merge master by Nic-Ma · Pull Request #352 · Nic-Ma/MONAI

Nic-Ma · 2022-01-14T12:09:34Z

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: Nic Ma <nma@nvidia.com>

* apply yesqa Signed-off-by: Jirka <jirka.borovec@seznam.cz> * rev Signed-off-by: Jirka <jirka.borovec@seznam.cz> * expand Signed-off-by: Jirka <jirka.borovec@seznam.cz> * plugins Signed-off-by: Jirka <jirka.borovec@seznam.cz>

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

* create images Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * use brats Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * update Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * working Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * rename file Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * optional import matplotlib Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * docstrings Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * store images in https://github.com/Project-MONAI/DocImages Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * extra transform example images Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * most transforms Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

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

* [DLMED] fix complex array issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix test issue Signed-off-by: Nic Ma <nma@nvidia.com>

* Adding documentation for AutoEncoder and VarAutoEncoder Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* [pre-commit.ci] pre-commit suggestions updates: - [github.com/asottile/pyupgrade: v2.27.0 → v2.29.0](asottile/pyupgrade@v2.27.0...v2.29.0) * fixes #3071 Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* update workflow Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes gpu tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* correct panelled example images Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* 2755 Add b-spline kernel option Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 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>

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

* fixes RandGaussianSmooth Signed-off-by: Wenqi Li <wenqil@nvidia.com> * minor fixes Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* 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>

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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>

* Create codeql-analysis.yml Signed-off-by: Wenqi Li <wenqil@nvidia.com> * build cpp Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes Multiplication result converted to larger type Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes url parsing Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add log handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] test CI Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix logging Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] temp test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix wrong unit test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix wrong test cases Signed-off-by: Nic Ma <nma@nvidia.com>

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

* [DLMED] enhance slice_channels 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> * [DLMED] remove test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add flag Signed-off-by: Nic Ma <nma@nvidia.com>

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

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

* [DLMED] add ascontiguous Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance CacheDataset Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] export to utility Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add to subclasses Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix antipatterns Signed-off-by: Nic Ma <nma@nvidia.com>

* adds a conda test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * openslide windows Signed-off-by: Wenqi Li <wenqil@nvidia.com> * conda create Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes lmdb Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes windows paging Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes matplotlib version Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes openslide conda Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * try to fix windows paging Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update cpuonly tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes windows install Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* 3616 test downloading issues Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* 0-d array Signed-off-by: Wenqi Li <wenqil@nvidia.com> * handling string types Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [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>

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

* [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>

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

* 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>

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

* avoid re-creation of AddChannel in EnsureChannelFirst

…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>

Nic-Ma and others added 30 commits October 2, 2021 10:56

[DLMED] fix broken link (#3059)

3b5af50

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

remove redundant noqa (#3027)

8271d8e

* apply yesqa Signed-off-by: Jirka <jirka.borovec@seznam.cz> * rev Signed-off-by: Jirka <jirka.borovec@seznam.cz> * expand Signed-off-by: Jirka <jirka.borovec@seznam.cz> * plugins Signed-off-by: Jirka <jirka.borovec@seznam.cz>

[DLMED] enhance label classes (#3061)

87e2ecd

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

[DLMED] enhance ScaleIntensity (#3062)

15c1f77

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

update backend (#3065)

26f20f4

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

3063 Fix the complex Tensor issue in type conversion (#3064)

7ad0f6e

* [DLMED] fix complex array issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix test issue Signed-off-by: Nic Ma <nma@nvidia.com>

Ae docs (#3067)

4618e85

* Adding documentation for AutoEncoder and VarAutoEncoder Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

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>

correct panelled example images (#3068)

57a26a0

* correct panelled example images Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

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>

fixes mmar tests (#3077)

07c5f53

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

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>

[DLMED] add more tests (#3080)

8d07aad

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

fix densenet264 error (#3081)

932abbe

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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>

wyli and others added 29 commits January 5, 2022 09:01

update issue template for questions (#3597)

cdcd524

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

conda environment yaml file (#3584)

a93b8cc

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

3616 test downloading issues (#3617)

a0d2558

* 3616 test downloading issues Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

[DLMED] fix dtype issue (#3625)

24404f4

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

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>

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>

capture windows permission error (#3633)

83f8b06

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

[DLMED] add missing doc-string (#3646)

523a047

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

update meshgrid (#3644)

d58e234

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

EnsureChannelFirst: avoid re-creation of AddChannel (#3649)

35c2b37

* avoid re-creation of AddChannel in EnsureChannelFirst

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>

Nic-Ma merged commit 630fc5c into Nic-Ma:3665-add-label-transform Jan 14, 2022

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

merge master#352

merge master#352
Nic-Ma merged 315 commits intoNic-Ma:3665-add-label-transformfrom
Project-MONAI:dev

Nic-Ma commented Jan 14, 2022

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

18 participants

Conversation

Nic-Ma commented Jan 14, 2022

Description

Status

Types of changes

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

18 participants