merge master by Nic-Ma · Pull Request #117 · Nic-Ma/MONAI

Nic-Ma · 2021-06-01T14:42:19Z

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 --codeformat --coverage.
Quick tests passed locally by running ./runtests.sh --quick.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

* 1651 implement RegUNet Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

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

* Update MONAI Docker with OpenSlide dependencies Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update cron job to install apt dependencies Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* use eval for getting class_idx for gradcam

* fixes unit test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes timed call tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

basic inverse API

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

* addresses testing instance memory errors Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update coverage config Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes https://github.com/Project-MONAI/MONAI/runs/2083800079?check_suite_focus=true#step:5:13886 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * test cases matching in runner Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes openslide tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes https://github.com/Project-MONAI/MONAI/runs/2086767998?check_suite_focus=true#step:7:5955 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes print stats Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove unused Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove global logging config Signed-off-by: Wenqi Li <wenqil@nvidia.com> * omit setup.py Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* 1651 implement RegUNet Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 1651 implement RegUNet Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk> * 1651 reformat code Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk> * 1651 reformat code Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk> * 1651 add globalnet Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk> * 1651 reformat code Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk> * 1651 reformat code Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk> * 1651 reformat code Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk> * 1651 reformat code Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

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

* [DLMED] add DistributedWeightedRandomSampler Signed-off-by: Nic Ma <nma@nvidia.com>

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

…seeds (#1761) * TEST: Check for identical MedNISTDataset length for different seeds Signed-off-by: Adam Aji <3487395+adamaji@users.noreply.github.com> * BUG: MedNISTDataset returns differently sized datasets for diff seeds Signed-off-by: Adam Aji <3487395+adamaji@users.noreply.github.com>

* [DLMED] add length API Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove replacement arg Signed-off-by: Nic Ma <nma@nvidia.com>

* reduce randomly cropped amount to appease CI Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fixes rand inverse Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] update ignite to 0.4.4 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix ignite compatible issues Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue 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] fix docs Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

lossless inverse transforms (non-croppad)

) * [DLMED] add greater_or_equal Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

* [DLMED] enhance CheckpointLoader Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

* Update WSIReader with cuCIM Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update unittests for cuCIM Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* Add to_onehot_y and include_background Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Add parameters to test seg loss Signed-off-by: Yiheng Wang <vennw@nvidia.com> * modify log softmax Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Modify weight format Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

Zoomd and RandZoomd

Inverse Rotated and RandRotated

* [DLMED] add CenterScaleCrop Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

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

* [DLMED] enhance CSVSaver Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix test errors 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> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] update accoring to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

)

* [DLMED] add meta_key arg to components Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] read-only transforms can share same meta data for keys Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more unit tests Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

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

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

* [DLMED] temp combine batch and output Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

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

* cache grid Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds cache tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* thread safety impl. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes croppad Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixed intensity Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes spatial Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes util Signed-off-by: Wenqi Li <wenqil@nvidia.com> * autofix Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update datastats Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes torch 1.7 issue Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes mac/win n_workers Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments 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: ambroslins <ambros.lins@gmail.com>

* add pypi quick tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * cron pypi tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit b6d86d6. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * revise cron Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit 44cddc0. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update setup.cfg Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* [DLMED] fix CopyItemsd transform Signed-off-by: Nic Ma <nma@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: Wenqi Li <wenqil@nvidia.com>

* enhance downloading APIs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add PostProcessing handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] skip min test Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] Adjust Invertd and TransformInverter Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] add detailed example to doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * enhance docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

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

This reverts commit 4c6af53. Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* removing convolutional compatability kernel for an optional matric multiplication Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * change to identity test against None Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * updating tests, non-determanism should be solved Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * moving compatability matrix to gpu in test to prevent errors when running without cuda Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * removing unused imports Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * pytyping fix for optional arg Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* removing convolutional compatability kernel for an optional matric multiplication Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * change to identity test against None Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * updating tests, non-determanism should be solved Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * moving compatability matrix to gpu in test to prevent errors when running without cuda Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * removing unused imports Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * pytyping fix for optional arg Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * moving back to permissive testing sue to cuda non determanism Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

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

* skip resampling if possible Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance doc-string of CacheDataset Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* revise cron-pip Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes pythonpath Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update path Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Started on a ResNet for classification from 1D, 2D, 3D images Signed-off-by: Douwe Spaanderman <dspaanderman@gmail.com>

kate-sann5100 and others added 30 commits March 9, 2021 15:31

1651 implement RegUNet (#1658)

