Mercurial > repos > imgteam > color_deconvolution

changeset 2:612aa1478fe1 draft

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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 be70a57d7174
files color-deconvolution.xml color_deconvolution.py
diffstat 2 files changed, 69 insertions(+), 71 deletions(-) [+]
line wrap: on
line diff
--- a/color-deconvolution.xml	Mon Jul 22 05:02:00 2019 -0400
+++ b/color-deconvolution.xml	Mon Nov 13 22:10:42 2023 +0000
@@ -1,5 +1,11 @@
-<tool id="ip_color_deconvolution" name="Color Deconvolution" version="0.8"> 
-    <description>Color deconvolution</description>
+<tool id="ip_color_deconvolution" name="Perform color decomposition" version="0.8-2"> 
+    <description></description>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">galaxy_image_analysis</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="0.14.2">scikit-image</requirement>
         <requirement type="package" version="4.0.0">pillow</requirement>
--- a/color_deconvolution.py	Mon Jul 22 05:02:00 2019 -0400
+++ b/color_deconvolution.py	Mon Nov 13 22:10:42 2023 +0000
@@ -1,87 +1,79 @@
 import argparse
 import sys
 import warnings
+
 import numpy as np
-import skimage.io
 import skimage.color
+import skimage.io
 import skimage.util
-from sklearn.decomposition import PCA, NMF, FastICA, FactorAnalysis
+from sklearn.decomposition import FactorAnalysis, FastICA, NMF, PCA
 
