Mercurial > repos > imgteam > projective_transformation

comparison projective_transformation.py @ 3:be9a815e2240 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit ee372547082b693ef1bbe10b5b7ea8660b9779df"
author imgteam
date Thu, 20 Jan 2022 17:14:55 +0000
parents 1ffdb07020ee
children 37b079c98c38
comparison
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2:1ffdb07020ee 3:be9a815e2240
5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT 5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
6 6
7 """ 7 """
8 8
9 import argparse 9 import argparse
10 import imghdr
11 import warnings 10 import warnings
12 11
13 import numpy as np 12 import numpy as np
14 import pandas as pd 13 import pandas as pd
15 import skimage.color 14 import skimage.color
48 47
49 48
50 def transform(moving_fn, fixed_fn, warp_mat, output_fn): 49 def transform(moving_fn, fixed_fn, warp_mat, output_fn):
51 50
52 moving = skimage.io.imread(moving_fn) 51 moving = skimage.io.imread(moving_fn)
53 extension = imghdr.what(moving_fn)
54 nDims = len(moving.shape) 52 nDims = len(moving.shape)
55 assert nDims in [2, 3, 4, 5, 6], 'this tool only supports up to 6 dimensions' 53 assert nDims in [2, 3, 4, 5, 6], 'this tool only supports up to 6 dimensions'
56 54
57 if moving.shape[-1] in [3, 4] and nDims > 2: 55 if moving.shape[-1] in [3, 4] and nDims > 2:
58 isRGB = True 56 isRGB = True
94 warped_moving = map_coordinates(moving, warped_coords, cval=0) 92 warped_moving = map_coordinates(moving, warped_coords, cval=0)
95 93
96 with warnings.catch_warnings(): 94 with warnings.catch_warnings():
97 warnings.simplefilter("ignore") 95 warnings.simplefilter("ignore")
98 if isMulCh: 96 if isMulCh:
99 tifffile.imwrite(output_fn + '.tif', warped_moving, imagej=True, metadata={'mode': 'composite'}) 97 tifffile.imwrite(output_fn, warped_moving, imagej=True, metadata={'mode': 'composite'})
100 else: 98 else:
101 skimage.io.imsave(output_fn + '.' + extension, warped_moving) 99 skimage.io.imsave(output_fn, warped_moving)
102 100
103 101
104 if __name__ == "__main__": 102 if __name__ == "__main__":
105 parser = argparse.ArgumentParser(description="Transform the image") 103 parser = argparse.ArgumentParser(description="Transform the image")
106 parser.add_argument("fixed_image", help="Path to the fixed image") 104 parser.add_argument("fixed_image", help="Path to the fixed image")