1862 chlorophyll image import

[kmurphy61]

Describe your changes
Updating the read_cropreporter.py function so that CHL (chlorophyll) frames are imported as numpy instead of xarray. This will save memory.

Type of update
Is this a:

• Feature enhancement

Associated issues
Associated with Issue 1862

For the reviewer
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• 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 8852d90...6afc88c on this pull request. Below is the summary for the review, and you can see the individual issues we found as inline review comments.

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PR Report Card

Overall Grade

Security   Reliability   Complexity   Hygiene   Coverage

Code Review Summary

Analyzer	Status	Updated (UTC)	Details
Python		Mar 27, 2026 4:24p.m.	Review ↗
Test coverage		Mar 27, 2026 4:24p.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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[Copilot]

Pull request overview

Updates CropReporter/PlantExplorer CHL (chlorophyll) import behavior in read_cropreporter to reduce memory usage by storing only the chlorophyll frame as a NumPy array rather than an xarray DataArray, with accompanying documentation updates.

Changes:

• Update CHL processing to extract/store only the Chl frame (dropping Fdark) as a NumPy array on ps.chlorophyll.
• Adjust CHL debug output to write a single-frame image instead of faceted xarray plots.
• Update read_cropreporter documentation to reflect the CHL storage change.

Reviewed changes

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

File	Description
plantcv/plantcv/photosynthesis/read_cropreporter.py	Changes CHL import from xarray DataArray cube to a single NumPy frame stored on ps.chlorophyll.
docs/photosynthesis_read_cropreporter.md	Updates user-facing documentation to describe CHL output changes (needs terminology/consistency fixes).

Comments suppressed due to low confidence (1)

plantcv/plantcv/photosynthesis/read_cropreporter.py:24

• read_cropreporter now stores ps.chlorophyll as a NumPy array (and not exclusively xarray), but the docstring still says the return is "photosynthesis data in xarray DataArray format" and uses PSII_Data instead of the PSII_data class name. Please update the return description/type wording to reflect the mixed xarray/NumPy contents and correct the class naming for accuracy.

    Read datacubes from PhenoVation B.V. CropReporter or PlantExplorer cameras into a PSII_Data instance.

    Inputs:
        filename        = .INF filename

    Returns:
        ps               = photosynthesis data in xarray DataArray format

    :param filename: str
    :return ps: plantcv.plantcv.classes.PSII_data
    """

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[Copilot]

Pull request overview

Copilot reviewed 5 out of 6 changed files in this pull request and generated 6 comments.

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[joshqsumner]

I think this is good per the rest of the cropreporter stuff, it works for me locally and seems clean.
I took a cursory stab at monkeypatching the tests and it wasn't super forthcoming with how many unexported functions are used in the main readers. Goal was to reduce the amount of stuff in the testdata that only pertains to these cropreporter functions since a 12Mb dataset felt very large.
Looking more broadly, I don't think adding this new test data is unreasonable but it may be worth some effort to clean all the cropreporter tests up to use fewer large files. I am not sure which of these could be combined if any, but there are some large files in here and some are duplicated just different by 1 character in the filename.

(plantcv) josh@Precision-7550:~/plantcv$ find tests/testdata -type f -exec du -ah {} + | grep -v "/$" | sort -rh | head -15
53M	tests/testdata/cropreporter_pmt/PMT_E0001P0007N0001_GCU24100090_20260226.DAT
51M	tests/testdata/cropreporter_v441/PSII_PSL_020321_WT_TOP_1.DAT
51M	tests/testdata/cropreporter_v441/PSII_PSD_020321_WT_TOP_1.DAT
42M	tests/testdata/cropreporter_v653/PSL_dark_light.DAT
42M	tests/testdata/cropreporter_v653/PSD_dark_light.DAT
24M	tests/testdata/cropreporter_v653/PML_dark_light.DAT
24M	tests/testdata/cropreporter_v653/PMD_dark_light.DAT
18M	tests/testdata/cropreporter_v653/CLR_dark_light.DAT
18M	tests/testdata/cropreporter_gfp/GFP_DYSeed_20251222191634684.DAT
15M	tests/testdata/cropreporter_npq/PSII_NPQ_020321_WT_TOP_1.DAT
12M	tests/testdata/cropreporter_v653/CHL_dark_light.DAT
12M	tests/testdata/cropreporter_rfp/RFP_DYSeed_20251222191634684.DAT
12M	tests/testdata/cropreporter_chl/CHL_2025-12-12_tob1-ojip_20251212213103380.DAT
12M	tests/testdata/cropreporter_aph/APH_2025-12-12_tob1_20251212205712029.DAT
9.7M	tests/testdata/colorcard_img.png

[joshqsumner]

Forgot to push local changes before submitting approval, just stylistic some docstring edits

[joshqsumner]

@nfahlgren per dev meeting conversation I removed the additional test data and used the chl data from v441.