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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
author thomaswollmann
date Mon, 07 Jan 2019 05:37:21 -0500
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bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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1 import argparse
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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2 from PIL import Image
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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3 import skimage.io
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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4 import skimage.color
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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5 from skimage.transform import ProjectiveTransform
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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6 from scipy.ndimage import map_coordinates
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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7 import numpy as np
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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8 import pandas as pd
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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11 def _stackcopy(a, b):
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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12 if a.ndim == 3:
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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13 a[:] = b[:, :, np.newaxis]
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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14 else:
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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15 a[:] = b
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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18 def warp_coords_batch(coord_map, shape, dtype=np.float64, batch_size=1000000):
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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19 rows, cols = shape[0], shape[1]
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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20 coords_shape = [len(shape), rows, cols]
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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21 if len(shape) == 3:
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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22 coords_shape.append(shape[2])
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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23 coords = np.empty(coords_shape, dtype=dtype)
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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25 tf_coords = np.indices((cols, rows), dtype=dtype).reshape(2, -1).T
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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27 for i in range(0, (tf_coords.shape[0]//batch_size+1)):
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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28 tf_coords[batch_size*i:batch_size*(i+1)] = coord_map(tf_coords[batch_size*i:batch_size*(i+1)])
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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29 tf_coords = tf_coords.T.reshape((-1, cols, rows)).swapaxes(1, 2)
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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31 _stackcopy(coords[1, ...], tf_coords[0, ...])
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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32 _stackcopy(coords[0, ...], tf_coords[1, ...])
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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33 if len(shape) == 3:
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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34 coords[2, ...] = range(shape[2])
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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36 return coords
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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39 def transform(moving_image, fixed_image, warp_matrix):
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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40 trans = ProjectiveTransform(matrix=warp_matrix)
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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41 warped_coords = warp_coords_batch(trans, fixed_image.shape)
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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42 return map_coordinates(moving_image, warped_coords)
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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43
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45 def overlay(moving_image, fixed_image, factor, overlay_out_path):
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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46 moving_image = Image.fromarray(moving_image).convert("RGBA")
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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47 fixed_image = Image.fromarray(fixed_image).convert("RGBA")
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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48 overlay_out = Image.blend(moving_image, fixed_image, factor)
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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49 overlay_out.save(overlay_out_path, "PNG")
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51
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52 if __name__=="__main__":
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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53 parser = argparse.ArgumentParser(description = "Overlay two images")
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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54 parser.add_argument("fixed_image", help = "Path to fixed image")
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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55 parser.add_argument("moving_image", help = "Path to moving image")
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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56 parser.add_argument("warp_matrix", help="Paste path to warp_matrix.csv that should be used for transformation")
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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57 parser.add_argument("--inverse_transform", dest='inverse_transform', action='store_true', help="Set if inverse transform should be visualized")
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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58 parser.add_argument("--factor", dest = "factor", help = "Enter the factor by which images should be blended, 1.0 returns a copy of second image", type = float, default = 0.5)
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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59 parser.add_argument("overlay_out", help = "Overlay output path")
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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60 args = parser.parse_args()
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62 fixed_image = skimage.io.imread(args.fixed_image)
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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63 moving_image = skimage.io.imread(args.moving_image)
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64
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65 warp_matrix = pd.read_csv(args.warp_matrix, delimiter=",", header=None)
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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66 warp_matrix = np.array(warp_matrix)
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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67 if args.inverse_transform:
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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68 fixed_image = transform(fixed_image, moving_image, warp_matrix)
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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69 else:
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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70 warp_matrix = np.linalg.inv(warp_matrix)
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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71 moving_image = transform(moving_image, fixed_image, warp_matrix)
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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72
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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73 overlay(moving_image, fixed_image, args.factor, args.overlay_out)