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.
plantcv.cluster_contour_splitimg(rgb_img, grouped_contour_indexes, contours, hierarchy, outdir=None, file=None, filenames=None)
returns output_paths, output_imgs, output_masks
- rgb_img - RGB image data
- 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 (default outdir=None)
- file - the name of the input image to use as a base name , output of filename from read_image function (default file=None)
- filenames - input txt file with list of filenames in order from top to bottom left to right (likely list of genotypes, default filenames=None)
- Takes clustered contours and splits them into multiple images.
- Function input usually comes from the output of the cluster contours function.
- Example use:
Output of Cluster Contours
from plantcv import plantcv as pcv # Set global debug behavior to None (default), "print" (to file), # or "plot" (Jupyter Notebooks or X11) pcv.params.debug = "print" # Cluster Contours and Split into Separate Images out = './examples/' output_path, imgs, masks = pcv.cluster_contour_splitimg(rgb_img, clusters_i, contours, hierarchy, out, file, filenames=None)
Split the Clusters into Separate Images (example of a few images)