| Previous changeset 1:0976b373a321 (2019-07-22) |
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Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf |
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modified:
color-deconvolution.xml color_deconvolution.py |
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| diff -r 0976b373a321 -r 612aa1478fe1 color-deconvolution.xml --- a/color-deconvolution.xml Mon Jul 22 05:02:00 2019 -0400 +++ b/color-deconvolution.xml Mon Nov 13 22:10:42 2023 +0000 |
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| @@ -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> |
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| diff -r 0976b373a321 -r 612aa1478fe1 color_deconvolution.py --- a/color_deconvolution.py Mon Jul 22 05:02:00 2019 -0400 +++ b/color_deconvolution.py Mon Nov 13 22:10:42 2023 +0000 |
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| b"@@ -1,87 +1,79 @@\n import argparse\n import sys\n import warnings\n+\n import numpy as np\n-import skimage.io\n import skimage.color\n+import skimage.io\n import skimage.util\n-from sklearn.decomposition import PCA, NMF, FastICA, FactorAnalysis\n+from sklearn.decomposition import FactorAnalysis, FastICA, NMF, PCA\n \n convOptions = {\n- 'hed2rgb' : lambda img_raw: skimage.color.hed2rgb(img_raw),\n- 'hsv2rgb' : lambda img_raw: skimage.color.hsv2rgb(img_raw),\n- 'lab2lch' : lambda img_raw: skimage.color.lab2lch(img_raw),\n- 'lab2rgb' : lambda img_raw: skimage.color.lab2rgb(img_raw),\n- 'lab2xyz' : lambda img_raw: skimage.color.lab2xyz(img_raw),\n- 'lch2lab' : lambda img_raw: skimage.color.lch2lab(img_raw),\n- 'luv2rgb' : lambda img_raw: skimage.color.luv2rgb(img_raw),\n- 'luv2xyz' : lambda img_raw: skimage.color.luv2xyz(img_raw),\n- 'rgb2hed' : lambda img_raw: skimage.color.rgb2hed(img_raw),\n- 'rgb2hsv' : lambda img_raw: skimage.color.rgb2hsv(img_raw),\n- 'rgb2lab' : lambda img_raw: skimage.color.rgb2lab(img_raw),\n- 'rgb2luv' : lambda img_raw: skimage.color.rgb2luv(img_raw),\n- 'rgb2rgbcie' : lambda img_raw: skimage.color.rgb2rgbcie(img_raw),\n- 'rgb2xyz' : lambda img_raw: skimage.color.rgb2xyz(img_raw),\n- #'rgb2ycbcr' : lambda img_raw: skimage.color.rgb2ycbcr(img_raw),\n- #'rgb2yiq' : lambda img_raw: skimage.color.rgb2yiq(img_raw),\n- #'rgb2ypbpr' : lambda img_raw: skimage.color.rgb2ypbpr(img_raw),\n- #'rgb2yuv' : lambda img_raw: skimage.color.rgb2yuv(img_raw),\n- #'rgba2rgb' : lambda img_raw: skimage.color.rgba2rgb(img_raw),\n- 'rgbcie2rgb' : lambda img_raw: skimage.color.rgbcie2rgb(img_raw),\n- 'xyz2lab' : lambda img_raw: skimage.color.xyz2lab(img_raw),\n- 'xyz2luv' : lambda img_raw: skimage.color.xyz2luv(img_raw),\n- 'xyz2rgb' : lambda img_raw: skimage.color.xyz2rgb(img_raw),\n- #'ycbcr2rgb' : lambda img_raw: skimage.color.ycbcr2rgb(img_raw),\n- #'yiq2rgb' : lambda img_raw: skimage.color.yiq2rgb(img_raw),\n- #'ypbpr2rgb' : lambda img_raw: skimage.color.ypbpr2rgb(img_raw),\n- #'yuv2rgb' : lambda img_raw: skimage.color.yuv2rgb(img_raw), \n- \n- 'rgb_from_hed' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hed),\n- 'rgb_from_hdx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hdx),\n- 'rgb_from_fgx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_fgx),\n- 'rgb_from_bex' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bex),\n- 'rgb_from_rbd' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_rbd),\n- 'rgb_from_gdx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_gdx),\n- 'rgb_from_hax' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hax),\n- 'rgb_from_bro' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bro),\n- 'rgb_from_bpx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bpx),\n- 'rgb_from_ahx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_ahx),\n- 