merge master #424

Nic-Ma · 2022-06-21T02:24:30Z

Fixes # .

Description

A few sentences describing the changes proposed in this pull request.

Status

Ready/Work in progress/Hold

Types of changes

Non-breaking change (fix or new feature that would not break existing functionality).
Breaking change (fix or new feature that would cause existing functionality to change).
New tests added to cover the changes.
Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

* 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]>

… and iterating across batches (#4137) `MetaTensor`: collate; decollate; dataset; dataloader; out=; indexing and iterating across batches (#4137)

* [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]>

* 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>

* add box rot90 Signed-off-by: Can Zhao <[email protected]> * docstring 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 * docstring typos Signed-off-by: Can Zhao <[email protected]> * add case k=0 Signed-off-by: Can Zhao <[email protected]> * typo Signed-off-by: Can Zhao <[email protected]> * fix bug Signed-off-by: Can Zhao <[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]>

[DLMED] enhance docs Signed-off-by: Nic Ma <[email protected]>

* [DLMED] enhance doc according to user's feedback Signed-off-by: Nic Ma <[email protected]> * [DLMED] update fast training tutorial Signed-off-by: Nic Ma <[email protected]> * [DLMED] add bundle description Signed-off-by: Nic Ma <[email protected]> * [DLMED] add swin unetr Signed-off-by: Nic Ma <[email protected]> * [DLMED] add ImageWriter Signed-off-by: Nic Ma <[email protected]> * [DLMED] add DeepEdit Signed-off-by: Nic Ma <[email protected]> * [DLMED] add Nuclick for Nuclei segmentation Signed-off-by: Nic Ma <[email protected]> * [DLMED] update pathology Signed-off-by: Nic Ma <[email protected]> * [DLMED] clear files Signed-off-by: Nic Ma <[email protected]> * [DLMED] add detection Signed-off-by: Nic Ma <[email protected]> * docs update Signed-off-by: Wenqi Li <[email protected]> * [DLMED] fix wrong links Signed-off-by: Nic Ma <[email protected]> * [DLMED] update detection chart Signed-off-by: Nic Ma <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* add box convert to world coordinate transform Signed-off-by: Can Zhao <[email protected]> * add test Signed-off-by: Can Zhao <[email protected]>

skip unused resampling Signed-off-by: Wenqi Li <[email protected]>

* iterables enhancements 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 * update based on comments 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 * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* enhance swin_unetr relative position Signed-off-by: ahatamizadeh <[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>

update versions Signed-off-by: Wenqi Li <[email protected]>

changed ngc download url and folder structure Signed-off-by: Yanxuan Liu <[email protected]>

Fixed generalized dice score to be 1 if denominator is 0 and prediction is empty, and 0 if denominator is 0 but prediction is not empty Signed-off-by: João Lourenço Silva <[email protected]>

[DLMED] update doc Signed-off-by: Nic Ma <[email protected]>

* changed ngc download url and folder structure Signed-off-by: Yanxuan Liu <[email protected]> * added ngc-cli to PATH Signed-off-by: Yanxuan Liu <[email protected]> Co-authored-by: Yanxuan Liu <[email protected]>

corner case in test Signed-off-by: Can Zhao <[email protected]>

* MetaTensor non-breaking changes Signed-off-by: Richard Brown <[email protected]>

fixes #4530 Signed-off-by: Wenqi Li <[email protected]>

ericspod and others added 30 commits April 4, 2022 19:38

[pre-commit.ci] pre-commit suggestions (#4072)

c5bf120

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>

Fix a logical error in level verification (#4075)

b229e9c

* Fix a logical error in level verification Signed-off-by: Behrooz <[email protected]>

[DLMED] add allow_missing_reference (#4079)

b5e7fe1

Signed-off-by: Nic Ma <[email protected]>

extending the mlp module (#4089)

17529e7

* 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]>

4073 Enhance DynUNet doc-strings (#4102)

af6560a

* Fix doc strings error Signed-off-by: Yiheng Wang <[email protected]> * remove duplicate places Signed-off-by: Yiheng Wang <[email protected]>

Make pixelshuffle scriptable (#4109)

4e7ca44

* Update the existing functionality to comply with the `torchscript.jit.script` function. Signed-off-by: Ramon Emiliani <[email protected]>

meta tensor (#4077)

