# Source code for graspy.utils.utils

```
# Copyright 2019 NeuroData (http://neurodata.io)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import warnings
from collections import Iterable
from functools import reduce
from pathlib import Path
import networkx as nx
import numpy as np
from sklearn.utils import check_array
[docs]def import_graph(graph, copy=True):
"""
A function for reading a graph and returning a shared data type.
Parameters
----------
graph: object
Either array-like, shape (n_vertices, n_vertices) numpy array,
or an object of type networkx.Graph.
copy: bool, (default=True)
Whether to return a copied version of array. If False and input is np.array,
the output returns the original input.
Returns
-------
out: array-like, shape (n_vertices, n_vertices)
A graph.
See Also
--------
networkx.Graph, numpy.array
"""
if isinstance(graph, (nx.Graph, nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph)):
out = nx.to_numpy_array(graph, nodelist=sorted(graph.nodes), dtype=np.float)
elif isinstance(graph, (np.ndarray, np.memmap)):
shape = graph.shape
if len(shape) > 3:
msg = "Input tensor must have at most 3 dimensions, not {}.".format(
len(shape)
)
raise ValueError(msg)
elif len(shape) == 3:
if shape[1] != shape[2]:
msg = "Input tensor must have same number of vertices."
raise ValueError(msg)
min_features = shape[1]
min_samples = 2
else:
min_features = np.max(shape)
min_samples = min_features
out = check_array(
graph,
dtype=[np.float64, np.float32],
ensure_2d=True,
allow_nd=True, # For omni tensor input
ensure_min_features=min_features,
ensure_min_samples=min_samples,
copy=copy,
)
else:
msg = "Input must be networkx.Graph or np.array, not {}.".format(type(graph))
raise TypeError(msg)
return out
[docs]def import_edgelist(
path, extension="edgelist", delimiter=None, nodetype=int, return_vertices=False
):
"""
Function for reading a single or multiple edgelists. When importing multiple
edgelists, the union of vertices from all graphs is computed so that each output
graph have matched vertex set. The order of nodes are sorted by node values.
Parameters
----------
path : str, Path object, or iterable
If ``path`` is a directory, then the importing order will be sorted in
alphabetical order.
extension : str, optional
If ``path`` is a directory, then the function will convert all files
with matching extension.
delimiter : str or None, default=None, optional
Delimiter of edgelist. If None, the delimiter is whitespace.
nodetype : int (default), float, str, Python type, optional
Convert node data from strings to specified type.
return_vertices : bool, default=False, optional
Returns the union of all ind
Returns
-------
out : list of array-like, or array-like, shape (n_vertices, n_vertices)
If ``path`` is a directory, a list of arrays is returned. If ``path`` is a file,
an array is returned.
vertices : array-like, shape (n_vertices, )
If ``return_vertices`` == True, then returns an array of all vertices that were
included in the output graphs.
"""
# p = Path(path)
if not isinstance(path, (str, Path, Iterable)):
msg = "path must be a string or Iterable, not {}".format(type(path))
raise TypeError(msg)
# get a list of files to import
if isinstance(path, (str, Path)):
p = Path(path)
if p.is_dir():
files = sorted(p.glob("*" + extension))
elif p.is_file():
files = [p]
else:
raise ValueError("No graphs founds to import.")
else: # path is an iterable
files = [Path(f) for f in path]
if len(files) == 0:
msg = "No files found with '{}' extension found.".format(extension)
raise ValueError(msg)
graphs = [
nx.read_weighted_edgelist(f, nodetype=nodetype, delimiter=delimiter)
for f in files
]
if all(len(G.nodes) == 0 for G in graphs):
msg = (
"All graphs have 0 vertices. Please double check if proper "
+ "'delimiter' is given."
)
warnings.warn(msg, UserWarning)
# Compute union of all vertices
vertices = np.sort(reduce(np.union1d, [G.nodes for G in graphs]))
out = [nx.to_numpy_array(G, nodelist=vertices, dtype=np.float) for G in graphs]
# only return adjacency matrix if input is only 1 graph
if len(out) == 1:
out = out[0]
if return_vertices:
return out, vertices
else:
return out
def is_symmetric(X):
return np.array_equal(X, X.T)
def is_loopless(X):
return not np.any(np.diag(X) != 0)
def is_unweighted(X):
return ((X == 0) | (X == 1)).all()
def is_almost_symmetric(X, atol=1e-15):
return np.allclose(X, X.T, atol=atol)
[docs]def symmetrize(graph, method="triu"):
"""
A function for forcing symmetry upon a graph.
