merge master #397

Nic-Ma · 2022-04-04T12:01:23Z

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 <[email protected]>

* [DLMED] add dataset generator Signed-off-by: Nic Ma <[email protected]> * [DLMED] add DatasetGenerator 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 wrong test Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove return Signed-off-by: Nic Ma <[email protected]> * [DLMED] update rtol for CI Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* [DLMED] add missing docs Signed-off-by: Nic Ma <[email protected]> * [DLMED] add missing components Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add channel-wise Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip test if before 1.7 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 Iteration base class 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]>

Signed-off-by: Yiheng Wang <[email protected]>

* [DLMED] support string dtype Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance dtype in ToCupy Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add Iteration base class 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]>

Signed-off-by: Yiheng Wang <[email protected]>

* [DLMED] support string dtype Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance dtype in ToCupy Signed-off-by: Nic Ma <[email protected]>

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

* Update to not include number for the name of the first range Signed-off-by: Behrooz <[email protected]> * Update CuCIM and TorchVision wrappers to include name Signed-off-by: Behrooz <[email protected]> * Update nvtx range to append undelying class for wrapper tranforms Signed-off-by: Behrooz <[email protected]> * Add new test cases to cover changes Signed-off-by: Behrooz <[email protected]> * Update cucim and torchvision check Signed-off-by: Behrooz <[email protected]>

* [DLMED] add missing images Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix 3471 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix AsDiscrete Signed-off-by: Nic Ma <[email protected]>

* make bending energy loss invariant to resolution fixes #3485 Signed-off-by: Ebrahim Ebrahim <[email protected]> * set BendingEnergyLoss default normalize to False Maybe it's more important that the default behavior match usage of the term "bending energy" elsewhere, rather than that it be the most convenient behavior. Signed-off-by: Ebrahim Ebrahim <[email protected]>

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

* [DLMED] correct kwargs Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix grammar Signed-off-by: Nic Ma <[email protected]>

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

* [DLMED] add SavitzkyGolaySmoothd 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]>

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

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

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

* Adding Torchscript utility functions 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]> * Adding Torchscript utility functions Signed-off-by: Eric Kerfoot <[email protected]> * Added test for extra files 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 * Update Signed-off-by: Eric Kerfoot <[email protected]> * Update 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 * Update Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> * Updates 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 * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Updates 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]> Co-authored-by: Nic Ma <[email protected]>

* [DLMED] change to utility transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance args Signed-off-by: Nic Ma <[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] enhance reader Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix docs Signed-off-by: Nic Ma <[email protected]>

* fixes #3934 Signed-off-by: Wenqi Li <[email protected]> * min_test update Signed-off-by: Wenqi Li <[email protected]> * cu115 tests Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]>

* use enum for dicece reduction Signed-off-by: Yiheng Wang <[email protected]> * use look up option Signed-off-by: Yiheng Wang <[email protected]>

* [DLMED] update to 21.10 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo in integration test config Signed-off-by: Nic Ma <[email protected]>

* attention unet Signed-off-by: Juan Pablo de la Cruz Gutiérrez <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * fixed issues and added suggested improvements Signed-off-by: Juan Pablo de la Cruz Gutierrez <[email protected]> * fixed flake issues * smaller tests Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]>

* [DLMED] add verify script 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] add unit tests and doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip min tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] update device names Signed-off-by: Nic Ma <[email protected]> * [DLMED] update doc-string examples Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance error message Signed-off-by: Nic Ma <[email protected]> * [DLMED] cpu:0 to cpu Signed-off-by: Nic Ma <[email protected]> * [DLMED] adjust "dataset_dir" Signed-off-by: Nic Ma <[email protected]>

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

Signed-off-by: Yiheng Wang <[email protected]>

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

* fixes #3942 Signed-off-by: Wenqi Li <[email protected]> * adds import statement Signed-off-by: Wenqi Li <[email protected]> * more tests Signed-off-by: Wenqi Li <[email protected]> * update to resolve import statement Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Yiheng Wang <[email protected]>

