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annotate 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
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1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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1 """
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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2 Copyright 2019-2022 Biomedical Computer Vision Group, Heidelberg University.
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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3
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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4 Distributed under the MIT license.
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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7 """
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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8
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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9 import argparse
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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10 import warnings
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12 import numpy as np
17f5d0c3f8a3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 import pandas as pd
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14 import skimage.color
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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15 import skimage.io
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16 import tifffile
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17 from scipy.ndimage import map_coordinates
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18 from skimage.transform import ProjectiveTransform
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17f5d0c3f8a3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 def _stackcopy(a, b):
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22 if a.ndim == 3:
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23 a[:] = b[:, :, np.newaxis]
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24 else:
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25 a[:] = b
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28 def warp_coords_batch(coord_map, shape, dtype=np.float64, batch_size=1000000):
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29 rows, cols = shape[0], shape[1]
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30 coords_shape = [len(shape), rows, cols]
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31 if len(shape) == 3:
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32 coords_shape.append(shape[2])
17f5d0c3f8a3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 coords = np.empty(coords_shape, dtype=dtype)
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35 tf_coords = np.indices((cols, rows), dtype=dtype).reshape(2, -1).T
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36
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37 for i in range(0, (tf_coords.shape[0] // batch_size + 1)):
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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38 tf_coords[batch_size * i:batch_size * (i + 1)] = coord_map(tf_coords[batch_size * i:batch_size * (i + 1)])
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39 tf_coords = tf_coords.T.reshape((-1, cols, rows)).swapaxes(1, 2)
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41 _stackcopy(coords[1, ...], tf_coords[0, ...])
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42 _stackcopy(coords[0, ...], tf_coords[1, ...])
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43 if len(shape) == 3:
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44 coords[2, ...] = range(shape[2])
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46 return coords
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48
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49 def transform(moving_fn, fixed_fn, warp_mat, output_fn):
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50 moving = skimage.io.imread(moving_fn)
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51 nDims = len(moving.shape)
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52 assert nDims in [2, 3, 4, 5, 6], 'this tool only supports up to 6 dimensions'
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53
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54 if moving.shape[-1] in [3, 4] and nDims > 2:
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55 isRGB = True
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56 moving = np.transpose(moving, (nDims - 1,) + tuple(_ for _ in range(nDims - 1)))
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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57 else:
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58 isRGB = False
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59
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60 if nDims > 3 or (nDims == 3 and not isRGB):
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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61 isMulCh = True
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62 else:
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63 isMulCh = False
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64
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65 fixed = skimage.io.imread(fixed_fn)
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66 if fixed.shape[-1] in [3, 4] and len(fixed.shape) > 2:
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67 hw_fixed = fixed.shape[-3:-1]
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68 else:
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69 hw_fixed = fixed.shape[-2:]
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70
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71 if isRGB or isMulCh:
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72 shapeCh = moving.shape[0:-2]
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73 nCh = np.prod(shapeCh)
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74 moving = np.reshape(moving, (nCh,) + moving.shape[-2:])
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75 warped_moving = np.zeros((nCh,) + hw_fixed, dtype=moving.dtype)
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76
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77 warp_mat = pd.read_csv(warp_mat, delimiter="\t", header=None)
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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78 warp_mat = np.array(warp_mat)
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79 assert warp_mat.shape[0] in [3], 'only 2D image transformaton is supported'
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80
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81 transI = ProjectiveTransform(matrix=np.linalg.inv(warp_mat))
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82 warped_coords = warp_coords_batch(transI, hw_fixed)
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83
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84 if isMulCh or isRGB:
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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85 for i in range(nCh):
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86 warped_moving[i, ...] = map_coordinates(moving[i, ...], warped_coords, cval=0)
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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87 warped_moving = np.reshape(warped_moving, shapeCh + warped_moving.shape[-2:])
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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88 if isRGB:
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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89 warped_moving = np.transpose(warped_moving, tuple(_ for _ in range(1, nDims)) + (0,))
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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90 else:
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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91 warped_moving = map_coordinates(moving, warped_coords, cval=0)
0
17f5d0c3f8a3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17f5d0c3f8a3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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93 with warnings.catch_warnings():
17f5d0c3f8a3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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94 warnings.simplefilter("ignore")
2
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95 if isMulCh:
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96 tifffile.imwrite(output_fn, warped_moving, imagej=True, metadata={'mode': 'composite'})
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1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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97 else:
3
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98 skimage.io.imsave(output_fn, warped_moving)
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99
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17f5d0c3f8a3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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101 if __name__ == "__main__":
17f5d0c3f8a3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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102 parser = argparse.ArgumentParser(description="Transform the image")
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103 parser.add_argument("fixed_image", help="Path to the fixed image")
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104 parser.add_argument("moving_image", help="Path to the moving image (to be transformed)")
1ffdb07020ee "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 40b2eeecc9e15be0b710f5e5195ac6f3b3b83c39"
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105 parser.add_argument("warp_matrix", help="Path to the transformation matrix")
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106 parser.add_argument("warped_image", help="Path to the output (transfirmed moving image)")
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107 args = parser.parse_args()
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108 transform(args.moving_image, args.fixed_image, args.warp_matrix, args.warped_image)