Mercurial > repos > imgteam > points2labelimage
annotate points2label.py @ 2:30ca5d5d03ec draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author | imgteam |
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date | Mon, 13 Nov 2023 22:11:46 +0000 |
parents | 9bd039f46843 |
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dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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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 |
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30ca5d5d03ec
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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3 import warnings |
30ca5d5d03ec
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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4 |
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dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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5 import numpy as np |
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30ca5d5d03ec
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
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6 import pandas as pd |
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dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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7 import skimage.io |
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30ca5d5d03ec
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
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8 |
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dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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9 |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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10 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
parents:
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11 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
imgteam
parents:
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12 |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
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13 if is_TSV: |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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14 if has_header: |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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15 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
parents:
diff
changeset
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16 else: |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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17 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
parents:
diff
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18 else: |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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19 if has_header: |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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20 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
parents:
diff
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21 else: |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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22 df = pd.read_csv(labels, header=None) |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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23 |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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24 for i in range(0, len(df)): |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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25 a_row = df.iloc[i] |
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30ca5d5d03ec
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
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26 labelimg[a_row[0], a_row[1]] = i + 1 |
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dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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27 |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
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28 if output_file is not None: |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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29 with warnings.catch_warnings(): |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
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30 warnings.simplefilter("ignore") |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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31 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
parents:
diff
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32 else: |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
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33 return labelimg |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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34 |
2
30ca5d5d03ec
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
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35 |
0
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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36 if __name__ == "__main__": |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
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37 parser = argparse.ArgumentParser() |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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38 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
parents:
diff
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39 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
parents:
diff
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40 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
parents:
diff
changeset
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41 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
parents:
diff
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42 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
parents:
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43 args = parser.parse_args() |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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44 |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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45 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
imgteam
parents:
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46 |
dcc8c1d6af48
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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47 points2label(args.label_file.name, original_shape, args.out_file.name, args.has_header, args.is_tsv) |