Convert Points between geojson and lists¶

Using a Napari or PlantCV-annotate viewer object with clicked points, output a shapefile. Or read in a Point- or MultiPoint-type geojson shapefile and output a list of coordinates in numpy space.

plantcv.geospatial.convert.points(img, source, dest=None, layername="Points")

• Parameters:

  • img - GEO image object, likely read in with geo.read_geotif. If source is the path to a shapefile, the metadata of this image will be used to convert points to numpy coordinates.
  • source - str, Napari.viewer, or plantcv.annotate.classes.Points object. If this is an str then it should be a path to a geojson file to read points from. A Napari.viewer or Points object will be saved to a geojson specified by dest.
  • dest - str, Path to save a geojson file if source is a Napari.viewer or Points object. This is not required if source is a geojson file path.
  • layername - str, Name of the Napari viewer layer from which to take points. Only used if source is a Napari viewer object.

• Returns:

  • coordinates - list of points in numpy coordinates from source, and a saved geojson file if dest is a viewer or Points object.

• Context:

  • Convert points to/from coordinates and geojson files.
• Example use:
  • below to click plant locations

import plantcv.geospatial as gcv
import plantcv.annotate as an

# Read geotif in
img = gcv.read_geotif("../read_geotif/rgb.tif", bands="R,G,B")
viewer = an.napari_open(img=img.pseudo_rgb)
viewer.add_points()

# A napari viewer window will pop up, use the points function to add clicks

# In a separate cell, save the output after clicking:
gcv.convert.points(img=img, source=viewer, dest="./points_example.geojson")

Source Code: Here