Apply format kernel to pcv

[joshqsumner]

Describe your changes
Applies _format_kernel function to kernel/ksize arguments in the main plantcv.plantcv module.

Type of update
This is a feature enhancement.

Associated issues
Part of #1911

Additional context
Builds off of #1944

For the reviewer
See this page for instructions on how to review the pull request.

• PR functionality reviewed in a Jupyter Notebook
• All tests pass
• Test coverage remains 100%
• Documentation tested
• New documentation pages added to plantcv/mkdocs.yml
• Changes to function input/output signatures added to updating.md
• Code reviewed
• PR approved

[deepsource-io]

DeepSource Code Review

We reviewed changes in 0a9cf06...6d26d42 on this pull request. Below is the summary for the review, and you can see the individual issues we found as inline review comments.

See full review on DeepSource ↗

PR Report Card

Overall Grade

Security   Reliability   Complexity   Hygiene   Coverage

Code Review Summary

Analyzer	Status	Updated (UTC)	Details
Python		Jul 22, 2026 7:56p.m.	Review ↗
Code coverage		Jul 22, 2026 7:56p.m.	Review ↗

Code Coverage Summary

Language	Line Coverage (New Code)	Line Coverage (Overall)
Aggregate	100% [✓ above threshold]	100%
Python	100% [✓ above threshold]	100%

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[Copilot]

Pull request overview

This PR standardizes kernel/ksize handling across several plantcv.plantcv image-processing functions by routing inputs through _format_kernel, enabling more flexible user inputs (int/tuple/ndarray) while updating documentation and a sharpen ROI test accordingly.

Changes:

• Apply _format_kernel to kernel/ksize arguments in multiple filters and morphology wrappers (e.g., blur, sharpen, Sobel/Laplace, erosion/dilation, ROI-aware functions).
• Update docstrings and user docs to describe the broadened kernel specification options.
• Update sharpen ROI test to exercise integer kernel input.

Reviewed changes

Copilot reviewed 21 out of 21 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tests/plantcv/test_sharpen.py	Updates a sharpen ROI test to pass an integer kernel size.
plantcv/plantcv/stdev_filter.py	Coerces ksize via _format_kernel before calling generic_filter; updates docstring.
plantcv/plantcv/sobel_filter.py	Coerces ksize via _format_kernel before calling cv2.Sobel; updates docstring.
plantcv/plantcv/sharpen.py	Coerces ksize via _format_kernel before unsharp masking.
plantcv/plantcv/segment_image_series.py	Coerces ksize via _format_kernel for time-block propagation logic.
plantcv/plantcv/opening.py	Coerces kernel via _format_kernel before calling skimage opening functions; adjusts import.
plantcv/plantcv/median_blur.py	Uses _format_kernel for flexible median filter sizing and updates debug filename.
plantcv/plantcv/laplace_filter.py	Coerces ksize via _format_kernel before calling cv2.Laplacian.
plantcv/plantcv/get_kernel.py	Adds explicit type validation for _format_kernel inputs.
plantcv/plantcv/gaussian_blur.py	Coerces ksize via _format_kernel before calling cv2.GaussianBlur.
plantcv/plantcv/erode.py	Coerces ksize via _format_kernel before calling _erode; updates debug filename.
plantcv/plantcv/dilate.py	Coerces ksize via _format_kernel before calling _dilate; updates debug filename.
plantcv/plantcv/closing.py	Updates docstring to reflect standardized kernel specification.
docs/stdev_filter.md	Updates docs to describe flexible ksize specification.
docs/sobel_filter.md	Updates docs to describe flexible ksize specification for Sobel.
docs/sharpen.md	Updates docs to describe flexible ksize specification for sharpen.
docs/segment_image_series.md	Updates docs to describe flexible ksize specification for time blocks.
docs/median_blur.md	Updates docs to describe flexible ksize specification for median blur.
docs/laplace_filter.md	Updates docs to describe flexible ksize specification for Laplace.
docs/gaussian_blur.md	Updates docs to describe flexible ksize specification for Gaussian blur.
docs/erode.md	Minor documentation punctuation/wording adjustment.

Comments suppressed due to low confidence (1)

plantcv/plantcv/laplace_filter.py:42

• ksize is coerced to k for the OpenCV call, but the debug filename still embeds the original ksize. If callers pass a tuple/array, the filename will not reflect the actual kernel size used.

    _debug(visual=lp_filtered,
           filename=os.path.join(params.debug_outdir,
                                 str(params.device) + '_lp_out_k' + str(ksize) + '_scale' + str(scale) + '.png'),
           cmap='gray')

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