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annotate imagecoordinates_flipaxis.py @ 3:984b342d03a6 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:11:12 +0000
parents f8f1100d0701
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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
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984b342d03a6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
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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
3 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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984b342d03a6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
diff changeset
6 def imagecoordinates_flipyaxis(input_file, output_file, image_height, offset=[0, 0]):
984b342d03a6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
diff changeset
7 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:
diff changeset
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984b342d03a6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
diff changeset
9 x = df.copy().y # create copy instead of view
984b342d03a6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
diff changeset
10 df.y = image_height - (df.x + 1) + offset[1] # since maximal y index = height-1
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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
11 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
12 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:
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:
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:
diff changeset
15 if __name__ == "__main__":
5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
diff changeset
16 parser = argparse.ArgumentParser()
5a210baa2ff1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
imgteam
parents:
diff changeset
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:
diff changeset
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
diff changeset
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:
diff changeset
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])