merge master by Nic-Ma · Pull Request #358 · Nic-Ma/MONAI

Nic-Ma · 2022-01-25T23:54:07Z

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.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance random computation Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

…3079) * Torch `CropForeground`, `HistogramNormalize`, `RandHistogramShift` Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add MLFlowHandler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add optional import Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix doc format Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI test Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

…rop` (#3078) Torch `AddCoordinateChannels`, `ExtremePointsChannel`, `RandWeightedCrop`

* [DLMED] fix wrong doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

* fixes 33097 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] update intensity transforms Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update all the other transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CPU test Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* adds new tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes the tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * split yml Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* feat: refactor seg-net for easier use Signed-off-by: BenTenmann <benji.tenmann@me.com>

* ignores E402 Module level import not at top of file Signed-off-by: Wenqi Li <wenqil@nvidia.com> * exlcude Signed-off-by: Wenqi Li <wenqil@nvidia.com> * ignore Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add state attr Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix integration test Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add integration test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more random test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

…gLabel (#3129) Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* add alias tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * monai.losses.dice Signed-off-by: Wenqi Li <wenqil@nvidia.com> * monai.utils.deprecated Signed-off-by: Wenqi Li <wenqil@nvidia.com> * monai.networks.nets.senet Signed-off-by: Wenqi Li <wenqil@nvidia.com> * monai.networks.nets.dynunet Signed-off-by: Wenqi Li <wenqil@nvidia.com> * monai.networks.nets.unet Signed-off-by: Wenqi Li <wenqil@nvidia.com> * monai.networks.nets.densenet Signed-off-by: Wenqi Li <wenqil@nvidia.com> * monai.networks.nets.ahnet Signed-off-by: Wenqi Li <wenqil@nvidia.com> * only check for the existing modules Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes docs Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* upgrade torch image to 2109 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * more time for fast training Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit a5b4447. Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* add griddistortion Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix pre-commit ci black error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add unittest Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [DLMED] add metric example Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

* update rand grid distortion Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes formatting and errors Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add Tensor to CropForegroundd transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance data conversion Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more tests and fix convert tensor issue Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Nic Ma <nma@nvidia.com>

…dComponents (#3647) * [DLMED] support single channel One-Hot Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add missing doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance correct centers Signed-off-by: Nic Ma <nma@nvidia.com>

* option to occlude all channels simultaneously

* removed duplicated Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update gitignore to ignore readthedocs autobuild Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* ignore some flake8 errors Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #3660 2003->2106 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add default values Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Nic Ma <nma@nvidia.com>

install fresh from conda or install dependencies using environment-dev.yml Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* DictPostFixes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * use fn Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Signed-off-by: Nic Ma <nma@nvidia.com>

* update folder layout Signed-off-by: Wenqi Li <wenqil@nvidia.com> * revise create_file_basename util Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [DLMED] change to warning Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more error message Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] simplify the messages Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix channel_dim issue in ITKReader, add it in NibabelReader Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] restore LoadImaged test Signed-off-by: Nic Ma <nma@nvidia.com>

allow test image creation to save to different folders and with different file names

* support stack of images with channels Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

… is 0 (#3690) * [DLMED] check 0 length Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add dist tests Signed-off-by: Nic Ma <nma@nvidia.com>

* remove tensor-array convertions Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update backend Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests, remove meshgrid warnings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typing issue Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes import Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] update ignite to 0.4.8 Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix format issue Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* add dev mode collate Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* add benchmarking warp against python itk Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* fix differentiability of generalized Dice loss Signed-off-by: Josafat-Mattias Burmeister <josafat-mattias.burmeister@student.hpi.de> * fix weight clamping for the case that is True Signed-off-by: Josafat-Mattias Burmeister <josafat-mattias.burmeister@student.hpi.de> * add test case for batch mode Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

… comma (#3711) * [DLMED] add support to config delimiter Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

wyli and others added 30 commits October 8, 2021 11:26

fixes figures (#3083)

6169c5d

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

fixes rst format issues (#3088)

54bd9db

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

oneof doc (#3090)

3b109f0

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3082 Enhance heavy random computation of transforms (#3086)

484bb5c

* [DLMED] enhance random computation Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

[DLMED] fix wrong doc-string (#3096)

ce38a93

Signed-off-by: Nic Ma <nma@nvidia.com>

KeepLargestConnectedComponent(d) example transforms (#3108)