Parameters
----------
graph: object
Either array-like, (n_vertices, n_vertices) numpy matrix,
or an object of type networkx.Graph.
method: {'triu' (default), 'tril', 'avg'}, optional
An option indicating which half of the edges to
retain when symmetrizing.
- 'triu'
Retain the upper right triangle.
- 'tril'
Retain the lower left triangle.
- 'avg'
Retain the average weight between the upper and lower
right triangle, of the adjacency matrix.
Returns
-------
graph: array-like, shape (n_vertices, n_vertices)
the graph with asymmetries removed.
"""
# graph = import_graph(graph)
if method == "triu":
graph = np.triu(graph)
elif method == "tril":
graph = np.tril(graph)
elif method == "avg":
graph = (np.triu(graph) + np.tril(graph)) / 2
else:
msg = "You have not passed a valid parameter for the method."
raise ValueError(msg)
# A = A + A' - diag(A)
graph = graph + graph.T - np.diag(np.diag(graph))
return graph
[docs]def remove_loops(graph):
"""
A function to remove loops from a graph.
Parameters
----------
graph: object
Either array-like, (n_vertices, n_vertices) numpy matrix,
or an object of type networkx.Graph.
Returns
-------
graph: array-like, shape(n_vertices, n_vertices)
the graph with self-loops (edges between the same node) removed.
"""
graph = import_graph(graph)
graph = graph - np.diag(np.diag(graph))
return graph
[docs]def to_laplace(graph, form="DAD", regularizer=None):
r"""
A function to convert graph adjacency matrix to graph laplacian.
Currently supports I-DAD, DAD, and R-DAD laplacians, where D is the diagonal
matrix of degrees of each node raised to the -1/2 power, I is the
identity matrix, and A is the adjacency matrix.
R-DAD is regularized laplacian: where :math:`D_t = D + regularizer*I`.
Parameters
----------
graph: object
Either array-like, (n_vertices, n_vertices) numpy array,
or an object of type networkx.Graph.
form: {'I-DAD' (default), 'DAD', 'R-DAD'}, string, optional
- 'I-DAD'
Computes :math:`L = I - D*A*D`
- 'DAD'
Computes :math:`L = D*A*D`
- 'R-DAD'
Computes :math:`L = D_t*A*D_t` where :math:`D_t = D + regularizer*I`
regularizer: int, float or None, optional (default=None)
Constant to be added to the diagonal of degree matrix. If None, average
node degree is added. If int or float, must be >= 0. Only used when
``form`` == 'R-DAD'.
Returns
-------
L: numpy.ndarray
2D (n_vertices, n_vertices) array representing graph
laplacian of specified form
References
----------
.. [1] Qin, Tai, and Karl Rohe. "Regularized spectral clustering
under the degree-corrected stochastic blockmodel." In Advances
in Neural Information Processing Systems, pp. 3120-3128. 2013
"""
valid_inputs = ["I-DAD", "DAD", "R-DAD"]
if form not in valid_inputs:
raise TypeError("Unsuported Laplacian normalization")
A = import_graph(graph)
if not is_almost_symmetric(A):
raise ValueError("Laplacian not implemented/defined for directed graphs")
D_vec = np.sum(A, axis=0)
# regularize laplacian with parameter
# set to average degree
if form == "R-DAD":
if regularizer is None:
regularizer = np.mean(D_vec)
elif not isinstance(regularizer, (int, float)):
raise TypeError(
"Regularizer must be a int or float, not {}".format(type(regularizer))
)
elif regularizer < 0:
raise ValueError("Regularizer must be greater than or equal to 0")
D_vec += regularizer
with np.errstate(divide="ignore"):
D_root = 1 / np.sqrt(D_vec) # this is 10x faster than ** -0.5
D_root[np.isinf(D_root)] = 0
D_root = np.diag(D_root) # just change to sparse diag for sparse support
if form == "I-DAD":
L = np.diag(D_vec) - A
L = D_root @ L @ D_root
elif form == "DAD" or form == "R-DAD":
L = D_root @ A @ D_root
return symmetrize(L, method="avg") # sometimes machine prec. makes this necessary
[docs]def is_fully_connected(graph):
r"""
Checks whether the input graph is fully connected in the undirected case
or weakly connected in the directed case.
