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merge master #355

Merged
merged 324 commits into from
Jan 20, 2022
Merged

merge master #355

merged 324 commits into from
Jan 20, 2022

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Nic-Ma
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@Nic-Ma Nic-Ma commented Jan 20, 2022

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.

wyli and others added 30 commits October 5, 2021 16:56
@wyli
update workflow (#3073)
51b2380 
* update workflow

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

* fixes gpu tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
correct panelled example images (#3068)
57a26a0 
* correct panelled example images

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@kate-sann5100
2755 Add b-spline kernel option (#2847)
1651f1b 
* 2755 Add b-spline kernel option

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>
@wyli
daily tests for mmar loading (#3066)
6cf6a8d 
* adds integration tests

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

* temp tests

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

* cache pip

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

* fixes conc

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

* Revert "temp tests"

This reverts commit 5a931c6.

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

* print outcome

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>
@wyli
fixes mmar tests (#3077)
07c5f53 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
2231 enhances a few transform backends (#3075)
af88eeb 
* fixes RandGaussianSmooth

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

* minor fixes

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
[DLMED] add more tests (#3080)
8d07aad 
Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
2357 Fixes unit test cases to run on GA100 (#3072)
6a2086d 
* relax atol for a100

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

* temp tests

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

* fixes #3071

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

* remove temp tests

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

* fixes tests

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

* update tests

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

* add tf32 tests

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

* fixes rtol wit tf32

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

* detect tf32

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

* update flag

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

* fixes testing util

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@yiheng-wang-nv
fix densenet264 error (#3081)
932abbe 
Signed-off-by: Yiheng Wang <vennw@nvidia.com>
@wyli
fixes figures (#3083)
6169c5d 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
fixes rst format issues (#3088)
54bd9db 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
oneof doc (#3090)
3b109f0 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma @wyli
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>
@rijobro @wyli
Torch CropForeground, HistogramNormalize, RandHistogramShift (#…
dc970c7 
…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>
@Nic-Ma
[DLMED] fix wrong doc-string (#3096)
ce38a93 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
2998 Add MLFlowHandler (#3099)
31f9c1e 
* [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>
@rijobro
KeepLargestConnectedComponent(d) example transforms (#3108)
7b1b772 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@rijobro
Torch AddCoordinateChannels, ExtremePointsChannel, `RandWeightedC…
c346956 
…rop` (#3078)

Torch `AddCoordinateChannels`, `ExtremePointsChannel`, `RandWeightedCrop`
@Nic-Ma
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>
@wyli
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>
@Nic-Ma
3087 enhance usage of intensity RandomizableTransform (#3094)
e0f84f2 
* [DLMED] update intensity transforms

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
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>
@Nic-Ma @wyli
[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>
@wyli
3122 pytorch versions tests (#3123)
c4dd43f 
* 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>
@BenTenmann
feat: refactor seg-net for easier use (#3057)
ed9cd41 
* feat: refactor seg-net for easier use

Signed-off-by: BenTenmann <benji.tenmann@me.com>
@wyli @monai-bot
3127 fixes autopep8 error (#3128)
e29a6ea 
* 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>
@Nic-Ma @ericspod @wyli
[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>
@Nic-Ma
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>
@Nic-Ma @wyli
3114 Add fast training integration test (#3120)
6dc65db 
* [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>
@rijobro
allow ROIs bigger than im for RandCropByLabelClasses, RandCropByPosNe…
6155724 
…gLabel (#3129)

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Nic-Ma and others added 29 commits January 10, 2022 09:48
@Nic-Ma
[DLMED] fix dtype issue (#3625)
24404f4 
Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
3628 0-d array to_contiguous (#3629)
3c6ee69 
* 0-d array

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

* handling string types

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
3624 Add kwargs to torch APIs of utilities (#3631)
2fef7ff 
* [DLMED] add kwargs for torch APIs

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

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
capture windows permission error (#3633)
83f8b06 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
3632 Enhance GridPatchDataset for iterable API and data source (#3636)
be1c362 
* [DLMED] update GridPatchDataset

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

* [DLMED] fix test typo

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

* [DLMED] update for windows

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

* [DLMED] fix windows test

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

* [DLMED] update test

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] add missing doc-string (#3646)
523a047 
Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
3621 update get_rank calls (#3641)
12955c5 
* update get_rank calls

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

* relaxing atol/rtol in tests.test_savitzky_golay_filter

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

* skip timing for cpu only tests

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

* fixes import ContentTooShortError

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
update meshgrid (#3644)
d58e234 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
EnsureChannelFirst: avoid re-creation of AddChannel (#3649)
35c2b37 
* avoid re-creation of AddChannel in EnsureChannelFirst
@Nic-Ma
3578 Support single channel with OneHot format in KeepLargestConnecte…
cd177c0 
…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>
@wyli
moveaxis and typing enhancements (#3648)
459b081 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
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>
@rijobro
option to occlude all channels simultaneously (#3543)
3a26702 
* option to occlude all channels simultaneously
@wyli
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>
@rijobro
black with pip (#3653)
b9ef673 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@rijobro
lint tests (#3656)
4ffe588 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@rijobro
pytype working for macOS (#3657)
6092b4d 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@wyli
Delete testdata.nrrd (#3658)
d646120 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
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>
@Nic-Ma
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>
@Nic-Ma
[DLMED] add label transform (#3666)
40257f5 
Signed-off-by: Nic Ma <nma@nvidia.com>
@rijobro @wyli
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>
@rijobro
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>
@Nic-Ma
[DLMED] change to warning (#3675)
c327cfa 
Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli @pre-commit-ci
3595 - adds a folder layout class (#3655)
c2b6459 
* 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>
@Nic-Ma
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>
@Nic-Ma
3670 Fix channel_dim in ITKReader and add in it NibabelReader (#3678)
2500edd 
* [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>
@rijobro
Update make_nifti (#3682)
ab14b8b 
allow test image creation to save to different folders and with different file names
@wyli
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>
@Nic-Ma Nic-Ma merged commit 47d4bc9 into Nic-Ma:3686-skip-workflow-run Jan 20, 2022
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