1862 import APH file in read_cropreporter

[kmurphy61]

Describe your changes
APH file types were previously imported as xarray, and are now converted as numpy in order to match styles and provide ease of downstream analysis.

Type of update
Is this a:

• Feature enhancement

Associated issues
Issue 1862

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 38b01e4...9a34460 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		May 12, 2026 6:21p.m.	Review ↗
Code coverage		May 12, 2026 6:21p.m.	Review ↗

Code Coverage Summary

Language	Line Coverage (New Code)	Line Coverage (Overall)
Aggregate	100% [✓ above threshold]	99.9% [▼ down 0.1% from main]
Python	100% [✓ above threshold]	99.9% [▼ down 0.1% from main]

➟ Additional coverage metrics may have been reported. See full coverage report ↗

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[kmurphy61]

@deepsourcebot review

[Copilot]

Pull request overview

Updates CropReporter APH ingestion so APH data is stored as a NumPy array (Red/FarRed only) rather than an xarray DataArray, aligning it with other NumPy-based protocol outputs and simplifying downstream analysis.

Changes:

• Convert APH import from xarray DataArray to a 3D NumPy array containing only the Red and FarRed frames.
• Add an xarray wrapper only for debug plotting so frame labels render in debug output.
• Update the APH screenshot filename reference in the documentation.

Reviewed changes

Copilot reviewed 2 out of 4 changed files in this pull request and generated 2 comments.

File	Description
plantcv/plantcv/photosynthesis/read_cropreporter.py	Changes APH parsing/storage to NumPy and adjusts debug visualization accordingly.
docs/photosynthesis_read_cropreporter.md	Updates APH screenshot reference in docs to match the new filename.
docs/img/documentation_images/photosynthesis_read_cropreporter/6_aph_frames.png	Asset presence in PR context; documentation reference now points to 6_APH-frames.png.

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