#! /usr/bin/env python # -*- coding: utf-8 -*- # # graph_tool -- a general graph manipulation python module # # Copyright (C) 2006-2015 Tiago de Paula Peixoto # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see . """ graph_tool - efficient graph analysis and manipulation ====================================================== Summary ------- .. autosummary:: :nosignatures: Graph GraphView Vertex Edge PropertyMap PropertyArray load_graph group_vector_property ungroup_vector_property infect_vertex_property edge_endpoint_property incident_edges_op perfect_prop_hash value_types show_config This module provides: 1. A :class:`~graph_tool.Graph` class for graph representation and manipulation 2. Property maps for Vertex, Edge or Graph. 3. Fast algorithms implemented in C++. How to use the documentation ---------------------------- Documentation is available in two forms: docstrings provided with the code, and the full documentation available in `the graph-tool homepage `_. We recommend exploring the docstrings using `IPython `_, an advanced Python shell with TAB-completion and introspection capabilities. The docstring examples assume that ``graph_tool.all`` has been imported as ``gt``:: >>> import graph_tool.all as gt Code snippets are indicated by three greater-than signs:: >>> x = x + 1 Use the built-in ``help`` function to view a function's docstring:: >>> help(gt.Graph) Contents -------- """ from __future__ import division, absolute_import, print_function import sys if sys.version_info < (3,): range = xrange __author__ = "Tiago de Paula Peixoto " __copyright__ = "Copyright 2006-2015 Tiago de Paula Peixoto" __license__ = "GPL version 3 or above" __URL__ = "http://graph-tool.skewed.de" # import numpy and scipy before everything to avoid weird segmentation faults # depending on the order things are imported. import numpy import numpy.ma import scipy import scipy.stats from .dl_import import * dl_import("from . import libgraph_tool_core as libcore") __version__ = libcore.mod_info().version from . import io # sets up libcore io routines import sys import os import re import gzip import weakref import copy import textwrap import io if sys.version_info < (3,): import StringIO from .decorators import _wraps, _require, _attrs, _limit_args from inspect import ismethod __all__ = ["Graph", "GraphView", "Vertex", "Edge", "Vector_bool", "Vector_int16_t", "Vector_int32_t", "Vector_int64_t", "Vector_double", "Vector_long_double", "Vector_string", "Vector_size_t", "value_types", "load_graph", "PropertyMap", "group_vector_property", "ungroup_vector_property", "infect_vertex_property", "edge_endpoint_property", "incident_edges_op", "perfect_prop_hash", "seed_rng", "show_config", "PropertyArray", "openmp_enabled", "openmp_get_num_threads", "openmp_set_num_threads", "openmp_get_schedule", "openmp_set_schedule", "__author__", "__copyright__", "__URL__", "__version__"] # this is rather pointless, but it works around a sphinx bug graph_tool = sys.modules[__name__] ################################################################################ # Utility functions ################################################################################ def _prop(t, g, prop): """Return either a property map, or an internal property map with a given name.""" if type(prop) == str: try: pmap = g.properties[(t, prop)] except KeyError: raise KeyError("no internal %s property named: %s" %\ ("vertex" if t == "v" else \ ("edge" if t == "e" else "graph"), prop)) else: pmap = prop if pmap == None: return libcore.any() else: if t != prop.key_type(): names = {'e': 'edge', 'v': 'vertex', 'g': 'graph'} raise ValueError("Expected '%s' property map, got '%s'" % (names[t], names[prop.key_type()])) return pmap._PropertyMap__map.get_map() def _degree(g, name): """Retrieve the degree type from string, or returns the corresponding property map.""" deg = name if name == "in-degree" or name == "in": deg = libcore.Degree.In elif name == "out-degree" or name == "out": deg = libcore.Degree.Out elif name == "total-degree" or name == "total": deg = libcore.Degree.Total else: deg = _prop("v", g, deg) return deg def _type_alias(type_name): alias = {"int8_t": "bool", "boolean": "bool", "short": "int16_t", "int": "int32_t", "long": "int64_t", "long long": "int64_t", "unsigned long": "int64_t", "object": "python::object", "float": "double"} if type_name in value_types(): return type_name if type_name in alias: return alias[type_name] ma = re.compile(r"vector<(.*)>").match(type_name) if ma: t = ma.group(1) if t in alias: return "vector<%s>" % alias[t] raise ValueError("invalid property value type: " + type_name) def _python_type(type_name): type_name = _type_alias(type_name) if "vector" in type_name: ma = re.compile(r"vector<(.*)>").match(type_name) t = ma.group(1) return list, _python_type(t) if "int" in type_name: return int if type_name == "bool": return bool if "double" in type_name: return float if "string" in type_name: return str return object def _gt_type(obj): t = type(obj) if t is numpy.longlong or t is numpy.uint64: return "long long" if issubclass(t, numpy.int16): return "short" if t is int or issubclass(t, numpy.int): return "int" if t is numpy.float128: return "long double" if t is float or issubclass(t, numpy.float): return "double" if t is str: return "string" if t is bool: return "bool" if issubclass(t, list) or issubclass(t, numpy.ndarray): return "vector<%s>" % _gt_type(obj[0]) return "object" def _convert(prop, val): # attempt to convert to a compatible python type. This is useful, # for instance, when dealing with numpy types. vtype = _python_type(prop.value_type()) if type(vtype) is tuple: return [vtype[1](x) for x in val] if vtype is object: return val return vtype(val) def show_config(): """Show ``graph_tool`` build configuration.""" info = libcore.mod_info() print("version:", info.version) print("gcc version:", info.gcc_version) print("compilation flags:", info.cxxflags) print("install prefix:", info.install_prefix) print("python dir:", info.python_dir) print("graph filtering:", libcore.graph_filtering_enabled()) print("openmp:", libcore.openmp_enabled()) print("uname:", " ".join(os.uname())) def terminal_size(): import fcntl, termios, struct h, w, hp, wp = struct.unpack('HHHH', fcntl.ioctl(0, termios.TIOCGWINSZ, struct.pack('HHHH', 0, 0, 0, 0))) return w, h ################################################################################ # Property Maps ################################################################################ class PropertyArray(numpy.ndarray): """This is a :class:`~numpy.ndarray` subclass which keeps a reference of its :class:`~graph_tool.PropertyMap` owner, and detects if the underlying data has been invalidated.""" __array_priority__ = -10 def _get_pmap(self): return self._prop_map def _set_pmap(self, value): self._prop_map = value prop_map = property(_get_pmap, _set_pmap, doc=":class:`~graph_tool.PropertyMap` owner instance.") def __new__(cls, input_array, prop_map): obj = numpy.asarray(input_array).view(cls) obj.prop_map = prop_map # check if data really belongs to property map if (prop_map._get_data().__array_interface__['data'][0] != obj._get_base_data()): obj.prop_map = None # do a copy obj = numpy.asarray(obj) return obj def _get_base(self): base = self while base.base is not None: base = base.base return base def _get_base_data(self): return self._get_base().__array_interface__['data'][0] def _check_data(self): if self.prop_map is None: return data = self.prop_map._get_data() if (data is None or data.