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)
returns shape data headers, shape data, analysis_images
- 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).
Output Data Units:
- Object Area - object area, pixels (units)
- Convex-Hull Area - area of convex-hull, pixels (units)
- Solidity - Ratio, object area divided by convex hull area.
- Object Perimeter Length - pixels (units)
- Object Width (extent x) - pixels (units)
- Object Height (extent y) - pixels (units)
- Longest Axis - pixels (units)
- Center of Mass-X - x-coordinate, pixels (units)
- Center of Mass-Y - y-coordinate, pixels (units)
- Hull Vertices - number of convex-hull vertices
- In Bounds - True or False (if False the object is touching top of image)
- Object Bounding Ellipse Center-X - x-coordinate, pixels (units)
- Object Bounding Ellipse Center-Y - y-coordinate, pixels (units)
- Object Bounding Ellipse Major Axis - length of major axis of bounding ellipse, pixels (units)
- Object Bounding Ellipse Minor Axis - length of minor axis of bounding ellipse, pixels (units)
- Object Bounding Ellipse Angle - rotation of ellipse in degrees
- Object Bounding Ellipse Eccentricity - ratio, 'roundness' of object (a perfect circle is 0, ellipse is greater than 0 but less than 1)
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_header, shape_data, 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