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merge master #429
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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]>
* MetaTensor non-breaking changes Signed-off-by: Richard Brown <[email protected]>
fixes #4530 Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] update type conversion Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
* adds strenum Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * fixes 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 Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* [DLMED] update inverse for MetaTensor Signed-off-by: Nic Ma <[email protected]>
* wrap `Type` to the typing of `writer` parameter of `SaveImage` Signed-off-by: function2 <[email protected]>
* add TORCH backend for RandHistogramShift Signed-off-by: Bryn Lloyd <[email protected]>
* clean up code examle in box_utils docstring Signed-off-by: Can Zhao <[email protected]> * clean up code examle in box_utils docstring Signed-off-by: Can Zhao <[email protected]>
* fix documentation for ResampleToMatch * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: Gustav Müller-Franzes <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
[DLMED] fix error in script Signed-off-by: Nic Ma <[email protected]>
* Add Unified Focal Loss Signed-off-by: JohnMasoner <[email protected]>
* implement pydicomreader Signed-off-by: Yiheng Wang <[email protected]> * [MONAI] code formatting Signed-off-by: monai-bot <[email protected]> * modify read function to return obj Signed-off-by: Yiheng Wang <[email protected]> * enhance docstrings and fix errors Signed-off-by: Yiheng Wang <[email protected]> * add unittest Signed-off-by: Yiheng Wang <[email protected]> * adds deps Signed-off-by: Wenqi Li <[email protected]> * optional meta Signed-off-by: Wenqi Li <[email protected]> * adds consistency 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]>
* 4589 enable dropout Signed-off-by: Wenqi Li <[email protected]> * fixes docstring typo Signed-off-by: Wenqi Li <[email protected]>
* Move dictionary inserts to its definition * [MONAI] 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]>
* [DLMED] add default value Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments 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 Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* mri utils added Signed-off-by: mersad95zd <[email protected]> * fft_utils with its unit test added Signed-off-by: mersad95zd <[email protected]> * fft_utils updated with monai data converter Signed-off-by: mersad95zd <[email protected]> * updated fft_util's docstring Signed-off-by: mersad95zd <[email protected]> * apps.rst updated with fft_utils docstrings under the reconstruction module Signed-off-by: mersad95zd <[email protected]> * fft_utils docstring updated by adding dimension hins Signed-off-by: mersad95zd <[email protected]> * fft_utils docstring updated by removing redundant output type Signed-off-by: mersad95zd <[email protected]> * test_fft_utils.py moved to the tests folder Signed-off-by: mersad95zd <[email protected]> * created fft_utils_t, the torch-only version of fft_utils Signed-off-by: mersad95zd <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fft_utils_t updated with type ignore for mypy Signed-off-by: mersad95zd <[email protected]> * docs/source/networks.rst updated with fft_utils_t Signed-off-by: mersad95zd <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * manual fix for fft_utils_t output data types Signed-off-by: mersad95zd <[email protected]> * added support for older pytorch versions Signed-off-by: mersad95zd <[email protected]> * fixes mypy Signed-off-by: Wenqi Li <[email protected]> * update to remove assert Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Can Zhao <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Hovernet and associated test script added Signed-off-by: JHancox <[email protected]>
* Fix the location type returned in GridPatch when padding This PR fixes this issue #4597 * signing and fixing docstring Signed-off-by: Valentina Salvatelli <[email protected]>
* debug device conflict Signed-off-by: Can Zhao <[email protected]> * debug device conflict Signed-off-by: Can Zhao <[email protected]>
* ignite 0.4.9 Signed-off-by: Wenqi Li <[email protected]> * pytorch docker 22.05 Signed-off-by: Wenqi Li <[email protected]> * pytorch 1.8.2, 1.12.0 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * update install command 1.8.2 Signed-off-by: Wenqi Li <[email protected]> * fixes mypy Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 5167d65. Signed-off-by: Wenqi Li <[email protected]> * test 22.06 Signed-off-by: Wenqi Li <[email protected]> * fixes unit tests Signed-off-by: Wenqi Li <[email protected]>
* fix: avoid duplicate log when multiple DataStats are used Signed-off-by: upupming <[email protected]>
updates: - [github.com/pre-commit/pre-commit-hooks: v4.1.0 → v4.3.0](pre-commit/pre-commit-hooks@v4.1.0...v4.3.0) - [github.com/asottile/pyupgrade: v2.31.1 → v2.34.0](asottile/pyupgrade@v2.31.1...v2.34.0) - [github.com/hadialqattan/pycln: v1.3.3 → v1.3.5](hadialqattan/pycln@v1.3.3...v1.3.5) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* [DLMED] adapt Pad transform for MetaTensor Signed-off-by: Nic Ma <[email protected]> * [DLMED] format code Signed-off-by: Nic Ma <[email protected]> * [DLMED] update inverse and spatial_pad Signed-off-by: Nic Ma <[email protected]> * [DLMED] update border pad Signed-off-by: Nic Ma <[email protected]> * [DLMED] update divisible pad Signed-off-by: Nic Ma <[email protected]> * [DLMED] update spatial crop Signed-off-by: Nic Ma <[email protected]> * [DLMED] make thread safe Signed-off-by: Nic Ma <[email protected]> * [DLMED] update CenterSpatialCrop Signed-off-by: Nic Ma <[email protected]> * [DLMED] update scale crop Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update random spatial crop Signed-off-by: Nic Ma <[email protected]> * [DLMED] update random scale crop Signed-off-by: Nic Ma <[email protected]> * [DLMED] update random spatial crop samples Signed-off-by: Nic Ma <[email protected]> * [DLMED] adjust Pad design Signed-off-by: Nic Ma <[email protected]> * [DLMED] update CropForeground Signed-off-by: Nic Ma <[email protected]> * [DLMED] update random weighted crop Signed-off-by: Nic Ma <[email protected]> * [DLMED] update RandCropPosNeg Signed-off-by: Nic Ma <[email protected]> * [DLMED] update rand crop by label classes Signed-off-by: Nic Ma <[email protected]> * [DLMED] update ResizeCropOrPad Signed-off-by: Nic Ma <[email protected]> * [DLMED] restore numpy pad Signed-off-by: Nic Ma <[email protected]> * [DLMED] update dict spatial pad Signed-off-by: Nic Ma <[email protected]> * [DLMED] update border pad and divisible pad Signed-off-by: Nic Ma <[email protected]> * [DLMED] update spatial crop dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] update center spatial crop Signed-off-by: Nic Ma <[email protected]> * [DLMED] update rand scale crop dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] update rand spatial crop samples dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] update crop foreground dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] update rand weighted crop dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] update pos neg crop dict 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 crop by labels dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] update resize with pad or crop dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] update format Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix all the mypy errors Signed-off-by: Nic Ma <[email protected]> * [DLMED] add crop / pad base tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update border pad test Signed-off-by: Nic Ma <[email protected]> * [DLMED] update spatial crop Signed-off-by: Nic Ma <[email protected]> * [DLMED] update pad transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] update samples crop Signed-off-by: Nic Ma <[email protected]> * [DLMED] update crop tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add test for deepcopy Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] update docs Signed-off-by: Nic Ma <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Wenqi Li <[email protected]>
fixes #4641 inverse padlist Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: vale-salvatelli <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
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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 html
command in thedocs/
folder.