コード例 #1
0
ファイル: graph_connectivity.py プロジェクト: openube/NNGT
def distance_rule(scale, rule="exp", shape=None, neuron_density=1000., nodes=0,
                  density=0.1, edges=-1, avg_deg=-1., weighted=True,
                  directed=True, multigraph=False, name="DR", positions=None,
                  population=None, from_graph=None, **kwargs):
    """
    Create a graph using a 2D distance rule to create the connection between
    neurons. Available rules are linear (@todo) and exponential.

    Parameters
    ----------
    scale : float
        Characteristic scale for the distance rule. E.g for linear distance-
        rule, :math:`P(i,j) \propto (1-d_{ij}/scale))`, whereas for the
        exponential distance-rule, :math:`P(i,j) \propto e^{-d_{ij}/scale}`.
    rule : string, optional (default: 'exp')
        Rule that will be apply to draw the connections between neurons.
        Choose among "exp" (exponential), "lin" (linear, not implemented yet),
        "power" (power-law, not implemented yet).
    shape : :class:`~nngt.core.Shape`, optional (default: None)
        Shape of the neurons' environment. If not specified, a square will be
        created with the appropriate dimensions for the number of neurons and
        the neuron spatial density.
    neuron_density : float, optional (default: 1000.)
        Density of neurons in space (:math:`neurons \cdot mm^{-2}).
    nodes : int, optional (default: None)
        The number of nodes in the graph.
    density: double, optional (default: 0.1)
        Structural density given by `edges` / (`nodes`*`nodes`).
    edges : int (optional)
        The number of edges between the nodes
    avg_deg : double, optional
        Average degree of the neurons given by `edges` / `nodes`.
    weighted : bool, optional (default: True)
        @todo
        Whether the graph edges have weights.
    directed : bool, optional (default: True)
        Whether the graph is directed or not.
    multigraph : bool, optional (default: False)
        Whether the graph can contain multiple edges between two
        nodes.
    name : string, optional (default: "ER")
        Name of the created graph.
    positions : :class:`numpy.ndarray`, optional (default: None)
        A 2D or 3D array containing the positions of the neurons in space.
    population : :class:`~nngt.NeuralPop`, optional (default: None)
        Population of neurons defining their biological properties (to create a
        :class:`~nngt.Network`).
    from_graph : :class:`Graph` or subclass, optional (default: None)
        Initial graph whose nodes are to be connected.
    """
    # set node number and library graph
    graph_obj_dr, graph_dr = None, from_graph
    if graph_dr is not None:
        nodes = graph_dr.node_nb()
        graph_dr.clear_edges()
        graph_obj_dr = graph_dr.graph
    else:
        nodes = population.size if population is not None else nodes
        graph_obj_dr = GraphObject(nodes, directed=directed)
    # generate container
    h = w = np.sqrt(float(nodes)/neuron_density)
    if graph_dr is None:
        shape = shape if shape is not None else Shape.rectangle(None,h,w)
        graph_dr = SpatialGraph(name=name, libgraph=graph_obj_dr, shape=shape,
                                **kwargs)
    else:
        if not issubclass(graph_dr.__class__, SpatialGraph):
            shape = shape if shape is not None else Shape.rectangle(self,h,w)
            SpatialGraph.make_spatial(graph_dr, shape, positions)
    # add edges
    positions = graph_dr.position
    ia_edges = None
    if nodes > 1:
        ids = range(nodes)
        ia_edges = _distance_rule(ids, ids, density, edges, avg_deg, scale,
                                  rule, shape, positions, directed, multigraph)
        graph_obj_dr.new_edges(ia_edges)
    # set options
    if weighted:
        graph_dr.set_weights()
    if issubclass(graph_dr.__class__, Network):
        Connections.delays(graph_dr)
    elif population is not None:
        Network.make_network(graph_dr, population)
    return graph_dr
コード例 #2
0
ファイル: graph_connectivity.py プロジェクト: openube/NNGT
def erdos_renyi(nodes=0, density=0.1, edges=-1, avg_deg=-1., reciprocity=-1.,
                weighted=True, directed=True, multigraph=False, name="ER",
                shape=None, positions=None, population=None, from_graph=None,
                **kwargs):
    """
    Generate a random graph as defined by Erdos and Renyi but with a
    reciprocity that can be chosen.

