Mercurial > repos > imgteam > landmark_registration
changeset 0:a71239f3543a draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
| author | imgteam |
|---|---|
| date | Tue, 12 Feb 2019 08:35:45 -0500 |
| parents | |
| children | b0503eec7bd6 |
| files | landmark_registration.py landmark_registration.xml test-data/points1.tsv test-data/points2.tsv test-data/warp.tsv |
| diffstat | 5 files changed, 80 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/landmark_registration.py Tue Feb 12 08:35:45 2019 -0500 @@ -0,0 +1,27 @@ +from skimage.measure import ransac +from skimage.transform import AffineTransform +import pandas as pd +import numpy as np +import argparse + +def landmark_registration(points_file1, points_file2, out_file, residual_threshold=2, max_trials=100, delimiter="\t"): + points1 = pd.read_csv(points_file1, delimiter=delimiter) + points2 = pd.read_csv(points_file2, 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) + + model = AffineTransform() + model_robust, inliers = ransac((src, dst), AffineTransform, min_samples=3, + residual_threshold=residual_threshold, max_trials=max_trials) + pd.DataFrame(model_robust.params).to_csv(out_file, header = None, index = False) + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Estimate transformation from points") + parser.add_argument("points_file1", help="Paste path to src points") + parser.add_argument("points_file2", help="Paste path to dst points") + parser.add_argument("warp_matrix", help="Paste path to warp_matrix.csv that should be used for transformation") + parser.add_argument("--residual_threshold", dest="residual_threshold", help="Maximum distance for a data point to be classified as an inlier.", type=float, default=2) + parser.add_argument("--max_trials", dest="max_trials", help="Maximum number of iterations for random sample selection.", type=int, default=100) + args = parser.parse_args() + landmark_registration(args.points_file1, args.points_file2, args.warp_matrix, residual_threshold=args.residual_threshold, max_trials=args.max_trials)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/landmark_registration.xml Tue Feb 12 08:35:45 2019 -0500 @@ -0,0 +1,42 @@ +<tool id="ip_landmark_registration" name="Landmark Registration" version="0.0.2"> + <description>Landmark Registration</description> + <requirements> + <requirement type="package" version="0.14.2">scikit-image</requirement> + <requirement type="package" version="0.23.4">pandas</requirement> + <requirement type="package" version="1.15.4">numpy</requirement> + </requirements> + <command><![CDATA[ + python '$__tool_directory__/landmark_registration.py' + --residual_threshold $residual_threshold + --max_trials $max_trials + '$points_file1' + '$points_file2' + '$warp_matrix' +]]></command> + <inputs> + <param name="points_file1" type="data" format="tabular" label="Path to tab-separated file with src points" /> + <param name="points_file2" type="data" format="tabular" label="Path to tab-separated file with dst points" /> + <param name="residual_threshold" type="float" value="2" label="Maximum distance for a data point to be classified as an inlier." /> + <param name="max_trials" type="integer" value="100" label="Maximum number of iterations for random sample selection." /> + </inputs> + <outputs> + <data format="tabular" name="warp_matrix" /> + </outputs> + <tests> + <test> + <param name="points_file1" value="points1.tsv"/> + <param name="points_file2" value="points2.tsv"/> + <param name="residual_threshold" value="2"/> + <param name="max_trials" value="100"/> + <output name="warp_matrix" value="warp.tsv" ftype="tabular" compare="diff" lines_diff="6"/> + </test> + </tests> + <help> + **What it does** + + This tool estimates the transformation matrix between two sets of 2d points. + </help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/points1.tsv Tue Feb 12 08:35:45 2019 -0500 @@ -0,0 +1,4 @@ + x y +0 1 6 +1 5 2 +2 13 15