| Next changeset 1:974cf4357707 (2019-12-18) |
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Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 |
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projective_transformation.py projective_transformation.xml test-data/sample1.png test-data/sample2.png test-data/warp_matrix.tsv test-data/yam.png |
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| diff -r 000000000000 -r 17f5d0c3f8a3 projective_transformation.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/projective_transformation.py Sat Feb 09 14:44:40 2019 -0500 |
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| @@ -0,0 +1,61 @@ +import skimage.io +from skimage.transform import ProjectiveTransform +from scipy.ndimage import map_coordinates +import numpy as np +import pandas as pd +import argparse +import warnings +import shutil + + +def _stackcopy(a, b): + if a.ndim == 3: + a[:] = b[:, :, np.newaxis] + else: + a[:] = b + + +def warp_coords_batch(coord_map, shape, dtype=np.float64, batch_size=1000000): + rows, cols = shape[0], shape[1] + coords_shape = [len(shape), rows, cols] + if len(shape) == 3: + coords_shape.append(shape[2]) + coords = np.empty(coords_shape, dtype=dtype) + + tf_coords = np.indices((cols, rows), dtype=dtype).reshape(2, -1).T + + for i in range(0, (tf_coords.shape[0]//batch_size+1)): + tf_coords[batch_size*i:batch_size*(i+1)] = coord_map(tf_coords[batch_size*i:batch_size*(i+1)]) + tf_coords = tf_coords.T.reshape((-1, cols, rows)).swapaxes(1, 2) + + _stackcopy(coords[1, ...], tf_coords[0, ...]) + _stackcopy(coords[0, ...], tf_coords[1, ...]) + if len(shape) == 3: + coords[2, ...] = range(shape[2]) + + return coords + + +def transform(moving_image, fixed_image, warp_matrix, out): + moving_image = skimage.io.imread(moving_image) + fixed_image = skimage.io.imread(fixed_image) + warp_matrix = pd.read_csv(warp_matrix, delimiter="\t", header=None) + warp_matrix = np.array(warp_matrix) + + trans = ProjectiveTransform(matrix=warp_matrix) + warped_coords = warp_coords_batch(trans, fixed_image.shape) + t = map_coordinates(moving_image, warped_coords, mode='reflect') + + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + skimage.io.imsave(out, t) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Transform the image") + parser.add_argument("fixed_image", help="Paste path to image.png that should be transformed") + parser.add_argument("moving_image", help="Paste path to fixed image.png") + parser.add_argument("warp_matrix", help="Paste path to warp_matrix.csv that should be used for transformation") + parser.add_argument("out", help="Paste path to file in which transformed image should be saved") + args = parser.parse_args() + transform(args.moving_image, args.fixed_image, args.warp_matrix, args.out) |
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| diff -r 000000000000 -r 17f5d0c3f8a3 projective_transformation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/projective_transformation.xml Sat Feb 09 14:44:40 2019 -0500 |
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| @@ -0,0 +1,42 @@ +<tool id="ip_projective_transformation" name="Projective Transformation" version="0.0.4"> + <description>Projective Transformation</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> + <!--<requirement type="package" version="1.1.0">scipy</requirement>--> + </requirements> + <command> + <![CDATA[ + python '$__tool_directory__/projective_transformation.py' + '$fixed_image' + '$moving_image' + '$warp_matrix' + ./out.png + ]]> + </command> + <inputs> + <param name="moving_image" type="data" format="png" label="Moving Image" /> + <param name="fixed_image" type="data" format="png" label="Fixed Image" /> + <param name="warp_matrix" type= "data" format="tabular" label="Warp Matrix" /> + </inputs> + <outputs> + <data format="png" name="out" from_work_dir="out.png" /> + </outputs> + <tests> + <test> + <param name="fixed_image" value="sample1.png"/> + <param name="moving_image" value="sample2.png"/> + <param name="warp_matrix" value="warp_matrix.tsv"/> + <output name="out" value="yam.png" ftype="png" compare="sim_size"/> + </test> + </tests> + <help> + **What it does** + + This tool performs a projective transformation of the input (moving) image so that it fits the fixed image. + </help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 17f5d0c3f8a3 test-data/warp_matrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/warp_matrix.tsv Sat Feb 09 14:44:40 2019 -0500 |
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