Source code for pygsp.graphs.graph

# -*- coding: utf-8 -*-

from pygsp.utils import build_logger
from pygsp.graphs import gutils

import numpy as np
import scipy as sp
from scipy import sparse

from collections import Counter

[docs]class Graph(object): r""" The main graph object. It is used to initialize by default every missing field of the subclass graphs. It can also be used alone to initialize customs graphs. Parameters ---------- W : sparse matrix or ndarray (data is float) Weight matrix. Mandatory. gtype : string Graph type (default is "unknown") lap_type : string Laplacian type (default is 'combinatorial') coords : ndarray Coordinates of the vertices (default is None) plotting : dict Dictionnary containing the plotting parameters Fields ------ A graph contains the following fields: N : the number of nodes (also called vertices sometimes) in the graph. They represent the different points between which connections may occur. Ne : the number of edges (also called links sometimes) in the graph. They reprensent the actual connections between the nodes. W : the weight matrix contains the weights of the connections. It is represented as a NxN matrix of floats. W_i,j = 0 means that there is no connection from i to j. A : the adjacency matrix defines which edges exist on the graph. It is represented as a NxN matrix of booleans. A_i,j is True if W_i,j > 0. d : the degree vector of the vertices. It is represented as a Nx1 vector counting the number of connections that each node possesses. gtype : the graph type is a short description of the graph object. directed : the flag to assess if the graph is directed or not. In this framework, we consider that a graph is directed if and only if its weight matrix is non symmetric. L : the laplacian matrix. It is represented as a NxN matrix computed from W. lap_type : the laplacian type determine which kind of laplacian to compute. From a given matrix W, there exist several laplacians that could be computed. coords : the coordinates of the vertices in the 2D or 3D space for plotting. plotting : all the plotting parameters go here. They depend on the library used for plotting. Examples -------- >>> from pygsp import graphs >>> import numpy as np >>> W = np.arange(4).reshape(2, 2) >>> G = graphs.Graph(W) """ def __init__(self, W, gtype='unknown', lap_type='combinatorial', coords=None, plotting={}, **kwargs): self.logger = build_logger(__name__, **kwargs) shapes = np.shape(W) if len(shapes) != 2 or shapes[0] != shapes[1]: self.logger.error('W has incorrect shape {}'.format(shapes)) self.N = shapes[0] self.W = sparse.lil_matrix(W) gutils.check_weights(self.W) self.A = self.W > 0 self.Ne = self.W.nnz self.d = self.A.sum(axis=1) self.gtype = gtype self.lap_type = lap_type self.is_connected() if not self.connected: self.logger.warning('Graph is not connected!') self.create_laplacian(lap_type) if isinstance(coords, np.ndarray) and 2 <= len(np.shape(coords)) <= 3: self.coords = coords else: self.coords = np.ndarray(None) # Plotting default parameters self.plotting = {'vertex_size': 10, 'edge_width': 1, 'edge_style': '-', 'vertex_color': 'b'} if isinstance(plotting, dict): self.plotting.update(plotting)
[docs] def update_graph_attr(self, *args, **kwargs): r""" Recompute some attribute of the graph. Parameters ---------- args: list of string the arguments that will be not changed and not re-compute. kwargs: Dictionnary The arguments with their new value. Return ------ The same Graph with some updated values. Note ---- This method is usefull if you want to give a new weight matrix (W) and compute the adjacency matrix (A) and more again. The valid attributes are ['W', 'A', 'N', 'd', 'Ne', 'gtype', 'directed', 'coords', 'lap_type', 'L', 'plotting'] Examples -------- >>> from pygsp import graphs >>> G = graphs.Ring(N=10) >>> newW = G.W >>> newW[1] = 