Mercurial > repos > imgteam > projective_transformation

comparison projective_transformation.py @ 7:6a8ae8cd7167 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
author imgteam
date Wed, 24 Apr 2024 08:13:05 +0000
parents 37b079c98c38
children
comparison
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6:2f504e075496 7:6a8ae8cd7167
7 """ 7 """
8 8
9 import argparse 9 import argparse
10 import warnings 10 import warnings
11 11
12 import giatools.io
12 import numpy as np 13 import numpy as np
13 import pandas as pd 14 import pandas as pd
14 import skimage.color 15 import skimage.color
15 import skimage.io 16 import skimage.io
16 import tifffile 17 import tifffile
45 46
46 return coords 47 return coords
47 48
48 49
49 def transform(moving_fn, fixed_fn, warp_mat, output_fn): 50 def transform(moving_fn, fixed_fn, warp_mat, output_fn):
50 moving = skimage.io.imread(moving_fn) 51 moving = giatools.io.imread(moving_fn)
51 nDims = len(moving.shape) 52 nDims = len(moving.shape)
52 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'
53 54
54 if moving.shape[-1] in [3, 4] and nDims > 2: 55 if moving.shape[-1] in [3, 4] and nDims > 2:
55 isRGB = True 56 isRGB = True
60 if nDims > 3 or (nDims == 3 and not isRGB): 61 if nDims > 3 or (nDims == 3 and not isRGB):
61 isMulCh = True 62 isMulCh = True
62 else: 63 else:
63 isMulCh = False 64 isMulCh = False
64 65
65 fixed = skimage.io.imread(fixed_fn) 66 fixed = giatools.io.imread(fixed_fn)
66 if fixed.shape[-1] in [3, 4] and len(fixed.shape) > 2: 67 if fixed.shape[-1] in [3, 4] and len(fixed.shape) > 2:
67 hw_fixed = fixed.shape[-3:-1] 68 hw_fixed = fixed.shape[-3:-1]
68 else: 69 else:
69 hw_fixed = fixed.shape[-2:] 70 hw_fixed = fixed.shape[-2:]
70 71