Combine segments

Manually combine segments from a segmented skeleton

plantcv.morphology.segment_combine(segment_list, objects, mask)

returns Labeled image, new segment objects list

  • Parameters:

  • Context:

    • Objects with more complexity will often cause issues with the algorithms used in functions within the plantcv.morphology sub-package. However, it is still possible to collect accurate data from such images with a manual step such as plantcv.morphology.segment_combine. An example workflow would use plantcv.morphology.check_cycles to identify images that have parts of plant that occlude others, and get corrected by combining segments that are recognized as belonging to the same leaf.

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 = "plot"

# Adjust text thickness (default = 5) and text size (default = .55) with the 
# global text parameters. Users can adjust text_size and text_thickness to 
# obtain labels that are easier to read. 
pcv.params.text_thickness = 3

# Plot an image with ID's labeled so the specific segment ID's can get used
# to combine segments 
segment_img, id_labeled_img = pcv.morphology.segment_id(skel_img=pruned_img, objects=segment_objects, mask=mask)

# Combine the segments of the really floppy leaf
labeled_img, new_objects = pcv.morphology.segment_combine(segment_list=[12,6], objects=segment_objects, mask=mask)

# Combine the segments of the leaf obscuring the floppy leaf 
labeled_img2, new_objects = pcv.morphology.segment_combine(segment_list=[7,6], objects=new_objects, mask=mask)

# Optionally, if all ID's were legible we could combine multiple segments in one step. 
# Users can provide a list of lists in which each list contains segments that should 
# get combined together.  

## labeled_img, objects = pcv.morphology.segment_combine(segment_list=[[12,6,3], [11,10]],
##                                                       objects = segment_objects,
##                                                       mask = plant_mask)    

ID Labeled Image


Floppy Leaf Combined


Other Leaf Combined


Source Code: Here