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UPDATE needed to PSII tutorial: chlorophyll index default distance failing #1443

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AFis-245 opened this issue Feb 1, 2024 · 1 comment
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@AFis-245
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AFis-245 commented Feb 1, 2024

Describe the bug
error when analyzing spectral image from crop reporter and trying to calculate chlorophyll index
function pcv.spectral_index.ci_rededge(hsi=ps.spectral) returns error
needed to change distance from 20 (default) to 30

To Reproduce
Steps to reproduce the behavior (including sample data and code really help):

  1. Starting with image: spectral image from crop reporter
  2. Run function(s): ci = pcv.spectral_index.ci_rededge(hsi=ps.spectral)
  3. See error
    error: fatal_error("Available wavelengths are not suitable for calculating CI_REDEDGE. Try increasing distance.")

Expected behavior
A clear and concise description of what you expected to happen.
expect to get the chlorophyll index data

Local environment (please complete the following information):

  • OS: [macOS]
  • Environment [e.g. conda, virtualenv, pip, docker, etc.]
  • PlantCV Version [4.2.1]

Additional context
Add any other context about the problem here.
ci = pcv.spectral_index.ci_rededge(hsi=ps.spectral, distance=30) >> changing distance to 30 resolved the error
I think the default distance of 20 is either too strict or the wavelengths used to calculate the ratio are too far off from the wavelengths used by the crop reporter camera

@AFis-245 AFis-245 added the bug Bug or potential bug reports label Feb 1, 2024
@HaleySchuhl
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We believe the issue is the tutorial is failing on this step. https://plantcv.readthedocs.io/en/latest/tutorials/psII_tutorial/ and actual code for the tutorial here. Is it valid to include thiss in our tutorial if the specific wavelengths are not within our tutorial data (crop reporter, not HSI)

@HaleySchuhl HaleySchuhl changed the title chlorophyll index default distance UPDATE needed to PSII tutorial: chlorophyll index default distance failing Feb 2, 2024
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