Mercurial > repos > imgteam > count_objects
annotate count_objects.py @ 3:b58447a2eed2 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author | imgteam |
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date | Mon, 13 Nov 2023 22:10:56 +0000 |
parents | 5bf8eb50b280 |
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895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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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:
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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 |
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5bf8eb50b280
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit 3c2a4fed433e518fcd0bc8d4deffcc5c2346b2b5
imgteam
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4 |
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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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5 import skimage.io |
2
5bf8eb50b280
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit 3c2a4fed433e518fcd0bc8d4deffcc5c2346b2b5
imgteam
parents:
1
diff
changeset
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6 from skimage.measure import regionprops |
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895a29ebd0c7
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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7 |
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 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
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9 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
|
10 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
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11 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
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12 help='Tabular output file') |
2
5bf8eb50b280
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit 3c2a4fed433e518fcd0bc8d4deffcc5c2346b2b5
imgteam
parents:
1
diff
changeset
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13 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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14 |
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 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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16 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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17 |
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 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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19 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
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20 text_file.close() |