    Parameters
    ----------
    nodes : int, optional (default: None)
        The number of nodes in the graph.
    density : double, optional (default: 0.1)
        Structural density given by `edges` / `nodes`:math:`^2`.
    edges : int (optional)
        The number of edges between the nodes
    avg_deg : double, optional
        Average degree of the neurons given by `edges` / `nodes`.
    reciprocity : double, optional (default: -1 to let it free)
        Fraction of edges that are bidirectional (only for
        directed graphs -- undirected graphs have a reciprocity of 1 by
        definition)
    weighted : bool, optional (default: True)
        Whether the graph edges have weights.
    directed : bool, optional (default: True)
        Whether the graph is directed or not.
    multigraph : bool, optional (default: False)
        Whether the graph can contain multiple edges between two
        nodes.
    name : string, optional (default: "ER")
        Name of the created graph.
    shape : :class:`~nngt.core.Shape`, optional (default: None)
        Shape of the neurons' environment.
    positions : :class:`numpy.ndarray`, optional (default: None)
        A 2D or 3D array containing the positions of the neurons in space.
    population : :class:`~nngt.NeuralPop`, optional (default: None)
        Population of neurons defining their biological properties (to create a
        :class:`~nngt.Network`).
    from_graph : :class:`Graph` or subclass, optional (default: None)
        Initial graph whose nodes are to be connected.

    Returns
    -------
    graph_er : :class:`~nngt.Graph`, or subclass
        A new generated graph or the modified `from_graph`.

    Notes
    -----
    `nodes` is required unless `from_graph` or `population` is provided.
    If an `from_graph` is provided, all preexistant edges in the
    object will be deleted before the new connectivity is implemented.
    """
    # set node number and library graph
    graph_obj_er, graph_er = None, from_graph
    if graph_er is not None:
        nodes = graph_er.node_nb()
        graph_er.clear_edges()
        graph_obj_er = graph_er.graph
    else:
        nodes = population.size if population is not None else nodes
        graph_obj_er = GraphObject(nodes, directed=directed)
    # add edges
    ia_edges = None
    if nodes > 1:
        ids = range(nodes)
        ia_edges = _erdos_renyi(ids, ids, density, edges, avg_deg, reciprocity,
                                directed, multigraph)
        graph_obj_er.new_edges(ia_edges)
    # generate container
    if graph_er is None:
        graph_er = Graph(name=name, libgraph=graph_obj_er, **kwargs)
    else:
        graph_er.set_weights()
    # set options
    if issubclass(graph_er.__class__, Network):
        Connections.delays(graph_er)
    elif population is not None:
        Network.make_network(graph_er, population)
    if shape is not None:
        SpatialGraph.make_spatial(graph_er, shape, positions)
    return graph_er
コード例 #3
0
ファイル: graph_connectivity.py プロジェクト: openube/NNGT
def newman_watts(coord_nb, proba_shortcut, nodes=0, directed=True,
                 multigraph=False, name="ER", shape=None, positions=None,
                 population=None, from_graph=None, **kwargs):
    """
    Generate a small-world graph using the Newman-Watts algorithm.
    @todo: generate the edges of a circular graph to not replace the graph
    of the `from_graph` and implement chosen reciprocity.
    
    Parameters
    ----------
    coord_nb : int
        The number of neighbours for each node on the initial topological 
        lattice.
    proba_shortcut : double
        Probability of adding a new random (shortcut) edge for each existing 
        edge on the initial lattice.
    nodes : int, optional (default: None)
        The number of nodes in the graph.
    density: double, optional (default: 0.1)
        Structural density given by `edges` / (`nodes`*`nodes`).
    edges : int (optional)
        The number of edges between the nodes
    avg_deg : double, optional
        Average degree of the neurons given by `edges` / `nodes`.
    weighted : bool, optional (default: True)
        @todo
        Whether the graph edges have weights.
    directed : bool, optional (default: True)
        Whether the graph is directed or not.
    multigraph : bool, optional (default: False)
        Whether the graph can contain multiple edges between two
        nodes.
    name : string, optional (default: "ER")
        Name of the created graph.
    shape : :class:`~nngt.core.Shape`, optional (default: None)
        Shape of the neurons' environment
    positions : :class:`numpy.ndarray`, optional (default: None)
        A 2D or 3D array containing the positions of the neurons in space.
    population : :class:`~nngt.NeuralPop`, optional (default: None)
        Population of neurons defining their biological properties (to create a
        :class:`~nngt.Network`).
    from_graph : :class:`Graph` or subclass, optional (default: None)
        Initial graph whose nodes are to be connected.
    
