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annotate projective_transformation_points.py @ 1:f1744c5654b9 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit 201f4231192bc368b14e72bb1314b9a97b8db8d0
author imgteam
date Wed, 27 Mar 2019 14:54:32 -0400
parents ed8a71e13f7b
children 0d2707c82d29
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 from skimage.transform import ProjectiveTransform
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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2 import numpy as np
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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3 import pandas as pd
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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4 import argparse
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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7 def warp_coords_batch(coord_map, coords, dtype=np.float64, batch_size=1000000):
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f1744c5654b9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit 201f4231192bc368b14e72bb1314b9a97b8db8d0
imgteam
parents: 0
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8 tf_coords = coords.astype(np.float32)[:, ::-1]
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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f1744c5654b9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit 201f4231192bc368b14e72bb1314b9a97b8db8d0
imgteam
parents: 0
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10 for i in range(0, (tf_coords.shape[0]//batch_size)+1):
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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11 tf_coords[batch_size*i:batch_size*(i+1)] = coord_map(tf_coords[batch_size*i:batch_size*(i+1)])
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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f1744c5654b9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit 201f4231192bc368b14e72bb1314b9a97b8db8d0
imgteam
parents: 0
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13 return np.unique(np.round(tf_coords).astype(coords.dtype),axis=0)[:, ::-1]
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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16 def transform(coords, warp_matrix, out):
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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17 indices = np.array(pd.read_csv(coords, delimiter="\t"))
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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18 a_matrix = np.array(pd.read_csv(warp_matrix, delimiter="\t", header=None))
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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20 trans = ProjectiveTransform(matrix=a_matrix)
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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21 warped_coords = warp_coords_batch(trans, indices)
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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23 df = pd.DataFrame()
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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24 df['x'] = warped_coords[:,0]
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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25 df['y'] = warped_coords[:,1]
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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26 df.to_csv(out, index = False, sep="\t")
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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29 if __name__ == "__main__":
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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30 parser = argparse.ArgumentParser(description="Transform coordinates")
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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31 parser.add_argument("coords", help="Paste path to .csv with coordinates to transform (tab separated)")
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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32 parser.add_argument("warp_matrix", help="Paste path to .csv that should be used for transformation (, separated)")
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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33 parser.add_argument("out", help="Paste path to file in which transformed coords should be saved (tab separated)")
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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34 args = parser.parse_args()
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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35 transform(args.coords, args.warp_matrix, args.out)