Mercurial > repos > imgteam > imagecoordinates_flipaxis

comparison imagecoordinates_flipaxis.py @ 1:d0960e1b25a8 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit da043bdec956714abb0fa82f278931bbe1a6d41d
author imgteam
date Mon, 25 Mar 2019 11:15:54 -0400
parents 5a210baa2ff1
children f8f1100d0701
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0:5a210baa2ff1 1:d0960e1b25a8
1 import argparse 1 import argparse
2 import pandas as pd 2 import pandas as pd
3 3
4 4
5 def imagecoordinates_flipyaxis(input_file, output_file, image_height): 5 def imagecoordinates_flipyaxis(input_file, output_file, image_height, offset=[0,0]):
6 df = pd.read_csv(input_file, sep='\t') 6 df = pd.read_csv(input_file, sep='\t')
7 7
8 x = df.copy().y # create copy instead of view 8 x = df.copy().y # create copy instead of view
9 df.y = image_height-(df.x + 1) # since maximal y index = height-1 9 df.y = image_height-(df.x + 1) + offset[1] # since maximal y index = height-1
10 df.x = x 10 df.x = x + offset[0]
11 df.to_csv(output_file, sep="\t", index=False) 11 df.to_csv(output_file, sep="\t", index=False)
12 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')
18 parser.add_argument('out_file_str', type=str, help='string of output file name') 18 parser.add_argument('out_file_str', type=str, help='string of output file name')
19 # parser.add_argument('image_height', help='height of image')
20 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)
21 parser.add_argument('offset_y', type=int, help='offset in y direction (height)', default=0)
21 args = parser.parse_args() 22 args = parser.parse_args()
22 imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, args.image_height) 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, int(args.image_height)) 24 # imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, int(args.image_height))