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Merge pull request #23 from C-Achard/model-implementation
Model implementation
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‎.gitattributes‎

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*.pth filter=lfs diff=lfs merge=lfs -text
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*.tif filter=lfs diff=lfs merge=lfs -text

‎.github/workflows/test_and_deploy.yml‎

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# This workflows will upload a Python Package using Twine when a release is created
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# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
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name: tests
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on:
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push:
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branches:
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- main
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- npe2
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tags:
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- "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
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pull_request:
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branches:
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- main
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- npe2
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workflow_dispatch:
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jobs:
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test:
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name: ${{ matrix.platform }} py${{ matrix.python-version }}
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runs-on: ${{ matrix.platform }}
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strategy:
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matrix:
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platform: [ubuntu-latest, windows-latest, macos-latest]
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python-version: [3.8, 3.9, '3.10']
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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# these libraries enable testing on Qt on linux
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- uses: tlambert03/setup-qt-libs@v1
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# strategy borrowed from vispy for installing opengl libs on windows
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- name: Install Windows OpenGL
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if: runner.os == 'Windows'
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run: |
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git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
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powershell gl-ci-helpers/appveyor/install_opengl.ps1
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# note: if you need dependencies from conda, considering using
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# setup-miniconda: https://github.com/conda-incubator/setup-miniconda
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# and
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# tox-conda: https://github.com/tox-dev/tox-conda
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install setuptools tox tox-gh-actions
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# this runs the platform-specific tests declared in tox.ini
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- name: Test with tox
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uses: GabrielBB/xvfb-action@v1
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with:
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run: python -m tox
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env:
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PLATFORM: ${{ matrix.platform }}
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- name: Coverage
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uses: codecov/codecov-action@v2
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deploy:
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# this will run when you have tagged a commit, starting with "v*"
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# and requires that you have put your twine API key in your
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# github secrets (see readme for details)
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needs: [test]
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runs-on: ubuntu-latest
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if: contains(github.ref, 'tags')
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -U setuptools setuptools_scm wheel twine build
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- name: Build and publish
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env:
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TWINE_USERNAME: __token__
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TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
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run: |
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git tag
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python -m build .
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twine upload dist/*
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## This workflows will upload a Python Package using Twine when a release is created
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## For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
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#
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#name: tests
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#
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#on:
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# push:
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# branches:
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# - main
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# - npe2
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# tags:
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# - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
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# pull_request:
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# branches:
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# - main
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# - npe2
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# workflow_dispatch:
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#
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#jobs:
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# test:
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# name: ${{ matrix.platform }} py${{ matrix.python-version }}
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# runs-on: ${{ matrix.platform }}
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# strategy:
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# matrix:
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# platform: [windows-latest, macos-latest, ubuntu-latest]
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# python-version: [3.9]
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#
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# steps:
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# - uses: actions/checkout@v2
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#
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# - name: Set up Python ${{ matrix.python-version }}
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# uses: actions/setup-python@v2
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# with:
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# python-version: ${{ matrix.python-version }}
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#
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# # these libraries enable testing on Qt on linux
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# - uses: tlambert03/setup-qt-libs@v1
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#
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# # strategy borrowed from vispy for installing opengl libs on windows
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# - name: Install Windows OpenGL
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# if: runner.os == 'Windows'
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# run: |
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# git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
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# powershell gl-ci-helpers/appveyor/install_opengl.ps1
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#
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# # note: if you need dependencies from conda, considering using
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# # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
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# # and
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# # tox-conda: https://github.com/tox-dev/tox-conda
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# - name: Install dependencies
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# run: |
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# python -m pip install --upgrade pip
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# python -m pip install setuptools tox tox-gh-actions
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#
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# # this runs the platform-specific tests declared in tox.ini
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# - name: Test with tox
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# uses: GabrielBB/xvfb-action@v1
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# with:
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# run: python -m tox
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# env:
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# PLATFORM: ${{ matrix.platform }}
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#
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# - name: Coverage
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# uses: codecov/codecov-action@v2
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#
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# deploy:
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# # this will run when you have tagged a commit, starting with "v*"
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# # and requires that you have put your twine API key in your
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# # github secrets (see readme for details)
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# needs: [test]
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# runs-on: ubuntu-latest
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# if: contains(github.ref, 'tags')
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# steps:
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# - uses: actions/checkout@v2
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# - name: Set up Python
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# uses: actions/setup-python@v2
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# with:
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# python-version: "3.8"
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# - name: Install dependencies
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# run: |
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# python -m pip install --upgrade pip
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# pip install -U setuptools setuptools_scm wheel twine build
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# - name: Build and publish
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# env:
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# TWINE_USERNAME: __token__
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# TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
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# run: |
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# git tag
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# python -m build .
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# twine upload dist/*
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#

