merge master by Nic-Ma · Pull Request #152 · Nic-Ma/MONAI

Nic-Ma · 2021-06-29T02:17:50Z

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 --codeformat --coverage.
Quick tests passed locally by running ./runtests.sh --quick.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

* [DLMED] enhance decathlon datalist Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Behrooz <[email protected]>

Signed-off-by: Behrooz <[email protected]>

* adds docker tag action Signed-off-by: Wenqi Li <[email protected]> * adds tag info Signed-off-by: Wenqi Li <[email protected]> * update versioneer Signed-off-by: Wenqi Li <[email protected]>

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

* refactor docker building Signed-off-by: Wenqi Li <[email protected]>

* update docs deps. Signed-off-by: Wenqi Li <[email protected]> * fixes https://github.com/Project-MONAI/MONAI/runs/2283148095\?check_suite_focus\=true\#step:7:8972 Signed-off-by: Wenqi Li <[email protected]> * Revert "fixes https://github.com/Project-MONAI/MONAI/runs/2283148095\?check_suite_focus\=true\#step:7:8972" This reverts commit 1407400. Signed-off-by: Wenqi Li <[email protected]>

* Update garbage collection assertion to a more reliable one Signed-off-by: Behrooz <[email protected]> * Remove print Signed-off-by: Behrooz <[email protected]>

* Working ParameterScheduler Added a new ParameterScheduler handler and the required tests. Signed-off-by: Petru-Daniel Tudosiu <[email protected]>

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

* [DLMED] add support for addtional events Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typehints Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* fixes #1965 Signed-off-by: Wenqi Li <[email protected]> * adds docstring Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] enhance doc-strings Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

* adding init efficientnet support Signed-off-by: masadcv <[email protected]> * fixing flake8 and further refactoring Signed-off-by: masadcv <[email protected]> * adding unittests for efficiennet Signed-off-by: masadcv <[email protected]> * making unittests backwards compatible python<3.8 Signed-off-by: masadcv <[email protected]> * fixed kitty unittests file path Signed-off-by: masadcv <[email protected]> * adding docstrings and minor refactoring Signed-off-by: masadcv <[email protected]> * fix flake8-py3 failing test Signed-off-by: masadcv <[email protected]> * generalize drop_connect for n-dim, fix/add unittests, remove assert Signed-off-by: masadcv <[email protected]> * fix failing unittest, CC0-license image for test Signed-off-by: masadcv <[email protected]> * refactoring code for review Signed-off-by: masadcv <[email protected]> * WIP fix mypy type hint errors Signed-off-by: masadcv <[email protected]> * fix cuda test error Signed-off-by: masadcv <[email protected]> * WIP fix test errors Signed-off-by: masadcv <[email protected]> * adding non-default shape tests Signed-off-by: masadcv <[email protected]> * remove 3d case from non-default shape test Signed-off-by: masadcv <[email protected]> * refactoring and updating docs Signed-off-by: masadcv <[email protected]> Co-authored-by: Yiheng Wang <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* [DLMED] add TransformInverter handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support in SegmentationSaver handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

* changelog for 0.5.0 Signed-off-by: Wenqi Li <[email protected]> * update changelog Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add TransformInverter handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support in SegmentationSaver handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] save mode into inverse dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix ToTensor inverse issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] change the replacement logic into util function Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

* [DLMED] update highlights for 0.5 Signed-off-by: Nic Ma <[email protected]> * [DLMED] add invert transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more highlights Signed-off-by: Nic Ma <[email protected]> * [DLMED] add checkpointloader Signed-off-by: Nic Ma <[email protected]> * downscale image Signed-off-by: Wenqi Li <[email protected]> * downscale image Signed-off-by: Wenqi Li <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> * update desc Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* update convs docstrings Signed-off-by: Wenqi Li <[email protected]> * increase tol for cuda crf Signed-off-by: Wenqi Li <[email protected]> * update requirements according to docs/requirements Signed-off-by: Wenqi Li <[email protected]> * prune image Signed-off-by: Wenqi Li <[email protected]>

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

* [DLMED] metrics support a list of tensor Signed-off-by: Nic Ma <[email protected]> * update workflow test Signed-off-by: Wenqi Li <[email protected]> * [DLMED] fix engine.state.output dict copy issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] add num_workers Signed-off-by: Nic Ma <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * update docstrings Signed-off-by: Wenqi Li <[email protected]> * tests Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

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

* handling error Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * Revert "temp test" This reverts commit 60661ae. Signed-off-by: Wenqi Li <[email protected]>

