Report Size Marker

Get and record the size of a size marker or set an area as a size marker.

report_size_marker(img, shape, device, debug, marker='define', x_adj=0, y_adj=0, w_adj=0, h_adj=0, base='white', objcolor='dark', thresh_channel=None, thresh=None, filename=False)

returns device, marker_header,marker_data,analysis_images

  • Parameters:

    • img = image object (most likely the original), color(RGB)
    • shape = 'rectangle', 'circle', 'ellipse'
    • device = device number. Used to count steps in the pipeline
    • debug = None, print, or plot. Print = save to file, Plot = print to screen.
    • marker = define or detect, if define it means you set an area, if detect it means you want to detect within an area
    • x_adj = x position of shape, integer
    • y_adj = y position of shape, integer
    • w_adj = width
    • h_adj = height
    • base = background color 'white' is default
    • objcolor = object color is 'dark' or 'light'
    • thresh_channel = 'h', 's','v'
    • thresh = integer value
    • filename = name of file
  • Context:

    • Allows user to add size marker data, so that shape data can be normalized between images/cameras

Output Data Units: - Marker-Area - area of marker, pixels (units) - Marker Bounding Ellipse Major Axis - length of major axis of bounding ellipse, pixels (units)
- Marker Bounding Ellipse Minor Axis - length of minor axis of bounding ellipse, pixels (units)
- Marker Bounding Ellipse Eccentricity - ratio, 'roundness' of object (a perfect circle is 0, ellipse is greater than 0 but less than 1)

Object (green) that is identified as partially inside ROI


from plantcv import plantcv as pcv

# Detect and Measure Size Marker
device, marker_header,marker_data,images=pcv.report_size_marker_area(img1, 'rectangle', device, debug='print', marker='detect', x_adj=3500, y_adj=600, w_adj=-100, h_adj=-1500, base='white', objcolor='light', thresh_channel='s', thresh=120, filename=False)```

Area selected to detect size markers


Object (green) that is identified as size marker