7b1b772

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Torch AddCoordinateChannels, ExtremePointsChannel, `RandWeightedC…

c346956

…rop` (#3078) Torch `AddCoordinateChannels`, `ExtremePointsChannel`, `RandWeightedCrop`

Fix wrong doc-strings in several handlers (#3109)

712d90b

* [DLMED] fix wrong doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

3097 - deprecated_arg replacing name (#3107)

3c8cc78

* fixes 33097 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3087 enhance usage of intensity RandomizableTransform (#3094)

e0f84f2

* [DLMED] update intensity transforms Signed-off-by: Nic Ma <nma@nvidia.com>

3087 Enhance other RandomizableTransform transforms (#3113)

ce76ec7

* [DLMED] update all the other transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CPU test Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] fix 1.5.1 cron test (#3121)

9b9516c

Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

feat: refactor seg-net for easier use (#3057)

ed9cd41

* feat: refactor seg-net for easier use Signed-off-by: BenTenmann <benji.tenmann@me.com>

[DLMED] add state attr (#3125)

356af91

Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

3124 3126 Fix integration tests (#3130)

cd6e90c

* [DLMED] add state attr Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix integration test Signed-off-by: Nic Ma <nma@nvidia.com>

allow ROIs bigger than im for RandCropByLabelClasses, RandCropByPosNe…

6155724

…gLabel (#3129) Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

skip tests for torch 1.5 (#3131)

ff08334

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

senet tests with testing data (#3136)

1259042

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

400 Add example in the doc-string of Metric (#3139)

467138f

* [DLMED] add metric example Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] fix data type issue (#3143)

2920dd3

Signed-off-by: Nic Ma <nma@nvidia.com>

Nic-Ma and others added 29 commits January 13, 2022 04:14

moveaxis and typing enhancements (#3648)

459b081

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3648 Enhance correct centers for crop (#3652)

f089659

* [DLMED] add missing doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance correct centers Signed-off-by: Nic Ma <nma@nvidia.com>

option to occlude all channels simultaneously (#3543)

3a26702

* option to occlude all channels simultaneously

removes duplicated docstring rendering (#3651)

ceb71ab

* removed duplicated Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update gitignore to ignore readthedocs autobuild Signed-off-by: Wenqi Li <wenqil@nvidia.com>

black with pip (#3653)

b9ef673

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

lint tests (#3656)

4ffe588

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

pytype working for macOS (#3657)

6092b4d

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Delete testdata.nrrd (#3658)

d646120

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3654 remove some flake8 errors ignore (#3659)

a8ff27c

* ignore some flake8 errors Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #3660 2003->2106 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3661 Add default values to CopyItems transform (#3662)

a644b40

* [DLMED] add default values Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] add label transform (#3666)

40257f5

Signed-off-by: Nic Ma <nma@nvidia.com>

install from/with conda (#3667)

e0db5a5

install fresh from conda or install dependencies using environment-dev.yml Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

DictPostFixes (#3671)

b2cc166

* DictPostFixes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * use fn Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

[DLMED] change to warning (#3675)

c327cfa

Signed-off-by: Nic Ma <nma@nvidia.com>

3672 Add more messages for AUC warning (#3676)

b4f8ff1

* [DLMED] change to warning Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more error message Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] simplify the messages Signed-off-by: Nic Ma <nma@nvidia.com>

Update make_nifti (#3682)

ab14b8b

allow test image creation to save to different folders and with different file names

support stack of images with channels (#3680)

50c201c

* support stack of images with channels Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3686 Skip workflow run if data is empty or the specified epoch_length…

e96dcca

… is 0 (#3690) * [DLMED] check 0 length Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add dist tests Signed-off-by: Nic Ma <nma@nvidia.com>

adds a dev mode collate for diagnostic info (#3684)

32a045d

* add dev mode collate Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

add benchmarking warp against python itk (#3692)

3907cb4

* add benchmarking warp against python itk Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

compiler warnings (#3698)

c2018cf

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

try to fix #3621 (#3673)

3180c27

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Nic-Ma merged commit a12e9d4 into Nic-Ma:3713-fix-string-mode Jan 25, 2022

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merge master#358

merge master#358
Nic-Ma merged 333 commits intoNic-Ma:3713-fix-string-modefrom
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Nic-Ma commented Jan 25, 2022

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Nic-Ma commented Jan 25, 2022

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