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# -*- coding: utf-8 -*-
# Copyright (c) Vispy Development Team. All Rights Reserved.
# Distributed under the (new) BSD License. See LICENSE.txt for more info.
"""
Graph utilities
===============
A module containing several graph utility functions.
"""
import numpy as np
try:
from scipy.sparse import issparse
from scipy import sparse
except ImportError:
def issparse(*args, **kwargs):
return False
def _get_edges(adjacency_mat):
func = _sparse_get_edges if issparse(adjacency_mat) else _ndarray_get_edges
return func(adjacency_mat)
def _sparse_get_edges(adjacency_mat):
return np.concatenate((adjacency_mat.row[:, np.newaxis],
adjacency_mat.col[:, np.newaxis]), axis=-1)
def _ndarray_get_edges(adjacency_mat):
# Get indices of all non zero values
i, j = np.where(adjacency_mat)
return np.concatenate((i[:, np.newaxis], j[:, np.newaxis]), axis=-1)
def _get_directed_edges(adjacency_mat):
func = _sparse_get_edges if issparse(adjacency_mat) else _ndarray_get_edges
if issparse(adjacency_mat):
triu = sparse.triu
tril = sparse.tril
else:
triu = np.triu
tril = np.tril
upper = triu(adjacency_mat)
lower = tril(adjacency_mat)
return np.concatenate((func(upper), func(lower)))
def _straight_line_vertices(adjacency_mat, node_coords, directed=False):
"""
Generate the vertices for straight lines between nodes.
If it is a directed graph, it also generates the vertices which can be
passed to an :class:`ArrowVisual`.
Parameters
----------
adjacency_mat : array
The adjacency matrix of the graph
node_coords : array
The current coordinates of all nodes in the graph
directed : bool
Wether the graph is directed. If this is true it will also generate
the vertices for arrows which can be passed to :class:`ArrowVisual`.
Returns
-------
vertices : tuple
Returns a tuple containing containing (`line_vertices`,
`arrow_vertices`)
"""
if not issparse(adjacency_mat):
adjacency_mat = np.asarray(adjacency_mat, float)
if (adjacency_mat.ndim != 2 or adjacency_mat.shape[0] !=
adjacency_mat.shape[1]):
raise ValueError("Adjacency matrix should be square.")
arrow_vertices = np.array([])
edges = _get_edges(adjacency_mat)
line_vertices = node_coords[edges.ravel()]
if directed:
arrows = np.array(list(_get_directed_edges(adjacency_mat)))
arrow_vertices = node_coords[arrows.ravel()]
arrow_vertices = arrow_vertices.reshape((len(arrow_vertices)//2, 4))
return line_vertices, arrow_vertices
def _rescale_layout(pos, scale=1):
"""
Normalize the given coordinate list to the range [0, `scale`].
Parameters
----------
pos : array
Coordinate list
scale : number
The upperbound value for the coordinates range
Returns
-------
pos : array
The rescaled (normalized) coordinates in the range [0, `scale`].
Notes
-----
Changes `pos` in place.
"""
pos -= pos.min(axis=0)
pos *= scale / pos.max()
return pos
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