Cluster Contours and Split Images

This function takes clustered contours and splits them into multiple images, also does a check to make sure that the number of inputted filenames matches the number of clustered contours.

cluster_contour_splitimg(device, img, grouped_contour_indexes, contours, hierarchy, outdir, file=None, filenames=None, debug=None)

returns device, output_paths

  • Parameters:
    • device = Counter for image processing steps
    • img = image object to be masked
    • grouped_contour_indexes = output of cluster_contours, indexes of clusters of contours
    • contours = contours to cluster, output of cluster_contours
    • hierarchy = object hierarchy
    • outdir = directory for output images
    • file = the name of the input image to use as a base name , output of filename from read_image function
    • filenames = input txt file with list of filenames in order from top to bottom left to right (likely list of genotypes)
    • debug = None, "print", or "plot". Print = save to file, Plot = print to screen. Default = None
  • Context:
  • Example use:

Output of Cluster Contours

Screenshot

from plantcv import plantcv as pcv

# Cluster Contours and Split into Separate Images 
out = './examples/'
device, output_path = pcv.cluster_contour_splitimg(device, img1, clusters_i, contours, hierarchy, out, file, filenames=None,
                                                       debug="print")

Split the Clusters into Separate Images (example of a few images)

Screenshot Screenshot Screenshot