ROIs from the center of gridded polygons¶

After using a Napari viewer, and possibly the combination of create_shapes.napari_grid and create_shapes.napari_polygon_grid, this function takes a viewer's shapes layer and turns the center point of every polygon into a circular Region of Interest (ROI) for downstream analysis of individual objects.

plantcv.geospatial.center_grid_rois(editor, radius=10, layername="Shapes")

returns roi_objects

• Parameters:

  • editor - InteractiveShapes class object.
  • radius - Pixel value of the radius of ROIs. Default is 10.
  • layername - Name of shape layer containing polygons, defaults to "Shapes".

• Context:

  • Though this function is designed to be used after drawing polygons in a grid using create_shapes.napari_grid and create_shapes.napari_polygon_grid, it can be used to draw ROIs using polygons formed by hand, read in from a shapefile, or drawn using custom algorithms.

• Example use:

  • Below is an example of using hand-drawn polygons. For an example of making grid polygons, see InteractiveShapes Documentation

import plantcv.plantcv as pcv
import plantcv.geospatial as gcv

pcv.params.debug = "plot"

# Read geotif in
img = gcv.read_geotif("./grid_field.tif", bands="B,G,R,RE,N")
# Add a shapes layer to your InteractiveShapes editor
editor = gcv.create_shapes.InteractiveShapes(img)
editor.add_layer()

# Now, when the Napari viewer opens, the user can add polygons around individual plants or plots.

# Draw ROIs
rois = gcv.center_grid_rois(editor, radius=9)

# Resulting ROIs can be used for downstream analysis of individual objects in PlantCV

Read in geotif:

Adding polygons to shapes layer:

Drawn ROIs:

Source Code: Here