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data exploration function: which spectral indices can be calculated from my HSI? #1596

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HaleySchuhl opened this issue Sep 10, 2024 · 2 comments
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new feature New feature ideas and solutions

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@HaleySchuhl
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Is your feature request related to a problem? Please describe.
The deluxe problem is that PlantCV has so many indices that it supports in the plantcv.spectral_index sub-package. It would be nice to be able to subset the spectral indices that are valid to calculate given a multi/hyperspectral array with metadata about it's wavelengths, and possibly also the width of the wavelengths represented.

Describe the solution you'd like
Given a dictionary of wavelengths (Spectral_data.wavelength_dict) and a user defined distance/maximum bandwidth, output a list of indices supported in the current version of PlantCV.

Describe alternatives you've considered
Some type of camera configuration file with additional metadata that is not stored in the .hdr or embedded in the image some other way.

Additional context
E.g. we have a MicaSense camera collecting geotifs and we are interested in automatically determining which spectral_index could be calculated with something more Pythonic and user-friendly than a try block of all.

The MicaSense Altum-PT's wavelengths are:
Blue: 475 nanometers (nm) center, 32 nm bandwidth
Green: 560 nm center, 27 nm bandwidth
Red: 668 nm center, 14 nm bandwidth
Red edge: 717 nm center, 12 nm bandwidth
Near-IR: 842 nm center, 57 nm bandwidth
Thermal: FLIR LWIR thermal infrared 7.5-13.5um radiometrically calibrated

@HaleySchuhl HaleySchuhl added the new feature New feature ideas and solutions label Sep 10, 2024
@rayn-alex
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I have something like this on my list for RVS Analytics v.1.3. I wouldn't mind implementing it directly in plantCV.

Currently, I'm using a curated list of all indices which can be used with the RVS Camera, but I always wanted to make it dynamic based on the input.

@nfahlgren
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That would be great, thanks Alex!

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