Report Size Marker¶
Get and record the size of a size marker or set an area as a size marker.
plantcv.report_size_marker_area(img, roi_contour, roi_hierarchy, marker='define', objcolor='dark', thresh_channel=None, thresh=None)
- img = An RGB or grayscale image to plot the marker object on
- roi_contour = A region of interest contour (e.g. output from pcv.roi.rectangle or other methods)
- roi_hierarchy = A region of interest contour hierarchy (e.g. output from pcv.roi.rectangle or other methods)
- marker = 'define' (default) or 'detect'. If 'define' it means you set an area, if 'detect' it means you want to detect within an area
- objcolor = Object color is 'dark' (default) or 'light' (is the marker darker or lighter than the background)
- thresh_channel = 'h', 's', or 'v' for hue, saturation or value, default set to None
- thresh = Binary threshold value (integer), default set to None.
- Output data stored: Summary of Output Observations
Object (green) that is identified as partially inside ROI
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" # Define an ROI for the marker roi_contour, roi_hierarchy = pcv.roi.rectangle(img1, 3550, 850, 500, 500) # Detect and Measure Size Marker image = pcv.report_size_marker_area(img1, roi_contour, roi_hierarchy, marker='detect', objcolor='light', thresh_channel='s', thresh=120)
Area selected to detect size markers
Object (green) that is identified as size marker