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annotate points2label.py @ 0:dcc8c1d6af48 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:44:10 -0500
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children 9bd039f46843
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dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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2 import sys
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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3 import numpy as np
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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4 import skimage.io
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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5 import pandas as pd
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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6 import warnings
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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7
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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8 def points2label(labels, shape, output_file=None, has_header=False, is_TSV=True):
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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9 labelimg = np.zeros([shape[0], shape[1]], dtype=np.int32)
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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11 if is_TSV:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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12 if has_header:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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13 df = pd.read_csv(labels, sep='\t', skiprows=1, header=None)
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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14 else:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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15 df = pd.read_csv(labels, sep='\t', header=None)
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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16 else:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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17 if has_header:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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18 df = pd.read_csv(labels, skiprows=1, header=None)
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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19 else:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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20 df = pd.read_csv(labels, header=None)
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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22 for i in range(0, len(df)):
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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23 a_row = df.iloc[i]
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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24 labelimg[a_row[0], a_row[1]] = i+1
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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26 if output_file is not None:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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27 with warnings.catch_warnings():
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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28 warnings.simplefilter("ignore")
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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29 skimage.io.imsave(output_file, labelimg, plugin='tifffile')
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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30 else:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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31 return labelimg
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 if __name__ == "__main__":
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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34 parser = argparse.ArgumentParser()
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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35 parser.add_argument('label_file', type=argparse.FileType('r'), default=sys.stdin, help='label file')
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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36 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file')
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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37 parser.add_argument('org_file', type=argparse.FileType('r'), default=sys.stdin, help='input original file')
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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38 parser.add_argument('--has_header', dest='has_header', type=bool, default=False, help='label file has header')
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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39 parser.add_argument('--is_tsv', dest='is_tsv', type=bool, default=True, help='label file is TSV')
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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40 args = parser.parse_args()
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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41
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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42 original_shape = skimage.io.imread(args.org_file.name, plugin='tifffile').shape
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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43
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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44 points2label(args.label_file.name, original_shape, args.out_file.name, args.has_header, args.is_tsv)