Mercurial > repos > thomaswollmann > split_labelmap

annotate split_labelmap.py @ 0:9e15e70bb22b draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
author thomaswollmann
date Mon, 07 Jan 2019 05:36:05 -0500
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9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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1 from imageio import imread as io_imread
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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2 from skimage.measure import regionprops
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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3 import numpy as np
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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4 #import matplotlib.pyplot as plt
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5 import scipy
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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6 import skimage.io
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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7 import skimage.draw
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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8 from tifffile import imsave
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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9 import os
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10 import argparse
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11 import warnings
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13 # split_label_image takes a label image and outputs a similar file with the given name where the labeled
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14 # parts of the image that touch (or overlap) are separated by at least 1 pixel (at most 2).
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17 def split_labelmap(labelmap,outputfile):
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19 # Information from the label map.
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20 label_img = io_imread(labelmap)
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21 xtot, ytot = label_img.shape
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22 props = regionprops(label_img)
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23 N = len(props)
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25 # Creating the backgrounds.
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26 background = np.zeros([xtot,ytot], 'uint8')
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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27 overlap = np.zeros([N,xtot,ytot],'uint8')
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28 compstruct = scipy.ndimage.generate_binary_structure(2, 2) # Mask for image dilation.
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30 i = 0
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31 for cell in props:
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32 cell_image = cell.image.astype('uint8')
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33 #plt.imshow(cell_image)
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35 # Replace the background area corresponding to the bounding box with the image representing the cell.
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36 background[int(cell.bbox[0]):int(cell.bbox[2]),int(cell.bbox[1]):int(cell.bbox[3])] += cell_image
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37 overlap[i][int(cell.bbox[0]):int(cell.bbox[2]), int(cell.bbox[1]):int(cell.bbox[3])] = cell_image
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39 # In the overlap array, dilate the cell in all directions.
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40 overlap[i] = scipy.ndimage.binary_dilation(
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41 overlap[i], structure=compstruct).astype(overlap[i].dtype)
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43 i += 1
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45 if len(props) > 1:
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46 # Sum together the overlap.
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47 total_overlap = sum(overlap)
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49 # Wherever the overlap is greater than 1 replace that point with zero in the final image.
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50 for x in range(xtot):
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51 for y in range(ytot):
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52 if total_overlap[x,y] > 1:
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53 background[x,y] = 0
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54
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55 # Force the image into 8-bit.
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56 result = skimage.util.img_as_ubyte(background)
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58 # Save image
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59 with warnings.catch_warnings():
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60 warnings.simplefilter("ignore")
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61 skimage.io.imsave(outputfile, result, plugin="tifffile")
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63 return None
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64
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65 # To run from command line.
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66 if __name__ == "__main__":
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67 parser = argparse.ArgumentParser()
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68 parser.add_argument('labelmap',
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69 help='Label map image.')
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70 parser.add_argument('outputfile',
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71 help='Output file. Without extension (although it corrects if you '
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72 'add it; will always return a .tif')
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73
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74 args = parser.parse_args()
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75 split_labelmap(args.labelmap, args.outputfile)