Connected means one can get from any vertex u to vertex v by traversing
the graph. For a directed graph, weakly connected means that the graph
is connected after it is converted to an unweighted graph (ignore the
direction of each edge)
Parameters
----------
graph: nx.Graph, nx.DiGraph, nx.MultiDiGraph, nx.MultiGraph, np.ndarray
Input graph in any of the above specified formats. If np.ndarray,
interpreted as an :math:`n \times n` adjacency matrix
Returns
-------
boolean: True if the entire input graph is connected
References
----------
http://mathworld.wolfram.com/ConnectedGraph.html
http://mathworld.wolfram.com/WeaklyConnectedDigraph.html
"""
if type(graph) is np.ndarray:
if is_symmetric(graph):
g_object = nx.Graph()
else:
g_object = nx.DiGraph()
graph = nx.from_numpy_array(graph, create_using=g_object)
if type(graph) in [nx.Graph, nx.MultiGraph]:
return nx.is_connected(graph)
elif type(graph) in [nx.DiGraph, nx.MultiDiGraph]:
return nx.is_weakly_connected(graph)
[docs]def get_lcc(graph, return_inds=False):
r"""
Finds the largest connected component for the input graph.
The largest connected component is the fully connected subgraph
which has the most nodes.
Parameters
----------
graph: nx.Graph, nx.DiGraph, nx.MultiDiGraph, nx.MultiGraph, np.ndarray
Input graph in any of the above specified formats. If np.ndarray,
interpreted as an :math:`n \times n` adjacency matrix
return_inds: boolean, default: False
Whether to return a np.ndarray containing the indices in the original
adjacency matrix that were kept and are now in the returned graph.
Ignored when input is networkx object
Returns
-------
graph: nx.Graph, nx.DiGraph, nx.MultiDiGraph, nx.MultiGraph, np.ndarray
New graph of the largest connected component of the input parameter.
inds: (optional)
Indices from the original adjacency matrix that were kept after taking
the largest connected component
"""
input_ndarray = False
if type(graph) is np.ndarray:
input_ndarray = True
if is_symmetric(graph):
g_object = nx.Graph()
else:
g_object = nx.DiGraph()
graph = nx.from_numpy_array(graph, create_using=g_object)
if type(graph) in [nx.Graph, nx.MultiGraph]:
lcc_nodes = max(nx.connected_components(graph), key=len)
elif type(graph) in [nx.DiGraph, nx.MultiDiGraph]:
lcc_nodes = max(nx.weakly_connected_components(graph), key=len)
lcc = graph.subgraph(lcc_nodes).copy()
lcc.remove_nodes_from([n for n in lcc if n not in lcc_nodes])
if return_inds:
nodelist = np.array(list(lcc_nodes))
if input_ndarray:
lcc = nx.to_numpy_array(lcc)
if return_inds:
return lcc, nodelist
return lcc
[docs]def get_multigraph_union_lcc(graphs, return_inds=False):
r"""
Finds the union of all multiple graphs, then compute the largest connected
component.
Parameters
----------
graphs: list or np.ndarray
List of array-like, (n_vertices, n_vertices), or list of np.ndarray
nx.Graph, nx.DiGraph, nx.MultiDiGraph, nx.MultiGraph.
return_inds: boolean, default: False
Whether to return a np.ndarray containing the indices in the original
adjacency matrix that were kept and are now in the returned graph.
