Find file Copy path
186 lines (157 sloc) 7.39 KB
import collections as coll
import numpy as np
from scipy import ndimage as ndi
from ..util import img_as_float, regular_grid
from ..segmentation._slic import (_slic_cython,
from ..color import rgb2lab
def slic(image, n_segments=100, compactness=10., max_iter=10, sigma=0,
spacing=None, multichannel=True, convert2lab=None,
enforce_connectivity=True, min_size_factor=0.5, max_size_factor=3,
"""Segments image using k-means clustering in Color-(x,y,z) space.
image : 2D, 3D or 4D ndarray
Input image, which can be 2D or 3D, and grayscale or multichannel
(see `multichannel` parameter).
n_segments : int, optional
The (approximate) number of labels in the segmented output image.
compactness : float, optional
Balances color proximity and space proximity. Higher values give
more weight to space proximity, making superpixel shapes more
square/cubic. In SLICO mode, this is the initial compactness.
This parameter depends strongly on image contrast and on the
shapes of objects in the image. We recommend exploring possible
values on a log scale, e.g., 0.01, 0.1, 1, 10, 100, before
refining around a chosen value.
max_iter : int, optional
Maximum number of iterations of k-means.
sigma : float or (3,) array-like of floats, optional
Width of Gaussian smoothing kernel for pre-processing for each
dimension of the image. The same sigma is applied to each dimension in
case of a scalar value. Zero means no smoothing.
Note, that `sigma` is automatically scaled if it is scalar and a
manual voxel spacing is provided (see Notes section).
spacing : (3,) array-like of floats, optional
The voxel spacing along each image dimension. By default, `slic`
assumes uniform spacing (same voxel resolution along z, y and x).
This parameter controls the weights of the distances along z, y,
and x during k-means clustering.
multichannel : bool, optional
Whether the last axis of the image is to be interpreted as multiple
channels or another spatial dimension.
convert2lab : bool, optional
Whether the input should be converted to Lab colorspace prior to
segmentation. The input image *must* be RGB. Highly recommended.
This option defaults to ``True`` when ``multichannel=True`` *and*
``image.shape[-1] == 3``.
enforce_connectivity: bool, optional
Whether the generated segments are connected or not
min_size_factor: float, optional
Proportion of the minimum segment size to be removed with respect
to the supposed segment size ```depth*width*height/n_segments```
max_size_factor: float, optional
Proportion of the maximum connected segment size. A value of 3 works
in most of the cases.
slic_zero: bool, optional
Run SLIC-zero, the zero-parameter mode of SLIC. [2]_
labels : 2D or 3D array
Integer mask indicating segment labels.
If ``convert2lab`` is set to ``True`` but the last array
dimension is not of length 3.
* If `sigma > 0`, the image is smoothed using a Gaussian kernel prior to
* If `sigma` is scalar and `spacing` is provided, the kernel width is
divided along each dimension by the spacing. For example, if ``sigma=1``
and ``spacing=[5, 1, 1]``, the effective `sigma` is ``[0.2, 1, 1]``. This
ensures sensible smoothing for anisotropic images.
* The image is rescaled to be in [0, 1] prior to processing.
* Images of shape (M, N, 3) are interpreted as 2D RGB images by default. To
interpret them as 3D with the last dimension having length 3, use
.. [1] Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi,
Pascal Fua, and Sabine Süsstrunk, SLIC Superpixels Compared to
State-of-the-art Superpixel Methods, TPAMI, May 2012.
.. [2]
>>> from skimage.segmentation import slic
>>> from import astronaut
>>> img = astronaut()
>>> segments = slic(img, n_segments=100, compactness=10)
Increasing the compactness parameter yields more square regions:
>>> segments = slic(img, n_segments=100, compactness=20)
image = img_as_float(image)
is_2d = False
if image.ndim == 2:
# 2D grayscale image
image = image[np.newaxis, ..., np.newaxis]
is_2d = True
elif image.ndim == 3 and multichannel:
# Make 2D multichannel image 3D with depth = 1
image = image[np.newaxis, ...]
is_2d = True
elif image.ndim == 3 and not multichannel:
# Add channel as single last dimension
image = image[..., np.newaxis]
if spacing is None:
spacing = np.ones(3)
elif isinstance(spacing, (list, tuple)):
spacing = np.array(spacing, dtype=np.double)
if not isinstance(sigma, coll.Iterable):
sigma = np.array([sigma, sigma, sigma], dtype=np.double)
sigma /= spacing.astype(np.double)
elif isinstance(sigma, (list, tuple)):
sigma = np.array(sigma, dtype=np.double)
if (sigma > 0).any():
# add zero smoothing for multichannel dimension
sigma = list(sigma) + [0]
image = ndi.gaussian_filter(image, sigma)
if multichannel and (convert2lab or convert2lab is None):
if image.shape[-1] != 3 and convert2lab:
raise ValueError("Lab colorspace conversion requires a RGB image.")
elif image.shape[-1] == 3:
image = rgb2lab(image)
depth, height, width = image.shape[:3]
# initialize cluster centroids for desired number of segments
grid_z, grid_y, grid_x = np.mgrid[:depth, :height, :width]
slices = regular_grid(image.shape[:3], n_segments)
step_z, step_y, step_x = [int(s.step if s.step is not None else 1)
for s in slices]
segments_z = grid_z[slices]
segments_y = grid_y[slices]
segments_x = grid_x[slices]
segments_color = np.zeros(segments_z.shape + (image.shape[3],))
segments = np.concatenate([segments_z[..., np.newaxis],
segments_y[..., np.newaxis],
segments_x[..., np.newaxis],
axis=-1).reshape(-1, 3 + image.shape[3])
segments = np.ascontiguousarray(segments)
# we do the scaling of ratio in the same way as in the SLIC paper
# so the values have the same meaning
step = float(max((step_z, step_y, step_x)))
ratio = 1.0 / compactness
image = np.ascontiguousarray(image * ratio)
labels = _slic_cython(image, segments, step, max_iter, spacing, slic_zero)
if enforce_connectivity:
segment_size = depth * height * width / n_segments
min_size = int(min_size_factor * segment_size)
max_size = int(max_size_factor * segment_size)
labels = _enforce_label_connectivity_cython(labels,
if is_2d:
labels = labels[0]
return labels