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annotate overlay_images.py @ 5:c1fd8b7c6bbc draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
author imgteam
date Wed, 17 Dec 2025 11:22:51 +0000
parents 61009b4361c1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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1 """
2
f42d21fe65d8 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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45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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3
45613da1bf23 "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.
45613da1bf23 "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
45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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6 """
45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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7
45613da1bf23 "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
45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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9
3
eb173a1fabc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
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10 import giatools.io
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f42d21fe65d8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
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11 import matplotlib.colors
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45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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12 import matplotlib.pyplot as plt
45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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13 import numpy as np
45613da1bf23 "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.color
45613da1bf23 "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.io
45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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16 import skimage.measure
45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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17 import tifffile
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18 from contours import ContourPaint
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45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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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)
45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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24 assert nDims in [2, 3], 'this tool only supports single 2D images'
45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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25 if nDims == 3 and img.shape[-1] in [3, 4]:
45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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26 img = skimage.color.rgb2gray(img)
45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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27 if len(img.shape) == 3:
45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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28 return img[:, :, 0]
45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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29 else:
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30 return img
45613da1bf23 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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31
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32
4
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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33 def get_rgb8_copy(img, fp_lower, fp_upper):
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34 img = np.squeeze(img)
f42d21fe65d8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
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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 assert fp_lower == 'min' or abs(float(fp_lower)) < np.inf # 'min' or number
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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37 assert fp_upper == 'max' or abs(float(fp_upper)) < np.inf # 'max' or number
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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38
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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39 # Convert from floating point
2
f42d21fe65d8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
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40 if str(img.dtype).startswith('float'):
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61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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41 a = img.min() if fp_lower == 'min' else float(fp_lower)
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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42 b = img.max() if fp_upper == 'max' else float(fp_upper)
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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43
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44 if a > b:
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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45 raise ValueError(
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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46 f'Lower bound ({a:g}) must be less than upper bound ({b:g}).'
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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47 )
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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48 if a == b:
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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49 raise ValueError(
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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50 'Floating point conversion is undefined'
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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51 ' because lower and upper bounds are identical.'
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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52 )
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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53
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54 # Perform linear mapping to [0, 1]
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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55 img = img.clip(a, b)
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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56 img = (img - a) / (b - a)
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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57
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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58 # Convert to uint8
3
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59 img = np.round(img * 255).astype(np.uint8)
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60
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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61 # Convert from uint16
3
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62 elif img.dtype == np.uint16:
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63 img = (img // 256).astype(np.uint8)
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64
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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65 # Other dtypes than float, uint8, uint16 are not supported
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66 elif img.dtype != np.uint8:
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67 raise ValueError(f'unknown dtype: {img.dtype}')
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68
2
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69 if img.ndim == 2:
3
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70 result = np.dstack([img] * 3).copy()
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71 else:
3
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72 result = img[:, :, :3].copy()
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73 assert result.dtype == np.uint8, result.dtype
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74 return result
2
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75
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76
0
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77 def coloc_vis(in_red_fn, in_green_fn, out_fn):
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78 im1 = read_im_gray(in_red_fn)
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79 im2 = read_im_gray(in_green_fn)
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80 assert im1.shape == im2.shape, 'Two images should have the same dimension'
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81
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82 vmin = np.min([np.min(im1), np.min(im2)])
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83 scal = 255.0 / (np.max([np.max(im1), np.max(im2)]) - vmin)
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84
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85 out_im = np.zeros(im1.shape + (3,), dtype=np.ubyte)
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86 out_im[:, :, 0] = (im1 - vmin) * scal
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87 out_im[:, :, 1] = (im2 - vmin) * scal
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88 skimage.io.imsave(out_fn, out_im) # output is RGB
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89
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90
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91 def blending(im1_fn, im2_fn, out_fn, alpha=0.5):
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92 im1 = giatools.io.imread(im1_fn)
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93 im2 = giatools.io.imread(im2_fn)
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94 assert im1.shape == im2.shape, 'Two images should have the same dimension'
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95 out_im = (1 - alpha) * im1 + alpha * im2
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96 if len(im1.shape) > 3:
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97 tifffile.imwrite(out_fn, out_im.astype(im1.dtype), imagej=True)
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98 else:
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99 skimage.io.imsave(out_fn, out_im.astype(im1.dtype)) # format of output is the same as input
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100
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101
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102 def seg_contour(im1_fn, im2_fn, out_fn, fp_lower, fp_upper, linewidth, color='#ff0000', show_label=False, label_color='#ffff00'):
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103 img = giatools.io.imread(im1_fn)
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104 labels = giatools.io.imread(im2_fn)
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105
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106 result = get_rgb8_copy(img, fp_lower, fp_upper)
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107 cp = ContourPaint(labels, linewidth, where='center')
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108 color_rgb = np.multiply(255, matplotlib.colors.to_rgb(color))
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109
2
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110 for label in np.unique(labels):
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111 if label > 0:
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112 cc = (labels == label)
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113 bd = cp.get_contour_mask(cc)
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114 for i in range(3):
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115 result[:, :, i][bd] = color_rgb[i]
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116
0
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117 if show_label:
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118 fig = plt.figure(figsize=np.divide(img.shape[:2][::-1], 100), dpi=100)
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119 ax = fig.add_axes([0, 0, 1, 1])
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120 ax.axis('off')
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121 ax.imshow(result)
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122 for reg in skimage.measure.regionprops(labels):
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123 ax.text(reg.centroid[1], reg.centroid[0], str(reg.label), color=label_color)
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124 fig.canvas.print_png(out_fn)
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125
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126 else:
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127 skimage.io.imsave(out_fn, result) # format of output is RGB8
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128
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129
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130 if __name__ == "__main__":
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131 parser = argparse.ArgumentParser(description="Overlay two images")
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132 parser.add_argument("im1", help="The first image")
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133 parser.add_argument("im2", help="The second image")
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134 parser.add_argument("out", help="Output image")
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135 parser.add_argument('--method', dest='method', default='coloc_vis', help='How to overlay images')
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136 parser.add_argument('--fp_lower', default='0', type=str, help='Lower bound for floating point conversion')
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137 parser.add_argument('--fp_upper', default='1', type=str, help='Upper bound for floating point conversion')
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138 parser.add_argument('--alpha', dest='alpha', default=0.5, type=float, help='Blending weight')
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139 parser.add_argument('--thickness', dest='thickness', default=2, type=int, help='Contour thickness')
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140 parser.add_argument('--color', dest='color', default='#FF0000', help='Contour color')
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141 parser.add_argument('--show_label', dest='show_label', action='store_true', help='Show labels')
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142 parser.add_argument('--label_color', dest='label_color', default='#FFFF00', help='Label color')
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143 args = parser.parse_args()
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144
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145 if args.method == 'coloc_vis':
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146 coloc_vis(args.im1, args.im2, args.out)
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147 elif args.method == 'blending':
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148 blending(args.im1, args.im2, args.out, alpha=args.alpha)
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149 elif args.method == 'seg_contour':
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150 seg_contour(
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151 args.im1,
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152 args.im2,
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153 args.out,
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154 fp_lower=args.fp_lower,
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155 fp_upper=args.fp_upper,
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156 linewidth=args.thickness,
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157 color=args.color,
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158 show_label=args.show_label,
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159 label_color=args.label_color,
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160 )