merge master by Nic-Ma · Pull Request #411 · Nic-Ma/MONAI

Nic-Ma · 2022-05-03T06:12:38Z

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]>

… 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]>

…4203)

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]>

dongyang0122 and others added 20 commits April 23, 2022 16:37

fix bundle download test issue (#4169)

8f5c992

Signed-off-by: Yiheng Wang <[email protected]>

4094 Enhance ckpt_export to save config files (#4159)

e688989

* [DLMED] enhance checkpoint export Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

Move RGB/RGBA checks to base class (#4171)

d63f490

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

[CICD] To support temp dgx runner (#4175)

10cbeff

* 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]>

Test fix for AMP kwargs (#4178)

6393927

Signed-off-by: Eric Kerfoot <[email protected]>

Add DeepEdit transforms and interaction (#4164)

5777041

* Add DeepEdit transforms and interaction Signed-off-by: Andres Diaz-Pinto <[email protected]>

Remove commented out code (#4187)

c9b2d06

* 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 (#4189)

be3d22f

* Remove unused global variable

add adn unet (#4185)

df177fd

Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>

[DLMED] enhance load_files (#4192)

05b9d31

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

enhance mean dice (#4163)

9af6332

Signed-off-by: Yiheng Wang <[email protected]>

Make transforms optional (#4190)

1331432

* Make all transforms optional Signed-off-by: Behrooz <[email protected]>

4200 workaround for ci apt (#4202)

0db84a0

* 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]>

Update the default value of lazy arg in the ConfigParser to True (#…

d4a924c

…4203)

udpate md5 (#4213)

30ad90d

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

Nic-Ma merged commit a82b38e into Nic-Ma:4217-update-pytorch May 3, 2022

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merge master#411

merge master#411
Nic-Ma merged 50 commits intoNic-Ma:4217-update-pytorchfrom
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Nic-Ma commented May 3, 2022

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