1 >>> G.update_graph_attr('N', 'd', W=newW) Updates all attributes of G excepted 'N' and 'd' """ graph_attr = {} valid_attributes = ['W', 'A', 'N', 'd', 'Ne', 'gtype', 'directed', 'coords', 'lap_type', 'L', 'plotting'] for i in args: if i in valid_attributes: graph_attr[i] = getattr(self, i) else: self.logger.warning('Your attribute {} do not figure is the valid_attributes who are {}'.format(i, valid_attributes)) for i in kwargs: if i in valid_attributes: if i in graph_attr:'You already give this attribute in the args. Therefore, it will not be recaculate.') else: graph_attr[i] = kwargs[i] else: self.logger.warning('Your attribute {} do not figure is the valid_attributes who are {}'.format(i, valid_attributes)) from nngraphs import NNGraph if isinstance(self, NNGraph): super(NNGraph, self).__init__(**graph_attr) else: super(type(self), self).__init__(**graph_attr)
[docs] def copy_graph_attributes(self, Gn, ctype=True): r""" Copy some parameters of the graph into a given one. Parameters ----------: G : Graph structure ctype : bool Flag to select what to copy (Default is True) Gn : Graph structure The graph where the parameters will be copied Returns ------- Gn : Partial graph structure Examples -------- >>> from pygsp import graphs >>> Torus = graphs.Torus() >>> G = graphs.TwoMoons() >>> G.copy_graph_attributes(ctype=False, Gn=Torus); """ if hasattr(self, 'plotting'): Gn.plotting = self.plotting if ctype: if hasattr(self, 'coords'): Gn.coords = self.coords else: if hasattr(Gn.plotting, 'limits'): del Gn.plotting['limits'] if hasattr(self, 'lap_type'): Gn.lap_type = self.lap_type Gn.create_laplacian()
[docs] def set_coords(self, kind='ring2D', **kwargs): r""" Set coordinates for the vertices. Parameters ---------- kind : string The kind of display. Default is 'ring2D'. Accepting ['community2D', 'manual', 'random2D', 'random3D', 'ring2D', 'spring']. coords : np.ndarray An array of coordinates in 2D or 3D. Used only if kind is manual. Set the coordinates to this array as is. Examples -------- >>> from pygsp import graphs >>> G = graphs.ErdosRenyi() >>> G.set_coords() >>> G.plot() """ if kind not in ['community2D', 'manual', 'random2D', 'random3D', 'ring2D', 'spring']: raise ValueError('Unexpected kind argument. Got {}.'.format(kind)) if kind == 'manual': coords = kwargs.pop('coords', None) if isinstance(coords, list): coords = np.array(coords) if isinstance(coords, np.ndarray) and len(coords.shape) == 2 and \ coords.shape[0] == self.N and 2 <= coords.shape[1] <= 3: self.coords = coords else: raise ValueError('Expecting coords to be a list or ndarray of size Nx2 or Nx3.') elif kind == 'ring2D': tmp = np.arange(self.N).reshape(self.N, 1) self.coords = np.concatenate((np.cos(tmp*2*np.pi/self.N), np.sin(tmp*2*np.pi/self.N)), axis=1) elif kind == 'random2D': self.coords = np.random.rand(self.N, 2) elif kind == 'random3D': self.coords = np.random.rand(self.N, 3) elif kind == 'spring': self.coords = self._fruchterman_reingold_layout(**kwargs) elif kind == 'community2D': if not hasattr(self, 'info') or 'node_com' not in ValueError('Missing arguments to the graph to be able to compute community coordinates.') if 'world_rad' not in['world_rad'] = np.sqrt(self.N) if 'comm_sizes' not in counts = Counter(['node_com'])['comm_sizes'] = np.array([cnt[1] for cnt in sorted(counts.items())]) Nc =['comm_sizes'].shape[0]['com_coords'] =['world_rad'] * np.array(list(zip( np.cos(2 * np.pi * np.arange(1, Nc + 1) / Nc), np.sin(2 * np.pi * np.arange(1, Nc + 1) / Nc)))) coords = np.random.rand(self.N, 2) # nodes' coordinates inside the community self.coords = np.array([[elem[0] * np.cos(2 * np.pi * elem[1]), elem[0] * np.sin(2 * np.pi * elem[1])] for elem in coords]) for i in range(self.N): # set coordinates as an offset from the center of the community it belongs to comm_idx =['node_com'][i] comm_rad = np.sqrt(['comm_sizes'][comm_idx]) self.coords[i] =['com_coords'][comm_idx] + comm_rad * self.coords[i]
