Improvements in VISpipeline tutorial

I am following the VIS pipeline tutorial (http://plantcv.readthedocs.io/en/latest/vis_tutorial/) and found some minor flaws.

1. Extra agruments

-r results.txt -w are undefined arguments

2. Problem with debug argument

This could probably be a problem of mine. But the flag ‘print’ of the -D argument is not working for me i have to overwrite it in the code if i want the debug mode to print my images

3. Output directory

Not sure why, i hv specified the output directory but it is printing to the main project folder.

4. Sample image different resolution

I belive the image you make available to run this tutorial is different the one you used. because the ROI rectangle definition does not match.

5. color_img not defined

throughout the code i dont think color_img was actually created. Got this error: NameError: global name 'color_img' is not defined

[nfahlgren]

Yep, you are right, both -r and -w should be defined in the options function if the script is to be used with plantcv-pipeline.py. Here’s what we normally use:

def options():
    parser = argparse.ArgumentParser(description="Imaging processing with opencv")
    parser.add_argument("-i", "--image", help="Input image file.", required=True)
    parser.add_argument("-o", "--outdir", help="Output directory for image files.", required=False)
    parser.add_argument("-r","--result", help="result file.", required= False )
    parser.add_argument("-w","--writeimg", help="write out images.", default=False, action="store_true")
    parser.add_argument("-D", "--debug", help="Turn on debug, prints intermediate images.", default=None)
    args = parser.parse_args()
    return args

[maliagehan]

Updates have been made to correct the problems with the VIS and VIS/NIR tutorial. Please let us know if you find any other problems. Thank you!