WNet merger #55
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WNet merger #55
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Fix ONNX reqs
Disable dev scripts coverage
Tests :
- Base plugin
- ONNX inference
- Cropping
Fixes :
- Fixed review image loading not working
- Fixed scaling when running inference on a folder and showing originals
Remapping was done in inference always, which was breaking some models outputs. This is now done in the correct place, i.e. the WNet_model file
Fix dtype issue for label layer
Better interrupt
Colormap changes
Fixed device
Update name of utils when called by quick menu
Preventing background to be shown first when using WNet inference, for better UX
* 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]>
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This is already merged in #43 ! |
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TODO for @C-Achard