* Minor change to UNet to permit greater modifiability Signed-off-by: Eric Kerfoot <[email protected]> * Type fix Signed-off-by: Eric Kerfoot <[email protected]> * Reverting minor change Signed-off-by: Eric Kerfoot <[email protected]>

* Check images dimensions and color channels Signed-off-by: Behrooz <[email protected]>

* fixes multiprocessing memory issue Signed-off-by: Wenqi Li <[email protected]> * Revert "Workaround OOM issue in classification 2D integration tests (#3949)" This reverts commit 6ea9742. Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes typo Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [DLMED] support relative ids Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo in test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add description Signed-off-by: Nic Ma <[email protected]> * [DLMED] optimize the logic Signed-off-by: Nic Ma <[email protected]>

* fixes docstrings 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]>

* [DLMED] add export script Signed-off-by: Nic Ma <[email protected]> * [DLMED] add base unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add custom config item types and reference resolver Signed-off-by: Nic Ma <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] enhance doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add logging Signed-off-by: Nic Ma <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] remove customized configitem and resolver Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove assert ret Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to ckpt_export Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to .ts Signed-off-by: Nic Ma <[email protected]> * [DLMED] update min test Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify args Signed-off-by: Nic Ma <[email protected]> * fixes integration tests Signed-off-by: Wenqi Li <[email protected]> * [DLMED] change to coverage Signed-off-by: Nic Ma <[email protected]> * update integration tests Signed-off-by: Wenqi Li <[email protected]> * [DLMED] fix blossom Signed-off-by: Nic Ma <[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]> Co-authored-by: Wenqi Li <[email protected]>

* [DLMED] add logging config Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] adjust config Signed-off-by: Nic Ma <[email protected]> * [DLMED] add doc-string Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

Signed-off-by: Yiheng Wang <[email protected]>

* update mmars, fixes #4003 Signed-off-by: Wenqi Li <[email protected]> * adds typing Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * workaround cucim Signed-off-by: Wenqi Li <[email protected]>

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

* fixes unit test Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * adds docker version tests Signed-off-by: Wenqi Li <[email protected]> * fixes #4016 Signed-off-by: Wenqi Li <[email protected]> * local tests Signed-off-by: Wenqi Li <[email protected]> * remove mmar cache daily Signed-off-by: Wenqi Li <[email protected]> * remove cache Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 238d883. Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]>

* update bundle doc Signed-off-by: Wenqi Li <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update meta Signed-off-by: Wenqi Li <[email protected]> * update intro Signed-off-by: Wenqi Li <[email protected]> * update examples Signed-off-by: Wenqi Li <[email protected]> * adds yaml demo Signed-off-by: Wenqi Li <[email protected]> * update schema Signed-off-by: Wenqi Li <[email protected]> * update toc Signed-off-by: Wenqi Li <[email protected]> * update doc page Signed-off-by: Wenqi Li <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * $import Signed-off-by: Wenqi Li <[email protected]> * adds recommendations Signed-off-by: Wenqi Li <[email protected]> * update config Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * adds a link on CLI parsing Signed-off-by: Wenqi Li <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

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

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

* fix pil via specifying cpuonly version Signed-off-by: Yiheng Wang <[email protected]> * add push branch to check Signed-off-by: Yiheng Wang <[email protected]> * remove extra line Signed-off-by: Yiheng Wang <[email protected]> * remove push branch for upstream Signed-off-by: Yiheng Wang <[email protected]>

* Add support for level as input Signed-off-by: Behrooz <[email protected]> * Add unittests for levels Signed-off-by: Behrooz <[email protected]> * Update docstring Signed-off-by: Behrooz <[email protected]> * Add kwargs for WSIReader in all datasets Signed-off-by: Behrooz <[email protected]> * Update docstring Signed-off-by: Behrooz <[email protected]>

wyli and others added 30 commits December 9, 2021 13:37

adds the missing imports (#3462)

d2543ad

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

revise MILModel docstring (#3459)

82576e7

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

deprecate reduction (#3464)

4b5ad0b

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

Add missing components to API doc (#3468)

