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annotate points2binaryimage.py @ 0:dd513c9f5230 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:43:25 -0500
parents
children 90385ec28b34
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dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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2 import sys
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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3 import numpy as np
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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4 import skimage.io
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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5 import pandas as pd
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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6 import os
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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7 import warnings
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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8
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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9
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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10 def points2binaryimage(point_file, out_file, shape=[500, 500], has_header=False, invert_xy=False):
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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12 img = np.zeros(shape, dtype=np.int16)
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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13 if os.path.exists(point_file) and os.path.getsize(point_file) > 0:
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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14 if has_header:
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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15 df = pd.read_csv(point_file, skiprows=1, header=None, delimiter="\t")
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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16 else:
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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17 df = pd.read_csv(point_file, header=None, delimiter="\t")
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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19 for i in range(0, len(df)):
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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20 a_row = df.iloc[i]
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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21 if int(a_row[0]) < 0 or int(a_row[1]) < 0:
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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22 raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[0]), int(a_row[1]), shape[0], shape[1]))
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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24 if invert_xy:
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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25 if img.shape[0]<=int(a_row[0]) or img.shape[1]<=int(a_row[1]):
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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26 raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[0]), int(a_row[1]), shape[0], shape[1]))
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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27 else:
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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28 img[int(a_row[1]), int(a_row[0])] = 32767
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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29 else:
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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30 if img.shape[0]<=int(a_row[1]) or img.shape[1]<=int(a_row[0]):
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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31 raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[1]), int(a_row[0]), shape[0], shape[1]))
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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32 else:
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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33 img[int(a_row[0]), int(a_row[1])] = 32767
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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34 else:
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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35 raise Exception("{} is empty or does not exist.".format(point_file)) # appropriate built-in error?
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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36
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37 with warnings.catch_warnings():
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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38 warnings.simplefilter("ignore")
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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39 skimage.io.imsave(out_file, img, plugin='tifffile') # otherwise we get problems with the .dat extension
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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40
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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41 if __name__ == "__main__":
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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42 parser = argparse.ArgumentParser()
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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43 parser.add_argument('point_file', type=argparse.FileType('r'), help='label file')
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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44 parser.add_argument('out_file', type=str, help='out file (TIFF)')
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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45 parser.add_argument('shapex', type=int, help='shapex')
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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46 parser.add_argument('shapey', type=int, help='shapey')
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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47 parser.add_argument('--has_header', dest='has_header', default=False, help='set True if CSV has header')
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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48 parser.add_argument('--invert_xy', dest='invert_xy', default=False, help='invert x and y in CSV')
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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49
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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50 args = parser.parse_args()
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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51
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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52 #TOOL
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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53 points2binaryimage(args.point_file.name, args.out_file, [args.shapey, args.shapex], has_header=args.has_header, invert_xy=args.invert_xy)