 convOptions = {
-           'hed2rgb' : lambda img_raw: skimage.color.hed2rgb(img_raw),
-           'hsv2rgb' : lambda img_raw: skimage.color.hsv2rgb(img_raw),
-           'lab2lch' : lambda img_raw: skimage.color.lab2lch(img_raw),
-           'lab2rgb' : lambda img_raw: skimage.color.lab2rgb(img_raw),
-           'lab2xyz' : lambda img_raw: skimage.color.lab2xyz(img_raw),
-           'lch2lab' : lambda img_raw: skimage.color.lch2lab(img_raw),
-           'luv2rgb' : lambda img_raw: skimage.color.luv2rgb(img_raw),
-           'luv2xyz' : lambda img_raw: skimage.color.luv2xyz(img_raw),
-           'rgb2hed' : lambda img_raw: skimage.color.rgb2hed(img_raw),
-           'rgb2hsv' : lambda img_raw: skimage.color.rgb2hsv(img_raw),
-           'rgb2lab' : lambda img_raw: skimage.color.rgb2lab(img_raw),
-           'rgb2luv' : lambda img_raw: skimage.color.rgb2luv(img_raw),
-           'rgb2rgbcie' : lambda img_raw: skimage.color.rgb2rgbcie(img_raw),
-           'rgb2xyz' : lambda img_raw: skimage.color.rgb2xyz(img_raw),
-           #'rgb2ycbcr' : lambda img_raw: skimage.color.rgb2ycbcr(img_raw),
-           #'rgb2yiq' : lambda img_raw: skimage.color.rgb2yiq(img_raw),
-           #'rgb2ypbpr' : lambda img_raw: skimage.color.rgb2ypbpr(img_raw),
-           #'rgb2yuv' : lambda img_raw: skimage.color.rgb2yuv(img_raw),
-           #'rgba2rgb' : lambda img_raw: skimage.color.rgba2rgb(img_raw),
-           'rgbcie2rgb' : lambda img_raw: skimage.color.rgbcie2rgb(img_raw),
-           'xyz2lab' : lambda img_raw: skimage.color.xyz2lab(img_raw),
-           'xyz2luv' : lambda img_raw: skimage.color.xyz2luv(img_raw),
-           'xyz2rgb' : lambda img_raw: skimage.color.xyz2rgb(img_raw),
-           #'ycbcr2rgb' : lambda img_raw: skimage.color.ycbcr2rgb(img_raw),
-           #'yiq2rgb' : lambda img_raw: skimage.color.yiq2rgb(img_raw),
-           #'ypbpr2rgb' : lambda img_raw: skimage.color.ypbpr2rgb(img_raw),
-           #'yuv2rgb' : lambda img_raw: skimage.color.yuv2rgb(img_raw),    
-    
-           'rgb_from_hed' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hed),
-           'rgb_from_hdx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hdx),
-           'rgb_from_fgx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_fgx),
-           'rgb_from_bex' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bex),
-           'rgb_from_rbd' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_rbd),
-           'rgb_from_gdx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_gdx),
-           'rgb_from_hax' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hax),
-           'rgb_from_bro' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bro),
-           'rgb_from_bpx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bpx),
-           'rgb_from_ahx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_ahx),
-           'rgb_from_hpx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hpx),
-    
-           'hed_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hed_from_rgb),
-           'hdx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hdx_from_rgb),
-           'fgx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.fgx_from_rgb),
-           'bex_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bex_from_rgb),
-           'rbd_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.rbd_from_rgb),
-           'gdx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.gdx_from_rgb),
-           'hax_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hax_from_rgb),
-           'bro_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bro_from_rgb),
-           'bpx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bpx_from_rgb),
-           'ahx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.ahx_from_rgb),
-           'hpx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hpx_from_rgb),    
-    
-           'pca' : lambda img_raw: np.reshape(PCA(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])), 
-                              [img_raw.shape[0],img_raw.shape[1],-1]),    
-           'nmf' : lambda img_raw: np.reshape(NMF(n_components=3, init='nndsvda').fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])), 
-                              [img_raw.shape[0],img_raw.shape[1],-1]),
-           'ica' : lambda img_raw: np.reshape(FastICA(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])), 
-                              [img_raw.shape[0],img_raw.shape[1],-1]),
-           'fa' : lambda img_raw: np.reshape(FactorAnalysis(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])), 
-                              [img_raw.shape[0],img_raw.shape[1],-1])
+    'hed2rgb': lambda img_raw: skimage.color.hed2rgb(img_raw),
+    'hsv2rgb': lambda img_raw: skimage.color.hsv2rgb(img_raw),
+    'lab2lch': lambda img_raw: skimage.color.lab2lch(img_raw),
+    'lab2rgb': lambda img_raw: skimage.color.lab2rgb(img_raw),
+    'lab2xyz': lambda img_raw: skimage.color.lab2xyz(img_raw),
+    'lch2lab': lambda img_raw: skimage.color.lch2lab(img_raw),
+    'luv2rgb': lambda img_raw: skimage.color.luv2rgb(img_raw),
+    'luv2xyz': lambda img_raw: skimage.color.luv2xyz(img_raw),
+    'rgb2hed': lambda img_raw: skimage.color.rgb2hed(img_raw),
+    'rgb2hsv': lambda img_raw: skimage.color.rgb2hsv(img_raw),
+    'rgb2lab': lambda img_raw: skimage.color.rgb2lab(img_raw),
+    'rgb2luv': lambda img_raw: skimage.color.rgb2luv(img_raw),
+    'rgb2rgbcie': lambda img_raw: skimage.color.rgb2rgbcie(img_raw),
+    'rgb2xyz': lambda img_raw: skimage.color.rgb2xyz(img_raw),
+    'rgbcie2rgb': lambda img_raw: skimage.color.rgbcie2rgb(img_raw),
+    'xyz2lab': lambda img_raw: skimage.color.xyz2lab(img_raw),
+    'xyz2luv': lambda img_raw: skimage.color.xyz2luv(img_raw),
+    'xyz2rgb': lambda img_raw: skimage.color.xyz2rgb(img_raw),
+
+    'rgb_from_hed': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hed),
+    'rgb_from_hdx': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hdx),
+    'rgb_from_fgx': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_fgx),
+    'rgb_from_bex': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bex),
+    'rgb_from_rbd': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_rbd),
+    'rgb_from_gdx': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_gdx),
+    'rgb_from_hax': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hax),
+    'rgb_from_bro': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bro),
+    'rgb_from_bpx': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bpx),
+    'rgb_from_ahx': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_ahx),
+    'rgb_from_hpx': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hpx),
+
+    'hed_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hed_from_rgb),
+    'hdx_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hdx_from_rgb),
+    'fgx_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.fgx_from_rgb),
+    'bex_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bex_from_rgb),
+    'rbd_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.rbd_from_rgb),
+    'gdx_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.gdx_from_rgb),
+    'hax_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hax_from_rgb),
+    'bro_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bro_from_rgb),
+    'bpx_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bpx_from_rgb),
+    'ahx_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.ahx_from_rgb),
+    'hpx_from_rgb': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hpx_from_rgb),
+
+    'pca': lambda img_raw: np.reshape(PCA(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])),
+                                      [img_raw.shape[0], img_raw.shape[1], -1]),
+    'nmf': lambda img_raw: np.reshape(NMF(n_components=3, init='nndsvda').fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])),
+                                      [img_raw.shape[0], img_raw.shape[1], -1]),
+    'ica': lambda img_raw: np.reshape(FastICA(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])),
+                                      [img_raw.shape[0], img_raw.shape[1], -1]),
+    'fa': lambda img_raw: np.reshape(FactorAnalysis(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])),
+                                     [img_raw.shape[0], img_raw.shape[1], -1])
 }
 
 parser = argparse.ArgumentParser()
 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
 parser.add_argument('conv_type', choices=convOptions.keys(), help='conversion type')
-args = parser.parse_args() 
+args = parser.parse_args()
 
-img_in = skimage.io.imread(args.input_file.name)[:,:,0:3]
+img_in = skimage.io.imread(args.input_file.name)[:, :, 0:3]
 res = convOptions[args.conv_type](img_in)
-res[res<-1]=-1
-res[res>1]=1
+res[res < -1] = -1
+res[res > +1] = +1
 
 with warnings.catch_warnings():
-	warnings.simplefilter("ignore")
-	res = skimage.util.img_as_uint(res) #Attention: precision loss
-	skimage.io.imsave(args.out_file.name, res, plugin='tifffile')
+    warnings.simplefilter('ignore')
+    res = skimage.util.img_as_uint(res)  # Attention: precision loss
+    skimage.io.imsave(args.out_file.name, res, plugin='tifffile')