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C-AchardTimokleiaMMathisLab
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WandB/Colab + docs (#48)
* WANDB integration for WNet * Colab training script * Update colab_training.py * Update colab_training.py * Update colab_training.py * Update colab_training.py * Update colab_training.py * Added minimal Colab notebook * ZeroCostDL4Mic-style notebook * Added WANDB to Colab notebook * Added softmax param * Fix reset of paths in training UI * WNet visualization * Disable intensity transforms in WNet * Fixed supervised loss saving * Update view_wnet.ipynb * Update view_wnet.ipynb * Fixed filepaths * Added more checks for csv + fix eval batch size * Utils+training fixes * Colab training improvements (#49) * Update colab_wnet_training.ipynb * Update colab_wnet_training.ipynb --------- Co-authored-by: Cyril Achard <[email protected]> * Reverted include_background=True in Dice * Reintroduced best Dice channel seeking + refacto * Improve filepath messages * Fix unsup image loading when not validating * Fixed deletion of Qt imports in interface * Added auto-check for which channel has foreground Preventing background to be shown first when using WNet inference, for better UX * Fixed eval_batch_size assignment * Fix training tests * Experimental auto-discard * Improved auto-discard utility * Create experimental sliding window Voronoi-Otsu for large volumes * Disable resize error handler * Docs update & jupyter-books port (#50) * Moved docs to source folder * Updated to jupyter-books * Update GH Action to jupyter-book * Updated guides * Update reqs for jupyter-books - Fixed typo * Fix typo and file duplicate * Added auto API docs * Update welcome.rst * Update interface docstrings * Update ruff to enforce docstring style * Updated docstrings in interface/config * Add additional docstring rule exceptions * Update utils docstring * Update plugins.py * Update dev_scripts * Updated code_plugin folder docstrings * Update code_models docstrings * Update tests docstrings * Update docstring rules to enforce docs * Fix warnings when building docs * Restore docs images * Remove old API docs * Added module docstring for all public modules * Update pyproject.toml * Update folder desc * Update inference and training guides * Update inference_module_guide.rst * Guides updates * Change indexing, guides updates * Fix unindent warning * Update _toc.yml * Fixed model list inconsistencies * Update model list * Trying to fully use autosummary (see #51) * Docs update * Fix missing refactor in CRF * Update cropping_module_guide.rst * Updated docs ref for code * Figs, refs, utils guide update * Update images to figures where relevant * Updated refs to source code * Improved utils guide layout and contents * Review update + crop/utils * Review update * Small inference tweaks for pipeline * Config changes * Update worker_inference.py * Small instance seg refactor * Added properties for instance seg params * Utils cleanup * Small refactor of unclear train/val split terminology * Fix log parameters incorrectly printing def dir * Enable sliding window for all instance seg methods * Update instance_segmentation.py Refactor sliding window to not shadow builtin "function" * Fixed mistake in auto-check for WNet results * Fix for restarting train worker after force stop * Docs & images update * mv welcome image * Improved inference docs * Update inference_module_guide.rst * Attempt to fix M1 yaml * Config docstring update * Welcome page update * Docs update * Add WandB for supervised models * Added auto contrast reset in cropping * Added checks for instance labels in training * Check for custom weights before locking window inference * Improve review plots makers * Documentation update (Timokleia) (#53) * Update cropping_module_guide.rst changes in the cropping module guide * Update cropping_module_guide.rst add `` * Update inference_module_guide.rst additions to inference module * Update metrics_module_guide.rst adjusting the metrics module * Update review_module_guide.rst review module updates * Update training_module_guide.rst changes in the training module * Update training_wnet.rst additions in the wnet module * Update utils_module_guide.rst utilities updates * review parameters image * Update cropping_module_guide.rst emoji * Update metrics_module_guide.rst emoji * Update training_module_guide.rst emoji * Update utils_module_guide.rst emoji * Update cropping_module_guide.rst mild style changes * Update review_module_guide.rst adjusting image code * Update welcome.rst changes to welcome * Add files via upload * Review and training tweaks - Fixed a few links, indents, typos - Replaced some emojis and added new ones for other pages * Welcome and inference tweaks - Fixed minor formatting, tables, broken links issues, etc * RM unused model wrappers attributes * Inference edits * Update WNet and inference * Images update * Update plots_train.png * Restore walkthrough * Update detailed_walkthrough.rst * Update detailed_walkthrough.rst editions * Minor edits --------- Co-authored-by: C-Achard <[email protected]> * Added floats in small remove * Try to fix issue with float/long * Add except handling for layer removal in train * Add first version of dedicated install page - Add install page - Refacto/clean up welcome page - Add more useful plugins - Update TODO * Improve training guide * Move M1 install * Added label stats utils * Added label stats doc * Added check for dtype in stats labels * Update utils_module_guide.rst * Experimental classifier to reject bad preds on empty * Experimental classifier to reject bad preds on empty * Update classifier_test.ipynb * WIP Trying to fix some QoL issues - Better exception handling in inference - Swapaxes at mode output - Remove small in Voronoi-Otsu * Fix exception handling * Locating csv issue * Enable ruff again * Handle empty labels in csv stats * Fix call to get_dict when stats is None * Ensure consistent rotation * Fix rotation checks + auto-channel select * Fix test for review * Update installation_guide.rst (#54) refining * Minor edits to install guide * [WIP] GUI-less training example script (#52) * Add remote train scripts * mv dockerfile * Paths for remote train * Change device * Update remote_training.py * Change results path to include more info * Update colab_training.py * Delete Dockerfile.cellseg3d * Make all wandb inits point to same project * Remove deprecated call to AddChannel * Fix tests issue with MONAI 1.3.0 * Create whole_brain_utils.py Add segmentation correction scripts * Update whole_brain_utils.py * Update whole_brain_utils.py * Update whole_brain_utils.py * Update whole_brain_utils.py * Update _config.yml --------- Co-authored-by: Timokleia <[email protected]> Co-authored-by: Mackenzie Mathis <[email protected]> --------- Co-authored-by: Timokleia <[email protected]> Co-authored-by: Mackenzie Mathis <[email protected]>
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‎.github/workflows/build_docs.yml‎

