Mercurial > repos > imgteam > landmark_registration_ls
changeset 0:2f36165c49fb draft
"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 |
| parents | |
| children | 69db8c7d4244 |
| files | landmark_registration_ls.py landmark_registration_ls.xml test-data/points1.tsv test-data/points2.tsv test-data/tmat.tsv |
| diffstat | 5 files changed, 87 insertions(+), 0 deletions(-) [+] |
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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) + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/landmark_registration_ls.xml Tue Dec 29 12:10:53 2020 +0000 @@ -0,0 +1,33 @@ +<tool id="ip_landmark_registration_ls" name="Landmark Registration" version="0.0.1"> + <description>using least squares</description> + <requirements> + <requirement type="package" version="1.2.1">scipy</requirement> + <requirement type="package" version="0.23.4">pandas</requirement> + <requirement type="package" version="1.15.2">numpy</requirement> + </requirements> + <command><![CDATA[ + python '$__tool_directory__/landmark_registration_ls.py' + '$fn_pts1' + '$fn_pts2' + '$fn_tmat' +]]></command> + <inputs> + <param name="fn_pts1" type="data" format="tabular" label="Path to tab-separated file with src points" /> + <param name="fn_pts2" type="data" format="tabular" label="Path to tab-separated file with dst points" /> + </inputs> + <outputs> + <data format="tabular" name="fn_tmat" /> + </outputs> + <tests> + <test> + <param name="fn_pts1" value="points1.tsv"/> + <param name="fn_pts2" value="points2.tsv"/> + <output name="fn_tmat" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/> + </test> + </tests> + <help> + **What it does** + + This tool estimates the (affine) transformation matrix using least squares given two sets of 2d coordinates of landmarks. + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/points1.tsv Tue Dec 29 12:10:53 2020 +0000 @@ -0,0 +1,4 @@ + x y +0 1 6 +1 5 2 +2 13 15