__array_interface__['data'][0] != self._get_base_data()): raise ValueError(("The graph correspondig to the underlying" + " property map %s has changed. The" + " PropertyArray at 0x%x is no longer valid!") % (repr(self.prop_map), id(self))) def __array_finalize__(self, obj): if type(obj) is PropertyArray: obj._check_data() if obj is not None: # inherit prop_map only if the data is the same if (type(obj) is PropertyArray and self._get_base_data() == obj._get_base_data()): self.prop_map = getattr(obj, 'prop_map', None) else: self.prop_map = None self._check_data() def __array_prepare__(self, out_arr, context=None): self._check_data() return numpy.ndarray.__array_prepare__(self, out_arr, context) def __array_wrap__(self, out_arr, context=None): #demote to ndarray obj = numpy.ndarray.__array_wrap__(self, out_arr, context) return numpy.asarray(obj) # Overload members and operators to add data checking def _wrap_method(method): method = getattr(numpy.ndarray, method) def checked_method(self, *args, **kwargs): self._check_data() return method(self, *args, **kwargs) if ismethod(method): checked_method = _wraps(method)(checked_method) checked_method.__doc__ = getattr(method, "__doc__", None) return checked_method for method in ['all', 'any', 'argmax', 'argmin', 'argsort', 'astype', 'byteswap', 'choose', 'clip', 'compress', 'conj', 'conjugate', 'copy', 'cumprod', 'cumsum', 'diagonal', 'dot', 'dump', 'dumps', 'fill', 'flat', 'flatten', 'getfield', 'imag', 'item', 'itemset', 'itemsize', 'max', 'mean', 'min', 'newbyteorder', 'nonzero', 'prod', 'ptp', 'put', 'ravel', 'real', 'repeat', 'reshape', 'resize', 'round', 'searchsorted', 'setfield', 'setflags', 'sort', 'squeeze', 'std', 'sum', 'swapaxes', 'take', 'tofile', 'tolist', 'tostring', 'trace', 'transpose', 'var', 'view', '__getitem__']: if hasattr(numpy.ndarray, method): locals()[method] = _wrap_method(method) class PropertyMap(object): """This class provides a mapping from vertices, edges or whole graphs to arbitrary properties. See :ref:`sec_property_maps` for more details. The possible property value types are listed below. .. table:: ======================= ====================== Type name Alias ======================= ====================== ``bool`` ``uint8_t`` ``int16_t`` ``short`` ``int32_t`` ``int`` ``int64_t`` ``long``, ``long long`` ``double`` ``float`` ``long double`` ``string`` ``vector`` ``vector`` ``vector`` ``short`` ``vector`` ``vector`` ``vector`` ``vector``, ``vector`` ``vector`` ``vector`` ``vector`` ``vector`` ``python::object`` ``object`` ======================= ====================== """ def __init__(self, pmap, g, key_type): self.__map = pmap self.__g = weakref.ref(g) self.__base_g = lambda: None try: if isinstance(g, GraphView): self.__base_g = weakref.ref(g.base) # keep reference to the # base graph, in case the # graph view is deleted. except NameError: pass # ignore if GraphView is yet undefined self.__key_type = key_type self.__register_map() def __key_trans(self, key): if self.key_type() == "g": return key._Graph__graph else: return key def __register_map(self): for g in [self.__g(), self.__base_g()]: if g is not None: g._Graph__known_properties[id(self)] = weakref.ref(self) def __unregister_map(self): for g in [self.__g(), self.__base_g()]: if g is not None and id(self) in g._Graph__known_properties: del g._Graph__known_properties[id(self)] def __del__(self): self.__unregister_map() def __getitem__(self, k): return self.__map[self.__key_trans(k)] def __setitem__(self, k, v): key = self.__key_trans(k) try: self.__map[key] = v except TypeError: self.__map[key] = _convert(self, v) def __repr__(self): # provide some more useful information if self.key_type() == "e": k = "Edge" elif self.key_type() == "v": k = "Vertex" else: k = "Graph" g = self.get_graph() if g == None: g = "a non-existent graph" else: g = "Graph 0x%x" % id(g) try: vals = ", with values:\n%s" % str(self.fa) except ValueError: vals = "" return ("") % (k, self.value_type(), g, id(self), vals) def copy(self, value_type=None): """Return a copy of the property map. If ``value_type`` is specified, the value type is converted to the chosen type.""" return self.get_graph().copy_property(self, value_type=value_type) def __copy__(self): return self.copy() def get_graph(self): """Get the graph class to which the map refers.""" g = self.__g() if g is None: g = self.__base_g() return g def key_type(self): """Return the key type of the map. Either 'g', 'v' or 'e'.""" return self.__key_type def value_type(self): """Return the value type of the map.""" return self.__map.value_type() def python_value_type(self): """Return the python-compatible value type of the map.""" return _python_type(self.__map.value_type()) def get_array(self): """Get a :class:`~graph_tool.PropertyArray` with the property values. .. note:: An array is returned *only if* the value type of the property map is a scalar. For vector, string or object types, ``None`` is returned instead. For vector and string objects, indirect array access is provided via the :func:`~graph_tool.PropertyMap.get_2d_array()` and :func:`~graph_tool.PropertyMap.set_2d_array()` member functions. .. warning:: The returned array does not own the data, which belongs to the property map. Therefore, if the graph changes, the array may become *invalid* and any operation on it will fail with a :class:`ValueError` exception. Do **not** store the array if the graph is to be modified; store a **copy** instead. """ a = self._get_data() if a is None: raise ValueError("Cannot get array for value type: " + self.value_type()) return PropertyArray(a, prop_map=self) def _get_data(self): g = self.get_graph() if g is None: raise ValueError("Cannot get array for an orphaned property map") if self.__key_type == 'v': n = g._Graph__graph.GetNumberOfVertices(False) elif self.__key_type == 'e': n = g.max_edge_index else: n = 1 a = self.__map.get_array(n) return a def __set_array(self, v): a = self.get_array() a[:] = v a = property(get_array, __set_array, doc=r"""Shortcut to the :meth:`~PropertyMap.get_array` method as an attribute. This makes assignments more convenient, e.g.: >>> g = gt.Graph() >>> g.add_vertex(10) <...> >>> prop = g.new_vertex_property("double") >>> prop.a = np.random.random(10) # Assignment from array """) def __get_set_f_array(self, v=None, get=True): g = self.get_graph() if g is None: return None a = self.get_array() filt = [None] if self.__key_type == 'v': filt = g.get_vertex_filter() elif self.__key_type == 'e': filt = g.get_edge_filter() if g.get_vertex_filter()[0] is not None: filt = (g.new_edge_property("bool"), filt[1]) u = GraphView(g, directed=True, skip_properties=True) libcore.mark_edges(u._Graph__graph, _prop("e", u, filt[0])) if filt[1]: filt[0].a = 1 - filt[0].a elif g._get_max_edge_index() != g.num_edges(): filt = (g.new_edge_property("bool"), False) u = GraphView(g, directed=True, skip_properties=True) libcore.mark_edges(u._Graph__graph, _prop("e", u, filt[0])) if get: if a is None: return a if filt[0] is None: return a return a[filt[0].a == (not filt[1])] else: if a is None: return if filt[0] is None: try: a[:] = v except ValueError: a[:] = v[:len(a)] else: m = filt[0].a == (not filt[1]) try: a[m] = v except ValueError: a[m] = v[:len(m)][m] fa = property(__get_set_f_array, lambda self, v: self.__get_set_f_array(v, False), doc=r"""The same as the :attr:`~PropertyMap.a` attribute, but instead an *indexed* array is returned, which contains only entries for vertices/edges which are not filtered out. If there are no filters in place, the array is not indexed, and is identical to the :attr:`~PropertyMap.a` attribute. Note that because advanced indexing is triggered, a **copy** of the array is returned, not a view, as for the :attr:`~PropertyMap.a` attribute. Nevertheless, the assignment of values to the *whole* array at once works as expected.""") def __get_set_m_array(self, v=None, get=True): g = self.get_graph() if g is None: return None a = self.get_array() filt = [None] if self.