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63 lines
1.6 KiB
Python
63 lines
1.6 KiB
Python
from __future__ import division, print_function, absolute_import
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import numpy as np
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from ..util import img_as_ubyte
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from ._skeletonize_3d_cy import _compute_thin_image
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def skeletonize_3d(img):
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"""Compute the skeleton of a binary image.
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Thinning is used to reduce each connected component in a binary image
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to a single-pixel wide skeleton.
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Parameters
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----------
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img : ndarray, 2D or 3D
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A binary image containing the objects to be skeletonized. Zeros
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represent background, nonzero values are foreground.
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Returns
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-------
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skeleton : ndarray
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The thinned image.
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See also
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--------
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skeletonize, medial_axis
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References
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----------
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.. [Lee94] Lee et al, Building skeleton models via 3-D medial surface/axis
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thinning algorithms. Computer Vision, Graphics, and Image Processing,
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56(6):462-478, 1994.
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"""
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# make sure the image is 3D or 2D (if it is, temporarily upcast to 3D)
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if img.ndim < 2 or img.ndim > 3:
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raise ValueError('expect 2D, got ndim = %s' % img.ndim)
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img = img_as_ubyte(img)
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img = np.ascontiguousarray(img)
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img = img.copy()
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if img.ndim == 2:
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img = img[None, ...]
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# normalize to binary
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maxval = img.max()
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img[img != 0] = 1
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# pad w/ zeros to simplify dealing w/ boundaries
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img_o = np.pad(img, pad_width=1, mode='constant')
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# do the computation
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img_o = np.asarray(_compute_thin_image(img_o))
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# clip it back and restore the original intensity range
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img_o = img_o[1:-1, 1:-1, 1:-1]
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img_o = img_o.squeeze()
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img_o *= maxval
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return img_o
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