Mercurial > repos > imgteam > overlay_segmentation_mask

comparison overlay_segmentation_mask.py @ 2:22e573b7dcb1 draft default tip

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
author imgteam
date Sat, 26 Feb 2022 17:14:53 +0000
parents 8ad39f493587
children
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1:8ad39f493587 2:22e573b7dcb1
1 import argparse 1 import argparse
2 import sys
3 import os
4 2
5 import matplotlib 3 import matplotlib
4 import matplotlib.pyplot as plt
5 import skimage.io
6 import skimage.measure
7
6 matplotlib.use('Agg') 8 matplotlib.use('Agg')
7 import matplotlib.pyplot as plt 9 # TODO make importable by python script
8
9 #TODO make importable by python script
10
11 import skimage.io
12 import skimage.measure
13 10
14 parser = argparse.ArgumentParser() 11 parser = argparse.ArgumentParser()
15 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file') 12 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') 13 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 14 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
18 parser.add_argument('--grey', dest='greyscale', action='store_true', help='image is greyscale') 15 parser.add_argument('--grey', dest='greyscale', action='store_true', help='image is greyscale')
19 parser.add_argument('--label', dest='label', action='store_true', help='plot label') 16 parser.add_argument('--label', dest='label', action='store_true', help='plot label')
20 parser.add_argument('--label_color', dest='label_color', default='#FFFF00', help='label color') 17 parser.add_argument('--label_color', dest='label_color', default='#FFFF00', help='label color')
21 parser.add_argument('--thickness', dest='thickness', default=0.3, type=float, help='thickness') 18 parser.add_argument('--thickness', dest='thickness', default=0.3, type=float, help='thickness')
22 parser.add_argument('--stroke_color', dest='stroke_color', default='#ff0000', help='stroke color') 19 parser.add_argument('--stroke_color', dest='stroke_color', default='#ff0000', help='stroke color')