__key_type == 'v': filt = g.get_vertex_filter() elif self.__key_type == 'e': filt = g.get_edge_filter() if g.get_vertex_filter()[0] is not None: filt = (g.new_edge_property("bool"), filt[1]) u = GraphView(g, directed=True, skip_properties=True) libcore.mark_edges(u._Graph__graph, _prop("e", g, filt[0])) if filt[1]: filt[0].a = 1 - filt[0].a if filt[0] is None or a is None: if get: return a else: return ma = numpy.ma.array(a, mask=(filt[0].a == False) if not filt[1] else (filt[0].a == True)) if get: return ma else: ma[:] = v ma = property(__get_set_m_array, lambda self, v: self.__get_set_m_array(v, False), doc=r"""The same as the :attr:`~PropertyMap.a` attribute, but instead a :class:`~numpy.ma.MaskedArray` object is returned, which contains only entries for vertices/edges which are not filtered out. If there are no filters in place, a regular :class:`~graph_tool.PropertyArray` is returned, which is identical to the :attr:`~PropertyMap.a` attribute.""") def get_2d_array(self, pos): r"""Return a two-dimensional array with a copy of the entries of the vector-valued property map. The parameter ``pos`` must be a sequence of integers which specifies the indexes of the property values which will be used. """ if self.key_type() == "g": raise ValueError("Cannot create multidimensional array for graph property maps.") if "vector" not in self.value_type() and (len(pos) > 1 or pos[0] != 0): raise ValueError("Cannot create array of dimension %d (indexes %s) from non-vector property map of type '%s'." \ % (len(pos), str(pos), self.value_type())) if "string" in self.value_type(): if "vector" in self.value_type(): p = ungroup_vector_property(self, pos) else: p = [self] g = self.get_graph() if self.key_type() == "v": N = g.num_vertices() else: N = g.num_edges() a = [["" for j in range(N)] for i in range(len(p))] if self.key_type() == "v": iters = g.vertices() else: iters = g.edges() for v in iters: for i in range(len(p)): a[i][int(v)] = p[i][v] if len(a) == 1: a = a[0] return numpy.array(a) try: return numpy.array(self.fa) except ValueError: p = ungroup_vector_property(self, pos) return numpy.array([x.a for x in p]) def set_2d_array(self, a, pos=None): r"""Set the entries of the vector-valued property map from a two-dimensional array ``a``. If given, the parameter ``pos`` must be a sequence of integers which specifies the indexes of the property values which will be set.""" if self.key_type() == "g": raise ValueError("Cannot set multidimensional array for graph property maps.") if "vector" not in self.value_type(): if len(a.shape) != 1: raise ValueError("Cannot set array of shape %s to non-vector property map of type %s" % \ (str(a.shape), self.value_type())) if self.value_type() != "string": self.fa = a else: g = self.get_graph() if self.key_type() == "v": iters = g.vertices() else: iters = g.edges() for i, v in enumerate(iters): self[v] = a[i] return val = self.value_type()[7:-1] ps = [] for i in range(a.shape[0]): ps.append(self.get_graph().new_property(self.key_type(), val)) if self.value_type() != "string": ps[-1].fa = a[i] else: g = self.get_graph() if self.key_type() == "v": iters = g.vertices() else: iters = g.edges() for j, v in enumerate(iters): ps[-1][v] = a[i, j] group_vector_property(ps, val, self, pos) def is_writable(self): """Return True if the property is writable.""" return self.__map.is_writable() def __call__(self, a): p = self.copy() p.fa = a return p def __getstate__(self): g = self.get_graph() if g is None: raise ValueError("cannot pickle orphaned property map") value_type = self.value_type() key_type = self.key_type() if not self.is_writable(): vals = None else: u = GraphView(g, skip_vfilt=True, skip_efilt=True) if key_type == "v": vals = [_convert(self, self[v]) for v in u.vertices()] elif key_type == "e": vals = [_convert(self, self[e]) for e in u.edges()] else: vals = _convert(self, self[g]) state = dict(g=g, value_type=value_type, key_type=key_type, vals=vals, is_vindex=self is g.vertex_index, is_eindex=self is g.edge_index) return state def __setstate__(self, state): g = state["g"] key_type = state["key_type"] value_type = state["value_type"] vals = state["vals"] if state["is_vindex"]: pmap = g.vertex_index elif state["is_eindex"]: pmap = g.edge_index else: u = GraphView(g, skip_vfilt=True, skip_efilt=True) if key_type == "v": pmap = g.new_vertex_property(value_type) for i, v in enumerate(u.vertices()): pmap[v] = vals[i] elif key_type == "e": pmap = g.new_edge_property(value_type) for i, e in enumerate(u.edges()): pmap[e] = vals[i] else: pmap = g.new_graph_property(value_type) pmap[g] = vals self.__map = pmap.__map self.__g = pmap.__g self.__base_g = pmap.__base_g self.__key_type = key_type self.__register_map() def _check_prop_writable(prop, name=None): if not prop.is_writable(): raise ValueError("property map%s is not writable." %\ ((" '%s'" % name) if name != None else "")) def _check_prop_scalar(prop, name=None, floating=False): scalars = ["bool", "int32_t", "int64_t", "unsigned long", "double", "long double"] if floating: scalars = ["double", "long double"] if prop.value_type() not in scalars: raise ValueError("property map%s is not of scalar%s type." %\ (((" '%s'" % name) if name != None else ""), (" floating" if floating else ""))) def _check_prop_vector(prop, name=None, scalar=True, floating=False): scalars = ["bool", "int32_t", "int64_t", "unsigned long", "double", "long double"] if not scalar: scalars += ["string"] if floating: scalars = ["double", "long double"] vals = ["vector<%s>" % v for v in scalars] if prop.value_type() not in vals: raise ValueError("property map%s is not of vector%s type." %\ (((" '%s'" % name) if name != None else ""), (" floating" if floating else ""))) def group_vector_property(props, value_type=None, vprop=None, pos=None): """Group list of properties ``props`` into a vector property map of the same type. Parameters ---------- props : list of :class:`~graph_tool.PropertyMap` Properties to be grouped. value_type : string (optional, default: None) If supplied, defines the value type of the grouped property. vprop : :class:`~graph_tool.PropertyMap` (optional, default: None) If supplied, the properties are grouped into this property map. pos : list of ints (optional, default: None) If supplied, should contain a list of indexes where each corresponding element of ``props`` should be inserted. Returns ------- vprop : :class:`~graph_tool.PropertyMap` A vector property map with the grouped values of each property map in ``props``. Examples -------- >>> from numpy.random import seed, randint >>> from numpy import array >>> seed(42) >>> gt.seed_rng(42) >>> g = gt.random_graph(100, lambda: (3, 3)) >>> props = [g.new_vertex_property("int") for i in range(3)] >>> for i in range(3): ... props[i].a = randint(0, 100, g.num_vertices()) >>> gprop = gt.group_vector_property(props) >>> print(gprop[g.vertex(0)].a) [51 25 8] >>> print(array([p[g.vertex(0)] for p in props])) [51 25 8] """ g = props[0].get_graph() vtypes = set() keys = set() for i, p in enumerate(props): if "vector" in p.value_type(): raise ValueError("property map 'props[%d]' is a vector property." % i) vtypes.add(p.value_type()) keys.add(p.key_type()) if len(keys) > 1: raise ValueError("'props' must be of the same key type.") k = keys.pop() if vprop == None: if value_type == None and len(vtypes) == 1: value_type = vtypes.pop() if value_type != None: value_type = "vector<%s>" % value_type if k == 'v': vprop = g.new_vertex_property(value_type) elif k == 'e': vprop = g.new_edge_property(value_type) else: vprop = g.new_graph_property(value_type) else: ValueError("Can't automatically determine property map value" + " type. Please provide the 'value_type' parameter.") _check_prop_vector(vprop, name="vprop", scalar=False) for i, p in enumerate(props): if k != "g": u = GraphView(g, directed=True, reversed=g.is_reversed(), skip_properties=True) libcore.group_vector_property(u._Graph__graph, _prop(k, g, vprop), _prop(k, g, p), i if pos == None else pos[i], k == 'e') else: vprop[g][i if pos is None else pos[i]] = p[g] return vprop def ungroup_vector_property(vprop, pos, props=None): """Ungroup vector property map ``vprop`` into a list of individual property maps. Parameters ---------- vprop : :class:`~graph_tool.PropertyMap` Vector property map to be ungrouped. pos : list of ints A list of indexes corresponding to where each element of ``vprop`` should be inserted into the ungrouped list. props : list of :class:`~graph_tool.PropertyMap` (optional, default: None) If supplied, should contain a list of property maps to which ``vprop`` should be ungroupped. Returns ------- props : list of :class:`~graph_tool.PropertyMap` A list of property maps with the ungrouped values of ``vprop``. Examples -------- >>> from numpy.random import seed, randint >>> from numpy import array >>> seed(42) >>> gt.seed_rng(42) >>> g = gt.random_graph(100, lambda: (3, 3)) >>> prop = g.new_vertex_property("vector") >>> for v in g.vertices(): ... prop[v] = randint(0, 100, 3) >>> uprops = gt.ungroup_vector_property(prop, [0, 1, 2]) >>> print(prop[g.vertex(0)].a) [51 92 14] >>> print(array([p[g.vertex(0)] for p in uprops])) [51 92 14] """ g = vprop.get_graph() _check_prop_vector(vprop, name="vprop", scalar=False) k = vprop.key_type() value_type = vprop.value_type().split("<")[1].split(">")[0] if props == None: if k == 'v': props = [g.new_vertex_property(value_type) for i in pos] elif k == 'e': props = [g.new_edge_property(value_type) for i in pos] else: props = [g.new_graph_property(value_type) for i in pos] for i, p in enumerate(pos): if props[i].key_type() != k: raise ValueError("'props' must be of the same key type as 'vprop'.") if k != 'g': u = GraphView(g, directed=True, reversed=g.is_reversed(), skip_properties=True) libcore.ungroup_vector_property(u._Graph__graph, _prop(k, g, vprop), _prop(k, g, props[i]), p, k == 'e') else: if len(vprop[g]) <= pos[i]: vprop[g].resize(pos[i] + 1) props[i][g] = vprop[g][pos[i]] return props def infect_vertex_property(g, prop, vals=None): """Propagate the `prop` values of vertices with value `val` to all their out-neighbours. Parameters ---------- prop : :class:`~graph_tool.PropertyMap` Property map to be modified. vals : list (optional, default: `None`) List of values to be propagated. If not provided, all values will be propagated. Returns ------- None : ``None`` Examples -------- >>> from numpy.random import seed >>> seed(42) >>> gt.seed_rng(42) >>> g = gt.random_graph(100, lambda: (3, 3)) >>> prop = g.vertex_index.copy("int32_t") >>> gt.infect_vertex_property(g, prop, [10]) >>> print(sum(prop.a == 10)) 4 """ libcore.infect_vertex_property(g._Graph__graph, _prop("v", g, prop), vals) @_limit_args({"endpoint": ["source", "target"]}) def edge_endpoint_property(g, prop, endpoint, eprop=None): """Return an edge property map corresponding to the vertex property `prop` of either the target and source of the edge, according to `endpoint`. Parameters ---------- prop : :class:`~graph_tool.PropertyMap` Vertex property map to be used to propagated to the edge. endpoint : `"source"` or `"target"` Edge endpoint considered. If the graph is undirected, the source is always the vertex with the lowest index. eprop : :class:`~graph_tool.PropertyMap` (optional, default: `None`) If provided, the resulting edge properties will be stored here. Returns ------- eprop : :class:`~graph_tool.PropertyMap` Propagated edge property. Examples -------- >>> gt.seed_rng(42) >>> g = gt.random_graph(100, lambda: (3, 3)) >>> esource = gt.edge_endpoint_property(g, g.vertex_index, "source") >>> print(esource.a) [ 0 0 0 96 96 96 92 92 92 88 88 88 84 84 84 80 80 80 76 76 76 72 72 72 68 68 68 64 64 64 60 60 60 56 56 56 52 52 52 48 48 48 44 44 44 40 40 40 36 36 36 32 32 32 28 28 28 24 24 24 20 20 20 16 16 16 12 12 12 8 8 8 4 4 4 99 99 99 1 1 1 2 2 2 3 3 3 5 5 5 6 6 6 7 7 7 9 9 9 10 10 10 14 14 14 19 19 19 25 25 25 30 30 30 35 35 35 41 41 41 46 46 46 51 51 51 57 57 57 62 62 62 67 67 67 73 73 73 78 78 78 83 83 83 89 89 89 94 94 94 11 11 11 98 98 98 97 97 97 95 95 95 93 93 93 91 91 91 90 90 90 87 87 87 86 86 86 85 85 85 82 82 82 81 81 81 79 79 79 77 77 77 75 75 75 74 74 74 71 71 71 69 69 69 61 61 61 54 54 54 47 47 47 39 39 39 33 33 33 26 26 26 18 18 18 70 70 70 13 13 13 15 15 15 17 17 17 21 21 21 22 22 22 23 23 23 27 27 27 29 29 29 31 31 31 34 34 34 37 37 37 38 38 38 42 42 42 43 43 43 45 45 45 49 49 49 50 50 50 53 53 53 55 55 55 58 58 58 59 59 59 63 63 63 65 65 65 66 66 66] """ val_t = prop.value_type() if val_t == "unsigned long": val_t = "int64_t" if eprop is None: eprop = g.new_edge_property(val_t) if eprop.value_type() != val_t: raise ValueError("'eprop' must be of the same value type as 'prop': " + val_t) libcore.edge_endpoint(g._Graph__graph, _prop("v", g, prop), _prop("e", g, eprop), endpoint) return eprop @_limit_args({"direction": ["in", "out"], "op": ["sum", "prod", "min", "max"]}) def incident_edges_op(g, direction, op, eprop, vprop=None): """Return a vertex property map corresponding to a specific operation (sum, product, min or max) on the edge property `eprop` of incident edges on each vertex, following the direction given by `direction`. Parameters ---------- direction : `"in"` or `"out"` Direction of the incident edges. op : `"sum"`, `"prod"`, `"min"` or `"max"` Operation performed on incident edges. eprop : :class:`~graph_tool.PropertyMap` Edge property map to be summed. vprop : :class:`~graph_tool.PropertyMap` (optional, default: `None`) If provided, the resulting vertex properties will be stored here. Returns ------- vprop : :class:`~graph_tool.PropertyMap` Summed vertex property. Examples -------- >>> gt.seed_rng(42) >>> g = gt.random_graph(100, lambda: (3, 3)) >>> vsum = gt.incident_edges_op(g, "out", "sum", g.edge_index) >>> print(vsum.a) [ 3 237 246 255 219 264 273 282 210 291 300 453 201 687 309 696 192 705 669 318 183 714 723 732 174 327 660 741 165 750 336 759 156 651 768 345 147 777 786 642 138 354 795 804 129 813 363 633 120 822 831 372 111 840 624 849 102 381 858 867 93 615 390 876 84 885 894 399 75 606 678 597 66 408 588 579 57 570 417 561 48 552 543 426 39 534 525 516 30 435 507 498 21 489 444 480 12 471 462 228] """ val_t = eprop.value_type() if val_t == "unsigned long": val_t = "int64_t" if vprop is None: vprop = g.new_vertex_property(val_t) orig_vprop = vprop if vprop.value_type != val_t: vprop = g.new_vertex_property(val_t) if direction == "in" and not g.is_directed(): return orig_vprop if direction == "in": g = GraphView(g, reversed=True, skip_properties=True) libcore.out_edges_op(g._Graph__graph, _prop("e", g, eprop), _prop("v", g, vprop), op) if vprop is not orig_vprop: g.copy_property(vprop, orig_vprop) return orig_vprop @_limit_args({"htype": ["int8_t", "int32_t", "int64_t"]}) def perfect_prop_hash(props, htype="int32_t"): """Given a list of property maps `props` of the same type, a derived list of property maps with integral type `htype` is returned, where each value is replaced by a perfect (i.e. unique) hash value. .. note:: The hash value is deterministic, but it will not be necessarily the same for different values of `props`. """ val_types = set([p.value_type() for p in props]) if len(val_types) > 1: raise ValueError("All properties must have the same value type") hprops = [p.get_graph().new_property(p.key_type(), htype) for p in props] eprops = [p for p in props if p.key_type() == "e"] heprops = [p for p in hprops if p.key_type() == "e"] vprops = [p for p in props if p.key_type() == "v"] hvprops = [p for p in hprops if p.key_type() == "v"] hdict = libcore.any() for eprop, heprop in zip(eprops, heprops): g = eprop.get_graph() g = GraphView(g, directed=True, skip_properties=True) libcore.perfect_ehash(g._Graph__graph, _prop('e', g, eprop), _prop('e', g, heprop), hdict) for vprop, hvprop in zip(vprops, hvprops): g = vprop.get_graph() g = GraphView(g, directed=True, skip_properties=True) libcore.perfect_vhash(g._Graph__graph, _prop('v', g, vprop), _prop('v', g, hvprop), hdict) return hprops class PropertyDict(dict): """Wrapper for the dict of vertex, graph or edge properties, which sets the value on the property map when changed in the dict. .. note:: The class is only an one-way proxy to the internally-kept properties. If you modify this object, the change will be propagated to the internal dictionary, but not vice-versa. Keep this in mind if you intend to keep a copy of the class instance. """ def __init__(self, g, old, get_func, set_func, del_func): dict.