* update dev version Signed-off-by: Wenqi Li <[email protected]> * typo fix Signed-off-by: Wenqi Li <[email protected]>

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

TTA progress bar, use torch for mode, add label meta_data

* follow up of #1992 Signed-off-by: Wenqi Li <[email protected]> * update spacing inverse Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] update TransformInverter Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix deepcopy Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

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

* [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add nearest test cases Signed-off-by: Nic Ma <[email protected]>

* adds a what's new page Signed-off-by: Wenqi Li <[email protected]>

* Add blossom pre-merge pipeline Signed-off-by: Mohammad Adil <[email protected]>

* [DLMED] add min tests command Signed-off-by: Nic Ma <[email protected]> * [DLMED] update CI script Signed-off-by: Nic Ma <[email protected]>

* [DKMED] add CSV datalist Signed-off-by: Nic Ma <[email protected]> * [DLMED] add group feature Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add optional install Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] add doc-strings Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add CSVDataset for non-iterable data Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix min test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add CSVIterableDataset base Signed-off-by: Nic Ma <[email protected]> * [DLMED] add CSVIterableDataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] support multiple processes Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix docs-build Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix min tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI tests 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] change sys.platform Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip if windows Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] add col_types arg Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* [DLMED] test mypy fix Signed-off-by: Nic Ma <[email protected]> * [DLMED] test commit Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix np.random Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix other numpy data type errors Signed-off-by: Nic Ma <[email protected]>

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

* added spikes transform Signed-off-by: Yaniel Cabrera <[email protected]>

* [DLMED] add image_only and unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]>

* add json config model support Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add -1 support for pixdim Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add scale_np = scale_np[:d] Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update accortding to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove image_only in Spacing and Orientation Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: am <am>

Signed-off-by: Dong Yang <[email protected]>

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

* [DLMED] add TorchVisionClassificationModel Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* Add parameter unpacking for transforms Signed-off-by: Sebastian Penhouet <[email protected]>

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

* [DLMED] add copy logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]>

* Add query to NGC to get matched model URL and version. Allow mmar download with latest version or a specific version. Signed-off-by: Isaac Yang <[email protected]>

no need for default orig_size stored for invertible transforms

Signed-off-by: Can Zhao <[email protected]>

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

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

#2455) * add clara_train_covid19_3d_ct_classification and clara_train_covid19_annotation_ct_lung_1 point to pt version of covid19 lung annotation model Signed-off-by: Holger Roth <[email protected]>

* [DLMED] add pad options Signed-off-by: Nic Ma <[email protected]> * [DLMED] add to dict transforms Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

Signed-off-by: ahatamizadeh <[email protected]>

* [DLMED] update ignite to 0.4.5 Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add dynamic data list in CacheDataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support to PersistentDataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance dataset 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_data -> set_data Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Holger Roth <[email protected]>

…grow (#2442) Signed-off-by: vnath <[email protected]>

Nic-Ma and others added 30 commits April 5, 2021 21:44

Add progress bar to LesionFROC (#1951)

fbce3c2

Signed-off-by: Behrooz <[email protected]>

pipeline for releasing the docker images (#1953)

501026b

* adds docker tag action Signed-off-by: Wenqi Li <[email protected]> * adds tag info Signed-off-by: Wenqi Li <[email protected]> * update versioneer Signed-off-by: Wenqi Li <[email protected]>

remove unused RandomizableTransform (#1952)

81cfbf0

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

1956 - docker image building pipelines (#1957)

5c411d1

* refactor docker building Signed-off-by: Wenqi Li <[email protected]>

Update garbage collection assertion (#1959)

d6ed956

* Update garbage collection assertion to a more reliable one Signed-off-by: Behrooz <[email protected]> * Remove print Signed-off-by: Behrooz <[email protected]>

Working ParameterScheduler (#1949)

7581255

* Working ParameterScheduler Added a new ParameterScheduler handler and the required tests. Signed-off-by: Petru-Daniel Tudosiu <[email protected]>

[DLMED] remove warning (#1962)

baca6e0

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

1965 - register_backward_hook (#1966)

8cbd59a

* fixes #1965 Signed-off-by: Wenqi Li <[email protected]> * adds docstring Signed-off-by: Wenqi Li <[email protected]>

1968 Enhance meta data doc-string in SegmentationSaver (#1969)

d56c002

* [DLMED] enhance doc-strings Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

1889 - changelog for v0.5.0 (#1923)

