merge master#415
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Nic-Ma merged 99 commits intoNic-Ma:4346-enhance-contribution-docfrom May 27, 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]>
* track transforms Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * transforms -> applied operations Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]>
* add box center related funcs to box_utils Signed-off-by: Can Zhao <[email protected]>
* Make the order of slices row-major Signed-off-by: Behrooz <[email protected]> * Remove a comment Signed-off-by: Behrooz <[email protected]>
* local pre-commit 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 * indent 4 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>
* merge certain files from feature/MetaTensor to dev Signed-off-by: Richard Brown <[email protected]> * remove_extra_metadata Signed-off-by: Richard Brown <[email protected]>
* add box iou funcs Signed-off-by: Can Zhao <[email protected]> * add box iou funcs to init Signed-off-by: Can Zhao <[email protected]>
* fix RandAffine with randomize==False Signed-off-by: Richard Brown <[email protected]>
* add box transform Signed-off-by: Can Zhao <[email protected]>
* add box_ops for zoom box transforms Signed-off-by: Can Zhao <[email protected]>
* update swin_unetr block name Signed-off-by: ahatamizadeh <[email protected]>
* fix squeeze issue Signed-off-by: Yiheng Wang <[email protected]>
modify unetresblock Signed-off-by: Yiheng Wang <[email protected]>
* fixes multiprocessing fixes unit test update reduce fixes mypy Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * remove unused Signed-off-by: Wenqi Li <[email protected]>
* add box transforms for affine and zoom Signed-off-by: Can Zhao <[email protected]> * add missed alias Signed-off-by: Can Zhao <[email protected]> * add in all Signed-off-by: Can Zhao <[email protected]> * add comment Signed-off-by: Can Zhao <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * move inver affine from array to dict Signed-off-by: Can Zhao <[email protected]> * only for debugging Signed-off-by: Can Zhao <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * debugged for inverse transform, add unit test Signed-off-by: Can Zhao <[email protected]> * debugged Signed-off-by: Can Zhao <[email protected]> * debugged inverse transform Signed-off-by: Can Zhao <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * reformat Signed-off-by: Can Zhao <[email protected]> * typo Signed-off-by: Can Zhao <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* improve test cases Signed-off-by: Wenqi Li <[email protected]> * revise docstring Signed-off-by: Wenqi Li <[email protected]>
* add clip box to image into box_utils Signed-off-by: Can Zhao <[email protected]>
* [DLMED] enhance test cases Signed-off-by: Nic Ma <[email protected]>
* add box flip transforms Signed-off-by: Can Zhao <[email protected]>
* update bundle download Signed-off-by: Yiheng Wang <[email protected]> * modify a few doc strings Signed-off-by: Yiheng Wang <[email protected]> * ignore mypy error of net object Signed-off-by: Yiheng Wang <[email protected]> * update docstrings Signed-off-by: Yiheng Wang <[email protected]> * rewrite source and repo descriptions Signed-off-by: Yiheng Wang <[email protected]> * refine docstrings Signed-off-by: Yiheng Wang <[email protected]> * change progress pop arg format Signed-off-by: Yiheng Wang <[email protected]> * add more descriptions about load fun Signed-off-by: Yiheng Wang <[email protected]> * add get_state_dict according to comments Signed-off-by: Yiheng Wang <[email protected]> * [MONAI] code formatting Signed-off-by: monai-bot <[email protected]> * revert mis-modified space Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: monai-bot <[email protected]>
* add nms Signed-off-by: Can Zhao <[email protected]> * add COMPUTE_DTYPE Signed-off-by: Can Zhao <[email protected]>
* adds interp mode Signed-off-by: Wenqi Li <[email protected]> * update docstrings Signed-off-by: Wenqi Li <[email protected]>
* workaround protobuf issue Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * update env var Signed-off-by: Wenqi Li <[email protected]> * config env Signed-off-by: Wenqi Li <[email protected]> * [DLMED] update for test Signed-off-by: Nic Ma <[email protected]> * revert init workaround Signed-off-by: Wenqi Li <[email protected]> * [DLMED] update visualize Signed-off-by: Nic Ma <[email protected]> * revert init change Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>
Signed-off-by: Behrooz <[email protected]>
* add FPN Signed-off-by: Can Zhao <[email protected]>
* fix the cases of multiple labels Signed-off-by: Can Zhao <[email protected]> * add examples Signed-off-by: Can Zhao <[email protected]> * docstring Signed-off-by: Can Zhao <[email protected]> * docstring and remove inverse Signed-off-by: Can Zhao <[email protected]> * docstring Signed-off-by: Can Zhao <[email protected]> * docstring Signed-off-by: Can Zhao <[email protected]>
* Adding tests 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]> * Trying to read output from failed process 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 * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Marking bundle_init as excluded Signed-off-by: Eric Kerfoot <[email protected]> * Marking bundle_init as excluded Signed-off-by: Eric Kerfoot <[email protected]> * Forgot a file Signed-off-by: Eric Kerfoot <[email protected]> * Marking bundle_utils as excluded Signed-off-by: Eric Kerfoot <[email protected]> * Marking bundle_init as excluded Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* deprecate SegmentationSaver, TorchVisionFullyConvModel Signed-off-by: Wenqi Li <[email protected]> * fixes mintests Signed-off-by: Wenqi Li <[email protected]> * remove typing Signed-off-by: Wenqi Li <[email protected]>
improve dtype conversion
…ms (#4362) [DLMED] improve doc and tests Signed-off-by: Nic Ma <[email protected]>
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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.