__init__(self) dict.update(self, old) self.g = g self.get_func = get_func self.set_func = set_func self.del_func = del_func def __getitem__(self, key): if self.get_func != None: val = self.get_func(self.g, key) dict.__setitem__(self, key, val) return val else: raise KeyError("Property dict cannot be gotten") def __setitem__(self, key, val): if self.set_func != None: self.set_func(self.g, key, val) else: raise KeyError("Property dict cannot be set") dict.__setitem__(self, key, val) def __delitem__(self, key): self.del_func(self.g, key) dict.__delitem__(self, key) def clear(self): for k in self.keys(): self.del_func(self.g, k) dict.clear(self) ################################################################################ # Graph class # The main graph interface ################################################################################ from .libgraph_tool_core import Vertex, EdgeBase, Vector_bool, Vector_int16_t, \ Vector_int32_t, Vector_int64_t, Vector_double, Vector_long_double, \ Vector_string, Vector_size_t, new_vertex_property, new_edge_property, \ new_graph_property class Graph(object): """Generic multigraph class. This class encapsulates either a directed multigraph (default or if ``directed=True``) or an undirected multigraph (if ``directed=False``), with optional internal edge, vertex or graph properties. If ``g`` is specified, the graph (and its internal properties) will be copied. If ``prune`` is set to ``True``, and ``g`` is specified, only the filtered graph will be copied, and the new graph object will not be filtered. Optionally, a tuple of three booleans can be passed as value to ``prune``, to specify a different behavior to vertex, edge, and reversal filters, respectively. If ``vorder`` is specified, it should correspond to a vertex :class:`~graph_tool.PropertyMap` specifying the ordering of the vertices in the copied graph. The graph is implemented as an `adjacency list`_, where both vertex and edge lists are C++ STL vectors. .. _adjacency list: http://en.wikipedia.org/wiki/Adjacency_list """ def __init__(self, g=None, directed=True, prune=False, vorder=None): self.__properties = {} self.__known_properties = {} self.__filter_state = {"reversed": False, "edge_filter": (None, False), "vertex_filter": (None, False), "directed": True} if g is None: self.__graph = libcore.GraphInterface() self.set_directed(directed) # internal index maps self.__vertex_index = \ PropertyMap(libcore.get_vertex_index(self.__graph), self, "v") self.__edge_index = \ PropertyMap(libcore.get_edge_index(self.__graph), self, "e") else: if isinstance(prune, bool): vprune = eprune = rprune = prune else: vprune, eprune, rprune = prune if not (vprune or eprune or rprune): gv = GraphView(g, skip_vfilt=True, skip_efilt=True) if not rprune: gv.set_reversed(False) else: gv = g # The filters may or may not not be in the internal property maps vfilt = g.get_vertex_filter()[0] efilt = g.get_edge_filter()[0] if (vorder is None and ((vfilt is None and efilt is None) or (not vprune and not eprune))): # Do a simpler, faster copy. self.__graph = libcore.GraphInterface(gv.__graph, False, [], [], None) # internal index maps self.__vertex_index = \ PropertyMap(libcore.get_vertex_index(self.__graph), self, "v") self.__edge_index = \ PropertyMap(libcore.get_edge_index(self.__graph), self, "e") nvfilt = nefilt = None for k, m in g.properties.items(): nmap = self.copy_property(m, g=gv) self.properties[k] = nmap if m is vfilt: nvfilt = nmap if m is efilt: nefilt = nmap if vfilt is not None: if nvfilt is None: nvfilt = self.copy_property(vfilt, g=gv) if efilt is not None: if nefilt is None: nefilt = self.copy_property(efilt, g=gv) self.set_filters(nefilt, nvfilt, inverted_edges=g.get_edge_filter()[1], inverted_vertices=g.get_vertex_filter()[1]) else: # Copy all internal properties from original graph. vprops = [] eprops = [] ef_pos = vf_pos = None for k, m in gv.vertex_properties.items(): if not m.is_writable(): m = m.copy("int32_t") if not vprune and m is vfilt: vf_pos = len(vprops) vprops.append([_prop("v", gv, m), libcore.any()]) for k, m in gv.edge_properties.items(): if not m.is_writable(): m = m.copy("int32_t") if not eprune and m is efilt: ef_pos = len(eprops) eprops.append([_prop("e", gv, m), libcore.any()]) if not vprune and vf_pos is None and vfilt is not None: vf_pos = len(vprops) vprops.append([_prop("v", gv, vfilt), libcore.any()]) if not eprune and ef_pos is None and efilt is not None: ef_pos = len(eprops) eprops.append([_prop("e", gv, efilt), libcore.any()]) # The vertex ordering if vorder is None: vorder = gv.new_vertex_property("int") vorder.fa = numpy.arange(gv.num_vertices()) # The actual copying of the graph and property maps self.__graph = libcore.GraphInterface(gv.__graph, False, vprops, eprops, _prop("v", gv, vorder)) # internal index maps self.__vertex_index = \ PropertyMap(libcore.get_vertex_index(self.__graph), self, "v") self.__edge_index = \ PropertyMap(libcore.get_edge_index(self.__graph), self, "e") # Put the copied properties in the internal dictionary for i, (k, m) in enumerate(gv.vertex_properties.items()): pmap = new_vertex_property(m.value_type() if m.is_writable() else "int32_t", self.__graph.GetVertexIndex(), vprops[i][1]) self.vertex_properties[k] = PropertyMap(pmap, self, "v") for i, (k, m) in enumerate(gv.edge_properties.items()): pmap = new_edge_property(m.value_type() if m.is_writable() else "int32_t", self.__graph.GetEdgeIndex(), eprops[i][1]) self.edge_properties[k] = PropertyMap(pmap, self, "e") for k, v in gv.graph_properties.items(): new_p = self.new_graph_property(v.value_type()) new_p[self] = v[gv] self.graph_properties[k] = new_p epmap = vpmap = None if vf_pos is not None: vpmap = new_vertex_property("bool", self.__graph.GetVertexIndex(), vprops[vf_pos][1]) vpmap = PropertyMap(vpmap, self, "v") if ef_pos is not None: epmap = new_edge_property("bool", self.__graph.GetEdgeIndex(), eprops[ef_pos][1]) epmap = PropertyMap(epmap, self, "e") self.set_filters(epmap, vpmap, inverted_edges=g.get_edge_filter()[1], inverted_vertices=g.get_vertex_filter()[1]) if not rprune: self.set_reversed(g.is_reversed()) # directedness is always a filter self.set_directed(g.is_directed()) # modification permissions self.__perms = {"add_edge": True, "del_edge": True, "add_vertex": True, "del_vertex": True} def copy(self): """Return a deep copy of self. All :ref:`internal property maps ` are also copied.""" return Graph(self) def __copy__(self): return self.copy() def __repr__(self): # provide more useful information d = "directed" if self.is_directed() else "undirected" fr = ", reversed" if self.is_reversed() and self.is_directed() else "" f = "" if self.get_edge_filter()[0] is not None: f += ", edges filtered by %s" % (str(self.get_edge_filter())) if self.get_vertex_filter()[0] is not None: f += ", vertices filtered by %s" % (str(self.get_vertex_filter())) n = self.num_vertices() e = self.num_edges() return "<%s object, %s%s, with %d %s and %d edge%s%s at 0x%x>"\ % (type(self).