Segment Insertion Angles¶
Measure leaf insertion angles.
plantcv.morphology.segment_insertion_angle(skel_img, segmented_img, leaf_objects, stem_objects, size)
returns labeled image
- Parameters:
- skel_img - Skeletonize image (output from plantcv.morphology.skeletonize).
- segmented_img - Segmented image (output either from plantcv.morphology.segment_skeleton or plantcv.morphology.segment_id), used for creating the labeled debugging image.
- leaf_objects - Leaf segment objects (output from plantcv.morphology.segment_sort).
- stem_objects - Stem segment objects (output from plantcv.morphology.segment_sort).
- size - Size of ends (number of pixels) used to calculate insertion point "tangent" lines
- Context:
- Find "tangent" angles to leaf insertion points in degrees of skeleton segments compared to the stem angle.
Use
size
pixels of the inner portion of each leaf to find a linear regression line, and calculate angle between insertion angle and the stem. Insertion angles are automatically stored in the outputs class.
- Find "tangent" angles to leaf insertion points in degrees of skeleton segments compared to the stem angle.
Use
- Output data stored: 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"
# Adjust line thickness with the global line thickness parameter (default = 5)
pcv.params.line_thickness = 3
labeled_img = pcv.morphology.segment_insertion_angle(skel_img=skeleton,
segmented_img=leaves_segment,
leaf_objects=leaf_obj,
stem_objects=stem_objs,
size=20)
Labeled Image