Mercurial > repos > imgteam > projective_transformation

comparison projective_transformation.py @ 4:37b079c98c38 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit ded1703bcd6e295b26201505edb58381991b265e"
author imgteam
date Mon, 28 Feb 2022 17:36:23 +0000
parents be9a815e2240
children 6a8ae8cd7167
comparison
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3:be9a815e2240 4:37b079c98c38
45 45
46 return coords 46 return coords
47 47
48 48
49 def transform(moving_fn, fixed_fn, warp_mat, output_fn): 49 def transform(moving_fn, fixed_fn, warp_mat, output_fn):
50
51 moving = skimage.io.imread(moving_fn) 50 moving = skimage.io.imread(moving_fn)
52 nDims = len(moving.shape) 51 nDims = len(moving.shape)
53 assert nDims in [2, 3, 4, 5, 6], 'this tool only supports up to 6 dimensions' 52 assert nDims in [2, 3, 4, 5, 6], 'this tool only supports up to 6 dimensions'
54 53
55 if moving.shape[-1] in [3, 4] and nDims > 2: 54 if moving.shape[-1] in [3, 4] and nDims > 2:
77 76
78 warp_mat = pd.read_csv(warp_mat, delimiter="\t", header=None) 77 warp_mat = pd.read_csv(warp_mat, delimiter="\t", header=None)
79 warp_mat = np.array(warp_mat) 78 warp_mat = np.array(warp_mat)
80 assert warp_mat.shape[0] in [3], 'only 2D image transformaton is supported' 79 assert warp_mat.shape[0] in [3], 'only 2D image transformaton is supported'
81 80
82 trans = ProjectiveTransform(matrix=warp_mat) 81 transI = ProjectiveTransform(matrix=np.linalg.inv(warp_mat))
83 warped_coords = warp_coords_batch(trans, hw_fixed) 82 warped_coords = warp_coords_batch(transI, hw_fixed)
84 83
85 if isMulCh or isRGB: 84 if isMulCh or isRGB:
86 for i in range(nCh): 85 for i in range(nCh):
87 warped_moving[i, ...] = map_coordinates(moving[i, ...], warped_coords, cval=0) 86 warped_moving[i, ...] = map_coordinates(moving[i, ...], warped_coords, cval=0)
88 warped_moving = np.reshape(warped_moving, shapeCh + warped_moving.shape[-2:]) 87 warped_moving = np.reshape(warped_moving, shapeCh + warped_moving.shape[-2:])