Analyze Color

Extract color data of objects and produce pseudocolored images, can extract data for RGB (Red, Green, Blue), HSV (Hue, Saturation, Value) and LAB (Lightness, Green-Magenta, Blue Yellow) channels.

plantcv.analyze_color(rgb_img, mask, bins, hist_plot_type =None, pseudo_channel='v', pseudo_bkg='img', filename=False)

returns color channel histogram headers, color channel histogram data, analysis images

  • Parameters:
    • img - RGB image data
    • mask - binary mask of selected contours
    • bins - number of color bins (0-256), if you would like to bin data, you would alter this number
    • hist_plot_type - 'None', 'all', 'rgb','lab' or 'hsv', this is the data to be printed to an SVG histogram file, however all (every channel) data is still stored to the database.
    • pseudo_channel - 'None', 'r'(red), 'g'(green), 'b'(blue), 'l' (lightness), 'm' (green-magenta), 'y' (blue-yellow), 'h'(hue),'s'(saturation), or 'v'(value), creates pseduocolored image based on the specified channel.
    • pseudo_bkg = 'img' => channel image, 'white' => white background image, 'both' => both img and white options
    • filename - False or image name. If defined print image
  • Context:
    • Used to extract color data from RGB, LAB, and HSV color channels.
    • Generates histogram of color channel data.
    • Generaes pseudocolored output image of one of the channels specified.
  • Example use:

  • Use In VIS Tutorial

  • Output Data Units:

    • Red Channel - histogram of object pixel intensity values 0 (unsaturated) to 255 (saturated)
    • Green Channel - histogram of object pixel intensity values 0 (unsaturated) to 255 (saturated)
    • Blue Channel - histogram of object pixel intensity values 0 (unsaturated) to 255 (saturated)
    • Hue Channel - histogram of object pixel intensity values 0 (unsaturated) to 255 (saturated)
    • Saturation Channel - histogram of object pixel intensity values 0 (unsaturated) to 255 (saturated)
    • Value Channel - histogram of object pixel intensity values 0 (unsaturated) to 255 (saturated)
    • Lightness Channel - histogram of object pixel intensity values 0 (unsaturated) to 255 (saturated)
    • Green-Magenta Channel - histogram of object pixel intensity values 0 (unsaturated) to 255 (saturated)
    • Blue-Yellow Channel - histogram of object pixel intensity values 0 (unsaturated) to 255 (saturated)

Original image

Screenshot

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"

# Analyze Color

color_header, color_data, analysis_images= pcv.analyze_color(rgb_img, imagename, mask, 256, None, 'v', 'img', /home/user/analyze_color.png)

Histograms of (R, G, B), (H, S, V), and (L, A, B) color channels

Screenshot

Pseudocolored value-channel image

Screenshot