89f0bd4

* [DLMED] add missing docs Signed-off-by: Nic Ma <[email protected]> * [DLMED] add missing components Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test Signed-off-by: Nic Ma <[email protected]>

[DLMED] remove cls (#3475)

a4c1300

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

Add Iteration base class (#3472)

360c52f

* [DLMED] add Iteration base class 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]>

fix link error (#3488)

cb70e13

Signed-off-by: Yiheng Wang <[email protected]>

3465 Support string as dtype (#3478)

9ef0070

* [DLMED] support string dtype Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance dtype in ToCupy Signed-off-by: Nic Ma <[email protected]>

Add Iteration base class (#3472)

2cbb54c

* [DLMED] add Iteration base class 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]>

fix link error (#3488)

45af170

Signed-off-by: Yiheng Wang <[email protected]>

3465 Support string as dtype (#3478)

9ccc5ee

* [DLMED] support string dtype Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance dtype in ToCupy Signed-off-by: Nic Ma <[email protected]>

[DLMED] update to 0.4.7 (#3483)

7a66f18

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

3471 3491 Add example images for intensity transforms (#3494)

9927691

* [DLMED] add missing images Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix 3471 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix AsDiscrete Signed-off-by: Nic Ma <[email protected]>

Removes redundant casting -- ensure tuple (#3495)

3761ee0

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

3498 Correct kwargs arg for convert_to_torchscript (#3499)

a255648

* [DLMED] correct kwargs Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix grammar Signed-off-by: Nic Ma <[email protected]>

update tests with 1.10.1 (#3500)

531c276

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

3501 Add dict version SavitzkyGolaySmoothd (#3502)

d663d78

* [DLMED] add SavitzkyGolaySmoothd 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]>

remove file (#3507)

d2861a2

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

avoid 60.0.0 (#3514)

29779d1

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

[DLMED] add 6 new transform images (#3512)

c9d38f0

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

support of reversed indexing (#3508)

1d3a9d7

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

3517 Refine AddCoordinateChannels transform (#3524)

8e2ade5

* [DLMED] change to utility transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance args Signed-off-by: Nic Ma <[email protected]>

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]>

Nic-Ma and others added 29 commits March 15, 2022 15:43

3943 Enhance LoadImage transform for customized readers (#3944)

3b771bb

* [DLMED] enhance reader Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix docs Signed-off-by: Nic Ma <[email protected]>

3919 Use enums for reduction in DiceCELoss (#3953)

6ff8535

* use enum for dicece reduction Signed-off-by: Yiheng Wang <[email protected]> * use look up option Signed-off-by: Yiheng Wang <[email protected]>

Workaround OOM issue in classification 2D integration tests (#3949)

6ea9742

* [DLMED] update to 21.10 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo in integration test config Signed-off-by: Nic Ma <[email protected]>

optional meta_file (#3952)

55e6018

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

update cachedataset num workers (#3963)

7ee3488

Signed-off-by: Yiheng Wang <[email protected]>

[DLMED] update installation doc (#3970)

be25a72

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

fix fstring bugs (#3972)

459b188

Signed-off-by: Yiheng Wang <[email protected]>

Contain WSIReader to colored 2D images (#3979)

bdeb662

* Check images dimensions and color channels Signed-off-by: Behrooz <[email protected]>

3987 - fixes docstrings and adds checks (#3988)

7d8bb9b

* fixes docstrings Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

[DLMED] fix flake8 (#3991)

f11f58c

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

remove ambiguous or ops for optional args (#3997)

b91faa2

Signed-off-by: Yiheng Wang <[email protected]>

Update cuCIM min dependency to support randomized transforms (#4004)

a676e38

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

[DLMED] disable recursive macro (#4033)

af725d7

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

[DLMED] update to 22.02 (#4041)

4526b68

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

fixes typo ver (#4045)

167a320

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

Nic-Ma merged commit ec463d6 into Nic-Ma:main Apr 4, 2022

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merge master #397

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Nic-Ma commented Apr 4, 2022

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merge master #397

merge master #397

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Nic-Ma commented Apr 4, 2022

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