3a7cd46

* changelog for 0.5.0 Signed-off-by: Wenqi Li <[email protected]> * update changelog Signed-off-by: Wenqi Li <[email protected]>

test runner (#1986)

a625d38

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

add timeout (#1989)

f5d5737

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

1889 update preview version number (#1991)

b4d8780

* update dev version Signed-off-by: Wenqi Li <[email protected]> * typo fix Signed-off-by: Wenqi Li <[email protected]>

fix comprehension error (#1995)

d1f4e6f

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

TTA progress bar, use torch for mode, add label meta_data (#1992)

b3eb73a

TTA progress bar, use torch for mode, add label meta_data

include meta when inverting (#1997)

d72f61e

* follow up of #1992 Signed-off-by: Wenqi Li <[email protected]> * update spacing inverse Signed-off-by: Wenqi Li <[email protected]>

update (#2000)

2707407

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

Add more test for nearest interpolation in TransformInverter (#2001)

583e35b

* [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add nearest test cases Signed-off-by: Nic Ma <[email protected]>

2003 - adds a what's new page (#2005)

2c6d688

* adds a what's new page Signed-off-by: Wenqi Li <[email protected]>

madil90 and others added 29 commits June 21, 2021 21:05

Add blossom pre-merge pipeline (21/June) (#2382)

fb7d9f1

* Add blossom pre-merge pipeline Signed-off-by: Mohammad Adil <[email protected]>

Add min tests cmd to runtests script (#2400)

8cda6c1

* [DLMED] add min tests command Signed-off-by: Nic Ma <[email protected]> * [DLMED] update CI script Signed-off-by: Nic Ma <[email protected]>

fixes concurrency group (#2409)

0bd312a

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

Spike (Herringbone) artifact transform (#2337)

88fe0fc

* added spikes transform Signed-off-by: Yaniel Cabrera <[email protected]>

2420 Add image_only option to several spatial transforms (#2421)

a0afa60

* [DLMED] add image_only and unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]>

2415 - add json config model support for mmar loading (#2416)

ea028f5

* add json config model support Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

Brain MMAR pretrained examples (#2406)

855a025

Signed-off-by: am <am>

add model desc for liver and pancreas seg (#2431)

5ff1bba

Signed-off-by: Dong Yang <[email protected]>

[DLMED] enhance docs (#2429)

c20f70b

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

Fix permissions for blossom CI (#2438)

0662ed2

2407 Add support to set number classes for TorchVision models (#2408)

79b83d9

* [DLMED] add TorchVisionClassificationModel Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

Add parameter unpacking for transforms (#2437)

38403bb

* Add parameter unpacking for transforms Signed-off-by: Sebastian Penhouet <[email protected]>

[DLMED] enhance assert (#2444)

05b2da6

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

2445 Fix inplace modification issue of SmartCacheDataset (#2446)

eec33b6

* [DLMED] add copy logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]>

Add query to NGC to get matched model URL and version. (#2433)

43aba96

* Add query to NGC to get matched model URL and version. Allow mmar download with latest version or a specific version. Signed-off-by: Isaac Yang <[email protected]>

no need for default orig_size stored for invertible transforms (#2441)

6401c5e

no need for default orig_size stored for invertible transforms

add annotation for brain and spleen (#2448)

079fcd4

Signed-off-by: Can Zhao <[email protected]>

Fix docstring error (#2461)

eb29e99

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

2453 Enhance ToTensor transform to support data with no dim (#2454)

9f9b63a

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

add clara_train_covid19_3d_ct_classification and clara_train_covid19_… (

1a707f0

#2455) * add clara_train_covid19_3d_ct_classification and clara_train_covid19_annotation_ct_lung_1 point to pt version of covid19 lung annotation model Signed-off-by: Holger Roth <[email protected]>

update_model_desc_prostate_spleen (#2466)

7b08d40

Signed-off-by: ahatamizadeh <[email protected]>

2399 update ignite to v0.4.5 (#2451)

91ea1b6

* [DLMED] update ignite to 0.4.5 Signed-off-by: Nic Ma <[email protected]>

update clara_pt_covid19_3d_ct_classification model description (#2472)

cdf05b0

Signed-off-by: Holger Roth <[email protected]>

Model Description in apps/mmars updated with NGC description for Deep…

0aa936f

…grow (#2442) Signed-off-by: vnath <[email protected]>

Nic-Ma merged commit 793ee6e into Nic-Ma:2474-deprecate-handlers Jun 29, 2021

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merge master#152

merge master#152
Nic-Ma merged 401 commits intoNic-Ma:2474-deprecate-handlersfrom
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Nic-Ma commented Jun 29, 2021

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