Mercurial > repos > imgteam > split_labelmap

comparison split_labelmap.py @ 0:597b7ef44b05 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:47:34 -0500
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children 9db1c22dbe17
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-1:000000000000 0:597b7ef44b05
1 from imageio import imread as io_imread
2 from skimage.measure import regionprops
3 import numpy as np
4 #import matplotlib.pyplot as plt
5 import scipy
6 import skimage.io
7 import skimage.draw
8 from tifffile import imsave
9 import os
10 import argparse
11 import warnings
12
13 # split_label_image takes a label image and outputs a similar file with the given name where the labeled
14 # parts of the image that touch (or overlap) are separated by at least 1 pixel (at most 2).
15
16
17 def split_labelmap(labelmap,outputfile):
18
19 # Information from the label map.
20 label_img = io_imread(labelmap)
21 xtot, ytot = label_img.shape
22 props = regionprops(label_img)
23 N = len(props)
24
25 # Creating the backgrounds.
26 background = np.zeros([xtot,ytot], 'uint8')
27 overlap = np.zeros([N,xtot,ytot],'uint8')
28 compstruct = scipy.ndimage.generate_binary_structure(2, 2) # Mask for image dilation.
29
30 i = 0
31 for cell in props:
32 cell_image = cell.image.astype('uint8')
33 #plt.imshow(cell_image)
34
35 # Replace the background area corresponding to the bounding box with the image representing the cell.
36 background[int(cell.bbox[0]):int(cell.bbox[2]),int(cell.bbox[1]):int(cell.bbox[3])] += cell_image
37 overlap[i][int(cell.bbox[0]):int(cell.bbox[2]), int(cell.bbox[1]):int(cell.bbox[3])] = cell_image
38
39 # In the overlap array, dilate the cell in all directions.
40 overlap[i] = scipy.ndimage.binary_dilation(
41 overlap[i], structure=compstruct).astype(overlap[i].dtype)
42
43 i += 1
44
45 if len(props) > 1:
46 # Sum together the overlap.
47 total_overlap = sum(overlap)
48
49 # Wherever the overlap is greater than 1 replace that point with zero in the final image.
50 for x in range(xtot):
51 for y in range(ytot):
52 if total_overlap[x,y] > 1:
53 background[x,y] = 0
54
55 # Force the image into 8-bit.
56 result = skimage.util.img_as_ubyte(background)
57
58 # Save image
59 with warnings.catch_warnings():
60 warnings.simplefilter("ignore")
61 skimage.io.imsave(outputfile, result, plugin="tifffile")
62
63 return None
64
65 # To run from command line.
66 if __name__ == "__main__":
67 parser = argparse.ArgumentParser()
68 parser.add_argument('labelmap',
69 help='Label map image.')
70 parser.add_argument('outputfile',
71 help='Output file. Without extension (although it corrects if you '
72 'add it; will always return a .tif')
73
74 args = parser.parse_args()
75 split_labelmap(args.labelmap, args.outputfile)