Mercurial > repos > imgteam > count_objects
annotate count_objects.py @ 1:664232d2a3f7 draft
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author | imgteam |
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date | Wed, 18 Dec 2019 05:01:56 -0500 |
parents | 895a29ebd0c7 |
children | 5bf8eb50b280 |
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895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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1 #!/usr/bin/python |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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2 |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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3 import argparse |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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4 import numpy as np |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
5 import os |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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6 import skimage.io |
1
664232d2a3f7
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
parents:
0
diff
changeset
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7 from skimage.measure import regionprops |
0
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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8 |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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9 parser = argparse.ArgumentParser(description='Count Objects') |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
10 parser.add_argument('input_file', type=argparse.FileType('r'), |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
11 help='Label input file') |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
12 parser.add_argument('output_file', type=argparse.FileType('w'), |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
13 help='Tabular output file') |
1
664232d2a3f7
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
parents:
0
diff
changeset
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14 args = parser.parse_args() |
0
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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15 |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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16 img_raw = skimage.io.imread(args.input_file.name) |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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17 res = len(regionprops(img_raw)) |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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18 |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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19 text_file = open(args.output_file.name, "w") |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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20 text_file.write("objects\n%s" % res) |
895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
21 text_file.close() |