| Previous changeset 1:f1744c5654b9 (2019-03-27) Next changeset 3:a84822a0060c (2020-05-08) |
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Commit message:
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit f1298dca5a7f5be3acbb5e3d80c98b1cd6d2795b" |
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modified:
projective_transformation_points.py projective_transformation_points.xml test-data/out.tsv |
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| diff -r f1744c5654b9 -r 0d2707c82d29 projective_transformation_points.py --- a/projective_transformation_points.py Wed Mar 27 14:54:32 2019 -0400 +++ b/projective_transformation_points.py Fri May 08 05:21:51 2020 -0400 |
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| @@ -1,28 +1,69 @@ from skimage.transform import ProjectiveTransform +from scipy.ndimage import map_coordinates import numpy as np import pandas as pd import argparse +def _stackcopy(a, b): + if a.ndim == 3: + a[:] = b[:, :, np.newaxis] + else: + a[:] = b + + +def warp_img_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 warp_coords_batch(coord_map, coords, dtype=np.float64, batch_size=1000000): tf_coords = coords.astype(np.float32)[:, ::-1] 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)]) - return np.unique(np.round(tf_coords).astype(coords.dtype),axis=0)[:, ::-1] - + return tf_coords[:, ::-1] + def transform(coords, warp_matrix, out): - indices = np.array(pd.read_csv(coords, delimiter="\t")) - a_matrix = np.array(pd.read_csv(warp_matrix, delimiter="\t", header=None)) + roi_coords = np.array(pd.read_csv(coords, delimiter="\t")) + trans_matrix = np.array(pd.read_csv(warp_matrix, delimiter="\t", header=None)) + + tol = 10 + moving = np.zeros(np.max(roi_coords,axis=0)+tol, dtype=np.int8) + idx_roi_coords = (roi_coords[:,0]-1) * moving.shape[1] + roi_coords[:,1] - 1 + moving.flat[idx_roi_coords] = 1 - trans = ProjectiveTransform(matrix=a_matrix) - warped_coords = warp_coords_batch(trans, indices) - + transP = ProjectiveTransform(matrix=trans_matrix) + roi_coords_warped_direct = warp_coords_batch(transP, roi_coords) + shape_fixed = np.round(np.max(roi_coords_warped_direct,axis=0)).astype(roi_coords.dtype)+tol + + transI = ProjectiveTransform(matrix=np.linalg.inv(trans_matrix)) + img_coords_warped = warp_img_coords_batch(transI, shape_fixed) + + moving_warped = map_coordinates(moving, img_coords_warped, mode='constant', cval=0) + idx_roi_coords_warped = np.where(moving_warped==1) + df = pd.DataFrame() - df['x'] = warped_coords[:,0] - df['y'] = warped_coords[:,1] + df['x'] = idx_roi_coords_warped[0] + 1 + df['y'] = idx_roi_coords_warped[1] + 1 df.to_csv(out, index = False, sep="\t") |
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| diff -r f1744c5654b9 -r 0d2707c82d29 projective_transformation_points.xml --- a/projective_transformation_points.xml Wed Mar 27 14:54:32 2019 -0400 +++ b/projective_transformation_points.xml Fri May 08 05:21:51 2020 -0400 |
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| @@ -1,9 +1,11 @@ -<tool id="ip_projective_transformation_points" name="Projective Transformation" version="0.0.3"> +<tool id="ip_projective_transformation_points" name="Projective Transformation" version="0.0.4"> <description>of input points</description> <requirements> <requirement type="package" version="0.14.2">scikit-image</requirement> + <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><!--conflict of 1.15.4 with mkl_fft!?--> + <requirement type="package" version="0.15.1">tifffile</requirement> </requirements> <command> <![CDATA[ @@ -19,7 +21,7 @@ </inputs> <outputs> <data format="tabular" name="out" /> - </outputs> + </outputs> <tests> <test> <param name="moving_points" value="points_tsv.tsv" /> |
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| diff -r f1744c5654b9 -r 0d2707c82d29 test-data/out.tsv --- a/test-data/out.tsv Wed Mar 27 14:54:32 2019 -0400 +++ b/test-data/out.tsv Fri May 08 05:21:51 2020 -0400 |
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| @@ -1,7 +1,7 @@ x y -30 12 28 14 28 15 28 16 28 17 +30 12 35 25 |