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.
- rgb_img - RGB image data for plotting.
- stem_objects - List of stem segments (output from segment_sort function)
- Used to output stem morphological characteristics, including height, angle, and length.
Output data stored: Data ('stem_angle', 'stem_height', and 'stem_length') automatically gets stored to the
Outputsclass when this function is ran. All data stored in the Outputs class gets printed out while running print_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 = "print"
stem_debug_img1 = pcv.morphology.analyze_stem(rgb_img=img1, stem_objects=stem_objects1) stem_debug_img2 = pcv.morphology.analyze_stem(rgb_img=img2, stem_objects=stem_objects2)
Access data stored out from analyze_object¶
stem_angle = pcv.outputs.observations['stem_angle']['value']
Image 1 with identified stem characteristics
Image 2 with identified stem characteristics
Source Code: Here