merge master#421
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Nic-Ma merged 134 commits intoNic-Ma:4463-enhance-normalize-docfrom Jun 7, 2022
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* Adding discussion on format to bundle specification Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
updates: - [github.com/asottile/pyupgrade: v2.31.0 → v2.31.1](asottile/pyupgrade@v2.31.0...v2.31.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* [DLMED] change PatchIter to be a transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] add dict transform Signed-off-by: Nic Ma <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] store coords in dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] restore the doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] store more info Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix a logical error in level verification Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* Refactor `if` expression * update clang format Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]>
* SplitDim Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * fix update meta Signed-off-by: Richard Brown <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* update mmar tests Signed-off-by: Wenqi Li <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes pylint error Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* extend mlp Signed-off-by: Wenqi Li <[email protected]> * 0 mlp_dim Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* added 2D (normalized) surface dice metric Signed-off-by: Silvia Seidlitz <[email protected]> * exclude from min tests Signed-off-by: Wenqi Li <[email protected]> * more detailled docstring Signed-off-by: Silvia Seidlitz <[email protected]>
* Fix doc strings error Signed-off-by: Yiheng Wang <[email protected]> * remove duplicate places Signed-off-by: Yiheng Wang <[email protected]>
* update sys req Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * update code for torch>=1.7 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * autofix Signed-off-by: Wenqi Li <[email protected]> * fixes import Signed-off-by: Wenqi Li <[email protected]> * clear cache Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * remove temp cmd Signed-off-by: Wenqi Li <[email protected]>
* Update the existing functionality to comply with the `torchscript.jit.script` function. Signed-off-by: Ramon Emiliani <[email protected]>
* meta tensor Signed-off-by: Richard Brown <[email protected]>
* [DLMED] add kwargs for to() API Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* update meta tensor api Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
to and from meta
* no skip if before pytorch 1.7 Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] fix typo in bundle scripts Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support for AMP args Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* [DLMED] update Workflow.py Signed-off-by: Nic Ma <[email protected]> * [DLMED] update all the engines Signed-off-by: Nic Ma <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Implement WSIReader with OpenSlide backend . Signed-off-by: Behrooz <[email protected]> * Add unittest for openslide Signed-off-by: Behrooz <[email protected]> * Add docs Signed-off-by: Behrooz <[email protected]> * formatting Signed-off-by: Behrooz <[email protected]> * Update imports and few fixes Signed-off-by: Behrooz <[email protected]> * Fix x,y in docstrings Signed-off-by: Behrooz <[email protected]> * Address comments Signed-off-by: Behrooz <[email protected]> * Remove x and y Signed-off-by: Behrooz <[email protected]>
* Implement PatchWSIDataset Signed-off-by: Behrooz <[email protected]> * Add unittests Signed-off-by: Behrooz <[email protected]> * Add docs Signed-off-by: Behrooz <[email protected]> * Reorder imports Signed-off-by: Behrooz <[email protected]> * formatting: Signed-off-by: Behrooz <[email protected]> * Address comments Signed-off-by: Behrooz <[email protected]> * Update to be compatible with Dataset Signed-off-by: Behrooz <[email protected]> * Update reader to accept str, class, object Signed-off-by: Behrooz <[email protected]> * Add test cases for various reader and level arguments Signed-off-by: Behrooz <[email protected]> * Update comment about OpenSlide cache Signed-off-by: Behrooz <[email protected]> * Rename reader_name to backend Signed-off-by: Behrooz <[email protected]> * Add new test cases Signed-off-by: Behrooz <[email protected]> * Add unittests for openslide Signed-off-by: Behrooz <[email protected]> * Add new test cases Signed-off-by: Behrooz <[email protected]> * sorts Signed-off-by: Behrooz <[email protected]> * Add docstring for kwargs Signed-off-by: Behrooz <[email protected]>
* draft download Signed-off-by: Yiheng Wang <[email protected]> * update bundle download Signed-off-by: Yiheng Wang <[email protected]> * add url and load Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename args and remove a few places Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix flake8 issue Signed-off-by: Yiheng Wang <[email protected]> * enhance with reviews Signed-off-by: Yiheng Wang <[email protected]> * add instantiate for load Signed-off-by: Yiheng Wang <[email protected]> * fix black error Signed-off-by: Yiheng Wang <[email protected]> * add unittest Signed-off-by: Yiheng Wang <[email protected]> * add load to docs Signed-off-by: Yiheng Wang <[email protected]> * add skip Signed-off-by: Yiheng Wang <[email protected]> * add schemaerror Signed-off-by: Yiheng Wang <[email protected]> * fix partial places Signed-off-by: Yiheng Wang <[email protected]> * download zip bundle Signed-off-by: Yiheng Wang <[email protected]> * [DLMED] restore Exception for test Signed-off-by: Nic Ma <[email protected]> * update ts features Signed-off-by: Yiheng Wang <[email protected]> * add config_files test case Signed-off-by: Yiheng Wang <[email protected]> * enhance docstring example for args_file Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nic Ma <[email protected]>
* workaround Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix tifffile issue Signed-off-by: Nic Ma <[email protected]>
