CodeCamp #141 [Feature] Add BioMedical3DRandomFlip. #2404
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Yes, I check the information about errors, but I cannot find the reason for the bug of my code. |
MeowZheng
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we are figuring out the bug of the ci test |
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| def __init__(self, | ||
| prob: float, | ||
| axes: Optional[Tuple[int, ...]] = None, |
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| axes: Optional[Tuple[int, ...]] = None, | |
| axes: Tuple[int, ...], |
I think the axes cannot be None in this transform, and could you give an example about axes in docstring, like the order of axes is ZYX or ZXY?
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Okay, the order 'ZXY' is given in docstring.
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| """Flip biomedical 3D images and segmentations. Modified from | ||
| https://github.com/MIC-DKFZ/batchgenerators/blob/master/batchgenerators/tra | ||
| nsforms/spatial_transforms.py # noqa:E501 Copyright 2021 Division of | ||
| Medical Image Computing, German Cancer Research Center (DKFZ) and Applied | ||
| Computer Vision Lab, Helmholtz Imaging Platform. Licensed under the | ||
| Apache-2.0 License Required Keys: | ||
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| - img | ||
| - gt_seg_map (optional) | ||
| Modified Keys: | ||
| - img | ||
| - gt_seg_map (optional)) | ||
| Added Keys: | ||
| - do_flip | ||
| - flip_axes |
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Please other Bio3D transform and refine the docstring
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I have refined docstring.
Codecov ReportBase: 83.41% // Head: 83.40% // Decreases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## dev-1.x #2404 +/- ##
===========================================
- Coverage 83.41% 83.40% -0.01%
===========================================
Files 145 145
Lines 8451 8503 +52
Branches 1259 1272 +13
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- Misses 1194 1197 +3
- Partials 208 214 +6
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| - img | ||
| - gt_seg_map (optional) |
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| - img | |
| - gt_seg_map (optional) | |
| Required Keys: | |
| - img (np.ndarry): Biomedical image with shape (N, Z, Y, X) by default, | |
| N is the number of modalities. | |
| - gt_seg_map (np.ndarray, optional): Biomedical seg map with shape | |
| (Z, Y, X) by default. |
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| - img | ||
| - gt_seg_map (optional) |
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| - img | |
| - gt_seg_map (optional) | |
| Required Keys: | |
| - img (np.ndarry): Biomedical image with shape (N, Z, Y, X) by default, | |
| N is the number of modalities. | |
| - gt_seg_map (np.ndarray, optional): Biomedical seg map with shape | |
| (Z, Y, X) by default. |
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| """Flip biomedical 3D images and segmentations. Modified from | ||
| https://github.com/MIC-DKFZ/batchgenerators/blob/master/batchgenerators/tra | ||
| nsforms/spatial_transforms.py # noqa:E501 Copyright 2021 Division of | ||
| Medical Image Computing, German Cancer Research Center (DKFZ) and Applied | ||
| Computer Vision Lab, Helmholtz Imaging Platform. Licensed under the | ||
| Apache-2.0 License. |
There was a problem hiding this comment.
Suggested change
| """Flip biomedical 3D images and segmentations. Modified from | |
| https://github.com/MIC-DKFZ/batchgenerators/blob/master/batchgenerators/tra | |
| nsforms/spatial_transforms.py # noqa:E501 Copyright 2021 Division of | |
| Medical Image Computing, German Cancer Research Center (DKFZ) and Applied | |
| Computer Vision Lab, Helmholtz Imaging Platform. Licensed under the | |
| Apache-2.0 License. | |
| """Flip biomedical 3D images and segmentations. | |
| Modified from | |
| https://github.com/MIC-DKFZ/batchgenerators/blob/master/batchgenerators/transforms/spatial_transforms.py # noqa:E501 | |
| Copyright 2021 Division of | |
| Medical Image Computing, German Cancer Research Center (DKFZ) and Applied | |
| Computer Vision Lab, Helmholtz Imaging Platform. | |
| Licensed under the Apache-2.0 License. |
MeowZheng
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Jan 20, 2023
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Mar 27, 2023
Fix typo in AttnProcessor2_0 symbol.
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Apr 5, 2024
…mlab#2404) ## Motivation Support for biomedical 3d images augmentation. ## Modification Add BioMedical3DRandomFlip in mmseg/datasets/transforms/transforms.py. Co-authored-by: MeowZheng <meowzheng@outlook.com>
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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
Support for biomedical 3d images augmentation.
Modification
Add BioMedical3DRandomFlip in mmseg/datasets/transforms/transforms.py.
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)
Add the function to support the flipping for biomedical 3d images and segmentation maps.
Checklist