Mercurial > repos > imgteam > binaryimage2points

comparison binaryimage2points.py @ 0:cb1eaebdb4c4 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:31:13 -0500
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children f38f42d55813
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-1:000000000000 0:cb1eaebdb4c4
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 import warnings
9
10
11
12 def binaryimage2points(input_file):
13 # ignore warnings that arise when importing a package that was compiled against an older version of numpy than installed; https://github.com/numpy/numpy/pull/432
14 warnings.filterwarnings("ignore")
15
16 img_in = skimage.io.imread(input_file, plugin='tifffile')
17
18 #make label image
19 label = skimage.measure.label(img_in)
20
21 #amount of regions
22 amount_label = np.max(label)
23
24 # iterate over all regions in order to calc center of mass
25 center_mass = []
26 for i in range(1,amount_label+1):
27 #get coordinates of region
28 coord = np.where(label==i)
29 # be carefull with x,y coordinates
30 center_mass.append([np.mean(coord[1]),np.mean(coord[0])])
31
32 #make data frame of detections
33 out_dataFrame = pd.DataFrame(center_mass)
34
35
36 #return
37 return(out_dataFrame)
38
39
40 if __name__ == "__main__":
41 parser = argparse.ArgumentParser()
42 parser.add_argument('input_file', help='input file')
43 parser.add_argument('out_file', help='out file (TSV)')
44
45 args = parser.parse_args()
46 input_file = args.input_file
47 out_file = args.out_file
48
49 #TOOL
50 out_dataFrame = binaryimage2points(input_file)
51
52 #Print to csv file
53 out_dataFrame.to_csv(out_file, index=False, header=False, sep="\t")