Convert Shapes between geojson and lists¶

Using a Napari viewer with drawn polygons, output a shapefile. Or read in a Polygon- or MultiPolygon-type geojson shapefile and output a list of polygon vertex coordinates in numpy space.

plantcv.geospatial.convert.shapes(img, source, dest=None, shapetype="polygon", layername="Shapes")

• 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 vertex points to numpy coordinates.
  • source - str or Napari.viewer. If this is an str then it should be a path to a geojson file to read shapes from. A Napari viewer should have a polygon like layer that will be saved to a geojson specified by dest.
  • dest - str, Path to save a geojson file if source is a Napari.viewer. This is not required if source is a geojson file path.
  • shapetype - str, Geometry type from Napari viewer shape layer to be written to geojson output. Only used if source is a viewer.
  • layername - str, Name of the shapes layer in the napari viewer. Only used if source is a viewer.

• Context:

  • Convert shapes to/from coordinates and geojson files.
  • Useful for saving custom plot boundaries to be reused.
• Example use:
  • below to outline plot 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.thumb)
viewer.add_shapes()

# A napari viewer window will pop up, use the custom polygon function to add shapes

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

Source Code: Here