/morphoclass/xai/__init__.py +++ b/src/morphoclass/xai/__init__.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """XAI tools for morphology GNNs.""" from __future__ import annotations diff --git a/src/morphoclass/xai/embedding_extractor.py b/src/morphoclass/xai/embedding_extractor.py index ee4c6ad..3caf4a1 100644 --- a/src/morphoclass/xai/embedding_extractor.py +++ b/src/morphoclass/xai/embedding_extractor.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `EmbeddingExtractor` class.""" from __future__ import annotations diff --git a/src/morphoclass/xai/embedding_visualization.py b/src/morphoclass/xai/embedding_visualization.py index ddcf146..ce6942b 100644 --- a/src/morphoclass/xai/embedding_visualization.py +++ b/src/morphoclass/xai/embedding_visualization.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Plot embeddings for outlier detection.""" from __future__ import annotations diff --git a/src/morphoclass/xai/grad_cam_explainer.py b/src/morphoclass/xai/grad_cam_explainer.py index 8bff494..eff67fd 100644 --- a/src/morphoclass/xai/grad_cam_explainer.py +++ b/src/morphoclass/xai/grad_cam_explainer.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `GradCAMExplainer` class.""" from __future__ import annotations diff --git a/src/morphoclass/xai/grad_cam_on_models.py b/src/morphoclass/xai/grad_cam_on_models.py index 82fc286..591bb10 100644 --- a/src/morphoclass/xai/grad_cam_on_models.py +++ b/src/morphoclass/xai/grad_cam_on_models.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Explain model layers using GradCam.""" from __future__ import annotations diff --git a/src/morphoclass/xai/model_attributions.py b/src/morphoclass/xai/model_attributions.py index 7897980..6b6b1c8 100644 --- a/src/morphoclass/xai/model_attributions.py +++ b/src/morphoclass/xai/model_attributions.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Explain model layers using GradShap.""" from __future__ import annotations diff --git a/src/morphoclass/xai/plot_node_saliency.py b/src/morphoclass/xai/plot_node_saliency.py index 35ddae2..c2eff0c 100644 --- a/src/morphoclass/xai/plot_node_saliency.py +++ b/src/morphoclass/xai/plot_node_saliency.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """Implementation of the `plot_node_saliency` function.""" from __future__ import annotations diff --git a/src/morphoclass/xai/reports/__init__.py b/src/morphoclass/xai/reports/__init__.py index e1227f2..7292336 100644 --- a/src/morphoclass/xai/reports/__init__.py +++ b/src/morphoclass/xai/reports/__init__.py @@ -1,2 +1,15 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """XAI report.""" from __future__ import annotations diff --git a/src/morphoclass/xai/reports/xai_report.py b/src/morphoclass/xai/reports/xai_report.py index f82edd8..4a6b86d 100644 --- a/src/morphoclass/xai/reports/xai_report.py +++ b/src/morphoclass/xai/reports/xai_report.py @@ -1,3 +1,16 @@ +# Copyright © 2022 Blue Brain Project/EPFL +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """XAI report creation.""" from __future__ import annotations