Mercurial > repos > imgteam > imagecoordinates_flipaxis

comparison 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
children
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2:f8f1100d0701 3:984b342d03a6
1 import argparse 1 import argparse
2
2 import pandas as pd 3 import pandas as pd
3 4
4 5
5 def imagecoordinates_flipyaxis(input_file, output_file, image_height, offset=[0,0]): 6 def imagecoordinates_flipyaxis(input_file, output_file, image_height, offset=[0, 0]):
6 df = pd.read_csv(input_file, sep='\t') 7 df = pd.read_csv(input_file, sep='\t')
7 8
8 x = df.copy().y # create copy instead of view 9 x = df.copy().y # create copy instead of view
9 df.y = image_height-(df.x + 1) + offset[1] # since maximal y index = height-1 10 df.y = image_height - (df.x + 1) + offset[1] # since maximal y index = height-1
10 df.x = x + offset[0] 11 df.x = x + offset[0]
11 df.to_csv(output_file, sep="\t", index=False) 12 df.to_csv(output_file, sep="\t", index=False)
12
13 13
14 14
15 if __name__ == "__main__": 15 if __name__ == "__main__":
16 parser = argparse.ArgumentParser() 16 parser = argparse.ArgumentParser()
17 parser.add_argument('input_file', type=argparse.FileType('r'), help='original file') 17 parser.add_argument('input_file', type=argparse.FileType('r'), help='original file')
19 parser.add_argument('image_height', type=int, help='height of image') 19 parser.add_argument('image_height', type=int, help='height of image')
20 parser.add_argument('offset_x', type=int, help='offset in x direction (width)', default=0) 20 parser.add_argument('offset_x', type=int, help='offset in x direction (width)', default=0)
21 parser.add_argument('offset_y', type=int, help='offset in y direction (height)', default=0) 21 parser.add_argument('offset_y', type=int, help='offset in y direction (height)', default=0)
22 args = parser.parse_args() 22 args = parser.parse_args()
23 imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, args.image_height, [args.offset_x, args.offset_y]) 23 imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, args.image_height, [args.offset_x, args.offset_y])
24 # imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, int(args.image_height))