[docs] def subgraph(self, ind): r""" Create a subgraph from G keeping only the given indices. Parameters ---------- ind : list Nodes to keep Returns ------- sub_G : Graph Subgraph Examples -------- >>> from pygsp import graphs >>> import numpy as np >>> W = np.arange(16).reshape(4, 4) >>> G = graphs.Graph(W) >>> ind = [1, 3] >>> sub_G = G.subgraph(ind) """ if not isinstance(ind, list) and not isinstance(ind, np.ndarray): raise TypeError('The indices must be a list or a ndarray.') N = len(ind) sub_W = self.W.tocsr()[ind, :].tocsc()[:, ind] return Graph(sub_W, gtype="sub-{}".format(self.gtype))
[docs] def is_connected(self, force_recompute=False): r""" Check the strong connectivity of the input graph. It uses DFS travelling on graph to ensure that each node is visited. For undirected graphs, starting at any vertex and trying to access all others is enough. For directed graphs, one needs to check that a random vertex is accessible by all others and can access all others. Thus, we can transpose the adjacency matrix and compute again with the same starting point in both phases. Parameters --------- force_recompute: bool Force to recompute the connectivity if already known. Returns ------- connected : bool A bool value telling if the graph is connected. Examples -------- >>> from scipy import sparse >>> from pygsp import graphs >>> W = sparse.rand(10, 10, 0.2) >>> G = graphs.Graph(W=W) >>> connected = G.is_connected() """ if hasattr(self, 'force_recompute'): if force_recompute: self.logger.warning("Connectivity for this graph is already known. Recomputing.") else: self.logger.error("Connectivity for this graph is already known. Stopping.") return self.connected if not hasattr(self, 'directed'): self.is_directed() if self.A.shape[0] != self.A.shape[1]: self.logger.error('Inconsistant shape to test connectedness. Set to False.') self.connected = False return False for adj_matrix in [self.A, self.A.T] if self.directed else [self.A]: visited = np.zeros(self.A.shape[0], dtype=bool) stack = set([0]) while len(stack): v = stack.pop() if not visited[v]: visited[v] = True # Add indices of nodes not visited yet and accessible from v stack.update(set([idx for idx in adj_matrix[v, :].nonzero()[1] if not visited[idx]])) if not visited.all(): self.connected = False return False self.connected = True return True
[docs] def is_directed(self, force_recompute=False): r""" Define if the graph has directed edges. Parameters --------- force_recompute: bool Force to recompute the directedness if already known. Notes ----- Can also be used to check if a matrix is symmetrical Examples -------- >>> from scipy import sparse >>> from pygsp import graphs >>> W = sparse.rand(10, 10, 0.2) >>> G = graphs.Graph(W=W) >>> directed = G.is_directed() """ if hasattr(self, 'force_recompute'): if force_recompute: self.logger.warning("Directedness for this graph is already known. Recomputing.") else: self.logger.error("Directedness for this graph is already known. Stopping.") return self.directed if np.diff(np.shape(self.W))[0]: raise ValueError("Matrix dimensions mismatch, expecting square matrix.") is_dir = np.abs(self.W - self.W.T).sum() != 0 self.directed = is_dir
