Mercurial > repos > imgteam > overlay_segmentation_mask

comparison overlay_segmentation_mask.py @ 1:8077f714ad94 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit b2acc1845a25828181597fe5b6982fe116a7796d
author imgteam
date Mon, 22 Jul 2019 04:58:02 -0400
parents 9e67f52b3eaf
children 4c01cc565771
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0:9e67f52b3eaf 1:8077f714ad94
7 import matplotlib.pyplot as plt 7 import matplotlib.pyplot as plt
8 8
9 #TODO make importable by python script 9 #TODO make importable by python script
10 10
11 import skimage.io 11 import skimage.io
12 import skimage.measure 12 import skimage.measure
13 13
14 parser = argparse.ArgumentParser() 14 parser = argparse.ArgumentParser()
15 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file') 15 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
16 parser.add_argument('mask_file', type=argparse.FileType('r'), help='mask file') 16 parser.add_argument('mask_file', type=argparse.FileType('r'), help='mask file')
17 parser.add_argument('out_file', type=str, help='out file (PNG)') # file would be created immediately with argparse.FileType('w') s.t. file cannot be renamed on galaxy 17 parser.add_argument('out_file', type=str, help='out file (PNG)') # file would be created immediately with argparse.FileType('w') s.t. file cannot be renamed on galaxy