merge master #346

Nic-Ma · 2022-01-10T13:53:48Z

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.

* release note v0.7 Signed-off-by: Wenqi Li <[email protected]> * adds whatsnew 07 Signed-off-by: Wenqi Li <[email protected]>

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

* [DLMED] update README Signed-off-by: Nic Ma <[email protected]> * [DLMED] update what's new Signed-off-by: Nic Ma <[email protected]> * [DLMED] use whatsnew link Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add more doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] edit change log Signed-off-by: Nic Ma <[email protected]> * [DLMED] add command to get transform backend Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance the doc Signed-off-by: Nic Ma <[email protected]>

…dGaussianSharpen` (#2971) Torch `GaussianSmooth`, `RandGaussianSmooth`, `GaussianSharpen`, `RandGaussianSharpen`

* apply pyupgrade Signed-off-by: Jirka <[email protected]> * exclude monai/_version.py Signed-off-by: Jirka <[email protected]>

* enhance the release version string check Signed-off-by: GitHub <[email protected]> * update the releasing steps Signed-off-by: GitHub <[email protected]> Co-authored-by: Nic Ma <[email protected]>

* [DLMED] update ignite 0.4.6 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issues Signed-off-by: Nic Ma <[email protected]>

* print dtype along with type Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]>

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

…SpikeNoise (#2974) GibbsNoise, RandGibbsNoise, KSpaceSpikeNoise, RandKSpaceSpikeNoise

…std (#3044) Signed-off-by: Richard Brown <[email protected]>

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

Torch `Spacing`, `Spacingd`

* torch fgbgtoindices Signed-off-by: Wenqi Li <[email protected]> * unravel indices Signed-off-by: Wenqi Li <[email protected]> * simplified Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>

* [DLMED] fix spacing dtype Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix dtype Signed-off-by: Nic Ma <[email protected]>

create example transform images

* [DLMED] fix crop performance issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] use default to avoid overflow Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI error Signed-off-by: Nic Ma <[email protected]>

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

* apply yesqa Signed-off-by: Jirka <[email protected]> * rev Signed-off-by: Jirka <[email protected]> * expand Signed-off-by: Jirka <[email protected]> * plugins Signed-off-by: Jirka <[email protected]>

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

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

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

* [DLMED] fix complex array issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test issue Signed-off-by: Nic Ma <[email protected]>

* Adding documentation for AutoEncoder and VarAutoEncoder Signed-off-by: Eric Kerfoot <[email protected]>

* [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 <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <[email protected]>

* update workflow Signed-off-by: Wenqi Li <[email protected]> * fixes gpu tests Signed-off-by: Wenqi Li <[email protected]>

* correct panelled example images Signed-off-by: Richard Brown <[email protected]>

* adds missing item Signed-off-by: Wenqi Li <[email protected]> * update the contributing guide Signed-off-by: Wenqi Li <[email protected]> * update copyright headers Signed-off-by: Wenqi Li <[email protected]>

* util to check the licence info Signed-off-by: Wenqi Li <[email protected]> * update flags Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

… APIs (#3526) * [DLMED] clarify old APIs Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update to 21.12 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add PyTorch 1.9 test Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add missing args Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update progress arg Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix oneof Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update index Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * Revert "[DLMED] update according to comments" This reverts commit c6c3a35. Signed-off-by: Nic Ma <[email protected]> * Revert "[DLMED] update index" This reverts commit 649a7c5. Signed-off-by: Nic Ma <[email protected]>

* drop py36 support Signed-off-by: Wenqi Li <[email protected]> * drop 20.09 test because of python min version 3.6 Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * error->warning, revise copyright Signed-off-by: Wenqi Li <[email protected]>

* has cupy check Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* adds min. memory testing utils Signed-off-by: Wenqi Li <[email protected]> * include valueerror for robust outcome Signed-off-by: Wenqi Li <[email protected]> * ensure float Signed-off-by: Wenqi Li <[email protected]> * msg improvements Signed-off-by: Wenqi Li <[email protected]> * update threshold Signed-off-by: Wenqi Li <[email protected]> * remove ref Signed-off-by: Wenqi Li <[email protected]> * separate disttests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] remove warning Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* Adding smooth deform transform Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Docs update Signed-off-by: Eric Kerfoot <[email protected]> * Type fixing Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix for moveaxis Signed-off-by: Eric Kerfoot <[email protected]> * Fix for moveaxis Signed-off-by: Eric Kerfoot <[email protected]> * Adding example images, random field sized reduced to (10,10,10) Signed-off-by: Eric Kerfoot <[email protected]> * Changed backend Signed-off-by: Eric Kerfoot <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Tweak Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]>

