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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author thomaswollmann
date Wed, 16 Jan 2019 15:34:44 -0500
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f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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1 #!/usr/bin/python
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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3 import argparse
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
parents:
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4 import numpy as np
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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5 import os
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
parents:
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6 import skimage.io
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
parents:
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7 from skimage.measure import regionprops
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
parents:
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8
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
parents:
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9 parser = argparse.ArgumentParser(description='Count Objects')
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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10 parser.add_argument('input_file', type=argparse.FileType('r'),
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
parents:
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11 help='Label input file')
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
parents:
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12 parser.add_argument('output_file', type=argparse.FileType('w'),
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
parents:
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13 help='Tabular output file')
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
parents:
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14 args = parser.parse_args()
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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16 img_raw = skimage.io.imread(args.input_file.name)
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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17 res = len(regionprops(img_raw))
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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19 text_file = open(args.output_file.name, "w")
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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20 text_file.write("objects\n%s" % res)
f02a2d0f407c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
parents:
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21 text_file.close()