review readme Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] support globals in eval(lambda) Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update test Signed-off-by: Nic Ma <[email protected]> * [DLMED] update test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more test Signed-off-by: Nic Ma <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…4.0.0` is used (#4397)
* Implement GridPatch and RandGridPatch Signed-off-by: Behrooz <[email protected]>
* Implement foreground mask Signed-off-by: Behrooz <[email protected]>
* Try 1 Signed-off-by: vnath <[email protected]> * dataset prep addition Signed-off-by: vnath <[email protected]> * Refactoring of transforms as there were loose hanging functions Signed-off-by: vnath <[email protected]> * Minor changes to transforms Signed-off-by: vnath <[email protected]> * Added test cases for all transforms Signed-off-by: vnath <[email protected]> * Removed dataset prep, it will be a part of tutorial, added opencv to dev requirements Signed-off-by: vnath <[email protected]> * Added Init for NuClick Signed-off-by: vnath <[email protected]> * Code formatting changes Signed-off-by: vnath <[email protected]> * Linting & Formatting Signed-off-by: vnath <[email protected]> * Fixed Flake 8 & opencv addition to requirement & env files Signed-off-by: vnath <[email protected]> * Fixed Flake 8 & opencv addition to requirement & env files Signed-off-by: vnath <[email protected]> * Fixed Flake 8 & opencv addition to requirement & env files Signed-off-by: vnath <[email protected]> * Fixed Flake 8 & opencv addition to requirement & env files Signed-off-by: vnath <[email protected]> * Minor in line docs need to be updated Signed-off-by: vnath <[email protected]> * Minor in line docs need to be updated Signed-off-by: vnath <[email protected]> * Adding Two Transforms & Test Cases Signed-off-by: vnath <[email protected]> * Formatted the PR Signed-off-by: vnath <[email protected]> * opencv changes Signed-off-by: vnath <[email protected]> * opencv changes Signed-off-by: vnath <[email protected]> * More optional import based changes Signed-off-by: vnath <[email protected]> * Removed opencv-python-headles as that does not workout Signed-off-by: vnath <[email protected]> * adding sk image back to requirement.txt till we figure out an alternative Signed-off-by: vnath <[email protected]> * Replaced MapTransform instead of Transform for SplitLabeld Signed-off-by: vnath <[email protected]> * Added skimage and cv2 requirements.txt as tests fail otherwise Signed-off-by: vnath <[email protected]> * Added MapTransform Inheritance to AddClickSignalsd Signed-off-by: vnath <[email protected]> * Spatial Pad Incorporated to ExtractPatchd Signed-off-by: vnath <[email protected]> * Remvoed comments and added doc-strings Signed-off-by: vnath <[email protected]> * codeformat Signed-off-by: vnath <[email protected]> * Adding NuClick Test to Min tests and removing opencv & scikit from requirements.txt Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removed cv2 dependency after modification of FlattenLabeld Transform to use skimage functionality instead Signed-off-by: vnath <[email protected]> * Minor addition to doc string Signed-off-by: vnath <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * adds unit test case Signed-off-by: Wenqi Li <[email protected]> * remove unused import Signed-off-by: Wenqi Li <[email protected]> * fixes unit test Signed-off-by: Wenqi Li <[email protected]> * Adding changes as docs and init arguments, 2 additional test cases Signed-off-by: vnath <[email protected]> * Minor changes Signed-off-by: vnath <[email protected]> * kwargs added to ExtractPatchd Signed-off-by: vnath <[email protected]> * Added a unit test for kwargs of SpatialPad in ExtractPatchd and a doc-string Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]> Co-authored-by: Nic Ma <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: Behrooz Hashemian <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* Update wsi metadata names Signed-off-by: Behrooz <[email protected]> * Implement prob map handler Signed-off-by: Behrooz <[email protected]>
* enhance download Signed-off-by: Yiheng Wang <[email protected]> * [MONAI] code formatting Signed-off-by: monai-bot <[email protected]> * fixes #4432 Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* Implement MaskedPatchWSIDataset Signed-off-by: Behrooz <[email protected]> * Add unittests Signed-off-by: Behrooz <[email protected]> * Update the min verison for skimage to 0.19.0 Signed-off-by: Behrooz <[email protected]> * Add channel last for wsireader Signed-off-by: Behrooz <[email protected]> * Replace all wsi patch key related with WSIPatchKeys Signed-off-by: Behrooz <[email protected]> * Update ProbMapKeys.NAME Signed-off-by: Behrooz <[email protected]> * Update GridPatch and iter_patch to support no padding Signed-off-by: Behrooz <[email protected]> * Add threshold for filtering to grid patch Signed-off-by: Behrooz <[email protected]>
* Added GeneralizedDiceFocalLoss to losses. Added GeneralizedDiceScore to metrics. Added function to check whether tensors are binarized to metrics.util and refactored metrics to use it. Signed-off-by: João Lourenço Silva <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Refactored monai.metrics.utils.is_binary_tensor function to receive name of the tensor as argument and issue warnings directly * Refactored metric classes to use is_binary_tensor function
adds download link Signed-off-by: Wenqi Li <[email protected]>
* support of subplots axes input Signed-off-by: Wenqi Li <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Adding thread worker option to ThreadDataLoader Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fixes Signed-off-by: Eric Kerfoot <[email protected]> * Fixes Signed-off-by: Eric Kerfoot <[email protected]> * Reworking of implementation with global data fix Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix Signed-off-by: Eric Kerfoot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * Tweak to cleanup Signed-off-by: Eric Kerfoot <[email protected]> * Try to disable thread test to see if global data is causing failure Signed-off-by: Eric Kerfoot <[email protected]> * Undoing Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
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Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.