__name__, d, fr, n, "vertex" if n == 1 else "vertices", e, "" if e == 1 else "s", f, id(self)) # Graph access # ============ def __check_perms(self, ptype): if not self.__perms[ptype]: raise RuntimeError("the graph cannot be modified at this point!") def vertices(self): """Return an :meth:`iterator ` over the vertices. .. note:: The order of the vertices traversed by the iterator **always** corresponds to the vertex index ordering, as given by the :attr:`~graph_tool.Graph.vertex_index` property map. Examples -------- >>> g = gt.Graph() >>> vlist = list(g.add_vertex(5)) >>> vlist2 = [] >>> for v in g.vertices(): ... vlist2.append(v) ... >>> assert(vlist == vlist2) """ return libcore.get_vertices(weakref.ref(self)) def vertex(self, i, use_index=True): """Return the vertex with index ``i``. If ``use_index=False``, the ``i``-th vertex is returned (which can differ from the vertex with index ``i`` in case of filtered graphs). """ vfilt = self.get_vertex_filter() if vfilt[0] is None or not use_index: return libcore.get_vertex(weakref.ref(self), int(i)) try: self.set_vertex_filter(None) v = libcore.get_vertex(weakref.ref(self), int(i)) finally: self.set_vertex_filter(vfilt[0], vfilt[1]) if not v.is_valid(): return v if vfilt[0] is not None and vfilt[0][v] == vfilt[1]: return None return v def edge(self, s, t, all_edges=False): """Return the edge from vertex ``s`` to ``t``, if it exists. If ``all_edges=True`` then a list is returned with all the parallel edges from ``s`` to ``t``, otherwise only one edge is returned. This operation will take :math:`O(k(s))` time, where :math:`k(s)` is the out-degree of vertex :math:`s`. """ s = self.vertex(int(s)) t = self.vertex(int(t)) if s is None or t is None: return None efilt = self.get_edge_filter() edges = [] for e in s.out_edges(): if efilt[0] is not None and efilt[0][e] == efilt[1]: continue if e.target() == t: if not all_edges: return e edges.append(e) if all_edges: return edges return None def edges(self): """Return an :meth:`iterator ` over the edges. .. note:: The order of the edges traversed by the iterator **does not** necessarily correspond to the edge index ordering, as given by the :attr:`~graph_tool.Graph.edge_index` property map. This will only happen after :meth:`~graph_tool.Graph.reindex_edges` is called, or in certain situations such as just after a graph is loaded from a file. However, further manipulation of the graph may destroy the ordering. """ return libcore.get_edges(weakref.ref(self)) def add_vertex(self, n=1): """Add a vertex to the graph, and return it. If ``n != 1``, ``n`` vertices are inserted and an iterator over the new vertices is returned. This operation is :math:`O(n)`. """ if n == 0: return (None for i in range(0, 0)) self.__check_perms("add_vertex") v = libcore.add_vertex(weakref.ref(self), n) if n <= 1: return v else: pos = self.num_vertices() - n return (self.vertex(i) for i in range(pos, pos + n)) def remove_vertex(self, vertex, fast=False): r"""Remove a vertex from the graph. If ``vertex`` is an iterable, it should correspond to a sequence of vertices to be removed. .. note:: If the option ``fast == False`` is given, this operation is :math:`O(N + E)` (this is the default). Otherwise it is :math:`O(k + k_{\text{last}})`, where :math:`k` is the (total) degree of the vertex being deleted, and :math:`k_{\text{last}}` is the (total) degree of the vertex with the largest index. .. warning:: This operation may invalidate vertex descriptors. Vertices are always indexed contiguously in the range :math:`[0, N-1]`, hence vertex descriptors with an index higher than ``vertex`` will be invalidated after removal (if ``fast == False``, otherwise only descriptors pointing to vertices with the largest index will be invalidated). Because of this, the only safe way to remove more than one vertex at once is to sort them in decreasing index order: .. code:: # 'del_list' is a list of vertex descriptors for v in reversed(sorted(del_list)): g.remove_vertex(v) Alternatively (and preferably), a list (or iterable) may be passed directly as the ``vertex`` parameter, and the above is performed internally (in C++). .. warning:: If ``fast == True``, the vertex being deleted is 'swapped' with the last vertex (i.e. with the largest index), which will in turn inherit the index of the vertex being deleted. All property maps associated with the graph will be properly updated, but the index ordering of the graph will no longer be the same. """ self.__check_perms("del_vertex") try: vs = numpy.array([int(vertex)], dtype="int64") except TypeError: try: vs = numpy.asarray(vertex, dtype="int64") except TypeError: vs = numpy.asarray([int(v) for v in vertex], dtype="int64") if len(vs) == 0: return vs = numpy.sort(vs)[::-1] back = self.__graph.GetNumberOfVertices(False) - 1 if vs.max() > back: raise ValueError("Vertex index %d is invalid" % vs.max()) # move / shift all known property maps if len(vs) > 0 or vs[0] != back: for pmap in self.__known_properties.values(): if pmap() is not None and pmap().key_type() == "v" and pmap().is_writable(): if fast: self.__graph.MoveVertexProperty(pmap()._PropertyMap__map.get_map(), vs) else: self.__graph.ShiftVertexProperty(pmap()._PropertyMap__map.get_map(), vs) libcore.remove_vertex(self.__graph, vs, fast) def clear_vertex(self, vertex): """Remove all in and out-edges from the given vertex.""" del_es = set() for e in vertex.all_edges(): del_es.add(e) for e in del_es: self.remove_edge(e) def add_edge(self, source, target): """Add a new edge from ``source`` to ``target`` to the graph, and return it. This operation is :math:`O(1)`.""" self.__check_perms("add_edge") e = libcore.add_edge(weakref.ref(self), self.vertex(int(source)), self.vertex(int(target))) efilt = self.get_edge_filter() if efilt[0] is not None: efilt[0][e] = not efilt[1] return e def remove_edge(self, edge): r"""Remove an edge from the graph. .. note:: This operation is normally :math:`O(k_s + k_t)`, where :math:`k_s` and :math:`k_s` are the total degrees of the source and target vertices, respectively. However, if :meth:`~Graph.set_fast_edge_removal` is set to `True`, this operation becomes :math:`O(1)`. .. warning:: The relative ordering of the remaining edges in the graph is kept unchanged, unless :meth:`~Graph.set_fast_edge_removal` is set to `True`, in which case it can change. """ self.__check_perms("del_edge") return libcore.remove_edge(self.__graph, edge) def add_edge_list(self, edge_list): """Add a list of edges to the graph, given by ``edge_list``, which can be a list of ``(source, target)`` pairs where both ``source`` and ``target`` are vertex indexes, or a :class:`~numpy.ndarray` of shape ``(E,2)``, where ``E`` is the number of edges, and each line specifies a ``(source, target)`` pair. If the list references vertices which do not exist in the graph, they will be created.""" self.__check_perms("add_edge") edges = numpy.asarray(edge_list) libcore.add_edge_list(self.__graph, edges) def set_fast_edge_removal(self, fast=True): r"""If ``fast == True`` the fast :math:`O(1)` removal of edges will be enabled. This requires an additional data structure of size :math:`O(E)` to be kept at all times. If ``fast == False``, this data structure is destroyed.""" self.__graph.SetKeepEpos(fast) def get_fast_edge_removal(self): r"""Return whether the fast :math:`O(1)` removal of edges is currently enabled.""" return self.__graph.GetKeepEpos() def clear(self): """Remove all vertices and edges from the graph.""" self.__check_perms("del_vertex") self.__check_perms("del_edge") self.__graph.Clear() def clear_edges(self): """Remove all edges from the graph.""" self.__check_perms("del_edge") self.