Mercurial > repos > imgteam > projective_transformation_points

annotate projective_transformation_points.py @ 5:c88235457379 draft default tip

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c4424f5dd4110c92ae39815ebfe2ea8c1010be9c"
author imgteam
date Wed, 26 Jan 2022 15:25:08 +0000
parents b9121ff67280
children
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c88235457379 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c4424f5dd4110c92ae39815ebfe2ea8c1010be9c"
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1 """
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2 Copyright 2019-2022 Biomedical Computer Vision Group, Heidelberg University.
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c88235457379 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c4424f5dd4110c92ae39815ebfe2ea8c1010be9c"
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4 Distributed under the MIT license.
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5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
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7 """
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9 import argparse
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11 import numpy as np
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12 import pandas as pd
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13 from scipy.ndimage import map_coordinates
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14 from skimage.transform import ProjectiveTransform
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17 def _stackcopy(a, b):
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18 if a.ndim == 3:
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19 a[:] = b[:, :, np.newaxis]
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20 else:
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21 a[:] = b
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24 def warp_img_coords_batch(coord_map, shape, dtype=np.float64, batch_size=1000000):
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25 rows, cols = shape[0], shape[1]
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26 coords_shape = [len(shape), rows, cols]
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27 if len(shape) == 3:
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28 coords_shape.append(shape[2])
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29 coords = np.empty(coords_shape, dtype=dtype)
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31 tf_coords = np.indices((cols, rows), dtype=dtype).reshape(2, -1).T
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33 for i in range(0, (tf_coords.shape[0] // batch_size + 1)):
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34 tf_coords[batch_size * i:batch_size * (i + 1)] = coord_map(tf_coords[batch_size * i:batch_size * (i + 1)])
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35 tf_coords = tf_coords.T.reshape((-1, cols, rows)).swapaxes(1, 2)
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37 _stackcopy(coords[1, ...], tf_coords[0, ...])
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38 _stackcopy(coords[0, ...], tf_coords[1, ...])
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39 if len(shape) == 3:
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40 coords[2, ...] = range(shape[2])
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42 return coords
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45 def warp_coords_batch(coord_map, coords, dtype=np.float64, batch_size=1000000):
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46 tf_coords = coords.astype(np.float32)[:, ::-1]
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48 for i in range(0, (tf_coords.shape[0] // batch_size) + 1):
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49 tf_coords[batch_size * i:batch_size * (i + 1)] = coord_map(tf_coords[batch_size * i:batch_size * (i + 1)])
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51 return tf_coords[:, ::-1]
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54 def transform(fn_roi_coords, fn_warp_matrix, fn_out):
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55 data = pd.read_csv(fn_roi_coords, delimiter="\t")
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56 all_data = np.array(data)
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58 nrows, ncols = all_data.shape[0:2]
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59 roi_coords = all_data.take([0, 1], axis=1).astype('int64')
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61 tol = 10
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62 moving = np.zeros(np.max(roi_coords, axis=0) + tol, dtype=np.uint32)
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63 idx_roi_coords = (roi_coords[:, 0] - 1) * moving.shape[1] + roi_coords[:, 1] - 1
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64 moving.flat[idx_roi_coords] = np.transpose(np.arange(nrows) + 1)
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66 trans_matrix = np.array(pd.read_csv(fn_warp_matrix, delimiter="\t", header=None))
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67 transP = ProjectiveTransform(matrix=trans_matrix)
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68 roi_coords_warped_direct = warp_coords_batch(transP, roi_coords)
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69 shape_fixed = np.round(np.max(roi_coords_warped_direct, axis=0)).astype(roi_coords.dtype) + tol
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71 transI = ProjectiveTransform(matrix=np.linalg.inv(trans_matrix))
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72 img_coords_warped = warp_img_coords_batch(transI, shape_fixed)
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74 moving_warped = map_coordinates(moving, img_coords_warped, order=0, mode='constant', cval=0)
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75 idx_roi_coords_warped = np.where(moving_warped > 0)
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76 roi_annots_warped = moving_warped.compress((moving_warped > 0).flat)
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78 df = pd.DataFrame()
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79 col_names = data.columns.tolist()
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80 df['x'] = idx_roi_coords_warped[0] + 1
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81 df['y'] = idx_roi_coords_warped[1] + 1
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82 if ncols > 2:
c88235457379 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c4424f5dd4110c92ae39815ebfe2ea8c1010be9c"
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83 for i in range(2, ncols):
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84 df[col_names[i]] = all_data[:, i].take(roi_annots_warped - 1)
c88235457379 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c4424f5dd4110c92ae39815ebfe2ea8c1010be9c"
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85 df.to_csv(fn_out, index=False, sep="\t")
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86
dd792352f2a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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87
dd792352f2a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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88 if __name__ == "__main__":
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89 parser = argparse.ArgumentParser(description="Transform ROIs defined by pixel (point) coordinates")
c88235457379 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c4424f5dd4110c92ae39815ebfe2ea8c1010be9c"
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90 parser.add_argument("coords", help="Path to the TSV file of the coordinates (and labels) to be transformed")
c88235457379 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c4424f5dd4110c92ae39815ebfe2ea8c1010be9c"
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91 parser.add_argument("tmat", help="Path to the TSV file of the transformation matrix")
c88235457379 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c4424f5dd4110c92ae39815ebfe2ea8c1010be9c"
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92 parser.add_argument("out", help="Path to the TSV file of the transformed coordinates (and labels)")
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dd792352f2a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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93 args = parser.parse_args()
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94 transform(args.coords, args.tmat, args.out)