Mercurial > repos > imgteam > landmark_registration_ls
diff landmark_registration_ls.py @ 0:2f36165c49fb draft
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration_ls/ commit abd8b0b42f6a700d61c7b042dbf5e5a291b148a3"
author | imgteam |
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date | Tue, 29 Dec 2020 12:10:53 +0000 |
parents | |
children | 69db8c7d4244 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/landmark_registration_ls.py Tue Dec 29 12:10:53 2020 +0000 @@ -0,0 +1,43 @@ +from scipy.linalg import lstsq +import pandas as pd +import numpy as np +import argparse + +def landmark_registration_ls(pts_f1, pts_f2, out_f, delimiter="\t"): + + points1 = pd.read_csv(pts_f1, delimiter=delimiter) + points2 = pd.read_csv(pts_f2, delimiter=delimiter) + + src = np.concatenate([np.array(points1['x']).reshape([-1,1]), + np.array(points1['y']).reshape([-1,1])], + axis=-1) + dst = np.concatenate([np.array(points2['x']).reshape([-1,1]), + np.array(points2['y']).reshape([-1,1])], + axis=-1) + + A = np.zeros((src.size,6)) + A[0:src.shape[0],[0,1]] = src + A[0:src.shape[0],2] = 1 + A[src.shape[0]:,[3,4]] = src + A[src.shape[0]:,5] = 1 + b = dst.T.flatten().astype('float64') + x = lstsq(A,b) + + tmat = np.eye(3) + tmat[0,:] = x[0].take([0,1,2]) + tmat[1,:] = x[0].take([3,4,5]) + pd.DataFrame(tmat).to_csv(out_f, header=None, index=False, sep="\t") + + +if __name__ == "__main__": + + parser = argparse.ArgumentParser(description="Estimate transformation from points using least squares") + + parser.add_argument("fn_pts1", help="File name src points") + parser.add_argument("fn_pts2", help="File name dst points") + parser.add_argument("fn_tmat", help="File name transformation matrix") + args = parser.parse_args() + + landmark_registration_ls(args.fn_pts1, args.fn_pts2, args.fn_tmat) + +