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b/ants/segmentation/kmeans.py |
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__all__ = ['kmeans_segmentation'] |
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import ants |
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def kmeans_segmentation(image, k, kmask=None, mrf=0.1): |
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""" |
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K-means image segmentation that is a wrapper around `ants.atropos` |
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ANTsR function: `kmeansSegmentation` |
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Arguments |
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--------- |
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image : ANTsImage |
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input image |
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k : integer |
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integer number of classes |
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kmask : ANTsImage (optional) |
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segment inside this mask |
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mrf : scalar |
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smoothness, higher is smoother |
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Returns |
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------- |
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ANTsImage |
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Example |
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------- |
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>>> import ants |
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>>> fi = ants.image_read(ants.get_ants_data('r16'), 'float') |
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>>> fi = ants.n3_bias_field_correction(fi, 2) |
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>>> seg = ants.kmeans_segmentation(fi, 3) |
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""" |
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dim = image.dimension |
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kmimage = ants.iMath(image, 'Normalize') |
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if kmask is None: |
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kmask = ants.get_mask(kmimage, 0.01, 1, cleanup=2) |
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kmask = ants.iMath(kmask, 'FillHoles').threshold_image(1,2) |
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nhood = 'x'.join(['1']*dim) |
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mrf = '[%s,%s]' % (str(mrf), nhood) |
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kmimage = ants.atropos(a = kmimage, m = mrf, c = '[5,0]', i = 'kmeans[%s]'%(str(k)), x = kmask) |
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kmimage['segmentation'] = kmimage['segmentation'].clone(image.pixeltype) |
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return kmimage |