Mercurial > repos > thomaswollmann > color_deconvolution

comparison color_deconvolution.py @ 0:d7bd56ed3d85 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
author thomaswollmann
date Tue, 07 Feb 2017 09:56:10 -0500
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children 8fcbcf6509d8
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-1:000000000000 0:d7bd56ed3d85
1 import argparse
2 import sys
3 import warnings
4 import numpy as np
5 import skimage.io
6 import skimage.color
7 import skimage.util
8 from sklearn.decomposition import PCA
9
10 convOptions = {
11 'hed2rgb' : lambda img_raw: skimage.color.hed2rgb(img_raw),
12 'hsv2rgb' : lambda img_raw: skimage.color.hsv2rgb(img_raw),
13 'lab2lch' : lambda img_raw: skimage.color.lab2lch(img_raw),
14 'lab2rgb' : lambda img_raw: skimage.color.lab2rgb(img_raw),
15 'lab2xyz' : lambda img_raw: skimage.color.lab2xyz(img_raw),
16 'lch2lab' : lambda img_raw: skimage.color.lch2lab(img_raw),
17 'luv2rgb' : lambda img_raw: skimage.color.luv2rgb(img_raw),
18 'luv2xyz' : lambda img_raw: skimage.color.luv2xyz(img_raw),
19 'rgb2hed' : lambda img_raw: skimage.color.rgb2hed(img_raw),
20 'rgb2hsv' : lambda img_raw: skimage.color.rgb2hsv(img_raw),
21 'rgb2lab' : lambda img_raw: skimage.color.rgb2lab(img_raw),
22 'rgb2luv' : lambda img_raw: skimage.color.rgb2luv(img_raw),
23 'rgb2rgbcie' : lambda img_raw: skimage.color.rgb2rgbcie(img_raw),
24 'rgb2xyz' : lambda img_raw: skimage.color.rgb2xyz(img_raw),
25 #'rgb2ycbcr' : lambda img_raw: skimage.color.rgb2ycbcr(img_raw),
26 #'rgb2yiq' : lambda img_raw: skimage.color.rgb2yiq(img_raw),
27 #'rgb2ypbpr' : lambda img_raw: skimage.color.rgb2ypbpr(img_raw),
28 #'rgb2yuv' : lambda img_raw: skimage.color.rgb2yuv(img_raw),
29 #'rgba2rgb' : lambda img_raw: skimage.color.rgba2rgb(img_raw),
30 'rgbcie2rgb' : lambda img_raw: skimage.color.rgbcie2rgb(img_raw),
31 'xyz2lab' : lambda img_raw: skimage.color.xyz2lab(img_raw),
32 'xyz2luv' : lambda img_raw: skimage.color.xyz2luv(img_raw),
33 'xyz2rgb' : lambda img_raw: skimage.color.xyz2rgb(img_raw),
34 #'ycbcr2rgb' : lambda img_raw: skimage.color.ycbcr2rgb(img_raw),
35 #'yiq2rgb' : lambda img_raw: skimage.color.yiq2rgb(img_raw),
36 #'ypbpr2rgb' : lambda img_raw: skimage.color.ypbpr2rgb(img_raw),
37 #'yuv2rgb' : lambda img_raw: skimage.color.yuv2rgb(img_raw),
38
39 'rgb_from_hed' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hed),
40 'rgb_from_hdx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hdx),
41 'rgb_from_fgx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_fgx),
42 'rgb_from_bex' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bex),
43 'rgb_from_rbd' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_rbd),
44 'rgb_from_gdx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_gdx),
45 'rgb_from_hax' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hax),
46 'rgb_from_bro' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bro),
47 'rgb_from_bpx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bpx),
48 'rgb_from_ahx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_ahx),
49 'rgb_from_hpx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hpx),
50
51 'hed_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hed_from_rgb),
52 'hdx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hdx_from_rgb),
53 'fgx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.fgx_from_rgb),
54 'bex_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bex_from_rgb),
55 'rbd_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.rbd_from_rgb),
56 'gdx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.gdx_from_rgb),
57 'hax_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hax_from_rgb),
58 'bro_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bro_from_rgb),
59 'bpx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bpx_from_rgb),
60 'ahx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.ahx_from_rgb),
61 'hpx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hpx_from_rgb),
62
63 'pca' : lambda img_raw: np.reshape(PCA(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])),
64 [img_raw.shape[0],img_raw.shape[1],-1])
65 }
66
67 parser = argparse.ArgumentParser()
68 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
69 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
70 parser.add_argument('conv_type', choices=convOptions.keys(), help='conversion type')
71 args = parser.parse_args()
72
73 img_in = skimage.io.imread(args.input_file.name)[:,:,0:3]
74 res = convOptions[args.conv_type](img_in)
75 res[res<-1]=-1
76 res[res>1]=1
77
78 with warnings.catch_warnings():
79 warnings.simplefilter("ignore")
80 res = skimage.util.img_as_uint(res) #Attention: precision loss
81 skimage.io.imsave(args.out_file.name, res, plugin='tifffile')