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name: Deploy Sphinx documentation to Pages
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name: deploy
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on:
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push:
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branches: # branch to trigger deployment
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- main
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# This job installs dependencies, build the book, and pushes it to `gh-pages`
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jobs:
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pages:
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runs-on: ubuntu-20.04
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build-and-deploy-book:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest]
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python-version: [3.8]
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steps:
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- id: deployment
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uses: sphinx-notes/pages@v3
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- uses: actions/checkout@v2
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# Install dependencies
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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publish: false
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- uses: peaceiris/actions-gh-pages@v3
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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pip install jupyter-book
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# Build the book
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- name: Build the book
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run: |
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jupyter-book build docs/
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# Deploy the book's HTML to gh-pages branch
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- name: GitHub Pages action
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uses: peaceiris/[email protected]
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ${{ steps.deployment.outputs.artifact }}
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publish_dir: docs/_build/html

‎.gitignore‎

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# written by setuptools_scm
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**/_version.py
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# WANDB
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/wandb/
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########
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#project specific
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#dataset, weights, old logos, requirements
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/napari_cellseg3d/code_models/models/dataset/
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/napari_cellseg3d/code_models/models/saved_weights/
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/docs/res/logo/old_logo/
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/docs/source/logo/old_logo/
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/docs/source/code/_autosummary/
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/reqs/
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/loss_plots/
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/wandb/
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!napari_cellseg3d/_tests/res/wnet_test/lab/*.tif
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!napari_cellseg3d/_tests/res/wnet_test/vol/*.tif
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cov.syspath.txt
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#include docs images
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!docs/source/logo/*
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!docs/source/images/*
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napari_cellseg3d/dev_scripts/wandb

‎.pre-commit-config.yaml‎

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- id: trailing-whitespace
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- id: check-yaml
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- id: check-added-large-files
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args: [--maxkb=5000]
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- id: check-toml
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# - repo: https://github.com/pycqa/isort
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# rev: 5.12.0

‎conda/napari_cellseg3d_m1.yml‎

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- tifffile>=2022.2.9
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- imageio-ffmpeg>=0.4.5
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- torch>=1.11
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- monai[nibabel,einops]>=0.9.0
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- monai>=0.9.0
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- tqdm
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- nibabel
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- scikit-image

‎docs/Makefile‎

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‎docs/TODO.md‎

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[//]: # (
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TODO:
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- [ ] Add a way to get the current version of the library
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- [x] Update all modules
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- [x] Better WNet tutorial
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- [x] Setup GH Actions
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- [ ] Add a bibliography
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)

‎docs/_config.yml‎

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# Book settings
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# Learn more at https://jupyterbook.org/customize/config.html
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title: napari-cellseg3d Documentation
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author: Cyril Achard, Maxime Vidal, Timokleia Kousi, Mackenzie Mathis | Mathis Laboratory
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logo: source/logo/logo_alpha.png
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# Force re-execution of notebooks on each build.
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# See https://jupyterbook.org/content/execute.html
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execute:
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execute_notebooks: force
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# Define the name of the latex output file for PDF builds
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latex:
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latex_documents:
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targetname: book.tex
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# Add a bibtex file so that we can create citations
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bibtex_bibfiles:
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- references.bib
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# Information about where the book exists on the web
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repository:
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url: https://github.com/AdaptiveMotorControlLab/CellSeg3d # Online location of your book
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path_to_book: docs # Optional path to your book, relative to the repository root
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branch: main # Which branch of the repository should be used when creating links (optional)
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# Add GitHub buttons to your book
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# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
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html:
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use_issues_button: true
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use_repository_button: true
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# Add auto-generated API docs
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sphinx:
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extra_extensions:
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- 'sphinx.ext.napoleon'
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- 'sphinx.ext.autodoc'
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- 'sphinx.ext.autosummary'
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- 'sphinx.ext.viewcode'
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- 'sphinx.ext.autosectionlabel'
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config:
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add_module_names: False
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autosectionlabel_prefix_document: True
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autosummary_generate: True
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autoclass_content: "both"
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# templates_path: ['_templates']
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exclude_patterns:
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- '_build'
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- '_templates'
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# - 'napari_cellseg3d/__pycache__'

‎docs/_templates/custom-class-template.rst‎

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{{ fullname | escape | underline}}
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.. currentmodule:: {{ module }}
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.. autoclass:: {{ objname }}
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:members:
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:show-inheritance:
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{% block methods %}
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{% if methods %}
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.. rubric:: {{ _('Methods') }}
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.. autosummary::
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:nosignatures:
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{% for item in methods %}
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{%- if not item.startswith('_') %}
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~{{ name }}.{{ item }}
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{%- endif -%}
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{%- endfor %}
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{% endif %}
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{% endblock %}
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{% block attributes %}
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{% if attributes %}
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.. rubric:: {{ _('Attributes') }}
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.. autosummary::
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{% for item in attributes %}
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~{{ name }}.{{ item }}
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{%- endfor %}
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{% endif %}
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{% endblock %}

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