'rgb_from_hpx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hpx),\n- \n- 'hed_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hed_from_rgb),\n- 'hdx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hdx_from_rgb),\n- 'fgx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.fgx_from_rgb),\n- 'bex_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bex_fro"..b'g_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hdx),\n+ \'rgb_from_fgx\': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_fgx),\n+ \'rgb_from_bex\': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bex),\n+ \'rgb_from_rbd\': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_rbd),\n+ \'rgb_from_gdx\': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_gdx),\n+ \'rgb_from_hax\': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hax),\n+ \'rgb_from_bro\': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bro),\n+ \'rgb_from_bpx\': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bpx),\n+ \'rgb_from_ahx\': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_ahx),\n+ \'rgb_from_hpx\': lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hpx),\n+\n+ \'hed_from_rgb\': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hed_from_rgb),\n+ \'hdx_from_rgb\': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hdx_from_rgb),\n+ \'fgx_from_rgb\': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.fgx_from_rgb),\n+ \'bex_from_rgb\': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bex_from_rgb),\n+ \'rbd_from_rgb\': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.rbd_from_rgb),\n+ \'gdx_from_rgb\': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.gdx_from_rgb),\n+ \'hax_from_rgb\': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hax_from_rgb),\n+ \'bro_from_rgb\': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bro_from_rgb),\n+ \'bpx_from_rgb\': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bpx_from_rgb),\n+ \'ahx_from_rgb\': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.ahx_from_rgb),\n+ \'hpx_from_rgb\': lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hpx_from_rgb),\n+\n+ \'pca\': lambda img_raw: np.reshape(PCA(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])),\n+ [img_raw.shape[0], img_raw.shape[1], -1]),\n+ \'nmf\': lambda img_raw: np.reshape(NMF(n_components=3, init=\'nndsvda\').fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])),\n+ [img_raw.shape[0], img_raw.shape[1], -1]),\n+ \'ica\': lambda img_raw: np.reshape(FastICA(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])),\n+ [img_raw.shape[0], img_raw.shape[1], -1]),\n+ \'fa\': lambda img_raw: np.reshape(FactorAnalysis(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])),\n+ [img_raw.shape[0], img_raw.shape[1], -1])\n }\n \n parser = argparse.ArgumentParser()\n parser.add_argument(\'input_file\', type=argparse.FileType(\'r\'), default=sys.stdin, help=\'input file\')\n parser.add_argument(\'out_file\', type=argparse.FileType(\'w\'), default=sys.stdin, help=\'out file (TIFF)\')\n parser.add_argument(\'conv_type\', choices=convOptions.keys(), help=\'conversion type\')\n-args = parser.parse_args() \n+args = parser.parse_args()\n \n-img_in = skimage.io.imread(args.input_file.name)[:,:,0:3]\n+img_in = skimage.io.imread(args.input_file.name)[:, :, 0:3]\n res = convOptions[args.conv_type](img_in)\n-res[res<-1]=-1\n-res[res>1]=1\n+res[res < -1] = -1\n+res[res > +1] = +1\n \n with warnings.catch_warnings():\n-\twarnings.simplefilter("ignore")\n-\tres = skimage.util.img_as_uint(res) #Attention: precision loss\n-\tskimage.io.imsave(args.out_file.name, res, plugin=\'tifffile\')\n+ warnings.simplefilter(\'ignore\')\n+ res = skimage.util.img_as_uint(res) # Attention: precision loss\n+ skimage.io.imsave(args.out_file.name, res, plugin=\'tifffile\')\n' |