merge master by Nic-Ma · Pull Request #172 · Nic-Ma/MONAI

Nic-Ma · 2021-07-12T23:35:50Z

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.

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

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

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

* [DLMED] check the label data for Tensor Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

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

* [DLMED] add `device` and `to_tensor` args Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support for non-tensor output Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove detach.cpu Signed-off-by: Nic Ma <[email protected]>

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

* fix duplication of key_transforms in RandSpatialCropSamplesd Signed-off-by: Richard Brown <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] only deep copy unmodified Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Nic Ma <[email protected]>

* [DLMED] save inverted meta dict Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * safe key get Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

@jhlegarreta

Based on the ITK welcome: https://github.com/InsightSoftwareConsortium/ITK/blob/master/CONTRIBUTING.md by @jhlegarreta

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

* [DLMED] add divisible K Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue 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] fix CI tests Signed-off-by: Nic Ma <[email protected]>

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

* enhance persistent temp Signed-off-by: Wenqi Li <[email protected]> * fixes windows file rename issue Signed-off-by: Wenqi Li <[email protected]> * enhance multiprocess LMDB Signed-off-by: Wenqi Li <[email protected]> * remove usued vars Signed-off-by: Wenqi Li <[email protected]> * fixes LGTM errors Signed-off-by: Wenqi Li <[email protected]> * remove comparison-with-callable (W0143) Signed-off-by: Wenqi Li <[email protected]> * fixes pylint W0231 Signed-off-by: Wenqi Li <[email protected]> * fixes PYL-R1705 Signed-off-by: Wenqi Li <[email protected]> * fixes PYL-R1720 Signed-off-by: Wenqi Li <[email protected]> * fixes PTC-W0060 Signed-off-by: Wenqi Li <[email protected]> * fixes PYL-W0105 Signed-off-by: Wenqi Li <[email protected]> * fixes PTC-W0016 Signed-off-by: Wenqi Li <[email protected]>

* update box_start/end for deepgrow Signed-off-by: Richard Brown <[email protected]> * add test Signed-off-by: Richard Brown <[email protected]>

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

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

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

* [DLMED] add detach for Tensor Signed-off-by: Nic Ma <[email protected]> * fixes test Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* adding error messaging for unsupported tensor shapes Signed-off-by: chaliebudd <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]>

* [DLMED] Enhance unit test and doc-string Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] enhance unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* [DLMED] fix shallow copy issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] add patch_index to RandWeightedCrop Signed-off-by: Nic Ma <[email protected]>

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

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

* update readme Signed-off-by: Wenqi Li <[email protected]> * update index Signed-off-by: Wenqi Li <[email protected]> * relative links Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>

* Added RicianNoise transform Signed-off-by: Lyndon Boone <[email protected]> * Use ensure_tuple_rep in channel-wise RandRicianNoise transform Signed-off-by: Lyndon Boone <[email protected]> * Added RandRicianNoised transform Signed-off-by: Lyndon Boone <[email protected]> * Autofixed coding style errors Signed-off-by: Lyndon Boone <[email protected]> * Added paper reference for RandRicianNoise in docstring Signed-off-by: Lyndon Boone <[email protected]> * Added unit test for RandRicianNoise transform Signed-off-by: Lyndon Boone <[email protected]> * Added unit test for RandRicianNoised transform Signed-off-by: Lyndon Boone <[email protected]> * Fixed mypy typing issues Signed-off-by: Lyndon Boone <[email protected]>

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

Signed-off-by: Jeff VanOss <[email protected]>

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

* [DLMED] add ignite dist support 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] change key_metric_score_sign to a bool flag 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]>

* [DLMED] add decollate logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix plot Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update classification integration test Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] restore decollate logic 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]>

* [DLMED] fix strict_shape Signed-off-by: Nic Ma <[email protected]> * [DLMED] add warning message 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]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add links Signed-off-by: Nic Ma <[email protected]> * [DLMED] Enhance doc-strings Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance CI 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] make get_model_spec API Signed-off-by: Nic Ma <[email protected]> * [DLMED] unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]>

