1862 import APH file in read_cropreporter#1906
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switch aph import to numpy instead of an xarray
Wrap debug in xarray so that the debug can have titles for the frames
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Code Review Summary
| Analyzer | Status | Updated (UTC) | Details |
|---|---|---|---|
| Python |  |
May 4, 2026 8:43p.m. | Review ↗ |
| Code coverage | |
May 4, 2026 8:43p.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] |
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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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Based on copilot suggestion
Used monkeypatch to test a scenario for less APH frames
Do not use pytest
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:
Associated issues
Issue 1862
For the reviewer
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plantcv/mkdocs.ymlupdating.md