merge master by Nic-Ma · Pull Request #165 · Nic-Ma/MONAI

Nic-Ma · 2021-07-08T07:38:55Z

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 unit tests 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] add warning 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]>

* Jupyter and other additions Signed-off-by: Eric Kerfoot <[email protected]>

* allow slicing with SpatialCrop(d) Signed-off-by: Richard Brown <[email protected]>

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

* fixes docstring Signed-off-by: Wenqi Li <[email protected]> * update example Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add alias Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] add unit tests 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: Nic Ma <[email protected]>

* [DLMED] add more alias 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]>

* Implement RandTorchVisionD Signed-off-by: Behrooz <[email protected]> * Add unittest for RandTorchVisiond Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Formatting Signed-off-by: Behrooz <[email protected]>

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

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]>

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

* enhance version compare Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * remove unused Signed-off-by: Wenqi Li <[email protected]> * remove unused vars Signed-off-by: Wenqi Li <[email protected]> * update debug info Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * non integer comparison Signed-off-by: Wenqi Li <[email protected]> * adds tests Signed-off-by: Wenqi Li <[email protected]> * no temp tests Signed-off-by: Wenqi Li <[email protected]> * update test Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>

* [DLMED] add deprecated decorator 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] enhance doc-string Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

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

* [DLMED] add support to compare metrics 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]>

* add UNETR, ViT Signed-off-by: ahatamizadeh <[email protected]> * add UNETR, ViT Signed-off-by: ahatamizadeh <[email protected]> * add UNETR, ViT Signed-off-by: ahatamizadeh <[email protected]> * add UNETR, ViT Signed-off-by: ahatamizadeh <[email protected]> * add UNETR, ViT Signed-off-by: ahatamizadeh <[email protected]> * add UNETR, ViT Signed-off-by: ahatamizadeh <[email protected]> * add UNETR, ViT Signed-off-by: ahatamizadeh <[email protected]>

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

* [DLMED] fix PatchEmbeddingBlock Signed-off-by: Nic Ma <[email protected]> * [DLMED] correct typehint Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pos_embed and Rearrange types Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix nn.module Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix vit Signed-off-by: Nic Ma <[email protected]> * [DLMED] update docs Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix UNetr Signed-off-by: Nic Ma <[email protected]>

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

* 21.04->21.06 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * Revert "temp test" This reverts commit f5385c2. Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 4468dcc. Signed-off-by: Wenqi Li <[email protected]> * update version number 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]>

Nic-Ma and others added 30 commits April 14, 2021 17:33

2007 Enhance the unit tests of MapLabelValue transform (#2008)

5f47407

* [DLMED] enhance unit tests 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]>

2011 Add warning for resample in SegnmentationSaver (#2013)

88806e1

* [DLMED] add warning 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]>

Plot engine fix (#2015)

357e6d4

* Jupyter and other additions Signed-off-by: Eric Kerfoot <[email protected]>

allow slicing with SpatialCrop(d) (#1954)

9f4da6a

* allow slicing with SpatialCrop(d) Signed-off-by: Richard Brown <[email protected]>

raising error tolerance to prevent rare failure (#2025)

abcca9b

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

fixes tutorial issue 183 (#2031)

9f409c1

* fixes docstring Signed-off-by: Wenqi Li <[email protected]> * update example Signed-off-by: Wenqi Li <[email protected]>

[DLMED] enhance error message (#2038)

a7a9430

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

2032 Add more alias for other networks (#2040)

170fc91

* [DLMED] add more alias 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] add post_func arg (#2049)

fc1546a

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

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]>

ericspod and others added 29 commits June 29, 2021 17:42

Update blossom-ci.yml (#2484)

50d8391

match keys in doc code examples (#2469)

11af59a

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

update google drive links (#2491)

f4894bb

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

fixes pillow version (#2503)

ce45640

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

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]>

Nic-Ma merged commit 6e8e59b into Nic-Ma:2432-add-class-ratio-crop Jul 8, 2021

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merge master#165

merge master#165
Nic-Ma merged 432 commits intoNic-Ma:2432-add-class-ratio-cropfrom
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Nic-Ma commented Jul 8, 2021

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