Measure Tangent Angles of Segments¶
Measure tangent angles of segments as a way to quantify leaf behavior.
plantcv.morphology.segment_tangent_angle(segmented_img, objects, size, label=None)
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).
- size - Size of ends (number of pixels) used to calculate "tangent" lines
- label - Optional label parameter, modifies the variable name of observations recorded. (default =
pcv.params.sample_label
)
- Context:
- Find 'tangent' angles in degrees of skeleton segments. Use
size
pixels on either end of each segment to find a linear regression line, and calculate angle between the two lines drawn per segment. Users can pass only leaf objects (returned from plantcv.morphology.segment_sort) to only collect angles of leaves.
- Find 'tangent' angles in degrees of skeleton segments. Use
- Output data stored: Data ('segment_tangent_angle') 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 image
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"
# Optionally, set a sample label name
pcv.params.sample_label = "plant"
# Adjust line thickness with the global line thickness parameter (default = 5)
pcv.params.line_thickness = 3
labeled_img = pcv.morphology.segment_tangent_angle(segmented_img=leaves_segment,
objects=leaf_obj,
size=15)
# Access data stored out from segment_tangent_angle
leaf_tangent_angles = pcv.outputs.observations['plant']['segment_tangent_angle']['value']
Labeled Image
Source Code: Here