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Thanks for your contribution and we appreciate it a lot. The following instructions would make your pull request more healthy and more easily get feedback. If you do not understand some items, don't worry, just make the pull request and seek help from maintainers.

Motivation

Add random crop for the biomedical image.

Modification

implement nnUNet random crop before data augmentation

BC-breaking (Optional)

Does the modification introduce changes that break the backward-compatibility of the downstream repos?
If so, please describe how it breaks the compatibility and how the downstream projects should modify their code to keep compatibility with this PR.

Use cases (Optional)

If this PR introduces a new feature, it is better to list some use cases here, and update the documentation.

Checklist

  1. Pre-commit or other linting tools are used to fix the potential lint issues.
  2. The modification is covered by complete unit tests. If not, please add more unit test to ensure the correctness.
  3. If the modification has potential influence on downstream projects, this PR should be tested with downstream projects, like MMDet or MMDet3D.
  4. The documentation has been modified accordingly, like docstring or example tutorials.

@Yejin0111 Yejin0111 changed the base branch from master to dev-1.x December 5, 2022 11:05
# at least 1% of the class voxels need to be selected,
# otherwise it may be too sparse
min_percent_coverage = 0.01
rndst = np.random.RandomState(1234)
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remove randomness seed

@MeowZheng MeowZheng added this to the 1.0.0rc3 milestone Dec 22, 2022
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codecov bot commented Dec 27, 2022

Codecov Report

Base: 83.26% // Head: 83.38% // Increases project coverage by +0.11% 🎉

Coverage data is based on head (678344c) compared to base (933e4d3).
Patch coverage: 88.60% of modified lines in pull request are covered.

Additional details and impacted files
@@             Coverage Diff             @@
##           dev-1.x    #2378      +/-   ##
===========================================
+ Coverage    83.26%   83.38%   +0.11%     
===========================================
  Files          142      143       +1     
  Lines         8068     8204     +136     
  Branches      1205     1219      +14     
===========================================
+ Hits          6718     6841     +123     
- Misses        1163     1171       +8     
- Partials       187      192       +5     
Flag Coverage Δ
unittests 83.38% <88.60%> (+0.11%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
mmseg/datasets/transforms/transforms.py 95.23% <88.31%> (-1.20%) ⬇️
mmseg/datasets/__init__.py 100.00% <100.00%> (ø)
mmseg/datasets/transforms/__init__.py 100.00% <100.00%> (ø)
mmseg/datasets/ade.py 100.00% <0.00%> (ø)
mmseg/datasets/hrf.py 75.00% <0.00%> (ø)
mmseg/datasets/lip.py 100.00% <0.00%> (ø)
mmseg/datasets/voc.py 100.00% <0.00%> (ø)
mmseg/datasets/drive.py 75.00% <0.00%> (ø)
mmseg/datasets/isaid.py 100.00% <0.00%> (ø)
mmseg/datasets/isprs.py 100.00% <0.00%> (ø)
... and 11 more

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@MeowZheng MeowZheng merged commit 7e22612 into open-mmlab:dev-1.x Dec 30, 2022
MeowZheng added a commit to MeowZheng/mmsegmentation that referenced this pull request Dec 30, 2022
)

* [Feature] Add Biomedical 3D array random crop transform

* fix lint

* fix gen crop bbox

* fix gen crop bbox

* docstring

* typo

Co-authored-by: MeowZheng <[email protected]>
MeowZheng added a commit to MeowZheng/mmsegmentation that referenced this pull request Dec 30, 2022
)

* [Feature] Add Biomedical 3D array random crop transform

* fix lint

* fix gen crop bbox

* fix gen crop bbox

* docstring

* typo

Co-authored-by: MeowZheng <[email protected]>
MeowZheng added a commit to MeowZheng/mmsegmentation that referenced this pull request Dec 30, 2022
)

* [Feature] Add Biomedical 3D array random crop transform

* fix lint

* fix gen crop bbox

* fix gen crop bbox

* docstring

* typo

Co-authored-by: MeowZheng <[email protected]>
MeowZheng added a commit that referenced this pull request Dec 30, 2022
* [Feature] Add Biomedical 3D array random crop transform

* fix lint

* fix gen crop bbox

* fix gen crop bbox

* docstring

* typo

Co-authored-by: MeowZheng <[email protected]>
MeowZheng added a commit that referenced this pull request Dec 30, 2022
* [Feature] Add Biomedical 3D array random crop transform

* fix lint

* fix gen crop bbox

* fix gen crop bbox

* docstring

* typo

Co-authored-by: MeowZheng <[email protected]>
MeowZheng added a commit that referenced this pull request Dec 30, 2022
* [Feature] Add Biomedical 3D array random crop transform

* fix lint

* fix gen crop bbox

* fix gen crop bbox

* docstring

* typo

Co-authored-by: MeowZheng <[email protected]>
aravind-h-v pushed a commit to aravind-h-v/mmsegmentation that referenced this pull request Mar 27, 2023
@OpenMMLab-Assistant-007
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Hi @Yejin0111 !
First of all, we want to express our gratitude for your significant PR in the OpenMMLab project. Your contribution is highly appreciated, and we are grateful for your efforts in helping improve this open-source project during your personal time. We believe that many developers will benefit from your PR.

We would also like to invite you to join our Special Interest Group (SIG) private channel on Discord, where you can share your experiences, ideas, and build connections with like-minded peers. To join the SIG channel, simply message moderator— OpenMMLab on Discord or briefly share your open-source contributions in the #introductions channel and we will assist you. Look forward to seeing you there! Join us :https://discord.gg/UjgXkPWNqA

If you have WeChat account,welcome to join our community on WeChat. You can add our assistant :openmmlabwx. Please add "mmsig + Github ID" as a remark when adding friends:)
Thank you again for your contribution❤

wjkim81 pushed a commit to wjkim81/mmsegmentation that referenced this pull request Dec 3, 2023
nahidnazifi87 pushed a commit to nahidnazifi87/mmsegmentation_playground that referenced this pull request Apr 5, 2024
)

* [Feature] Add Biomedical 3D array random crop transform

* fix lint

* fix gen crop bbox

* fix gen crop bbox

* docstring

* typo

Co-authored-by: MeowZheng <[email protected]>
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4 participants