Mercurial > repos > imgteam > landmark_registration_ls

annotate landmark_registration_ls.py @ 0:2f36165c49fb draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
author imgteam
date Tue, 29 Dec 2020 12:10:53 +0000
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children 69db8c7d4244
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2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
imgteam
parents:
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1 from scipy.linalg import lstsq
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
imgteam
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2 import pandas as pd
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
imgteam
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3 import numpy as np
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
imgteam
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4 import argparse
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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6 def landmark_registration_ls(pts_f1, pts_f2, out_f, delimiter="\t"):
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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8 points1 = pd.read_csv(pts_f1, delimiter=delimiter)
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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9 points2 = pd.read_csv(pts_f2, delimiter=delimiter)
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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11 src = np.concatenate([np.array(points1['x']).reshape([-1,1]),
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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12 np.array(points1['y']).reshape([-1,1])],
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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13 axis=-1)
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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14 dst = np.concatenate([np.array(points2['x']).reshape([-1,1]),
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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15 np.array(points2['y']).reshape([-1,1])],
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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16 axis=-1)
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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18 A = np.zeros((src.size,6))
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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19 A[0:src.shape[0],[0,1]] = src
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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20 A[0:src.shape[0],2] = 1
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21 A[src.shape[0]:,[3,4]] = src
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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22 A[src.shape[0]:,5] = 1
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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23 b = dst.T.flatten().astype('float64')
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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24 x = lstsq(A,b)
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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26 tmat = np.eye(3)
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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27 tmat[0,:] = x[0].take([0,1,2])
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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28 tmat[1,:] = x[0].take([3,4,5])
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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29 pd.DataFrame(tmat).to_csv(out_f, header=None, index=False, sep="\t")
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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32 if __name__ == "__main__":
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34 parser = argparse.ArgumentParser(description="Estimate transformation from points using least squares")
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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36 parser.add_argument("fn_pts1", help="File name src points")
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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37 parser.add_argument("fn_pts2", help="File name dst points")
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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38 parser.add_argument("fn_tmat", help="File name transformation matrix")
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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39 args = parser.parse_args()
2f36165c49fb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
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41 landmark_registration_ls(args.fn_pts1, args.fn_pts2, args.fn_tmat)
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