Replace imgaug with albumentations #1623
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #1623 +/- ##
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- Coverage 73.38% 73.37% -0.01%
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Files 134 134
Lines 24064 24063 -1
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- Hits 17659 17657 -2
- Misses 6405 6406 +1 ☔ View full report in Codecov by Sentry. |
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Review Status
Actionable comments generated: 0
Configuration used: CodeRabbit UI
Files ignored due to filter (3)
- environment.yml
- environment_mac.yml
- environment_no_cuda.yml
Files selected for processing (4)
- .conda/meta.yaml (2 hunks)
- sleap/nn/data/augmentation.py (6 hunks)
- sleap/nn/data/pipelines.py (8 hunks)
- tests/nn/data/test_augmentation.py (2 hunks)
Additional comments: 17
.conda/meta.yaml (2)
33-39: The addition of
albumentationsto thehostrequirements is consistent with the PR objective to replaceimgaugwithalbumentations. However, ensure that the presence ofopencvin the requirements is still necessary, as the PR objective mentioned eliminating the dependency on a specific version ofopencvrequired byimgaug.61-67: The addition of
albumentationsto therunrequirements is consistent with the PR objective to replaceimgaugwithalbumentations. Similar to thehostrequirements, verify the necessity ofopencvin therunrequirements.sleap/nn/data/augmentation.py (4)
1-11: The import changes from
imgaugtoalbumentationsare consistent with the PR objective to replace the image augmentation library.105-124: The introduction of the
AlbumentationsAugmenterclass is consistent with the PR objective and the summary provided.140-202: > Note: This review was outside the patches, so it was mapped to the patch with the greatest overlap. Original lines [129-202]
The
from_configmethod has been correctly updated to usealbumentationstransformations, aligning with the PR objective.
- 229-244: > Note: This review was outside the patches, so it was mapped to the patch with the greatest overlap. Original lines [229-260]
The
transform_datasetmethod has been updated to applyalbumentations-based image augmentation, which is in line with the PR objective.sleap/nn/data/pipelines.py (8)
18-24: The import changes from
imgaugtoalbumentationsare consistent with the PR objectives and the summary provided. TheAlbumentationsAugmenteris correctly imported and replaces the previousImgaugAugmenter.68-74: The
TRANSFORMERStuple has been correctly updated to includeAlbumentationsAugmenterinstead ofImgaugAugmenter, aligning with the PR objectives and the summary.406-411: The usage of
AlbumentationsAugmenter.from_configis consistent with the PR objectives to replaceimgaugwithalbumentations. The configuration is correctly passed to thefrom_configmethod.550-555: The usage of
AlbumentationsAugmenter.from_configwithin theCentroidConfmapsPipelineclass is consistent with the PR objectives and the summary.713-718: The usage of
AlbumentationsAugmenter.from_configwithin theTopdownConfmapsPipelineclass is consistent with the PR objectives and the summary.863-869: The usage of
AlbumentationsAugmenter.from_configwithin theBottomUpPipelineclass is consistent with the PR objectives and the summary.1028-1034: The usage of
AlbumentationsAugmenter.from_configwithin theBottomUpMultiClassPipelineclass is consistent with the PR objectives and the summary.1186-1192: The usage of
AlbumentationsAugmenter.from_configwithin theTopDownMultiClassPipelineclass is consistent with the PR objectives and the summary.tests/nn/data/test_augmentation.py (3)
17-20: The summary incorrectly states that the rotation angle parameters are adjusted from -90 to 90. The hunk shows that both
rotation_min_angleandrotation_max_angleare set to 90, not from -90 to 90. Please correct the summary to accurately reflect the changes made in the code.14-22: The changes in this hunk correctly reflect the PR's objective of replacing
imgaugwithalbumentations. TheAlbumentationsAugmenteris being used with the new configuration as expected.54-58: The changes in this hunk are also in line with the PR's objective and the summary provided. The
ImgaugAugmenterhas been replaced withAlbumentationsAugmentercorrectly.
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Review Status
Actionable comments generated: 1
Configuration used: CodeRabbit UI
Files ignored due to filter (3)
- environment.yml
- environment_mac.yml
- environment_no_cuda.yml
Files selected for processing (6)
- .conda/bld.bat (1 hunks)
- .conda/build.sh (1 hunks)
- .conda/meta.yaml (2 hunks)
- .conda_mac/build.sh (1 hunks)
- .conda_mac/meta.yaml (2 hunks)
- requirements.txt (1 hunks)
Files skipped from review due to trivial changes (3)
- .conda/meta.yaml
- .conda_mac/meta.yaml
- requirements.txt
Additional comments: 2
.conda/build.sh (1)
- 10-10: The addition of
--no-binary qudida,albumentationsto thepip installcommand ensures that these packages are installed from source. This is a good practice when specific binary compatibility is required or when the latest source version is needed. Confirm that this change is compatible with the build environment and that all necessary build tools and dependencies are available to compile these packages from source..conda_mac/build.sh (1)
- 10-10: The addition of
--no-binary qudida,albumentationsto thepip installcommand will force these packages to be compiled from source. Ensure that the build environment in the CI and any development setups have the necessary tools and dependencies to compile these packages.
| @@ -7,7 +7,7 @@ set PIP_IGNORE_INSTALLED=False | |||
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| @REM Install the pip dependencies. Note: Using urls to wheels might be better: | |||
| @REM https://docs.conda.io/projects/conda-build/en/stable/user-guide/wheel-files.html) | |||
| pip install --no-cache-dir -r .\requirements.txt | |||
| pip install --no-cache-dir -r .\requirements.txt --no-binary qudida,albumentations | |||
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Consider pinning the versions of qudida and albumentations to ensure consistent builds and compatibility with the rest of the codebase.
#!/bin/bash
# Check if the versions of qudida and albumentations are pinned in the requirements.txt file.
rg 'qudida(==|@)' .\requirements.txt
rg 'albumentations(==|@)' .\requirements.txt
Description
This PR replaces imgaug with albumentations as our library for image augmentation. We're doing this in the hopes of getting rid of our hard dependency on a specific variant of opencv which imgaug (which is no longer maintained) depends on.
Types of changes
Does this address any currently open issues?
#648
Outside contributors checklist
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Summary by CodeRabbit
New Features
imgaugtoalbumentationsfor enhanced image augmentation capabilities.Bug Fixes
Refactor
albumentationslibrary.Tests