    Returns
    -------
    graph_nw : :class:`~nngt.Graph` or subclass
    
    Notes
    -----
    `nodes` is required unless `from_graph` or `population` is provided.
    """
    # set node number and library graph
    graph_obj_nw, graph_nw = None, from_graph
    if graph_nw is not None:
        nodes = graph_nw.node_nb()
        graph_nw.clear_edges()
        graph_obj_nw = graph_nw.graph
    else:
        nodes = population.size if population is not None else nodes
        graph_obj_nw = GraphObject(nodes, directed=directed)
    # add edges
    ia_edges = None
    if nodes > 1:
        ids = range(nodes)
        ia_edges = _newman_watts(ids, ids, coord_nb, proba_shortcut, directed,
                                 multigraph)
        graph_obj_nw.new_edges(ia_edges)
    # generate container
    if graph_nw is None:
        graph_nw = Graph(name=name, libgraph=graph_obj_nw, **kwargs)
    else:
        graph_nw.set_weights()
    # set options
    if issubclass(graph_nw.__class__, Network):
        Connections.delays(graph_nw)
    elif population is not None:
        Network.make_network(graph_nw, population)
    if shape is not None:
        SpatialGraph.make_spatial(graph_nw, shape, positions)
    return graph_nw
コード例 #4
0
ファイル: graph_connectivity.py プロジェクト: openube/NNGT
def random_scale_free(in_exp, out_exp, nodes=0, density=0.1, edges=-1,
                      avg_deg=-1, reciprocity=0., weighted=True, directed=True,
                      multigraph=False, name="RandomSF", shape=None, 
                      positions=None, population=None, from_graph=None,
                      **kwargs):
    """
    Generate a free-scale graph of given reciprocity and otherwise
    devoid of correlations.

    Parameters 
    ----------
    in_exp : float
        Absolute value of the in-degree exponent :math:`\gamma_i`, such that
        :math:`p(k_i) \propto k_i^{-\gamma_i}
    out_exp : float
        Absolute value of the out-degree exponent :math:`\gamma_o`, such that
        :math:`p(k_o) \propto k_o^{-\gamma_o}
    nodes : int, optional (default: None)
        The number of nodes in the graph.
    density: double, optional (default: 0.1)
        Structural density given by `edges` / (`nodes`*`nodes`).
    edges : int (optional)
        The number of edges between the nodes
    avg_deg : double, optional
        Average degree of the neurons given by `edges` / `nodes`.
    weighted : bool, optional (default: True)
        @todo
        Whether the graph edges have weights.
    directed : bool, optional (default: True)
        Whether the graph is directed or not.
    multigraph : bool, optional (default: False)
        Whether the graph can contain multiple edges between two
        nodes. can contain multiple edges between two
    name : string, optional (default: "ER")
        Name of the created graph.
    shape : :class:`~nngt.core.Shape`, optional (default: None)
        Shape of the neurons' environment.
    positions : :class:`numpy.ndarray`, optional (default: None)
        A 2D or 3D array containing the positions of the neurons in space.
    population : :class:`~nngt.NeuralPop`, optional (default: None)
        Population of neurons defining their biological properties (to create a
        :class:`~nngt.Network`)
    from_graph : :class:`Graph` or subclass, optional (default: None)
        Initial graph whose nodes are to be connected.

    Returns
    -------
    graph_fs : :class:`~nngt.Graph`
    
    Notes
    -----
    As reciprocity increases, requested values of `in_exp` and `out_exp` will
    be less and less respected as the distribution will converge to a common
    exponent :math:`\gamma = \frac{\gamma_i + \gamma_o}{2}`.
    Parameter `nodes` is required unless `from_graph` or `population` is
    provided.
    """
    # set node number and library graph
    graph_obj_rsf, graph_rsf = None, from_graph
    if graph_rsf is not None:
        nodes = graph_rsf.node_nb()
        graph_rsf.clear_edges()
        graph_obj_rsf = graph_rsf.graph
    else:
        nodes = population.size if population is not None else nodes
        graph_obj_rsf = GraphObject(nodes, directed=directed)
    # add edges
    ia_edges = None
    if nodes > 1:
        ids = range(nodes)
        ia_edges = _random_scale_free(ids, ids, in_exp, out_exp, density,
                          edges, avg_deg, reciprocity, directed, multigraph)
        graph_obj_rsf.new_edges(ia_edges)
    # generate container
    if graph_rsf is None:
        graph_rsf = Graph(name=name, libgraph=graph_obj_rsf, **kwargs)
    else:
        graph_rsf.set_weights()
    # set options
    if issubclass(graph_rsf.__class__, Network):
        Connections.delays(graph_rsf)
    elif population is not None:
        Network.make_network(graph_rsf, population)
    if shape is not None:
        SpatialGraph.make_spatial(graph_rsf, shape, positions)
    return graph_rsf