Convert a networkx to graph-tool graph

.gitignore

__pycache__

__init__.py

from . import nx2gt

nx2gt.py

# code from http://bbengfort.github.io/snippets/2016/06/23/graph-tool-from-networkx.html

import networkx as nx
import graph_tool as gt


def get_prop_type(value, key=None):
    """
    Performs typing and value conversion for the graph_tool PropertyMap class.
    If a key is provided, it also ensures the key is in a format that can be
    used with the PropertyMap. Returns a tuple, (type name, value, key)
    """

    # Deal with the value
    if isinstance(value, bool):
        tname = 'bool'

    elif isinstance(value, int):
        tname = 'float'
        value = float(value)

    elif isinstance(value, float):
        tname = 'float'

    elif isinstance(value, dict):
        tname = 'object'

    else:
        tname = 'string'
        value = str(value)

    return tname, value, key


def nx2gt(nxG):
    """
    Converts a networkx graph to a graph-tool graph.
    """
    # Phase 0: Create a directed or undirected graph-tool Graph
    gtG = gt.Graph(directed=nxG.is_directed())

    # Add the Graph properties as "internal properties"
    for key, value in nxG.graph.items():
        # Convert the value and key into a type for graph-tool
        tname, value, key = get_prop_type(value, key)

        prop = gtG.new_graph_property(tname)  # Create the PropertyMap
        gtG.graph_properties[key] = prop      # Set the PropertyMap
        gtG.graph_properties[key] = value     # Set the actual value

    # Phase 1: Add the vertex and edge property maps
    # Go through all nodes and edges and add seen properties
    # Add the node properties first
    nprops = set()  # cache keys to only add properties once
    for node, data in nxG.nodes(data=True):

        # Go through all the properties if not seen and add them.
        for key, val in data.items():
            if key in nprops:
                continue  # Skip properties already added

            # Convert the value and key into a type for graph-tool
            tname, _, key = get_prop_type(val, key)

            prop = gtG.new_vertex_property(tname)  # Create the PropertyMap
            gtG.vertex_properties[key] = prop      # Set the PropertyMap

            # Add the key to the already seen properties
            nprops.add(key)

    # Also add the node id: in NetworkX a node can be any hashable type, but
    # in graph-tool node are defined as indices. So we capture any strings
    # in a special PropertyMap called 'id' -- modify as needed!
    gtG.vertex_properties['id'] = gtG.new_vertex_property('string')

    # Add the edge properties second
    eprops = set()  # cache keys to only add properties once
    for src, dst, data in nxG.edges(data=True):

        # Go through all the edge properties if not seen and add them.
        for key, val in data.items():
            if key in eprops:
                continue  # Skip properties already added

            # Convert the value and key into a type for graph-tool
            tname, _, key = get_prop_type(val, key)

            prop = gtG.new_edge_property(tname)  # Create the PropertyMap
            gtG.edge_properties[key] = prop      # Set the PropertyMap

            # Add the key to the already seen properties
            eprops.add(key)

    # Phase 2: Actually add all the nodes and vertices with their properties
    # Add the nodes
    vertices = {}  # vertex mapping for tracking edges later
    for node, data in nxG.nodes(data=True):

        # Create the vertex and annotate for our edges later
        v = gtG.add_vertex()
        vertices[node] = v

        # Set the vertex properties, not forgetting the id property
        data['id'] = str(node)
        for key, value in data.items():
            gtG.vp[key][v] = value  # vp is short for vertex_properties

    # Add the edges
    for src, dst, data in nxG.edges(data=True):

        # Look up the vertex structs from our vertices mapping and add edge.
        e = gtG.add_edge(vertices[src], vertices[dst])

        # Add the edge properties
        for key, value in data.items():
            gtG.ep[key][e] = value  # ep is short for edge_properties

    # Done, finally!
    return gtG