Ignored when input is networkx object
Returns
-------
out : list or np.ndarray
If input was a list
"""
if isinstance(graphs, list):
if not isinstance(graphs[0], np.ndarray):
raise NotImplementedError
out = [import_graph(g) for g in graphs]
if len(set(map(np.shape, out))) != 1:
msg = "All input graphs must have the same size"
raise ValueError(msg)
bar = np.stack(out).mean(axis=0)
elif isinstance(graphs, np.ndarray):
shape = graphs.shape
if shape[1] != shape[2]:
msg = "Input graphs must be square"
raise ValueError(msg)
bar = graphs.mean(axis=0)
else:
msg = "Expected list or np.ndarray, but got {} instead.".format(type(graphs))
raise ValueError(msg)
_, idx = get_lcc(bar, return_inds=True)
idx = np.array(idx)
if isinstance(graphs, np.ndarray):
graphs[:, idx[:, None], idx]
elif isinstance(graphs, list):
if isinstance(graphs[0], np.ndarray):
graphs = [g[idx[:, None], idx] for g in graphs]
if return_inds:
return graphs, idx
return graphs
def get_multigraph_intersect_lcc(graphs, return_inds=False):
r"""
Finds the intersection of multiple graphs's largest connected components.
Computes the largest connected component for each graph that was input, and
takes the intersection over all of these resulting graphs. Note that this
does not guarantee finding the largest graph where every node is shared among
all of the input graphs.
Parameters
----------
graphs: list or np.ndarray
if list, each element must be an :math:`n \times n` np.ndarray adjacency matrix
return_inds: boolean, default: False
Whether to return a np.ndarray containing the indices in the original
adjacency matrix that were kept and are now in the returned graph.
Ignored when input is networkx object
Returns
-------
graph: nx.Graph, nx.DiGraph, nx.MultiDiGraph, nx.MultiGraph, np.ndarray
New graph of the largest connected component of the input parameter.
inds: (optional)
Indices from the original adjacency matrix that were kept after taking
the largest connected component
"""
lcc_by_graph = []
inds_by_graph = []
for graph in graphs:
lcc, inds = get_lcc(graph, return_inds=True)
lcc_by_graph.append(lcc)
inds_by_graph.append(inds)
inds_intersection = reduce(np.intersect1d, inds_by_graph)
new_graphs = []
for graph in graphs:
if type(graph) is np.ndarray:
lcc = graph[inds_intersection, :][:, inds_intersection]
else:
lcc = graph.subgraph(inds_intersection).copy()
lcc.remove_nodes_from([n for n in lcc if n not in inds_intersection])
new_graphs.append(lcc)
# this is not guaranteed be connected after one iteration because taking the
# intersection of nodes among graphs can cause some components to become
# disconnected, so, we check for this and run again if necessary
recurse = False
for new_graph in new_graphs:
if not is_fully_connected(new_graph):
recurse = True
break
if recurse:
new_graphs, new_inds_intersection = get_multigraph_intersect_lcc(
new_graphs, return_inds=True
)
# new inds intersection are the indices of new_graph that were kept on recurse
# need to do this because indices could have shifted during recursion
if type(graphs[0]) is np.ndarray:
inds_intersection = inds_intersection[new_inds_intersection]
else:
inds_intersection = new_inds_intersection
if type(graphs) != list:
new_graphs = np.stack(new_graphs)
if return_inds:
return new_graphs, inds_intersection
else:
return new_graphs
[docs]def augment_diagonal(graph, weight=1):
r"""
Replaces the diagonal of adjacency matrix with
:math:`\frac{degree}{nverts - 1}` for the degree associated
with each node.
For directed graphs, the degree used is the out degree (number) of
edges leaving the vertex. Ignores self-loops when calculating degree
Parameters
----------
graph: nx.Graph, nx.DiGraph, nx.MultiDiGraph, nx.MultiGraph, np.ndarray
Input graph in any of the above specified formats. If np.ndarray,
interpreted as an :math:`n \times n` adjacency matrix
"""
graph = import_graph(graph)
graph = remove_loops(graph)
divisor = graph.shape[0] - 1
# use out degree for directed graph
# ignore self loops in either case
degrees = np.count_nonzero(graph, axis=1)
diag = weight * degrees / divisor
graph += np.diag(diag)
return graph
def binarize(graph):
"""
Binarize the input adjacency matrix
"""
graph = import_graph(graph)
graph[graph != 0] = 1
return graph
def cartprod(*arrays):
"""
Compute the cartesian product of multiple arrays
"""
N = len(arrays)
return np.transpose(
np.meshgrid(*arrays, indexing="ij"), np.roll(np.arange(N + 1), -1)
).reshape(-1, N)
```