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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]>
… layer options (#4157) * fixed a bug Signed-off-by: dongy <[email protected]> * autofix Signed-off-by: dongy <[email protected]> * update test case Signed-off-by: dongy <[email protected]> Co-authored-by: dongy <[email protected]>
* Redesign whole slide image reading (#4107) * Redesign BaseWSIReader, WSIReader, CuCIMWSIReader Signed-off-by: Behrooz <[email protected]> * Add unittests for WSIReader Signed-off-by: Behrooz <[email protected]> * Add image mode for output validation Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Update references to new WSIReader Signed-off-by: Behrooz <[email protected]> * Remove legacy WSIReader Signed-off-by: Behrooz <[email protected]> * Update unittests Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * sort imports Signed-off-by: Behrooz <[email protected]> * Clean up imports Signed-off-by: Behrooz <[email protected]> * Update docstrings Signed-off-by: Behrooz <[email protected]> * Update docs and docstrings Signed-off-by: Behrooz <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix a typo Signed-off-by: Behrooz <[email protected]> * Remove redundant checking Signed-off-by: Behrooz <[email protected]> * Update read and other methods Signed-off-by: Behrooz <[email protected]> * Update wsireader to support multi image and update docstrings Signed-off-by: Behrooz <[email protected]> * Make workaround for CuImage objects Signed-off-by: Behrooz <[email protected]> * Add unittests for multi image reading Signed-off-by: Behrooz <[email protected]> * Update a note about cucim Signed-off-by: Behrooz <[email protected]> * Update type hints and docstrings Signed-off-by: Behrooz <[email protected]> * Implement Split transform Signed-off-by: Behrooz <[email protected]> * Add unittests Signed-off-by: Behrooz <[email protected]> * Update formatting Signed-off-by: Behrooz <[email protected]> * Implement SplitDict Signed-off-by: Behrooz <[email protected]> * Add unittests for SplitDict Signed-off-by: Behrooz <[email protected]> * Add docs Signed-off-by: Behrooz <[email protected]> * Remove images from docs Signed-off-by: Behrooz <[email protected]> * Address all comments Signed-off-by: Behrooz <[email protected]> * Add example and size check Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Revert references to new wsireader Signed-off-by: Behrooz <[email protected]> * Add missing comma Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
* [DLMED] enhance checkpoint export Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]>
* Support new temp dgx runner Signed-off-by: Peixin Li <[email protected]> * atol 1e-5 Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
* [DLMED] enhance CLI runner_id Signed-off-by: Nic Ma <[email protected]> * [DLMED] optimize config logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix list order Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
* fixes #4172 aggregate with no in-place buffer change Signed-off-by: Wenqi Li <[email protected]> * update reduction option Signed-off-by: Wenqi Li <[email protected]> * fixes flake8 Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * adds tests Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] enhance test datalist 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]>
* Add DeepEdit transforms and interaction Signed-off-by: Andres Diaz-Pinto <[email protected]>
* Remove commented out code * [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]>
* Remove unused global variable
Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
* Make all transforms optional Signed-off-by: Behrooz <[email protected]>
* temp tests Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * workaround Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* add swin_unetr model
* [DLMED] update to 22.04 Signed-off-by: Nic Ma <[email protected]> * fixes unit test tests.test_lr_finder Signed-off-by: Wenqi Li <[email protected]> * test new_empty Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* implement the base class 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 * add unittest 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 * autofix Signed-off-by: Yiheng Wang <[email protected]> * switch to call apex directly Signed-off-by: Yiheng Wang <[email protected]> * uncomment unittest Signed-off-by: Yiheng Wang <[email protected]> * add apex install link in docstring Signed-off-by: Yiheng Wang <[email protected]> * add channels_last_3d test case Signed-off-by: Yiheng Wang <[email protected]> * rewrite types Signed-off-by: Yiheng Wang <[email protected]> * change types Signed-off-by: Yiheng Wang <[email protected]> * add docstrings 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: Wenqi Li <[email protected]>
* Update dice.py reduce redundant operations in DiceFocalLoss, initially caused oom Signed-off-by: Ryan Clanton <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: Ryan Clanton <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]>
* Make all transforms optional Signed-off-by: Behrooz <[email protected]> * Update wsireader tests Signed-off-by: Behrooz <[email protected]> * Remove optional from PersistentDataset and its derivatives Signed-off-by: Behrooz <[email protected]> * Add unittests for cache without transform Signed-off-by: Behrooz <[email protected]> * Add default replace_rate Signed-off-by: Behrooz <[email protected]> * Add default value Signed-off-by: Behrooz <[email protected]> * Set default replace_rate to 0.1 Signed-off-by: Behrooz <[email protected]> * Update metadata to include path Signed-off-by: Behrooz <[email protected]> * Adds SmartCachePatchWSIDataset Signed-off-by: Behrooz <[email protected]> * Add unittests for SmartCachePatchWSIDataset Signed-off-by: Behrooz <[email protected]> * Update references Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Remove smart cache Signed-off-by: Behrooz <[email protected]> * Remove unused imports Signed-off-by: Behrooz <[email protected]> * Add path metadata for OpenSlide Signed-off-by: Behrooz <[email protected]> * Update metadata to be unified across different backends Signed-off-by: Behrooz <[email protected]> * Update wsi metadata for multi wsi objects Signed-off-by: Behrooz <[email protected]> * Add unittests for wsi metadata Signed-off-by: Behrooz <[email protected]>
* replace modules Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * replace_module -> replace_modules Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Can Zhao <[email protected]>
* reproduce issue Signed-off-by: Yiheng Wang <[email protected]> * remove 22.01 02 Signed-off-by: Yiheng Wang <[email protected]> * remove other workflows Signed-off-by: Yiheng Wang <[email protected]> * run on pull request Signed-off-by: Yiheng Wang <[email protected]> * remove sleep Signed-off-by: Yiheng Wang <[email protected]> * test single layer forward Signed-off-by: Yiheng Wang <[email protected]> * add has_nvfuser Signed-off-by: Yiheng Wang <[email protected]> * add check within factory Signed-off-by: Yiheng Wang <[email protected]> * revert to original cron.yml 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 old pt issue Signed-off-by: Yiheng Wang <[email protected]> * change to return directly if no cuda Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Update to bundle specifiation 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 * Adding description in spec discussing the saved Torchscript object's file storage behaviour, and tweaking ckpt_export to add .json extension Signed-off-by: Eric Kerfoot <[email protected]> * Annotating optional bundle files Signed-off-by: Eric Kerfoot <[email protected]> * Adjusted ckpt_export test Signed-off-by: Eric Kerfoot <[email protected]> * 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.
Status
Ready/Work in progress/Hold
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.