Output Mask and Original Image

Write image and mask with the same name to the path specified (creates two folders within the path if they do not exist).

output_mask(device,img,mask, filename,outdir=None, mask_only=False,debug=None)

returns device, imgpath, maskpath, analysis_images

output_mask(device,img,mask, filename,outdir=None, mask_only=True,debug=None)

returns device, maskpath, analysis_images

  • Parameters:
    • device - pipeline step counter
    • img - original image, read in with plantcv function read_image
    • mask - binary mask image created in previous steps (single chanel)
    • filename - vis image file name (output of plantcv read_image function)
    • outdir - output directory
    • mask_only - If True, only outputs mask
    • debug - None, print, or plot. Print = save to file, Plot = print to screen.
  • Context:
    • This function was written to more easily create training sets for machine learning (eg. Naive Bayes Classifier)

import plantcv as pcv      

device, imgpath,maskpath=pcv.output_mask(device, img, mask, 'test.png', '/home/user/images', mask_only=True, debug='print')