Mercurial > repos > thomaswollmann > color_deconvolution
comparison color_deconvolution.py @ 2:8fcbcf6509d8 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit 92068c64f9a6c3cf59f756b9efc2d561196c6873
author | thomaswollmann |
---|---|
date | Thu, 09 Feb 2017 04:36:37 -0500 |
parents | d7bd56ed3d85 |
children | 85185e9a50a7 |
comparison
equal
deleted
inserted
replaced
1:e5d95eb1daad | 2:8fcbcf6509d8 |
---|---|
3 import warnings | 3 import warnings |
4 import numpy as np | 4 import numpy as np |
5 import skimage.io | 5 import skimage.io |
6 import skimage.color | 6 import skimage.color |
7 import skimage.util | 7 import skimage.util |
8 from sklearn.decomposition import PCA | 8 from sklearn.decomposition import PCA, NMF, FastICA, FactorAnalysis |
9 | 9 |
10 convOptions = { | 10 convOptions = { |
11 'hed2rgb' : lambda img_raw: skimage.color.hed2rgb(img_raw), | 11 'hed2rgb' : lambda img_raw: skimage.color.hed2rgb(img_raw), |
12 'hsv2rgb' : lambda img_raw: skimage.color.hsv2rgb(img_raw), | 12 'hsv2rgb' : lambda img_raw: skimage.color.hsv2rgb(img_raw), |
13 'lab2lch' : lambda img_raw: skimage.color.lab2lch(img_raw), | 13 'lab2lch' : lambda img_raw: skimage.color.lab2lch(img_raw), |
59 'bpx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bpx_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), | 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), | 61 'hpx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hpx_from_rgb), |
62 | 62 |
63 'pca' : lambda img_raw: np.reshape(PCA(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])), | 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]])), | |
64 [img_raw.shape[0],img_raw.shape[1],-1]) | 70 [img_raw.shape[0],img_raw.shape[1],-1]) |
65 } | 71 } |
66 | 72 |
67 parser = argparse.ArgumentParser() | 73 parser = argparse.ArgumentParser() |
68 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') | 74 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') |