…2518) * [DLMED] update lr_scheduler links Signed-off-by: Nic Ma <[email protected]> * [DLMED] update all the other links Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>

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

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

* [DLMED] add horovod tests Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] skip min tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] rename to skip auto CI Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

Signed-off-by: Mohammad Adil <[email protected]>

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

* update focalloss to use sigmoid 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]>

* [DLMED] add decollate logic to DeepGrow 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 AddRandomGuidanced to test Signed-off-by: Nic Ma <[email protected]> * [DLMED] update network Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix issue in addsignal Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix guidance issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix mypy and docs Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* Deepgrow - Fix probability scalar value during collate Signed-off-by: Sachidanand Alle <[email protected]> * Fix CI checks Signed-off-by: Sachidanand Alle <[email protected]> Co-authored-by: Sachidanand Alle <[email protected]>

* [DLMED] Add EnsureTensor transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] Enhance doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments 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] restore deprecated 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]> Co-authored-by: monai-bot <[email protected]>

* [DLMED] update highlight titles Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more content to highlight features Signed-off-by: Nic Ma <[email protected]> * [DLMED] Add other frameworks Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance distributed document Signed-off-by: Nic Ma <[email protected]> * update highlights Signed-off-by: Wenqi Li <[email protected]> * adds jit descriptions Signed-off-by: Wenqi Li <[email protected]> * adds gmm figure Signed-off-by: Wenqi Li <[email protected]> * add mmar transfer learning figure Signed-off-by: Wenqi Li <[email protected]> * fix typos Signed-off-by: Wenqi Li <[email protected]> * [DLMED] add decollate batch section Signed-off-by: Nic Ma <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* add use_deterministic_algorithms flag Signed-off-by: Wenqi Li <[email protected]> * fixes typing Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] fix ToNumpy 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]>

* [DLMED] enhance for scalar tensor Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] remove redundant logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] add doc-string for img Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* [DLMED] fix tests for PyTorch 1.5 Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify the tests Signed-off-by: Nic Ma <[email protected]>

* update lmdbdataset Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * docstring and less verbose progressbar Signed-off-by: Wenqi Li <[email protected]> * docstring Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* adds a release note for 0.6.0 Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Mohammad Adil <[email protected]>

* adds whats new 0.6 Signed-off-by: Wenqi Li <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> * add a list Signed-off-by: Wenqi Li <[email protected]> * update according to comments Signed-off-by: Wenqi Li <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]> * Revert "update lmdbdataset (#2531)" This reverts commit a980ae4. Signed-off-by: Wenqi Li <[email protected]>

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

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

* add WarmupCosineSchedule,unetr docstring Signed-off-by: ahatamizadeh <[email protected]> * add WarmupCosineSchedule,enhance unetr docstring Signed-off-by: ahatamizadeh <[email protected]>

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

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

wyli and others added 30 commits April 20, 2021 17:38

update docstring example (#2055)

de677ca

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

fixes tutorial issue 184 (#2053)

14976b5

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

Update cucim to 0.19.0 (#2057)

8057ae8

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

2044 Add check for label data type (#2060)

13bf996

* [DLMED] check the label data for Tensor Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

[DLMED] enhance metrics (#2061)

51ecc48

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

fixes tutorial 190 (#2063)

5cbcaf6

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

Add pointers to issues for community contributors (#2071)

7379ab8

Start with a welcoming statement in the contributing docs (#2072)

e0035b1

Based on the ITK welcome: https://github.com/InsightSoftwareConsortium/ITK/blob/master/CONTRIBUTING.md by @jhlegarreta

Remove transpose from the tissue masks (#2074)

fea9307

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

RandTorchVisionD update (#2076)

f45108b

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

update box_start/end for deepgrow (#2088)

dde1100

* update box_start/end for deepgrow Signed-off-by: Richard Brown <[email protected]> * add test Signed-off-by: Richard Brown <[email protected]>

