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metadata attribute is missing in calculated spectral indices #1672

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HaleySchuhl opened this issue Feb 14, 2025 · 0 comments · May be fixed by #1673
Open

metadata attribute is missing in calculated spectral indices #1672

HaleySchuhl opened this issue Feb 14, 2025 · 0 comments · May be fixed by #1673
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@HaleySchuhl
Labels
bug Bug or potential bug reports enhancement Enhancements to existing features update Updates an existing feature/method
Milestone
PlantCV v4.7

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@HaleySchuhl
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Describe the bug
The helper function _package_index is missing the newly added metadata attribute so it's missing in spectral index Objects.

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

  1. Starting with any geotif, such as this test data.
  2. run the following functions
pcv.spectral_index.ndvi(geotif)
viewer = an.napari_open(img=img.pseudo_rgb)
viewer.add_points()
geo.points_to_geojson(ndvi, viewer, out_path="./points_example.geojson")
  1. See error
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
Cell In[7], line 1
----> 1 geo.points_to_geojson(ndvi, viewer, out_path="./points_example.geojson")

File [~/Documents/GitHub/plantcv-geospatial/build/__editable__.plantcv_geospatial-0.1.dev315](http://localhost:8888/lab/tree/Projects/geospatial/public_data/~/Documents/GitHub/plantcv-geospatial/build/__editable__.plantcv_geospatial-0.1.dev315)+gbcbcb37-py3-none-any[/plantcv/geospatial/points_to_geojson.py:22](http://localhost:8888/plantcv/geospatial/points_to_geojson.py#line=21), in points_to_geojson(img, viewer, out_path)
     20 # Napari output, points must be reversed
     21 if hasattr(viewer, 'layers'):
---> 22     points = [(img.metadata["transform"]*reversed(i)) for i in viewer.layers["Points"].data]
     23 # Annotate output
     24 elif hasattr(viewer, 'coords'):

File [~/Documents/GitHub/plantcv-geospatial/build/__editable__.plantcv_geospatial-0.1.dev315](http://localhost:8888/lab/tree/Projects/geospatial/public_data/~/Documents/GitHub/plantcv-geospatial/build/__editable__.plantcv_geospatial-0.1.dev315)+gbcbcb37-py3-none-any[/plantcv/geospatial/points_to_geojson.py:22](http://localhost:8888/plantcv/geospatial/points_to_geojson.py#line=21), in <listcomp>(.0)
     20 # Napari output, points must be reversed
     21 if hasattr(viewer, 'layers'):
---> 22     points = [(img.metadata["transform"]*reversed(i)) for i in viewer.layers["Points"].data]
     23 # Annotate output
     24 elif hasattr(viewer, 'coords'):

KeyError: 'transform

Expected behavior
A clear and concise description of what you expected to happen.

Local environment (please complete the following information):

  • OS: [macOS]
  • Environment :[conda]
  • PlantCV Version [4.6]

Additional context
The plantcv-geospatial package will have an analyze.spectral function that requires metadata about the affine in the original geotif in order to use rasterstats.zonal_stats
@HaleySchuhl HaleySchuhl added bug Bug or potential bug reports enhancement Enhancements to existing features update Updates an existing feature/method labels Feb 14, 2025
@HaleySchuhl HaleySchuhl added this to the PlantCV v4.7 milestone Feb 14, 2025
@HaleySchuhl HaleySchuhl self-assigned this Feb 14, 2025
@github-project-automation github-project-automation bot moved this to New Issues in PlantCV4 Feb 14, 2025
@HaleySchuhl HaleySchuhl linked a pull request Feb 14, 2025 that will close this issue
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@HaleySchuhl HaleySchuhl

Labels
bug Bug or potential bug reports enhancement Enhancements to existing features update Updates an existing feature/method
Projects
PlantCV4
Status: New Issues
Milestone
PlantCV v4.7
Development

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add metadata to _package_index in spectral_index.py danforthcenter/plantcv
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@HaleySchuhl