merge master by Nic-Ma · Pull Request #177 · Nic-Ma/MONAI

Nic-Ma · 2021-07-14T15:22:02Z

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] 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]>

* adds tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * torch Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 6a2e7a2. Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 9fc84df. Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>

* create meta data key if necessary Signed-off-by: Richard Brown <[email protected]> * add orientationd too Signed-off-by: Richard Brown <[email protected]>

* update build option Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * Revert "temp test" This reverts commit f22cdeb. Signed-off-by: Wenqi Li <[email protected]>

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

* fixes subprocess transforms Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * add SelectItemsd alias Signed-off-by: Wenqi Li <[email protected]>

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

* Temporarily changing crf test to allow some errors Signed-off-by: chaliebudd <[email protected]> * changing to unittest assert Signed-off-by: chaliebudd <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

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

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

* [DLMED] add wiki link Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add map_classes_to_indices Signed-off-by: Nic Ma <[email protected]> * [DLMED] add tests for empty classes Signed-off-by: Nic Ma <[email protected]> * [DLMED] add all the transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add tests for ClassesToIndices transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests and documents Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 and add inverse tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] optimize random choice Signed-off-by: Nic Ma <[email protected]> * [DLMED] add check for num_samples Signed-off-by: Nic Ma <[email protected]> * [DLMED] add default value to ratios Signed-off-by: Nic Ma <[email protected]>

* update lmdbdataset (#2531) * 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]> * fixes lmdb integration tests Signed-off-by: Wenqi Li <[email protected]> * add docstring Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add DecollateBatch handler 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]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] skip in min tests 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] remove rep_scalar option Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

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

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

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

Nic-Ma and others added 30 commits April 22, 2021 00:03

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]>

create meta data key if necessary (#2119)

d93df0e

* create meta data key if necessary Signed-off-by: Richard Brown <[email protected]> * add orientationd too Signed-off-by: Richard Brown <[email protected]>

2118 speed up quick test (#2120)

fd9081b

* update build option Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * Revert "temp test" This reverts commit f22cdeb. Signed-off-by: Wenqi Li <[email protected]>

efficientnet mypy fix BlockArgs class and unittest (#2126)

2db93d8

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

2122 - fixes subprocess transforms (#2128)

45c6cf6

* fixes subprocess transforms Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * add SelectItemsd alias Signed-off-by: Wenqi Li <[email protected]>

remove requirements workaround (#2134)

e6b7787

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

Temporarily changing crf test to allow some errors (#2135)

7ef0142

* Temporarily changing crf test to allow some errors Signed-off-by: chaliebudd <[email protected]> * changing to unittest assert Signed-off-by: chaliebudd <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

remove default cache_dir None (#2137)

3affd03

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

madil90 and others added 29 commits July 6, 2021 20:48

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]>

2571 enhance decollate arg of workflows (#2577)

9818467

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

2571 add wiki link to the release note (#2585)

cbc8941

* [DLMED] add wiki link Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>

2590 Add more pad args in ResizeWithPadOrCrop transform (#2594)

ada5502

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

Fixes typos (#2591)

6e02506

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

[DLMED] enhance all the SpatialPad related (#2597)

813368b

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

Nic-Ma merged commit 4d9ab03 into Nic-Ma:get-raw-losses Jul 14, 2021

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merge master#177

merge master#177
Nic-Ma merged 451 commits intoNic-Ma:get-raw-lossesfrom
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Nic-Ma commented Jul 14, 2021

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