[docs] def extract_components(self): r""" Split the graph into several connected components. See the doc of `is_connected` for the method used to determine connectedness. Returns ------- graphs : list A list of graph structures. Each having its own node list and weight matrix. If the graph is directed, add into the info parameter the information about the source nodes and the sink nodes. Examples -------- >>> from scipy import sparse >>> from pygsp import graphs >>> W = sparse.rand(10, 10, 0.2) >>> G = graphs.Graph(W=W) >>> components = G.extract_components() >>> has_sinks = 'sink' in components[0].info >>> sinks_0 = components[0].info['sink'] if has_sinks else [] """ if not hasattr(self, 'directed'): self.is_directed() if self.A.shape[0] != self.A.shape[1]: self.logger.error('Inconsistant shape to extract components. Square matrix required.') return None if self.directed: raise NotImplementedError('Focusing on non directed graphs first.') graphs = [] visited = np.zeros(self.A.shape[0], dtype=bool) indices = [] while not visited.all(): stack = set([np.nonzero(visited == False)[0][0]]) comp = [] while len(stack): v = stack.pop() if not visited[v]: comp.append(v) visited[v] = True # Add indices of nodes not visited yet and accessible from v stack.update(set([idx for idx in self.A[v, :].nonzero()[1] if not visited[idx]])) comp = sorted(comp)'Constructing subgraph for component of size {}.'.format(len(comp))) G = self.subgraph(comp) = {'orig_idx': comp} graphs.append(G) return graphs
[docs] def compute_fourier_basis(self, smallest_first=True, force_recompute=False, **kwargs): r""" Compute the fourier basis of the graph. Parameters ---------- smallest_first: bool Define the order of the eigenvalues. Default is smallest first (True). force_recompute: bool Force to recompute the Fourier basis if already existing. Note ---- 'G.compute_fourier_basis()' computes a full eigendecomposition of the graph Laplacian G.L: .. L = U Lambda U* .. math:: {\cal L} = U \Lambda U^* where $\Lambda$ is a diagonal matrix of the Laplacian eigenvalues. *G.e* is a column vector of length *G.N* containing the Laplacian eigenvalues. The largest eigenvalue is stored in *G.lmax*. The eigenvectors are stored as column vectors of *G.U* in the same order that the eigenvalues. Finally, the coherence of the Fourier basis is in **. Example ------- >>> from pygsp import graphs >>> N = 50 >>> G = graphs.Sensor(N) >>> G.compute_fourier_basis() References ---------- cite ┬┤chung1997spectral┬┤ """ if hasattr(self, 'e') or hasattr(self, 'U'): if force_recompute: self.logger.warning("This graph already has a Fourier basis. Recomputing.") else: self.logger.error("This graph already has a Fourier basis. Stopping.") return if self.N > 3000: self.logger.warning("Performing full eigendecomposition of a large " "matrix may take some time.") if not hasattr(self, 'L'): raise AttributeError("Graph Laplacian is missing") eigenvectors, eigenvalues, _ = sp.linalg.svd(self.L.todense()) inds = np.argsort(eigenvalues) if not smallest_first: inds = inds[::-1] self.e = np.sort(eigenvalues) self.lmax = np.max(self.e) self.U = eigenvectors[:, inds] = np.max(np.abs(self.U))
[docs] def create_laplacian(self, lap_type='combinatorial'): r""" Create a new graph laplacian. Parameters ---------- lap_type : string The laplacian type to use. Default is "combinatorial". """ if np.shape(self.W) == (1, 1): self.L = sparse.lil_matrix(0) return if lap_type in ['combinatorial', 'normalized', 'none']: self.lap_type = lap_type else: raise AttributeError('Unknown laplacian type!') if self.directed: if lap_type == 'combinatorial': L = 0.5*(sparse.diags(np.ravel(self.W.sum(0)), 0) + sparse.diags(np.ravel(self.W.sum(1)), 0) - self.W - self.W.T).tocsc() elif lap_type == 'normalized': raise NotImplementedError('Yet. Ask Nathanael.') elif lap_type == 'none': L = sparse.lil_matrix(0) else: if lap_type == 'combinatorial': L = (sparse.diags(np.ravel(self.W.sum(1)), 0) - self.W).tocsc() elif lap_type == 'normalized': D = sparse.diags(np.ravel(np.power(self.W.sum(1), -0.5)), 0).tocsc() L = sparse.identity(self.N) - D * self.W * D elif lap_type == 'none': L = sparse.lil_matrix(0) self.L = L