‎.gitignore‎

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# C extensions
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*.so
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# unwanted results files
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*.csv
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# Distribution / packaging
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.Python
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env/
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# written by setuptools_scm
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**/_version.py
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########
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#project specific
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#dataset
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/src/napari_cellseg_annotator/models/dataset/
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/src/napari_cellseg_annotator/models/saved_weights/

‎.isort.cfg‎

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[settings]
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force_single_line = True
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force_sort_within_sections = False
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lexicographical = True
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single_line_exclusions = ('typing',)
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order_by_type = False
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group_by_package = True
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skip=__init__.py

‎LICENSE‎

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The MIT License (MIT)
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Copyright (c) 2022 Cyril Achard
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Copyright (c) 2022 Cyril Achard, Maxime Vidal
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal

‎README.md‎

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https://napari.org/plugins/stable/index.html
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-->
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## Requirements
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Requires manual installation of pytorch and MONAI.
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For Pytorch, please see [PyTorch]'s website for installation instructions.
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A CUDA-capable GPU is not needed but very strongly recommended, especially for training.
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If you get errors from MONAI regarding missing readers, please see [MONAI's optional dependencies] page for instructions on getting the readers required by your images.
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## Installation
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You can install `napari-cellseg-annotator` via [pip]:
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pip install napari-cellseg-annotator
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For local installation, please run:
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```
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pip install -e .
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```
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## Documentation
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You can generate docs by running ``make html`` in the docs folder
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## Usage
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To use the plugin, please run:
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```
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napari
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```
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Then go into Plugins > napari-cellseg-annotator, and choose which tool to use.
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- **Review**: This module allows you to review your labels, from predictions or manual labeling, and correct them if needed. It then saves the status of each file in a csv, for easier monitoring.
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- **Infer**: This module allows you to use pre-trained segmentation algorithms on volumes to automatically label cells.
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- **Train**: This module allows you to train segmentation algorithms from labeled volumes.
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- **Crop utility**: This module allows you to crop your volumes and labels dynamically, by selecting a fixed size volume and moving it around the image.
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## Testing
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To run tests locally:
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- Locally : run ``pytest`` in the plugin folder
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- Locally with coverage : In the plugin folder, run ``coverage run --source=src -m pytest`` then ``coverage.xml`` to generate a .xml coverage file.
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- With tox : run ``tox`` in the plugin folder (will simulate tests with several python and OS configs, requires substantial storage space)
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## Contributing
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[tox]: https://tox.readthedocs.io/en/latest/
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[pip]: https://pypi.org/project/pip/
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[PyPI]: https://pypi.org/
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[PyTorch]: https://pytorch.org/get-started/locally/
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[MONAI's optional dependencies]: https://docs.monai.io/en/stable/installation.html#installing-the-recommended-dependencies

‎dev.requirements.txt‎

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black
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coverage
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isort
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pytest
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pytest-qt
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tox
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sphinx
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sphinx-autodoc-typehints
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sphinx-rtd-theme
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tox
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twine

‎docs/conf.py‎

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# All configuration values have a default; values that are commented out
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# serve to show the default.
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import sys
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import os
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import shlex
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import sys
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# General information about the project.
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project = "napari-cellseg-annotator"
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copyright = "2022, Cyril Achard"
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author = "Cyril Achard"
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copyright = "2022, Cyril Achard, Maxime Vidal"
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author = "Cyril Achard, Maxime Vidal"
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# The version info for the project you're documenting, acts as replacement for
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# |version| and |release|, also used in various other places throughout the

‎docs/index.rst‎

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:caption: User guide:
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res/welcome
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res/loader_module_guide
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res/review_module_guide
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res/inference_module_guide
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res/training_module_guide
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res/cropping_module_guide
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res/custom_model_template
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.. toctree::
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:maxdepth: 1
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:caption: Source files:
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res/plugin_loader
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res/interface
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res/plugin_base
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res/plugin_review
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res/plugin_dock
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res/plugin_crop
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res/launch_review
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res/dock
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res/model_framework
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res/model_workers
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res/model_instance_seg
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res/plugin_model_inference
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res/plugin_model_training
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