Mercurial > repos > imgteam > color_deconvolution
comparison color_deconvolution.py @ 2:612aa1478fe1 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
| author | imgteam |
|---|---|
| date | Mon, 13 Nov 2023 22:10:42 +0000 |
| parents | 0976b373a321 |
| children | 5bd113d38acc |
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| 1:0976b373a321 | 2:612aa1478fe1 |
|---|---|
| 1 import argparse | 1 import argparse |
| 2 import sys | 2 import sys |
| 3 import warnings | 3 import warnings |
| 4 | |
| 4 import numpy as np | 5 import numpy as np |
| 6 import skimage.color | |
| 5 import skimage.io | 7 import skimage.io |
| 6 import skimage.color | |
| 7 import skimage.util | 8 import skimage.util |
| 8 from sklearn.decomposition import PCA, NMF, FastICA, FactorAnalysis | 9 from sklearn.decomposition import FactorAnalysis, FastICA, NMF, PCA |
| 9 | 10 |
| 10 convOptions = { | 11 convOptions = { |
| 11 'hed2rgb' : lambda img_raw: skimage.color.hed2rgb(img_raw), | 12 'hed2rgb': lambda img_raw: skimage.color.hed2rgb(img_raw), |
| 12 'hsv2rgb' : lambda img_raw: skimage.color.hsv2rgb(img_raw), | 13 'hsv2rgb': lambda img_raw: skimage.color.hsv2rgb(img_raw), |
| 13 'lab2lch' : lambda img_raw: skimage.color.lab2lch(img_raw), | 14 'lab2lch': lambda img_raw: skimage.color.lab2lch(img_raw), |
| 14 'lab2rgb' : lambda img_raw: skimage.color.lab2rgb(img_raw), | 15 'lab2rgb': lambda img_raw: skimage.color.lab2rgb(img_raw), |
| 15 'lab2xyz' : lambda img_raw: skimage.color.lab2xyz(img_raw), | 16 'lab2xyz': lambda img_raw: skimage.color.lab2xyz(img_raw), |
| 16 'lch2lab' : lambda img_raw: skimage.color.lch2lab(img_raw), | 17 'lch2lab': lambda img_raw: skimage.color.lch2lab(img_raw), |
| 17 'luv2rgb' : lambda img_raw: skimage.color.luv2rgb(img_raw), | 18 'luv2rgb': lambda img_raw: skimage.color.luv2rgb(img_raw), |
| 18 'luv2xyz' : lambda img_raw: skimage.color.luv2xyz(img_raw), | 19 'luv2xyz': lambda img_raw: skimage.color.luv2xyz(img_raw), |
| 19 'rgb2hed' : lambda img_raw: skimage.color.rgb2hed(img_raw), | 20 'rgb2hed': lambda img_raw: skimage.color.rgb2hed(img_raw), |
| 20 'rgb2hsv' : lambda img_raw: skimage.color.rgb2hsv(img_raw), | 21 'rgb2hsv': lambda img_raw: skimage.color.rgb2hsv(img_raw), |
| 21 'rgb2lab' : lambda img_raw: skimage.color.rgb2lab(img_raw), | 22 'rgb2lab': lambda img_raw: skimage.color.rgb2lab(img_raw), |
| 22 'rgb2luv' : lambda img_raw: skimage.color.rgb2luv(img_raw), | 23 'rgb2luv': lambda img_raw: skimage.color.rgb2luv(img_raw), |
| 23 'rgb2rgbcie' : lambda img_raw: skimage.color.rgb2rgbcie(img_raw), | 24 'rgb2rgbcie': lambda img_raw: skimage.color.rgb2rgbcie(img_raw), |
| 24 'rgb2xyz' : lambda img_raw: skimage.color.rgb2xyz(img_raw), | 25 'rgb2xyz': lambda img_raw: skimage.color.rgb2xyz(img_raw), |
| 25 #'rgb2ycbcr' : lambda img_raw: skimage.color.rgb2ycbcr(img_raw), | 26 'rgbcie2rgb': lambda img_raw: skimage.color.rgbcie2rgb(img_raw), |
| 26 #'rgb2yiq' : lambda img_raw: skimage.color.rgb2yiq(img_raw), | 27 'xyz2lab': lambda img_raw: skimage.color.xyz2lab(img_raw), |
| 27 #'rgb2ypbpr' : lambda img_raw: skimage.color.rgb2ypbpr(img_raw), | 28 'xyz2luv': lambda img_raw: skimage.color.xyz2luv(img_raw), |
| 28 #'rgb2yuv' : lambda img_raw: skimage.color.rgb2yuv(img_raw), | 29 'xyz2rgb': lambda img_raw: skimage.color.xyz2rgb(img_raw), |
| 29 #'rgba2rgb' : lambda img_raw: skimage.color.rgba2rgb(img_raw), | 30 |
| 30 'rgbcie2rgb' : lambda img_raw: skimage.color.rgbcie2rgb(img_raw), | 31 'rgb_from_hed': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hed), |
| 31 'xyz2lab' : lambda img_raw: skimage.color.xyz2lab(img_raw), | 32 'rgb_from_hdx': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hdx), |
| 32 'xyz2luv' : lambda img_raw: skimage.color.xyz2luv(img_raw), | 33 'rgb_from_fgx': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_fgx), |
| 33 'xyz2rgb' : lambda img_raw: skimage.color.xyz2rgb(img_raw), | 34 'rgb_from_bex': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bex), |
| 34 #'ycbcr2rgb' : lambda img_raw: skimage.color.ycbcr2rgb(img_raw), | 35 'rgb_from_rbd': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_rbd), |
| 35 #'yiq2rgb' : lambda img_raw: skimage.color.yiq2rgb(img_raw), | 36 'rgb_from_gdx': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_gdx), |
| 36 #'ypbpr2rgb' : lambda img_raw: skimage.color.ypbpr2rgb(img_raw), | 37 'rgb_from_hax': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hax), |
| 37 #'yuv2rgb' : lambda img_raw: skimage.color.yuv2rgb(img_raw), | 38 'rgb_from_bro': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bro), |
| 38 | 39 'rgb_from_bpx': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bpx), |
| 39 'rgb_from_hed' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hed), | 40 'rgb_from_ahx': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_ahx), |
| 40 'rgb_from_hdx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hdx), | 41 'rgb_from_hpx': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hpx), |
| 41 'rgb_from_fgx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_fgx), | 42 |
