Mercurial > repos > imgteam > overlay_moving_and_fixed_image

comparison overlay_moving_and_fixed_image.py @ 2:b4fc6e09e576 draft default tip

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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
children
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1:bc324ec66719 2:b4fc6e09e576
1 import argparse 1 import argparse
2 from PIL import Image 2
3 import skimage.io
4 import skimage.color
5 from skimage.transform import ProjectiveTransform
6 from scipy.ndimage import map_coordinates
7 import numpy as np 3 import numpy as np
8 import pandas as pd 4 import pandas as pd
5 import skimage.color
6 import skimage.io
7 from PIL import Image
8 from scipy.ndimage import map_coordinates
9 from skimage.transform import ProjectiveTransform
9 10
10 11
11 def _stackcopy(a, b): 12 def _stackcopy(a, b):
12 if a.ndim == 3: 13 if a.ndim == 3:
13 a[:] = b[:, :, np.newaxis] 14 a[:] = b[:, :, np.newaxis]
22 coords_shape.append(shape[2]) 23 coords_shape.append(shape[2])
23 coords = np.empty(coords_shape, dtype=dtype) 24 coords = np.empty(coords_shape, dtype=dtype)
24 25
25 tf_coords = np.indices((cols, rows), dtype=dtype).reshape(2, -1).T 26 tf_coords = np.indices((cols, rows), dtype=dtype).reshape(2, -1).T
26 27
27 for i in range(0, (tf_coords.shape[0]//batch_size+1)): 28 for i in range(0, (tf_coords.shape[0] // batch_size + 1)):
28 tf_coords[batch_size*i:batch_size*(i+1)] = coord_map(tf_coords[batch_size*i:batch_size*(i+1)]) 29 tf_coords[batch_size * i:batch_size * (i + 1)] = coord_map(tf_coords[batch_size * i:batch_size * (i + 1)])
29 tf_coords = tf_coords.T.reshape((-1, cols, rows)).swapaxes(1, 2) 30 tf_coords = tf_coords.T.reshape((-1, cols, rows)).swapaxes(1, 2)
30 31
31 _stackcopy(coords[1, ...], tf_coords[0, ...]) 32 _stackcopy(coords[1, ...], tf_coords[0, ...])
32 _stackcopy(coords[0, ...], tf_coords[1, ...]) 33 _stackcopy(coords[0, ...], tf_coords[1, ...])
33 if len(shape) == 3: 34 if len(shape) == 3:
34 coords[2, ...] = range(shape[2]) 35 coords[2, ...] = range(shape[2])
35 36
36 return coords 37 return coords
37 38
45 def overlay(moving_image, fixed_image, factor, overlay_out_path): 46 def overlay(moving_image, fixed_image, factor, overlay_out_path):
46 moving_image = Image.fromarray(moving_image).convert("RGBA") 47 moving_image = Image.fromarray(moving_image).convert("RGBA")
47 fixed_image = Image.fromarray(fixed_image).convert("RGBA") 48 fixed_image = Image.fromarray(fixed_image).convert("RGBA")
48 overlay_out = Image.blend(moving_image, fixed_image, factor) 49 overlay_out = Image.blend(moving_image, fixed_image, factor)
49 overlay_out.save(overlay_out_path, "PNG") 50 overlay_out.save(overlay_out_path, "PNG")
50
51 51
52 if __name__=="__main__": 52
53 parser = argparse.ArgumentParser(description = "Overlay two images") 53 if __name__ == "__main__":
54 parser.add_argument("fixed_image", help = "Path to fixed image") 54 parser = argparse.ArgumentParser(description="Overlay two images")
55 parser.add_argument("moving_image", help = "Path to moving image") 55 parser.add_argument("fixed_image", help="Path to fixed image")
56 parser.add_argument("moving_image", help="Path to moving image")
56 parser.add_argument("warp_matrix", help="Paste path to warp_matrix.csv that should be used for transformation") 57 parser.add_argument("warp_matrix", help="Paste path to warp_matrix.csv that should be used for transformation")
57 parser.add_argument("--inverse_transform", dest='inverse_transform', action='store_true', help="Set if inverse transform should be visualized") 58 parser.add_argument("--inverse_transform", dest='inverse_transform', action='store_true', help="Set if inverse transform should be visualized")
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) 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)
59 parser.add_argument("overlay_out", help = "Overlay output path") 60 parser.add_argument("overlay_out", help="Overlay output path")
60 args = parser.parse_args() 61 args = parser.parse_args()
61 62
62 fixed_image = skimage.io.imread(args.fixed_image) 63 fixed_image = skimage.io.imread(args.fixed_image)
63 moving_image = skimage.io.imread(args.moving_image) 64 moving_image = skimage.io.imread(args.moving_image)
64 65