Mercurial > repos > imgteam > imagecoordinates_flipaxis

annotate imagecoordinates_flipaxis.py @ 2:f8f1100d0701 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:02:25 -0500
parents d0960e1b25a8
children 984b342d03a6
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5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
diff changeset
1 import argparse
5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
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2 import pandas as pd
5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
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5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
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f8f1100d0701 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
parents: 1
diff changeset
5 def imagecoordinates_flipyaxis(input_file, output_file, image_height, offset=[0,0]):
f8f1100d0701 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
parents: 1
diff changeset
6 df = pd.read_csv(input_file, sep='\t')
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5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
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5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
diff changeset
8 x = df.copy().y # create copy instead of view
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d0960e1b25a8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit da043bdec956714abb0fa82f278931bbe1a6d41d
imgteam
parents: 0
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9 df.y = image_height-(df.x + 1) + offset[1] # since maximal y index = height-1
d0960e1b25a8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit da043bdec956714abb0fa82f278931bbe1a6d41d
imgteam
parents: 0
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10 df.x = x + offset[0]
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5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
diff changeset
11 df.to_csv(output_file, sep="\t", index=False)
5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
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5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
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5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
diff changeset
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5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
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15 if __name__ == "__main__":
5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
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16 parser = argparse.ArgumentParser()
5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
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17 parser.add_argument('input_file', type=argparse.FileType('r'), help='original file')
5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
diff changeset
18 parser.add_argument('out_file_str', type=str, help='string of output file name')
5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
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19 parser.add_argument('image_height', type=int, help='height of image')
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d0960e1b25a8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit da043bdec956714abb0fa82f278931bbe1a6d41d
imgteam
parents: 0
diff changeset
20 parser.add_argument('offset_x', type=int, help='offset in x direction (width)', default=0)
d0960e1b25a8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit da043bdec956714abb0fa82f278931bbe1a6d41d
imgteam
parents: 0
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21 parser.add_argument('offset_y', type=int, help='offset in y direction (height)', default=0)
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5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
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22 args = parser.parse_args()
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d0960e1b25a8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit da043bdec956714abb0fa82f278931bbe1a6d41d
imgteam
parents: 0
diff changeset
23 imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, args.image_height, [args.offset_x, args.offset_y])
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5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
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24 # imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, int(args.image_height))