Mercurial > repos > thomaswollmann > binaryimage2points
annotate binaryimage2points.py @ 0:c983b2d2cdd7 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
| author | thomaswollmann |
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| date | Wed, 12 Dec 2018 04:49:24 -0500 |
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| rev | line source |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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1 import argparse |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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2 import sys |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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3 import pandas as pd |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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4 import skimage.io |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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5 from skimage.measure import label |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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6 from skimage.data import checkerboard |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
diff
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7 import numpy as np |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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8 import warnings |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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9 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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10 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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11 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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12 def binaryimage2points(input_file): |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
diff
changeset
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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 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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14 warnings.filterwarnings("ignore") |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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15 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
diff
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16 img_in = skimage.io.imread(input_file, plugin='tifffile') |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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17 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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18 #make label image |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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19 label = skimage.measure.label(img_in) |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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20 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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21 #amount of regions |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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22 amount_label = np.max(label) |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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23 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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24 # iterate over all regions in order to calc center of mass |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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25 center_mass = [] |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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26 for i in range(1,amount_label+1): |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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27 #get coordinates of region |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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28 coord = np.where(label==i) |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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29 # be carefull with x,y coordinates |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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30 center_mass.append([np.mean(coord[1]),np.mean(coord[0])]) |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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31 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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32 #make data frame of detections |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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33 out_dataFrame = pd.DataFrame(center_mass) |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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34 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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35 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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36 #return |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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37 return(out_dataFrame) |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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38 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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39 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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40 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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41 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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42 if __name__ == "__main__": |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
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43 parser = argparse.ArgumentParser() |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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44 parser.add_argument('input_file', help='input file') |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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45 parser.add_argument('out_file', help='out file (CSV)') |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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46 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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47 args = parser.parse_args() |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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48 input_file = args.input_file |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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49 out_file = args.out_file |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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50 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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51 #TOOL |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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52 out_dataFrame = binaryimage2points(input_file) |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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53 |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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54 #Print to csv file |
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c983b2d2cdd7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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55 out_dataFrame.to_csv(out_file,index=False,header=False) |