78ec66f

* 1651 implement RegUNet Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

remove print msg (#1730)

ea1d04b

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

Fix MONAI docker dependency (#1731)

a462714

* Update MONAI Docker with OpenSlide dependencies Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update cron job to install apt dependencies Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

[1710] Gradcam eval (#1734)

d4c201e

* use eval for getting class_idx for gradcam

fixes unit test (#1735)

c362beb

* fixes unit test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes timed call tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

basic inverse API (#1720)

0b1fc4e

basic inverse API

improve decollate test for set_determinism (#1736)

c3e5a69

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

1236 integration test memory (#1738)

6d3bf2f

* addresses testing instance memory errors Signed-off-by: Wenqi Li <wenqil@nvidia.com>

1665 adjust localnet (#1752)

ce8f92a

* 1651 implement RegUNet Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

[DLMED] update WSIReader for typos and docs (#1758)

e001d2a

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

1742 Add DistributedWeightedRandomSampler (#1745)

21a3c16

* [DLMED] add DistributedWeightedRandomSampler Signed-off-by: Nic Ma <nma@nvidia.com>

Croppad inverse transform (#1737)

f56058d

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

TEST: Fix failing pytype check for predict_segmentation (#1762)

e17e158

Add __len__ for DistributedWeightedRandomSampler (#1766)

4670fd2

* [DLMED] add length API Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove replacement arg Signed-off-by: Nic Ma <nma@nvidia.com>

reduce randomly cropped amount to appease CI (#1769)

1badb41

* reduce randomly cropped amount to appease CI Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fixes rand inverse Signed-off-by: Wenqi Li <wenqil@nvidia.com>

update contrib guide to include some recent changes in dev tools (#1763)

3ea9ed4

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

1768 Update docs based on feedback (#1774)

13a2c59

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

lossless inverse (#1767)

3406398

lossless inverse transforms (non-croppad)

Update WSIReader with cuCIM (#1773)

bcbd685

* Update WSIReader with cuCIM Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update unittests for cuCIM Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Inverse Spacingd (#1779)

5588528

Inverse Resized (#1780)

46154ec

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

Inverse Zoomd and RandZoomd (#1778)

cf3bd1a

Zoomd and RandZoomd

Inverse Rotated (#1782)

592806a

Inverse Rotated and RandRotated

Nic-Ma and others added 29 commits May 17, 2021 16:05

allow sequence for network consistency (#2209)

fed0136

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

2041 - fixing main/releasing branch CI/CD; update contributing.md (#2123

e6258c9

)

cleaning allocated memory (#2216)

26ee695

Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

array transforms inherit Transform (#2219)

ba03150

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

inverse adjust contrast (#2217)

4c6af53

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

improve error msg (#2229)

ebfd550

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

2172 caching grid for randaffine (#2228)

2fb4b21

* cache grid Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds cache tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

fix type for margin argument in CropForegroundd (#2234)

33539db

Signed-off-by: ambroslins <ambros.lins@gmail.com>

SaveImage print_log (#2237)

fac9350

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

2236 Fix the duplicated key issue in CopyItemsd transform (#2238)

81994d2

* [DLMED] fix CopyItemsd transform Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

fixes network docs (#2240)

5d46589

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

enhance downloading APIs (#2242)

c3a5bdd

* enhance downloading APIs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Update type hints for act and norm (#2254)

fbfda15

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

Revert "inverse adjust contrast (#2217)" (#2259)

3ff988f

This reverts commit 4c6af53. Signed-off-by: Wenqi Li <wenqil@nvidia.com>

move mednist to gdrive (#2276)

2b13246

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

skip resampling for randaffine(d) if possible (#2264)

2aec103

* skip resampling if possible Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Enhance the doc-string of CacheDataset (#2279)

70f9fd1

* [DLMED] enhance doc-string of CacheDataset Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

Fixes cron tests (#2277)

7ee7989

* revise cron-pip Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes pythonpath Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update path Signed-off-by: Wenqi Li <wenqil@nvidia.com>

[WIP] ResNet (#2253)

2f60799

* Started on a ResNet for classification from 1D, 2D, 3D images Signed-off-by: Douwe Spaanderman <dspaanderman@gmail.com>

Nic-Ma merged commit 1449a0c into Nic-Ma:561-provide-metrics-base Jun 1, 2021

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merge master#117

merge master#117
Nic-Ma merged 289 commits into
Nic-Ma:561-provide-metrics-basefrom
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Nic-Ma commented Jun 1, 2021

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Nic-Ma commented Jun 1, 2021

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