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joshqsumner
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joshqsumner
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ready to review
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There was a lot of hassle with cyclic imports getting this to pass checks. I ended up changing a bunch of places where a function is imported from |
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Pull request overview
This pull request adds a new image sharpening function using the unsharp masking technique, as requested in issue #1824. The PR also includes a significant refactoring effort that moves the Params and Outputs singleton classes from classes.py to a new _globals.py module and updates all imports throughout the codebase. Additionally, the Points class is renamed to Point (singular), and the time_lapse_video function and its tests are removed.
Changes:
- Added a new
sharpenfunction implementing unsharp masking for image sharpening - Refactored global singleton instances (
paramsandoutputs) into a dedicated_globals.pymodule - Renamed the
Pointsclass toPointfor consistency with naming conventions
Reviewed changes
Copilot reviewed 116 out of 118 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
| plantcv/plantcv/sharpen.py | New function implementing image sharpening via unsharp masking with ROI support |
| tests/plantcv/test_sharpen.py | Basic test coverage for the sharpen function |
| plantcv/plantcv/_globals.py | New module containing Params and Outputs singleton classes |
| plantcv/plantcv/init.py | Updated imports to use _globals module and expose Point class |
| plantcv/plantcv/classes.py | Moved Params/Outputs to _globals.py, renamed Points to Point |
| plantcv/plantcv/deprecation_warning.py | Updated to use importlib.metadata.version instead of direct version import |
| plantcv/plantcv/visualize/time_lapse_video.py | Removed file |
| tests/plantcv/visualize/test_time_lapse_video.py | Removed file |
| plantcv/plantcv/visualize/init.py | Removed time_lapse_video import |
| tests/plantcv/annotate/test_points.py | Updated to use Point instead of Points |
| docs/sharpen.md | Documentation for the new sharpen function |
| docs/updating.md | Added entry for sharpen function signature |
| mkdocs.yml | Added sharpen documentation to navigation |
| 100+ other files | Updated imports from plantcv.plantcv import params/outputs to plantcv.plantcv._globals import params/outputs |
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| import cv2 | ||
| import numpy as np | ||
| from plantcv.plantcv.sharpen import sharpen | ||
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| def test_sharpen_zero_amount(test_data): | ||
| """Test for PlantCV.""" | ||
| # Read in test data | ||
| img = cv2.imread(test_data.small_rgb_img) | ||
| sharp_img = sharpen(img, (5, 5), amount = 0, threshold = 0) | ||
| assert np.average(img) == np.average(sharp_img) | ||
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| def test_sharpen_any_amount(test_data): | ||
| """Test for PlantCV.""" | ||
| # Read in test data | ||
| img = cv2.imread(test_data.small_rgb_img) | ||
| sharp_img = sharpen(img, (5, 5), amount = 1, threshold = 0) | ||
| assert np.average(img) != np.average(sharp_img) | ||
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| def test_sharpen_threshold(test_data): | ||
| """Test for PlantCV.""" | ||
| # Read in test data | ||
| img = cv2.imread(test_data.small_rgb_img) | ||
| zero_thresh = sharpen(img, (5, 5), amount = 1, threshold = 0) | ||
| thresh = sharpen(img, (5, 5), amount = 1, threshold = 100) | ||
| assert np.average(thresh) != np.average(zero_thresh) |
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Incomplete test coverage for the sharpen function. The tests only cover RGB images without ROI. Based on similar functions like gaussian_blur (see tests/plantcv/test_gaussian_blur.py), the test suite should also include: (1) test with ROI on RGB image, (2) test on grayscale image, (3) test with ROI on grayscale image, and (4) tests for sigma_x and sigma_y parameters which are currently not tested at all.
Describe your changes
Added a sharpening function using unsharp masking.
Type of update
This is a new feature.
Associated issues
Closes #1824
For the reviewer
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plantcv/mkdocs.ymlupdating.md