[docs] def estimate_lmax(self, force_recompute=False): r""" Estimate the maximal eigenvalue. Parameters ---------- force_recompute : boolean Force to recompute the maximal eigenvalue. Default is false. Examples -------- Just define a graph and apply the estimation on it. >>> from pygsp import graphs >>> import numpy as np >>> W = np.arange(16).reshape(4, 4) >>> G = graphs.Graph(W) >>> G.estimate_lmax() """ if hasattr(self, 'lmax'): if force_recompute: self.logger.error('Already computed lmax. Recomputing.') else: self.logger.error('Already computed lmax. Stopping.') return try: # On robustness purposes, increasing the error by 1 percent lmax = 1.01 * sparse.linalg.eigs(self.L, k=1, tol=5e-3, ncv=10)[0][0] except sparse.linalg.ArpackNoConvergence: self.logger.warning('GSP_ESTIMATE_LMAX: Cannot use default method.') lmax = 2. * np.max(self.d) lmax = np.real(lmax) self.lmax = lmax.sum()
[docs] def plot(self, **kwargs): r""" Plot the graph. See plotting doc. """ from pygsp import plotting plotting.plot_graph(self, **kwargs)
[docs] def plot_signal(self, signal, **kwargs): r""" Plot the graph signal. See plotting doc. """ from pygsp import plotting plotting.plot_signal(self, signal, **kwargs)
[docs] def show_spectrogramm(self, **kwargs): r""" Plot the spectrogramm for the graph object. See plotting doc on spectrogramm. """ from pygsp import plotting plotting.plot_spectrogramm(self, **kwargs)
def _fruchterman_reingold_layout(self, dim=2, k=None, pos=None, fixed=[], iterations=50, scale=1.0, center=None): # Position nodes using Fruchterman-Reingold force-directed algorithm. if center is None: center = np.zeros((1, dim)) if np.shape(center)[1] != dim: self.logger.error('Spring coordinates : center has wrong size.') center = np.zeros((1, dim)) dom_size = 1. if pos is not None: # Determine size of existing domain to adjust initial positions dom_size = np.max(pos) shape = (self.N, dim) pos_arr = np.random.random(shape) * dom_size + center for i in range(self.N): pos_arr[i] = np.asarray(pos[i]) else: pos_arr = None if k is None and fixed is not None: # We must adjust k by domain size for layouts that are not near 1x1 k = dom_size / np.sqrt(self.N) pos = _sparse_fruchterman_reingold(self.A, dim, k, pos_arr, fixed, iterations) if fixed is None: pos = _rescale_layout(pos, scale=scale) + center return pos
def _sparse_fruchterman_reingold(A, dim=2, k=None, pos=None, fixed=None, iterations=50): # Position nodes in adjacency matrix A using Fruchterman-Reingold nnodes = A.shape[0] # make sure we have a LIst of Lists representation try: A = A.tolil() except: A = (coo_matrix(A)).tolil() if pos is None: # random initial positions pos = np.random.random((nnodes, dim)) # no fixed nodes if fixed is None: fixed = [] # optimal distance between nodes if k is None: k = np.sqrt(1.0/nnodes) # simple cooling scheme. # linearly step down by dt on each iteration so last iteration is size dt. t = 0.1 dt = t/float(iterations+1) displacement = np.zeros((dim, nnodes)) for iteration in range(iterations): displacement *= 0 # loop over rows for i in range(nnodes): if i in fixed: continue # difference between this row's node position and all others delta = (pos[i]-pos).T # distance between points distance = np.sqrt((delta**2).sum(axis=0)) # enforce minimum distance of 0.01 distance = np.where(distance < 0.01, 0.01, distance) # the adjacency matrix row Ai = np.asarray(A[i, :].toarray()) # displacement "force" displacement[:, i] += \ (delta*(k*k/distance**2-Ai*distance/k)).sum(axis=1) # update positions length = np.sqrt((displacement**2).sum(axis=0)) length = np.where(length < 0.01, 0.1, length) pos += (displacement*t/length).T # cool temperature t -= dt return pos def _rescale_layout(pos, scale=1): # rescale to (-scale, scale) in all axes # shift origin to (0,0) lim = 0 # max coordinate for all axes for i in range(pos.shape[1]): pos[:, i] -= pos[:, i].mean() lim = max(pos[:, i].max(), lim) # rescale to (-scale,scale) in all directions, preserves aspect for i in range(pos.shape[1]): pos[:, i] *= scale/lim return pos