| 42 'rgb_from_bex' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bex), | 43 'hed_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hed_from_rgb), |
| 43 'rgb_from_rbd' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_rbd), | 44 'hdx_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hdx_from_rgb), |
| 44 'rgb_from_gdx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_gdx), | 45 'fgx_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.fgx_from_rgb), |
| 45 'rgb_from_hax' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hax), | 46 'bex_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bex_from_rgb), |
| 46 'rgb_from_bro' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bro), | 47 'rbd_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.rbd_from_rgb), |
| 47 'rgb_from_bpx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bpx), | 48 'gdx_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.gdx_from_rgb), |
| 48 'rgb_from_ahx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_ahx), | 49 'hax_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hax_from_rgb), |
| 49 'rgb_from_hpx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hpx), | 50 'bro_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bro_from_rgb), |
| 50 | 51 'bpx_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bpx_from_rgb), |
| 51 'hed_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hed_from_rgb), | 52 'ahx_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.ahx_from_rgb), |
| 52 'hdx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hdx_from_rgb), | 53 'hpx_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hpx_from_rgb), |
| 53 'fgx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.fgx_from_rgb), | 54 |
| 54 'bex_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bex_from_rgb), | 55 'pca': lambda img_raw: np.reshape(PCA(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])), |
| 55 'rbd_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.rbd_from_rgb), | 56 [img_raw.shape[0], img_raw.shape[1], -1]), |
| 56 'gdx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.gdx_from_rgb), | 57 'nmf': lambda img_raw: np.reshape(NMF(n_components=3, init='nndsvda').fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])), |
| 57 'hax_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hax_from_rgb), | 58 [img_raw.shape[0], img_raw.shape[1], -1]), |
| 58 'bro_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bro_from_rgb), | 59 'ica': lambda img_raw: np.reshape(FastICA(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])), |
| 59 'bpx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bpx_from_rgb), | 60 [img_raw.shape[0], img_raw.shape[1], -1]), |
| 60 'ahx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.ahx_from_rgb), | 61 'fa': lambda img_raw: np.reshape(FactorAnalysis(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])), |
| 61 'hpx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hpx_from_rgb), | 62 [img_raw.shape[0], img_raw.shape[1], -1]) |
| 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 'nmf' : lambda img_raw: np.reshape(NMF(n_components=3, init='nndsvda').fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])), | |
| 66 [img_raw.shape[0],img_raw.shape[1],-1]), | |
| 67 'ica' : lambda img_raw: np.reshape(FastICA(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])), | |
| 68 [img_raw.shape[0],img_raw.shape[1],-1]), | |
| 69 'fa' : lambda img_raw: np.reshape(FactorAnalysis(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])), | |
| 70 [img_raw.shape[0],img_raw.shape[1],-1]) | |
| 71 } | 63 } |
| 72 | 64 |
| 73 parser = argparse.ArgumentParser() | 65 parser = argparse.ArgumentParser() |
| 74 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') | 66 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') |
| 75 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') | 67 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') |
| 76 parser.add_argument('conv_type', choices=convOptions.keys(), help='conversion type') | 68 parser.add_argument('conv_type', choices=convOptions.keys(), help='conversion type') |
| 77 args = parser.parse_args() | 69 args = parser.parse_args() |
| 78 | 70 |
| 79 img_in = skimage.io.imread(args.input_file.name)[:,:,0:3] | 71 img_in = skimage.io.imread(args.input_file.name)[:, :, 0:3] |
| 80 res = convOptions[args.conv_type](img_in) | 72 res = convOptions[args.conv_type](img_in) |
| 81 res[res<-1]=-1 | 73 res[res < -1] = -1 |
| 82 res[res>1]=1 | 74 res[res > +1] = +1 |
| 83 | 75 |
| 84 with warnings.catch_warnings(): | 76 with warnings.catch_warnings(): |
| 85 warnings.simplefilter("ignore") | 77 warnings.simplefilter('ignore') |
| 86 res = skimage.util.img_as_uint(res) #Attention: precision loss | 78 res = skimage.util.img_as_uint(res) # Attention: precision loss |
| 87 skimage.io.imsave(args.out_file.name, res, plugin='tifffile') | 79 skimage.io.imsave(args.out_file.name, res, plugin='tifffile') |