__graph.ClearEdges() # Internal property maps # ====================== # all properties def __get_properties(self): return PropertyDict(self, self.__properties, lambda g, k: g.__properties[k], lambda g, k, v: g.__set_property(k[0], k[1], v), lambda g, k: g.__del_property(k[0], k[1])) @_limit_args({"t": ["v", "e", "g"]}) @_require("k", str) def __set_property(self, t, k, v): if t == "g" and not isinstance(v, PropertyMap): self.__properties[(t, k)][self] = v else: if t != v.key_type(): raise ValueError("wrong key type for property map") self.__properties[(t, k)] = v @_limit_args({"t": ["v", "e", "g"]}) @_require("k", str) def __del_property(self, t, k): del self.__properties[(t, k)] properties = property(__get_properties, doc= """Dictionary of internal properties. Keys must always be a tuple, where the first element if a string from the set {'v', 'e', 'g'}, representing a vertex, edge or graph property, respectively, and the second element is the name of the property map. Examples -------- >>> g = gt.Graph() >>> g.properties[("e", "foo")] = g.new_edge_property("vector") >>> del g.properties[("e", "foo")] """) def __get_specific_properties(self, t): props = dict([(k[1], v) for k, v in self.__properties.items() \ if k[0] == t]) return props # vertex properties def __get_vertex_properties(self): return PropertyDict(self, self.__get_specific_properties("v"), lambda g, k: g.__properties[("v", k)], lambda g, k, v: g.__set_property("v", k, v), lambda g, k: g.__del_property("v", k)) vertex_properties = property(__get_vertex_properties, doc="Dictionary of internal vertex properties. The keys are the property names.") vp = property(__get_vertex_properties, doc="Alias to :attr:`~Graph.vertex_properties`.") # edge properties def __get_edge_properties(self): return PropertyDict(self, self.__get_specific_properties("e"), lambda g, k: g.__properties[("e", k)], lambda g, k, v: g.__set_property("e", k, v), lambda g, k: g.__del_property("e", k)) edge_properties = property(__get_edge_properties, doc="Dictionary of internal edge properties. The keys are the property names.") ep = property(__get_edge_properties, doc="Alias to :attr:`~Graph.edge_properties`.") # graph properties def __get_graph_properties(self): return PropertyDict(self, self.__get_specific_properties("g"), lambda g, k: g.__properties[("g", k)][g], lambda g, k, v: g.__set_property("g", k, v), lambda g, k: g.__del_property("g", k)) graph_properties = property(__get_graph_properties, doc="Dictionary of internal graph properties. The keys are the property names.") gp = property(__get_graph_properties, doc="Alias to :attr:`~Graph.graph_properties`.") def own_property(self, prop): """Return a version of the property map 'prop' (possibly belonging to another graph) which is owned by the current graph.""" return PropertyMap(prop._PropertyMap__map, self, prop.key_type()) def list_properties(self): """Print a list of all internal properties. Examples -------- >>> g = gt.Graph() >>> g.properties[("e", "foo")] = g.new_edge_property("vector") >>> g.vertex_properties["foo"] = g.new_vertex_property("double") >>> g.vertex_properties["bar"] = g.new_vertex_property("python::object") >>> g.graph_properties["gnat"] = g.new_graph_property("string", "hi there!") >>> g.list_properties() gnat (graph) (type: string, val: hi there!) bar (vertex) (type: python::object) foo (vertex) (type: double) foo (edge) (type: vector) """ if len(self.__properties) == 0: return w = max([len(x[0]) for x in list(self.__properties.keys())]) + 4 w = w if w > 14 else 14 for k, v in self.__properties.items(): if k[0] == "g": pref="%%-%ds (graph) (type: %%s, val: " % w % \ (k[1], v.value_type()) val = str(v[self]) if len(val) > 1000: val = val[:1000] + "..." tw = terminal_size()[0] val = textwrap.indent(textwrap.fill(val, width=max(tw - len(pref), 1)), " " * len(pref)) val = val[len(pref):] print("%s%s)" % (pref, val)) for k, v in self.__properties.items(): if k[0] == "v": print("%%-%ds (vertex) (type: %%s)" % w % (k[1], v.value_type())) for k, v in self.__properties.items(): if k[0] == "e": print("%%-%ds (edge) (type: %%s)" % w % (k[1], v.value_type())) # index properties def _get_vertex_index(self): return self.__vertex_index vertex_index = property(_get_vertex_index, doc="""Vertex index map. It maps for each vertex in the graph an unique integer in the range [0, :meth:`~graph_tool.Graph.num_vertices` - 1]. .. note:: Like :attr:`~graph_tool.Graph.edge_index`, this is a special instance of a :class:`~graph_tool.PropertyMap` class, which is **immutable**, and cannot be accessed as an array.""") def _get_edge_index(self): return self.__edge_index edge_index = property(_get_edge_index, doc="""Edge index map. It maps for each edge in the graph an unique integer. .. note:: Like :attr:`~graph_tool.Graph.vertex_index`, this is a special instance of a :class:`~graph_tool.PropertyMap` class, which is **immutable**, and cannot be accessed as an array. Additionally, the indexes may not necessarily lie in the range [0, :meth:`~graph_tool.Graph.num_edges` - 1]. However this will always happen whenever no edges are deleted from the graph.""") def _get_max_edge_index(self): return self.__graph.GetMaxEdgeIndex() max_edge_index = property(_get_max_edge_index, doc="The maximum value of the edge index map.") def reindex_edges(self): """ Reset the edge indexes so that they lie in the [0, :meth:`~graph_tool.Graph.num_edges` - 1] range. The index ordering will be compatible with the sequence returned by the :meth:`~graph_tool.Graph.edges` function. .. WARNING:: Calling this function will invalidate all existing edge property maps, if the index ordering is modified! The property maps will still be usable, but their contents will still be tied to the old indexes, and thus may become scrambled. """ self.__graph.ReIndexEdges() # Property map creation def new_property(self, key_type, value_type, vals=None): """Create a new (uninitialized) vertex property map of key type ``key_type`` (``v``, ``e`` or ``g``), value type ``value_type``, and return it. If provided, the values will be initialized by ``vals``, which should be a sequence. """ if key_type == "v" or key_type == "vertex": return self.new_vertex_property(value_type, vals) if key_type == "e" or key_type == "edge": return self.new_edge_property(value_type, vals) if key_type == "g" or key_type == "graph": return self.new_graph_property(value_type, vals) raise ValueError("unknown key type: " + key_type) def new_vertex_property(self, value_type, vals=None): """Create a new (uninitialized) vertex property map of type ``value_type``, and return it. If provided, the values will be initialized by ``vals``, which should be either a sequence or a single value.""" prop = PropertyMap(new_vertex_property(_type_alias(value_type), self.__graph.GetVertexIndex(), libcore.any()), self, "v") if vals is not None: try: prop.a = vals except ValueError: for v, x in zip(self.vertices(), vals): prop[v] = x return prop def new_edge_property(self, value_type, vals=None): """Create a new (uninitialized) edge property map of type ``value_type``, and return it. If provided, the values will be initialized by ``vals``, which should be a sequence or a single value.""" prop = PropertyMap(new_edge_property(_type_alias(value_type), self.__graph.GetEdgeIndex(), libcore.any()), self, "e") if vals is not None: try: prop.a = vals except ValueError: for e, x in zip(self.edges(), vals): prop[e] = x return prop def new_graph_property(self, value_type, val=None): """Create a new graph property map of type ``value_type``, and return it. If ``val`` is not None, the property is initialized to its value.""" prop = PropertyMap(new_graph_property(_type_alias(value_type), self.