2092 Enhance NIfTI writer logging (#2093)

8f2856d

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

[DLMED] add flag (#2094)

5eb9198

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

2095 fix multi-gpu issue in ClassificationSaver (#2096)

9e1a7d4

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

Add detach to the tensors in handlers (#2100)

feb3a33

* [DLMED] add detach for Tensor Signed-off-by: Nic Ma <[email protected]> * fixes test Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

Adding error messaging for unsupported tensor shapes (#2089)

1f2247e

* adding error messaging for unsupported tensor shapes Signed-off-by: chaliebudd <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]>

2103 Add deepcopy to PosNegCrop transform (#2104)

12f267c

* [DLMED] fix shallow copy issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] add patch_index to RandWeightedCrop Signed-off-by: Nic Ma <[email protected]>

only pip install cucim if on linux (#2106)

304d1a8

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

re-enable dev branch tests (#2107)

8bb08a8

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

2041 - update readme/index page (#2108)

35cd9df

* update readme Signed-off-by: Wenqi Li <[email protected]> * update index Signed-off-by: Wenqi Li <[email protected]> * relative links Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>

[DLMED] improve doc-string of partition_dataset (#2109)

299f2c2

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

fix SegResNetVAE docstring to match args (#2113)

06fd8fe

Signed-off-by: Jeff VanOss <[email protected]>

2111 - adds a map_items option to compose (#2112)

198cd2f

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

Nic-Ma and others added 29 commits July 2, 2021 11:39

2512 Make get_model_spec API (#2515)

f3d436a

* [DLMED] make get_model_spec API Signed-off-by: Nic Ma <[email protected]> * [DLMED] unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]>

enhance one-hot documentation (#2521)

cfcce58

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

[DLMED] add first to from_engine (#2524)

025dee7

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

Add pip excludor to blackduck (#2533)

e8124da

Signed-off-by: Mohammad Adil <[email protected]>

previous dynunet (#2534)

0711e04

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

2509 update focalloss to use sigmoid (7/July) (#2513)

17dde67

* update focalloss to use sigmoid 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]>

2542 add use_deterministic_algorithms flag (#2543)

df76a20

* add use_deterministic_algorithms flag Signed-off-by: Wenqi Li <[email protected]> * fixes typing Signed-off-by: Wenqi Li <[email protected]>

2552 Fix ToNumpy issue with 0-dim data (#2553)

4ece449

* [DLMED] fix ToNumpy 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]>

2556 Fix EnsureType test error in PyTorch 1.5.1 (#2558)

66bc397

* [DLMED] fix tests for PyTorch 1.5 Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify the tests Signed-off-by: Nic Ma <[email protected]>

2488 adds a release note for 0.6.0 (#2520)

342b424

* adds a release note for 0.6.0 Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]>

Remove concurrency limit from blossom CI (#2559)

9a83660

Signed-off-by: Mohammad Adil <[email protected]>

update weekly dev version (#2561)

8365443

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

[DLMED] fix wrong link in README (#2564)

cad300a

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

[DLMED] add return to SaveImage (#2568)

3edff74

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

add WarmupCosineSchedule, UNETR & ViT Docstrings (#2545)

3902990

* add WarmupCosineSchedule,unetr docstring Signed-off-by: ahatamizadeh <[email protected]> * add WarmupCosineSchedule,enhance unetr docstring Signed-off-by: ahatamizadeh <[email protected]>

update highlights (#2579)

f420d99

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

2562 Add support to not save data in a separate folder (#2576)

daf2c4f

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

Nic-Ma merged commit d38d9c8 into Nic-Ma:2571-add-wiki-link Jul 12, 2021

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Nic-Ma merged 443 commits intoNic-Ma:2571-add-wiki-linkfrom
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Nic-Ma commented Jul 12, 2021

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