Mercurial > repos > thomaswollmann > overlay_segmentation_mask

comparison overlay_segmentation_mask.py @ 0:5f83d67e30f1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
author thomaswollmann
date Mon, 07 Jan 2019 05:38:10 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:5f83d67e30f1
1 import argparse
2 import sys
3 import os
4
5 import matplotlib
6 matplotlib.use('Agg')
7 import matplotlib.pyplot as plt
8
9 #TODO make importable by python script
10
11 import skimage.io
12 import skimage.measure
13
14 parser = argparse.ArgumentParser()
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')
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
18 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')
20 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')
22 parser.add_argument('--stroke_color', dest='stroke_color', default='#ff0000', help='stroke color')
23 args = parser.parse_args()
24 img = skimage.io.imread(args.input_file.name)
25 label = skimage.io.imread(args.mask_file.name)
26
27 fig = plt.figure()
28 ax = fig.add_axes([0, 0, 1, 1])
29 ax.axis('off')
30
31 if args.label:
32 for reg in skimage.measure.regionprops(label):
33 ax.text(reg.centroid[1], reg.centroid[0], str(reg.label), color=args.label_color)
34
35 if args.greyscale:
36 plt.imshow(img, cmap=plt.cm.gray)
37 else:
38 plt.imshow(img)
39 plt.contour(label, linewidths=args.thickness, colors=args.stroke_color)
40
41 fig.canvas.print_png(args.out_file)