Mercurial > repos > thomaswollmann > labelimage2points
comparison labelimage2points.py @ 0:732d95b2b030 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
| author | thomaswollmann |
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| date | Wed, 12 Dec 2018 04:38:34 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:732d95b2b030 |
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| 1 import argparse | |
| 2 import sys | |
| 3 import pandas as pd | |
| 4 import skimage.io | |
| 5 from skimage.measure import label | |
| 6 from skimage.data import checkerboard | |
| 7 import numpy as np | |
| 8 | |
| 9 | |
| 10 | |
| 11 def labelimage2points(input_file): | |
| 12 img_in = skimage.io.imread(input_file) | |
| 13 | |
| 14 #amount of regions | |
| 15 amount_label = np.max(img_in) | |
| 16 | |
| 17 # iterate over all regions in order to calc center of mass | |
| 18 center_mass = [] | |
| 19 for i in range(1,amount_label+1): | |
| 20 #get coordinates of region | |
| 21 coord = np.where(img_in==i) | |
| 22 # be carefull with x,y coordinates | |
| 23 center_mass.append([np.mean(coord[1]),np.mean(coord[0])]) | |
| 24 | |
| 25 #make data frame of detections | |
| 26 out_dataFrame = pd.DataFrame(center_mass) | |
| 27 | |
| 28 | |
| 29 #return | |
| 30 return(out_dataFrame) | |
| 31 | |
| 32 | |
| 33 | |
| 34 | |
| 35 if __name__ == "__main__": | |
| 36 parser = argparse.ArgumentParser() | |
| 37 parser.add_argument('input_file', help='input file') | |
| 38 parser.add_argument('out_file', help='out file (CSV)') | |
| 39 | |
| 40 args = parser.parse_args() | |
| 41 input_file = args.input_file | |
| 42 out_file = args.out_file | |
| 43 | |
| 44 #TOOL | |
| 45 out_dataFrame = labelimage2points(input_file) | |
| 46 | |
| 47 #Print to csv file | |
| 48 out_dataFrame.to_csv(out_file,index=False,header=False) |