Measure Path Length of Segments¶
Measure the geodesic distance of segments.
plantcv.morphology.segment_path_length(segmented_img, objects)
returns labeled_image
- Parameters:
- segmented_img - Segmented image (output either from plantcv.morphology.segment_skeleton or plantcv.morphology.segment_id), used for creating the labeled image.
- objects - Segment objects (output from either plantcv.morphology.prune, plantcv.morphology.segment_skeleton, or plantcv.morphology.segment_sort).
- Context:
- Calculates the geodesic distance of each segment. Users can pass only leaf objects (returned from plantcv.morphology.segment_sort) to only collect lengths of leaves only.
- Output data stored: Data ('segment_path_length') automatically gets stored to the
Outputs
class when this function is ran. These data can always get accessed during a workflow (example below). For more detail about data output see Summary of Output Observations
Reference Image: segmented_img
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"
labeled_img = pcv.morphology.segment_path_length(segmented_img=segmented_img,
objects=obj)
# Access data stored out from segment_path_length
path_lengths = pcv.outputs.observations['segment_path_length']['value']
Labeled Image
Source Code: Here