annotate overlay_images.py @ 6:2495f8b2aefd draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
author imgteam
date Wed, 24 Apr 2024 08:12:55 +0000
parents 37662cbf44b8
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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
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2 Copyright 2022-2023 Biomedical Computer Vision Group, Heidelberg University.
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3
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4 Distributed under the MIT license.
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5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
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6 """
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8 import argparse
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9
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2495f8b2aefd planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
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10 import giatools.io
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11 import matplotlib.colors
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12 import matplotlib.pyplot as plt
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13 import numpy as np
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14 import skimage.color
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15 import skimage.io
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16 import skimage.measure
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17 import tifffile
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18 from contours import ContourPaint
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21 def read_im_gray(fn):
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22 img = giatools.io.imread(fn)
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23 nDims = len(img.shape)
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24 assert nDims in [2, 3], 'this tool only supports single 2D images'
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25 if nDims == 3 and img.shape[-1] in [3, 4]:
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26 img = skimage.color.rgb2gray(img)
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27 if len(img.shape) == 3:
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28 return img[:, :, 0]
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29 else:
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30 return img
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32
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33 def get_rgb8_copy(img):
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34 img = np.squeeze(img)
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35 assert img.ndim == 2 or (img.ndim == 3 and img.shape[-1] in (3, 4))
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36 if str(img.dtype).startswith('float'):
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37 img = np.round(img * 255).astype(np.uint8)
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38 elif img.dtype == np.uint16:
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39 img = (img // 256).astype(np.uint8)
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40 elif img.dtype != np.uint8:
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41 raise ValueError(f'unknown dtype: {img.dtype}')
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42 if img.ndim == 2:
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43 result = np.dstack([img] * 3).copy()
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44 else:
4
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45 result = img[:, :, :3].copy()
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46 assert result.dtype == np.uint8, result.dtype
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47 return result
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48
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49
0
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50 def coloc_vis(in_red_fn, in_green_fn, out_fn):
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51 im1 = read_im_gray(in_red_fn)
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52 im2 = read_im_gray(in_green_fn)
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53 assert im1.shape == im2.shape, 'Two images should have the same dimension'
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54
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55 vmin = np.min([np.min(im1), np.min(im2)])
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56 scal = 255.0 / (np.max([np.max(im1), np.max(im2)]) - vmin)
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57
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58 out_im = np.zeros(im1.shape + (3,), dtype=np.ubyte)
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59 out_im[:, :, 0] = (im1 - vmin) * scal
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60 out_im[:, :, 1] = (im2 - vmin) * scal
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61 skimage.io.imsave(out_fn, out_im) # output is RGB
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62
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63
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64 def blending(im1_fn, im2_fn, out_fn, alpha=0.5):
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65 im1 = giatools.io.imread(im1_fn)
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66 im2 = giatools.io.imread(im2_fn)
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67 assert im1.shape == im2.shape, 'Two images should have the same dimension'
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68 out_im = (1 - alpha) * im1 + alpha * im2
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69 if len(im1.shape) > 3:
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70 tifffile.imwrite(out_fn, out_im.astype(im1.dtype), imagej=True)
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71 else:
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72 skimage.io.imsave(out_fn, out_im.astype(im1.dtype)) # format of output is the same as input
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73
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74
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75 def seg_contour(im1_fn, im2_fn, out_fn, linewidth, color='#ff0000', show_label=False, label_color='#ffff00'):
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76 img = giatools.io.imread(im1_fn)
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77 labels = giatools.io.imread(im2_fn)
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78
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79 result = get_rgb8_copy(img)
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80 cp = ContourPaint(labels, linewidth, where='center')
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81 color_rgb = np.multiply(255, matplotlib.colors.to_rgb(color))
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82
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83 for label in np.unique(labels):
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84 if label > 0:
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85 cc = (labels == label)
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86 bd = cp.get_contour_mask(cc)
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87 for i in range(3):
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88 result[:, :, i][bd] = color_rgb[i]
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89
0
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90 if show_label:
2
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91 fig = plt.figure(figsize=np.divide(img.shape[:2][::-1], 100), dpi=100)
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92 ax = fig.add_axes([0, 0, 1, 1])
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93 ax.axis('off')
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94 ax.imshow(result)
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95 for reg in skimage.measure.regionprops(labels):
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96 ax.text(reg.centroid[1], reg.centroid[0], str(reg.label), color=label_color)
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97 fig.canvas.print_png(out_fn)
0
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98
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99 else:
2
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100 skimage.io.imsave(out_fn, result) # format of output is RGB8
0
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101
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102
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103 if __name__ == "__main__":
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104 parser = argparse.ArgumentParser(description="Overlay two images")
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105 parser.add_argument("im1", help="The first image")
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106 parser.add_argument("im2", help="The second image")
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107 parser.add_argument("out", help="Output image")
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108 parser.add_argument('--method', dest='method', default='coloc_vis', help='How to overlay images')
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109 parser.add_argument('--alpha', dest='alpha', default=0.5, type=float, help='Blending weight')
2
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110 parser.add_argument('--thickness', dest='thickness', default=2, type=int, help='Contour thickness')
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111 parser.add_argument('--color', dest='color', default='#FF0000', help='Contour color')
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112 parser.add_argument('--show_label', dest='show_label', action='store_true', help='Show labels')
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113 parser.add_argument('--label_color', dest='label_color', default='#FFFF00', help='Label color')
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114 args = parser.parse_args()
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115
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116 if args.method == 'coloc_vis':
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117 coloc_vis(args.im1, args.im2, args.out)
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118 elif args.method == 'blending':
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119 blending(args.im1, args.im2, args.out, alpha=args.alpha)
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120 elif args.method == 'seg_contour':
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121 seg_contour(args.im1, args.im2, args.out,
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122 linewidth=args.thickness,
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123 color=args.color,
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124 show_label=args.show_label,
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125 label_color=args.label_color)