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annotate overlay_images.py @ 4:37662cbf44b8 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
author imgteam
date Fri, 17 Nov 2023 23:34:57 +0000
parents b74693340624
children 2495f8b2aefd
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589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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1 """
2
b74693340624 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
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2 Copyright 2022-2023 Biomedical Computer Vision Group, Heidelberg University.
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589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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3
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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4 Distributed under the MIT license.
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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6 """
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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7
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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8 import argparse
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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9
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b74693340624 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
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10 import matplotlib.colors
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589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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11 import matplotlib.pyplot as plt
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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12 import numpy as np
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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13 import skimage.color
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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14 import skimage.io
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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15 import skimage.measure
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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16 import tifffile
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17 from contours import ContourPaint
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20 def read_im_gray(fn):
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21 img = skimage.io.imread(fn)
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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22 nDims = len(img.shape)
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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23 assert nDims in [2, 3], 'this tool only supports single 2D images'
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24 if nDims == 3 and img.shape[-1] in [3, 4]:
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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25 img = skimage.color.rgb2gray(img)
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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26 if len(img.shape) == 3:
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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27 return img[:, :, 0]
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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28 else:
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29 return img
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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30
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31
2
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32 def get_rgb8_copy(img):
b74693340624 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
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33 img = np.squeeze(img)
b74693340624 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
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34 assert img.ndim == 2 or (img.ndim == 3 and img.shape[-1] in (3, 4))
b74693340624 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
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35 if str(img.dtype).startswith('float'):
4
37662cbf44b8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
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36 img = np.round(img * 255).astype(np.uint8)
37662cbf44b8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
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37 elif img.dtype == np.uint16:
37662cbf44b8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
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38 img = (img // 256).astype(np.uint8)
37662cbf44b8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
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39 elif img.dtype != np.uint8:
2
b74693340624 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
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40 raise ValueError(f'unknown dtype: {img.dtype}')
b74693340624 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
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41 if img.ndim == 2:
4
37662cbf44b8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
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42 result = np.dstack([img] * 3).copy()
2
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43 else:
4
37662cbf44b8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
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44 result = img[:, :, :3].copy()
37662cbf44b8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
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45 assert result.dtype == np.uint8, result.dtype
37662cbf44b8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
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46 return result
2
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47
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48
0
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49 def coloc_vis(in_red_fn, in_green_fn, out_fn):
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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50 im1 = read_im_gray(in_red_fn)
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51 im2 = read_im_gray(in_green_fn)
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52 assert im1.shape == im2.shape, 'Two images should have the same dimension'
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53
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54 vmin = np.min([np.min(im1), np.min(im2)])
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55 scal = 255.0 / (np.max([np.max(im1), np.max(im2)]) - vmin)
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56
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57 out_im = np.zeros(im1.shape + (3,), dtype=np.ubyte)
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58 out_im[:, :, 0] = (im1 - vmin) * scal
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59 out_im[:, :, 1] = (im2 - vmin) * scal
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60 skimage.io.imsave(out_fn, out_im) # output is RGB
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61
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62
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63 def blending(im1_fn, im2_fn, out_fn, alpha=0.5):
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64 im1 = skimage.io.imread(im1_fn)
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65 im2 = skimage.io.imread(im2_fn)
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66 assert im1.shape == im2.shape, 'Two images should have the same dimension'
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67 out_im = (1 - alpha) * im1 + alpha * im2
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68 if len(im1.shape) > 3:
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69 tifffile.imwrite(out_fn, out_im.astype(im1.dtype), imagej=True)
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70 else:
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71 skimage.io.imsave(out_fn, out_im.astype(im1.dtype)) # format of output is the same as input
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72
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73
2
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74 def seg_contour(im1_fn, im2_fn, out_fn, linewidth, color='#ff0000', show_label=False, label_color='#ffff00'):
0
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75 img = skimage.io.imread(im1_fn)
2
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76 labels = skimage.io.imread(im2_fn)
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77
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78 result = get_rgb8_copy(img)
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79 cp = ContourPaint(labels, linewidth, where='center')
b74693340624 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
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80 color_rgb = np.multiply(255, matplotlib.colors.to_rgb(color))
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81
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82 for label in np.unique(labels):
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83 if label > 0:
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84 cc = (labels == label)
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85 bd = cp.get_contour_mask(cc)
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86 for i in range(3):
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87 result[:, :, i][bd] = color_rgb[i]
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88
0
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89 if show_label:
2
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90 fig = plt.figure(figsize=np.divide(img.shape[:2][::-1], 100), dpi=100)
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91 ax = fig.add_axes([0, 0, 1, 1])
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92 ax.axis('off')
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93 ax.imshow(result)
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94 for reg in skimage.measure.regionprops(labels):
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95 ax.text(reg.centroid[1], reg.centroid[0], str(reg.label), color=label_color)
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96 fig.canvas.print_png(out_fn)
0
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97
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98 else:
2
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99 skimage.io.imsave(out_fn, result) # format of output is RGB8
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100
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101
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102 if __name__ == "__main__":
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103 parser = argparse.ArgumentParser(description="Overlay two images")
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104 parser.add_argument("im1", help="The first image")
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105 parser.add_argument("im2", help="The second image")
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106 parser.add_argument("out", help="Output image")
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107 parser.add_argument('--method', dest='method', default='coloc_vis', help='How to overlay images')
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108 parser.add_argument('--alpha', dest='alpha', default=0.5, type=float, help='Blending weight')
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109 parser.add_argument('--thickness', dest='thickness', default=2, type=int, help='Contour thickness')
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110 parser.add_argument('--color', dest='color', default='#FF0000', help='Contour color')
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111 parser.add_argument('--show_label', dest='show_label', action='store_true', help='Show labels')
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112 parser.add_argument('--label_color', dest='label_color', default='#FFFF00', help='Label color')
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113 args = parser.parse_args()
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114
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115 if args.method == 'coloc_vis':
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116 coloc_vis(args.im1, args.im2, args.out)
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117 elif args.method == 'blending':
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118 blending(args.im1, args.im2, args.out, alpha=args.alpha)
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119 elif args.method == 'seg_contour':
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120 seg_contour(args.im1, args.im2, args.out,
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121 linewidth=args.thickness,
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122 color=args.color,
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123 show_label=args.show_label,
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124 label_color=args.label_color)