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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
author imgteam
date Sat, 26 Feb 2022 17:14:27 +0000
parents bc324ec66719
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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diff changeset
1 import argparse
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b4fc6e09e576 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3 import numpy as np
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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4 import pandas as pd
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b4fc6e09e576 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
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5 import skimage.color
b4fc6e09e576 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
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6 import skimage.io
b4fc6e09e576 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
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7 from PIL import Image
b4fc6e09e576 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
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8 from scipy.ndimage import map_coordinates
b4fc6e09e576 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
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9 from skimage.transform import ProjectiveTransform
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 def _stackcopy(a, b):
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 if a.ndim == 3:
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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14 a[:] = b[:, :, np.newaxis]
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 else:
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 a[:] = b
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 def warp_coords_batch(coord_map, shape, dtype=np.float64, batch_size=1000000):
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 rows, cols = shape[0], shape[1]
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 coords_shape = [len(shape), rows, cols]
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 if len(shape) == 3:
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 coords_shape.append(shape[2])
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 coords = np.empty(coords_shape, dtype=dtype)
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 tf_coords = np.indices((cols, rows), dtype=dtype).reshape(2, -1).T
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 for i in range(0, (tf_coords.shape[0] // batch_size + 1)):
b4fc6e09e576 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
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29 tf_coords[batch_size * i:batch_size * (i + 1)] = coord_map(tf_coords[batch_size * i:batch_size * (i + 1)])
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 tf_coords = tf_coords.T.reshape((-1, cols, rows)).swapaxes(1, 2)
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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32 _stackcopy(coords[1, ...], tf_coords[0, ...])
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b4fc6e09e576 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
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33 _stackcopy(coords[0, ...], tf_coords[1, ...])
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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34 if len(shape) == 3:
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 coords[2, ...] = range(shape[2])
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37 return coords
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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40 def transform(moving_image, fixed_image, warp_matrix):
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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41 trans = ProjectiveTransform(matrix=warp_matrix)
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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42 warped_coords = warp_coords_batch(trans, fixed_image.shape)
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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43 return map_coordinates(moving_image, warped_coords)
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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46 def overlay(moving_image, fixed_image, factor, overlay_out_path):
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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47 moving_image = Image.fromarray(moving_image).convert("RGBA")
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48 fixed_image = Image.fromarray(fixed_image).convert("RGBA")
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49 overlay_out = Image.blend(moving_image, fixed_image, factor)
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50 overlay_out.save(overlay_out_path, "PNG")
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51
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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52
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53 if __name__ == "__main__":
b4fc6e09e576 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
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54 parser = argparse.ArgumentParser(description="Overlay two images")
b4fc6e09e576 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
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55 parser.add_argument("fixed_image", help="Path to fixed image")
b4fc6e09e576 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
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56 parser.add_argument("moving_image", help="Path to moving image")
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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57 parser.add_argument("warp_matrix", help="Paste path to warp_matrix.csv that should be used for transformation")
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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58 parser.add_argument("--inverse_transform", dest='inverse_transform', action='store_true', help="Set if inverse transform should be visualized")
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b4fc6e09e576 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
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59 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)
b4fc6e09e576 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
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60 parser.add_argument("overlay_out", help="Overlay output path")
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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61 args = parser.parse_args()
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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63 fixed_image = skimage.io.imread(args.fixed_image)
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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64 moving_image = skimage.io.imread(args.moving_image)
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65
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66 warp_matrix = pd.read_csv(args.warp_matrix, delimiter="\t", header=None)
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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67 warp_matrix = np.array(warp_matrix)
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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68 if args.inverse_transform:
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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69 fixed_image = transform(fixed_image, moving_image, warp_matrix)
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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70 else:
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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71 warp_matrix = np.linalg.inv(warp_matrix)
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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72 moving_image = transform(moving_image, fixed_image, warp_matrix)
165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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165a9330fc90 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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74 overlay(moving_image, fixed_image, args.factor, args.overlay_out)