* runtest.sh defaults to no build/install Signed-off-by: Wenqi Li <[email protected]> * following test case conventions for multiprocessing - adding `_dist` to multiprocessing test cases - decouple multiprocessing LMDB tests from `test_lmdbdataset` Signed-off-by: Wenqi Li <[email protected]> * exclude lmdbdataset tests in min_tests Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>

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

…#3558) Signed-off-by: Wenqi Li <[email protected]>

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

* [DLMED] update dataset summary Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance data type Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

updates: - [github.com/pre-commit/pre-commit-hooks: v4.0.1 → v4.1.0](pre-commit/pre-commit-hooks@v4.0.1...v4.1.0) - [github.com/asottile/pyupgrade: v2.29.0 → v2.31.0](asottile/pyupgrade@v2.29.0...v2.31.0) - [github.com/asottile/yesqa: v1.2.3 → v1.3.0](asottile/yesqa@v1.2.3...v1.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* adds metadata when loading dicom series Signed-off-by: Wenqi Li <[email protected]> * fixes timed tests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* Create codeql-analysis.yml Signed-off-by: Wenqi Li <[email protected]> * build cpp Signed-off-by: Wenqi Li <[email protected]> * fixes Multiplication result converted to larger type Signed-off-by: Wenqi Li <[email protected]> * fixes url parsing Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add log handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] test CI Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix logging Signed-off-by: Nic Ma <[email protected]> * [DLMED] temp test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix wrong unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix wrong test cases Signed-off-by: Nic Ma <[email protected]>

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

* [DLMED] enhance slice_channels 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]> * [DLMED] remove test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add flag Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add kwargs Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix doc typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Richard Brown <[email protected]>

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

* adds a conda test Signed-off-by: Wenqi Li <[email protected]> * openslide windows Signed-off-by: Wenqi Li <[email protected]> * conda create Signed-off-by: Wenqi Li <[email protected]> * fixes lmdb Signed-off-by: Wenqi Li <[email protected]> * fixes windows paging Signed-off-by: Wenqi Li <[email protected]> * fixes matplotlib version Signed-off-by: Wenqi Li <[email protected]> * fixes openslide conda Signed-off-by: Wenqi Li <[email protected]> * remove temp tests Signed-off-by: Wenqi Li <[email protected]> * try to fix windows paging Signed-off-by: Wenqi Li <[email protected]> * update cpuonly tests Signed-off-by: Wenqi Li <[email protected]> * fixes windows install Signed-off-by: Wenqi Li <[email protected]> * update comments Signed-off-by: Wenqi Li <[email protected]>

* 3616 test downloading issues Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

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

wyli and others added 30 commits September 23, 2021 22:29

2914 release note, and what's new for v0.7 (#2992)

64fa255

* release note v0.7 Signed-off-by: Wenqi Li <[email protected]> * adds whatsnew 07 Signed-off-by: Wenqi Li <[email protected]>

delaying the removal (#3015)

bfa054b

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

update preview version tag (#3016)

f06de43

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

Enhance 0.7 README doc (#3017)

aa4eb5d

* [DLMED] update README Signed-off-by: Nic Ma <[email protected]> * [DLMED] update what's new Signed-off-by: Nic Ma <[email protected]> * [DLMED] use whatsnew link Signed-off-by: Nic Ma <[email protected]>

Torch GaussianSmooth, RandGaussianSmooth, GaussianSharpen, `Ran…

453a9c0

…dGaussianSharpen` (#2971) Torch `GaussianSmooth`, `RandGaussianSmooth`, `GaussianSharpen`, `RandGaussianSharpen`

apply pyupgrade (#3026)

a477905

* apply pyupgrade Signed-off-by: Jirka <[email protected]> * exclude monai/_version.py Signed-off-by: Jirka <[email protected]>

3018 enhance version string check (#3022)

a0130d1

* enhance the release version string check Signed-off-by: GitHub <[email protected]> * update the releasing steps Signed-off-by: GitHub <[email protected]> Co-authored-by: Nic Ma <[email protected]>

3028 update ignite CI tests to 0.4.6 (#3029)

fe93596

* [DLMED] update ignite 0.4.6 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issues Signed-off-by: Nic Ma <[email protected]>

enhance DataStats to include dtype (#3043)

