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annotate landmark_registration.py @ 0:a71239f3543a draft

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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
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children b0503eec7bd6
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a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
1 from skimage.measure import ransac
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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2 from skimage.transform import AffineTransform
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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3 import pandas as pd
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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4 import numpy as np
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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5 import argparse
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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7 def landmark_registration(points_file1, points_file2, out_file, residual_threshold=2, max_trials=100, delimiter="\t"):
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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8 points1 = pd.read_csv(points_file1, delimiter=delimiter)
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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9 points2 = pd.read_csv(points_file2, delimiter=delimiter)
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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11 src = np.concatenate([np.array(points1['x']).reshape([-1,1]), np.array(points1['y']).reshape([-1,1])], axis=-1)
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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12 dst = np.concatenate([np.array(points2['x']).reshape([-1,1]), np.array(points2['y']).reshape([-1,1])], axis=-1)
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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14 model = AffineTransform()
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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15 model_robust, inliers = ransac((src, dst), AffineTransform, min_samples=3,
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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16 residual_threshold=residual_threshold, max_trials=max_trials)
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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17 pd.DataFrame(model_robust.params).to_csv(out_file, header = None, index = False)
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
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19 if __name__ == "__main__":
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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20 parser = argparse.ArgumentParser(description="Estimate transformation from points")
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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21 parser.add_argument("points_file1", help="Paste path to src points")
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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22 parser.add_argument("points_file2", help="Paste path to dst points")
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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23 parser.add_argument("warp_matrix", help="Paste path to warp_matrix.csv that should be used for transformation")
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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24 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)
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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25 parser.add_argument("--max_trials", dest="max_trials", help="Maximum number of iterations for random sample selection.", type=int, default=100)
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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26 args = parser.parse_args()
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
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27 landmark_registration(args.points_file1, args.points_file2, args.warp_matrix, residual_threshold=args.residual_threshold, max_trials=args.max_trials)