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118 lines
3.9 KiB
Cython
118 lines
3.9 KiB
Cython
#cython: cdivision=True
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#cython: boundscheck=False
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#cython: nonecheck=False
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#cython: wraparound=False
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from libc.float cimport DBL_MAX
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import numpy as np
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cimport numpy as cnp
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from skimage.util import regular_grid
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def _slic_cython(double[:, :, :, ::1] image_zyx,
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double[:, ::1] clusters,
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Py_ssize_t max_iter):
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"""Helper function for SLIC segmentation.
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Parameters
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----------
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image_zyx : 4D array of double, shape (Z, Y, X, C)
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The input image.
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clusters : 2D array of double, shape (N, 3 + C)
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The initial centroids obtained by SLIC as [Z, Y, X, C...].
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max_iter : int
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The maximum number of k-means iterations.
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Returns
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-------
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nearest_clusters : 3D array of int, shape (Z, Y, X)
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The label field/superpixels found by SLIC.
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"""
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# initialize on grid
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cdef Py_ssize_t depth, height, width
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depth = image_zyx.shape[0]
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height = image_zyx.shape[1]
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width = image_zyx.shape[2]
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cdef Py_ssize_t n_clusters = clusters.shape[0]
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# number of features [X, Y, Z, ...]
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cdef Py_ssize_t n_features = clusters.shape[1]
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# approximate grid size for desired n_segments
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cdef Py_ssize_t step_z, step_y, step_x
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slices = regular_grid((depth, height, width), n_clusters)
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step_z, step_y, step_x = [int(s.step) for s in slices]
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cdef Py_ssize_t[:, :, ::1] nearest_clusters \
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= np.empty((depth, height, width), dtype=np.intp)
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cdef double[:, :, ::1] distance \
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= np.empty((depth, height, width), dtype=np.double)
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cdef Py_ssize_t[:] n_cluster_elems = np.zeros(n_clusters, dtype=np.intp)
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cdef Py_ssize_t i, c, k, x, y, z, x_min, x_max, y_min, y_max, z_min, z_max
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cdef char change
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cdef double dist_mean, cx, cy, cz, dy, dz
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for i in range(max_iter):
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change = 0
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distance[:, :, :] = DBL_MAX
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# assign pixels to clusters
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for k in range(n_clusters):
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# cluster coordinate centers
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cz = clusters[k, 0]
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cy = clusters[k, 1]
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cx = clusters[k, 2]
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# compute windows
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z_min = <Py_ssize_t>max(cz - 2 * step_z, 0)
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z_max = <Py_ssize_t>min(cz + 2 * step_z + 1, depth)
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y_min = <Py_ssize_t>max(cy - 2 * step_y, 0)
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y_max = <Py_ssize_t>min(cy + 2 * step_y + 1, height)
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x_min = <Py_ssize_t>max(cx - 2 * step_x, 0)
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x_max = <Py_ssize_t>min(cx + 2 * step_x + 1, width)
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for z in range(z_min, z_max):
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dz = (cz - z) ** 2
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for y in range(y_min, y_max):
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dy = (cy - y) ** 2
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for x in range(x_min, x_max):
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dist_mean = dz + dy + (cx - x) ** 2
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for c in range(3, n_features):
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dist_mean += (image_zyx[z, y, x, c - 3]
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- clusters[k, c]) ** 2
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if distance[z, y, x] > dist_mean:
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nearest_clusters[z, y, x] = k
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distance[z, y, x] = dist_mean
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change = 1
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# stop if no pixel changed its cluster
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if change == 0:
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break
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# recompute clusters
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# sum features for all clusters
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n_cluster_elems[:] = 0
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clusters[:, :] = 0
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for z in range(depth):
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for y in range(height):
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for x in range(width):
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k = nearest_clusters[z, y, x]
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n_cluster_elems[k] += 1
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clusters[k, 0] += z
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clusters[k, 1] += y
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clusters[k, 2] += x
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for c in range(3, n_features):
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clusters[k, c] += image_zyx[z, y, x, c - 3]
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# divide by number of elements per cluster to obtain mean
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for k in range(n_clusters):
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for c in range(n_features):
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clusters[k, c] /= n_cluster_elems[k]
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return np.asarray(nearest_clusters)
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