28fb7d6

* print dtype along with type Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]>

enhance error handling (#3042)

e4dd504

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

2792 - Torch GibbsNoise, RandGibbsNoise, KSpaceSpikeNoise, RandKSpace…

fc478b0

…SpikeNoise (#2974) GibbsNoise, RandGibbsNoise, KSpaceSpikeNoise, RandKSpaceSpikeNoise

AdjustContrast, AdjustContrastd, RandAdjustContrast, RandAdjustContra…

0c03376

…std (#3044) Signed-off-by: Richard Brown <[email protected]>

remove false positive tests (#3046)

f85ad48

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

Torch Spacing, Spacingd (#3045)

bf561bb

Torch `Spacing`, `Spacingd`

2975 torch fgbgtoindices (#3038)

f909a6b

* torch fgbgtoindices Signed-off-by: Wenqi Li <[email protected]> * unravel indices Signed-off-by: Wenqi Li <[email protected]> * simplified Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>

3051 Fix dtype issue in Spacing transform (#3052)

d15cedd

* [DLMED] fix spacing dtype Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix dtype Signed-off-by: Nic Ma <[email protected]>

Create transform images (#3039)

a589c82

create example transform images

[DLMED] fix broken link (#3059)

3b5af50

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

remove redundant noqa (#3027)

8271d8e

* apply yesqa Signed-off-by: Jirka <[email protected]> * rev Signed-off-by: Jirka <[email protected]> * expand Signed-off-by: Jirka <[email protected]> * plugins Signed-off-by: Jirka <[email protected]>

[DLMED] enhance label classes (#3061)

87e2ecd

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

[DLMED] enhance ScaleIntensity (#3062)

15c1f77

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

update backend (#3065)

26f20f4

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

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

7ad0f6e

* [DLMED] fix complex array issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test issue Signed-off-by: Nic Ma <[email protected]>

Ae docs (#3067)

4618e85

* Adding documentation for AutoEncoder and VarAutoEncoder Signed-off-by: Eric Kerfoot <[email protected]>

update workflow (#3073)

51b2380

* update workflow Signed-off-by: Wenqi Li <[email protected]> * fixes gpu tests Signed-off-by: Wenqi Li <[email protected]>

correct panelled example images (#3068)

57a26a0

* correct panelled example images Signed-off-by: Richard Brown <[email protected]>

wyli and others added 29 commits December 21, 2021 10:04

3521 Copyright header update (#3522)

1516ca7

* adds missing item Signed-off-by: Wenqi Li <[email protected]> * update the contributing guide Signed-off-by: Wenqi Li <[email protected]> * update copyright headers Signed-off-by: Wenqi Li <[email protected]>

3521 - adds a util to check the licence info (#3523)

299a0d1

* util to check the licence info Signed-off-by: Wenqi Li <[email protected]> * update flags Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

3350 Remove PyTorch 1.5.x related logic and mark versions for all new…

58ded72

… APIs (#3526) * [DLMED] clarify old APIs Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

3533 Update PyTorch docker to 21.12 (#3534)

08f9bac

* [DLMED] update to 21.12 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add PyTorch 1.9 test Signed-off-by: Nic Ma <[email protected]>

3531 Add args to subclass of CacheDataset (#3532)

9caa1d0

* [DLMED] add missing args Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update progress arg Signed-off-by: Nic Ma <[email protected]>

3541 has cupy check (#3544)

21c5f6d

* has cupy check Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

3539 Remove decollate warning (#3545)

29bc93b

* [DLMED] remove warning Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>

[DLMED] enhance set_determinism (#3547)

df75199

Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

Remove apply_same_field (#3556)

c8e7fe1

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

skipping pretraining network loading when downloading is unsuccessful (…

885d5b9

…#3558) Signed-off-by: Wenqi Li <[email protected]>

[DLMED] fix mypy errors (#3562)

ba23afd

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

3565 - adds metadata when loading dicom series (#3566)

a7835ab

* adds metadata when loading dicom series Signed-off-by: Wenqi Li <[email protected]> * fixes timed tests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

update issue template for questions (#3597)

cdcd524

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

conda environment yaml file (#3584)

a93b8cc

Signed-off-by: Richard Brown <[email protected]>

3616 test downloading issues (#3617)

a0d2558

* 3616 test downloading issues Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

[DLMED] fix dtype issue (#3625)

24404f4

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

Nic-Ma merged commit 5235d67 into Nic-Ma:3613-fix-windows-temp Jan 10, 2022

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merge master #346

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Nic-Ma commented Jan 10, 2022

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Nic-Ma commented Jan 10, 2022

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