Analyze Stem Objects¶
Primary, or stem, objects identified during workflows that examine the morphology of plants or plant organs can have specific characteristics measured about the stem segments of a skeleton.
plantcv.morphology.analyze_stem(rgb_img, stem_objects, label=None)
returns labeled_img
- Parameters:
- rgb_img - RGB image data for plotting.
- stem_objects - List of stem segments (output from segment_sort function)
- label - Optional label parameter, modifies the variable name of observations recorded. (default =
pcv.params.sample_label
)
- Context:
- Used to output stem morphological characteristics, including height, angle, and length.
-
Example use:
-
Output data stored: Data ('stem_angle', 'stem_height', and 'stem_length') automatically gets stored to the
Outputs
class when this function is ran. All data stored in the Outputs class gets printed out while running pcv.outputs.save_results but these data can always get accessed during a workflow. For more detail about data output see Summary of Output Observations
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"
stem_debug_img1 = pcv.morphology.analyze_stem(rgb_img=img1, stem_objects=stem_objects1)
# Access data stored out from analyze_stem
stem_angle = pcv.outputs.observations['plant']['stem_angle']['value']
stem_debug_img2 = pcv.morphology.analyze_stem(rgb_img=img2, stem_objects=stem_objects2, label="rep1")
stem_angle = pcv.outputs.observations['rep1']['stem_angle']['value']
Image 1 with identified stem characteristics
Image 2 with identified stem characteristics
Source Code: Here