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.CondaPkg/env/Lib/site-packages/skimage/graph/_graph.py vendored
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import numpy as np
from scipy import sparse
from scipy.sparse import csgraph
from ..morphology._util import _raveled_offsets_and_distances
from ..util._map_array import map_array
def _weighted_abs_diff(values0, values1, distances):
"""A default edge function for complete image graphs.
A pixel graph on an image with no edge values and no mask is a very
boring regular lattice, so we define a default edge weight to be the
absolute difference between values *weighted* by the distance
between them.
Parameters
----------
values0 : array
The pixel values for each node.
values1 : array
The pixel values for each neighbor.
distances : array
The distance between each node and its neighbor.
Returns
-------
edge_values : array of float
The computed values: abs(values0 - values1) * distances.
"""
return np.abs(values0 - values1) * distances
def pixel_graph(
image, *, mask=None, edge_function=None, connectivity=1, spacing=None
):
"""Create an adjacency graph of pixels in an image.
Pixels where the mask is True are nodes in the returned graph, and they are
connected by edges to their neighbors according to the connectivity
parameter. By default, the *value* of an edge when a mask is given, or when
the image is itself the mask, is the euclidean distance between the pixels.
However, if an int- or float-valued image is given with no mask, the value
of the edges is the absolute difference in intensity between adjacent
pixels, weighted by the euclidean distance.
Parameters
----------
image : array
The input image. If the image is of type bool, it will be used as the
mask as well.
mask : array of bool
Which pixels to use. If None, the graph for the whole image is used.
edge_function : callable
A function taking an array of pixel values, and an array of neighbor
pixel values, and an array of distances, and returning a value for the
edge. If no function is given, the value of an edge is just the
distance.
connectivity : int
The square connectivity of the pixel neighborhood: the number of
orthogonal steps allowed to consider a pixel a neighbor. See
`scipy.ndimage.generate_binary_structure` for details.
spacing : tuple of float
The spacing between pixels along each axis.
Returns
-------
graph : scipy.sparse.csr_matrix
A sparse adjacency matrix in which entry (i, j) is 1 if nodes i and j
are neighbors, 0 otherwise.
nodes : array of int
The nodes of the graph. These correspond to the raveled indices of the
nonzero pixels in the mask.
"""
if image.dtype == bool and mask is None:
mask = image
if mask is None and edge_function is None:
mask = np.ones_like(image, dtype=bool)
edge_function = _weighted_abs_diff
# Strategy: we are going to build the (i, j, data) arrays of a scipy
# sparse COO matrix, then convert to CSR (which is fast).
# - grab the raveled IDs of the foreground (mask == True) parts of the
# image **in the padded space**.
# - broadcast them together with the raveled offsets to their neighbors.
# This gives us for each foreground pixel a list of neighbors (that
# may or may not be selected by the mask). (We also track the *distance*
# to each neighbor.)
# - select "valid" entries in the neighbors and distance arrays by indexing
# into the mask, which we can do since these are raveled indices.
# - use np.repeat() to repeat each source index according to the number
# of neighbors selected by the mask it has. Each of these repeated
# indices will be lined up with its neighbor, i.e. **this is the i
# array** of the COO format matrix.
# - use the mask as a boolean index to get a 1D view of the selected
# neighbors. **This is the j array.**
# - by default, the same boolean indexing can be applied to the distances
# to each neighbor, to give the **data array.** Optionally, a
# provided edge function can be computed on the pixel values and the
# distances to give a different value for the edges.
# Note, we use map_array to map the raveled coordinates in the padded
# image to the ones in the original image, and those are the returned
# nodes.
padded = np.pad(mask, 1, mode='constant', constant_values=False)
nodes_padded = np.flatnonzero(padded)
neighbor_offsets_padded, distances_padded = _raveled_offsets_and_distances(
padded.shape, connectivity=connectivity, spacing=spacing
)
neighbors_padded = nodes_padded[:, np.newaxis] + neighbor_offsets_padded
neighbor_distances_full = np.broadcast_to(
distances_padded, neighbors_padded.shape
)
nodes = np.flatnonzero(mask)
nodes_sequential = np.arange(nodes.size)
# neighbors outside the mask get mapped to 0, which is a valid index,
# BUT, they will be masked out in the next step.
neighbors = map_array(neighbors_padded, nodes_padded, nodes)
neighbors_mask = padded.reshape(-1)[neighbors_padded]
num_neighbors = np.sum(neighbors_mask, axis=1)
indices = np.repeat(nodes, num_neighbors)
indices_sequential = np.repeat(nodes_sequential, num_neighbors)
neighbor_indices = neighbors[neighbors_mask]
neighbor_distances = neighbor_distances_full[neighbors_mask]
neighbor_indices_sequential = map_array(
neighbor_indices, nodes, nodes_sequential
)
if edge_function is None:
data = neighbor_distances
else:
image_r = image.reshape(-1)
data = edge_function(
image_r[indices], image_r[neighbor_indices], neighbor_distances
)
m = nodes_sequential.size
mat = sparse.coo_matrix(
(data, (indices_sequential, neighbor_indices_sequential)),
shape=(m, m)
)
graph = mat.tocsr()
return graph, nodes
def central_pixel(graph, nodes=None, shape=None, partition_size=100):
"""Find the pixel with the highest closeness centrality.
Closeness centrality is the inverse of the total sum of shortest distances
from a node to every other node.
Parameters
----------
graph : scipy.sparse.csr_matrix
The sparse matrix representation of the graph.
nodes : array of int
The raveled index of each node in graph in the image. If not provided,
the returned value will be the index in the input graph.
shape : tuple of int
The shape of the image in which the nodes are embedded. If provided,
the returned coordinates are a NumPy multi-index of the same
dimensionality as the input shape. Otherwise, the returned coordinate
is the raveled index provided in `nodes`.
partition_size : int
This function computes the shortest path distance between every pair
of nodes in the graph. This can result in a very large (N*N) matrix.
As a simple performance tweak, the distance values are computed in
lots of `partition_size`, resulting in a memory requirement of only
partition_size*N.
Returns
-------
position : int or tuple of int
If shape is given, the coordinate of the central pixel in the image.
Otherwise, the raveled index of that pixel.
distances : array of float
The total sum of distances from each node to each other reachable
node.
"""
if nodes is None:
nodes = np.arange(graph.shape[0])
if partition_size is None:
num_splits = 1
else:
num_splits = max(2, graph.shape[0] // partition_size)
idxs = np.arange(graph.shape[0])
total_shortest_path_len_list = []
for partition in np.array_split(idxs, num_splits):
shortest_paths = csgraph.shortest_path(
graph, directed=False, indices=partition
)
shortest_paths_no_inf = np.nan_to_num(shortest_paths)
total_shortest_path_len_list.append(
np.sum(shortest_paths_no_inf, axis=1)
)
total_shortest_path_len = np.concatenate(total_shortest_path_len_list)
nonzero = np.flatnonzero(total_shortest_path_len)
min_sp = np.argmin(total_shortest_path_len[nonzero])
raveled_index = nodes[nonzero[min_sp]]
if shape is not None:
central = np.unravel_index(raveled_index, shape)
else:
central = raveled_index
return central, total_shortest_path_len