Analyze Shape Characteristics of Object¶
Shape analysis outputs numeric properties for an input object (contour or grouped contours), works best on grouped contours.
plantcv.analyze_object(img, obj, mask)
- img - RGB or grayscale image data for plotting.
- obj - Single or grouped contour object.
- mask - Binary image to use as mask for moments analysis.
- Used to output shape characteristics of an image, including height, object area, convex hull, convex hull area, perimeter, extent x, extent y, longest axis, centroid x coordinate, centroid y coordinate, in bounds QC (if object touches edge of image, image is flagged).
- Data automatically gets stored into the Outputs class. Users can look at the data collected at any point during the workflow by using pcv.print_results which prints all stored data to a .json file.
- Example use:
- Output data stored: 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" # Characterize object shapes shape_images = pcv.analyze_object(img, objects, mask) # Save returned images with more specific naming shape_image, mask = shape_images pcv.print_image(shape_image, '/home/malia/setaria_shape_img.png')
Image with identified objects
Image with shape characteristics