1880d38

* meta tensor Signed-off-by: Richard Brown <[email protected]>

fixes pytorch version tests (#4127)

ccac5ff

Signed-off-by: Wenqi Li <[email protected]>

update meta tensor api (#4131)

137164d

* update meta tensor api Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

runtests.sh isort (#4134)

5e180c6

Signed-off-by: Richard Brown <[email protected]>

update citation (#4133)

8544d9e

Signed-off-by: Wenqi Li <[email protected]>

ToMetaTensor and FromMetaTensor transforms (#4115)

443fc0c

to and from meta

no skip if before pytorch 1.7 (#4139)

cc9c066

* 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]>

[DLMED] fix file name in meta (#4145)

e1a62f2

Signed-off-by: Nic Ma <[email protected]>

New wsireader (#4147)

cb9040e

MetaTensor: collate; decollate; dataset; dataloader; out=; indexing…

6dfb6a8

… and iterating across batches (#4137) `MetaTensor`: collate; decollate; dataset; dataloader; out=; indexing and iterating across batches (#4137)

Disable pylint error and fix CI tests of new tifffile (#4162)

710781b

* workaround Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix tifffile issue Signed-off-by: Nic Ma <[email protected]>

Can-Zhao and others added 29 commits June 2, 2022 22:30

Add RetinaNet detector (#4400)

e2f160d

add RetinaNet detector loss computation (#4446)

4cddaa8

4451 adds testing file downloading (#4452)

db02f07

adds download link Signed-off-by: Wenqi Li <[email protected]>

4463 Enhance doc-string of Normalize and other places (#4464)

f00e9be

[DLMED] enhance docs Signed-off-by: Nic Ma <[email protected]>

Add coco detection metrics (#4447)

7d77322

add GIoU loss for box detection (#4454)

df4a7d7

4323 update changelog for 0.9.0 (#4470)

7504526

add box convert to world coordinate transform (#4476)

1daf220

* add box convert to world coordinate transform Signed-off-by: Can Zhao <[email protected]> * add test Signed-off-by: Can Zhao <[email protected]>

4480 skip unused resampling (#4481)

96c6cc3

skip unused resampling Signed-off-by: Wenqi Li <[email protected]>

Fixing SliceInferer Issue (#4482)

179e4de

More Efficient GridPatch and RandGridPatch V2 (#4473)

0b97bb6

4489 Enhance hyperlinks of config syntax doc (#4490)

af0e0e9

4323 update docs release versions (#4494)

1188b9c

update versions Signed-off-by: Wenqi Li <[email protected]>

changed ngc download url (#4508)

ed233d9

changed ngc download url and folder structure Signed-off-by: Yanxuan Liu <[email protected]>

Fixed generalized dice score (#4511)

4215599

Fixed generalized dice score to be 1 if denominator is 0 and prediction is empty, and 0 if denominator is 0 but prediction is not empty Signed-off-by: João Lourenço Silva <[email protected]>

Update bundle specification doc (#4512)

d0a554e

[DLMED] update doc Signed-off-by: Nic Ma <[email protected]>

add ngc to PATH (#4517)

0b6af0b

* changed ngc download url and folder structure Signed-off-by: Yanxuan Liu <[email protected]> * added ngc-cli to PATH Signed-off-by: Yanxuan Liu <[email protected]> Co-authored-by: Yanxuan Liu <[email protected]>

corner case in coco metric test (#4519)

78509ae

corner case in test Signed-off-by: Can Zhao <[email protected]>

Add youden_index and youden as aliases for bm (#4534)

29a724d

MetaTensor non-breaking changes (#4539)

8b5ddf5

* MetaTensor non-breaking changes Signed-off-by: Richard Brown <[email protected]>

4530 optional SummaryWriter (#4546)

1f07913

fixes #4530 Signed-off-by: Wenqi Li <[email protected]>

Nic-Ma merged commit 9c13c88 into Nic-Ma:metatensor-croppad Jun 21, 2022

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merge master #424

merge master #424

Nic-Ma commented Jun 21, 2022

merge master #424

merge master #424

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Nic-Ma commented Jun 21, 2022

Description

Status

Types of changes