__graph.GetGraphIndex(), libcore.any()), self, "g") if val is not None: prop[self] = val return prop # property map copying @_require("src", PropertyMap) @_require("tgt", (PropertyMap, type(None))) def copy_property(self, src, tgt=None, value_type=None, g=None): """Copy contents of ``src`` property to ``tgt`` property. If ``tgt`` is None, then a new property map of the same type (or with the type given by the optional ``value_type`` parameter) is created, and returned. The optional parameter g specifies the (identical) source graph to copy properties from (defaults to self). """ if tgt is None: tgt = self.new_property(src.key_type(), (src.value_type() if value_type == None else value_type)) ret = tgt else: ret = None if src.key_type() != tgt.key_type(): raise ValueError("source and target properties must have the same" + " key type") u = self if g is None else g g = GraphView(u, directed=True, reversed=u.is_reversed(), skip_properties=True) if src.key_type() == "v": self.__graph.CopyVertexProperty(g.__graph, _prop("v", g, src), _prop("v", self, tgt)) elif src.key_type() == "e": self.__graph.CopyEdgeProperty(g.__graph, _prop("e", g, src), _prop("e", self, tgt)) else: tgt[self] = src[g] return ret # degree property map @_limit_args({"deg": ["in", "out", "total"]}) def degree_property_map(self, deg, weight=None): """Create and return a vertex property map containing the degree type given by ``deg``, which can be any of ``"in"``, ``"out"``, or ``"total"``. If provided, ``weight`` should be an edge :class:`~graph_tool.PropertyMap` containing the edge weights which should be summed.""" pmap = self.__graph.DegreeMap(deg, _prop("e", self, weight)) return PropertyMap(pmap, self, "v") # I/O operations # ============== def __get_file_format(self, file_name): fmt = None for f in ["gt", "graphml", "xml", "dot", "gml"]: names = ["." + f, ".%s.gz" % f, ".%s.bz2" % f, ".%s.xz" % f] for name in names: if file_name.endswith(name): fmt = f break if fmt is None: raise ValueError("cannot determine file format of: " + file_name) return fmt def load(self, file_name, fmt="auto", ignore_vp=None, ignore_ep=None, ignore_gp=None): """Load graph from ``file_name`` (which can be either a string or a file-like object). The format is guessed from ``file_name``, or can be specified by ``fmt``, which can be either "gt", "graphml", "xml", "dot" or "gml". (Note that "graphml" and "xml" are synonyms). If provided, the parameters ``ignore_vp``, ``ignore_ep`` and ``ignore_gp``, should contain a list of property names (vertex, edge or graph, respectively) which should be ignored when reading the file. .. warning:: The only file formats which are capable of perfectly preserving the internal property maps are "gt" and "graphml". Because of this, they should be preferred over the other formats whenever possible. """ if isinstance(file_name, str): file_name = os.path.expanduser(file_name) f = open(file_name) # throw the appropriate exception, if not found if fmt == 'auto' and isinstance(file_name, str): fmt = self.__get_file_format(file_name) elif fmt == "auto": fmt = "gt" if isinstance(file_name, str) and file_name.endswith(".xz"): try: import lzma file_name = lzma.open(file_name, mode="rb") except ImportError: raise ValueError("lzma compression is only available in Python >= 3.3") if fmt == "graphml": fmt = "xml" if ignore_vp is None: ignore_vp = [] if ignore_ep is None: ignore_ep = [] if ignore_gp is None: ignore_gp = [] if isinstance(file_name, str): props = self.__graph.ReadFromFile(file_name, None, fmt, ignore_vp, ignore_ep, ignore_gp) else: props = self.__graph.ReadFromFile("", file_name, fmt, ignore_vp, ignore_ep, ignore_gp) for name, prop in props[0].items(): self.vertex_properties[name] = PropertyMap(prop, self, "v") for name, prop in props[1].items(): self.edge_properties[name] = PropertyMap(prop, self, "e") for name, prop in props[2].items(): self.graph_properties[name] = PropertyMap(prop, self, "g") if "_Graph__save__vfilter" in self.graph_properties: self.set_vertex_filter(self.vertex_properties["_Graph__save__vfilter"], self.graph_properties["_Graph__save__vfilter"]) del self.vertex_properties["_Graph__save__vfilter"] del self.graph_properties["_Graph__save__vfilter"] if "_Graph__save__efilter" in self.graph_properties: self.set_edge_filter(self.edge_properties["_Graph__save__efilter"], self.graph_properties["_Graph__save__efilter"]) del self.edge_properties["_Graph__save__efilter"] del self.graph_properties["_Graph__save__efilter"] if "_Graph__reversed" in self.graph_properties: self.set_reversed(True) del self.graph_properties["_Graph__reversed"] def save(self, file_name, fmt="auto"): """Save graph to ``file_name`` (which can be either a string or a file-like object). The format is guessed from the ``file_name``, or can be specified by ``fmt``, which can be either "gt", "graphml", "xml", "dot" or "gml". (Note that "graphml" and "xml" are synonyms). .. warning:: The only file formats which are capable of perfectly preserving the internal property maps are "gt" and "graphml". Because of this, they should be preferred over the other formats whenever possible. """ u = GraphView(self, reversed=self.is_reversed(), skip_vfilt=True, skip_efilt=True) if self.get_vertex_filter()[0] is not None: u.graph_properties["_Graph__save__vfilter"] = self.new_graph_property("bool") u.vertex_properties["_Graph__save__vfilter"] = self.get_vertex_filter()[0] u.graph_properties["_Graph__save__vfilter"] = self.get_vertex_filter()[1] if self.get_edge_filter()[0] is not None: u.graph_properties["_Graph__save__efilter"] = self.new_graph_property("bool") u.edge_properties["_Graph__save__efilter"] = self.get_edge_filter()[0] u.graph_properties["_Graph__save__efilter"] = self.get_edge_filter()[1] if self.is_reversed(): u.graph_properties["_Graph__reversed"] = self.new_graph_property("bool") u.graph_properties["_Graph__reversed"] = True if type(file_name) == str: file_name = os.path.expanduser(file_name) if fmt == 'auto' and isinstance(file_name, str): fmt = self.__get_file_format(file_name) elif fmt == "auto": fmt = "gt" if fmt == "graphml": fmt = "xml" if isinstance(file_name, str) and file_name.endswith(".xz"): try: import lzma file_name = lzma.open(file_name, mode="wb") except ImportError: raise ValueError("lzma compression is only available in Python >= 3.3") props = [(name[1], prop._PropertyMap__map) for name, prop in \ self.__properties.items()] if isinstance(file_name, str): f = open(file_name, "w") # throw the appropriate exception, if # unable to open f.close() u.__graph.WriteToFile(file_name, None, fmt, props) else: u.__graph.WriteToFile("", file_name, fmt, props) # Directedness # ============ def set_directed(self, is_directed): """Set the directedness of the graph.""" self.__graph.SetDirected(is_directed) def is_directed(self): """Get the directedness of the graph.""" return self.__graph.GetDirected() # Reversedness # ============ def set_reversed(self, is_reversed): """Reverse the direction of the edges, if ``is_reversed`` is ``True``, or maintain the original direction otherwise.""" self.__graph.SetReversed(is_reversed) def is_reversed(self): """Return ``True`` if the edges are reversed, and ``False`` otherwise. """ return self.__graph.GetReversed() # Filtering # ========= def set_filters(self, eprop, vprop, inverted_edges=False, inverted_vertices=False): """Set the boolean properties for edge and vertex filters, respectively. Only the vertices and edges with value different than ``True`` are kept in the filtered graph. If either the ``inverted_edges`` or ``inverted_vertex`` options are supplied with the value ``True``, only the edges or vertices with value ``False`` are kept. If any of the supplied property is ``None``, an empty filter is constructed which allows all edges or vertices.""" if eprop is None and vprop is None: return if eprop is None: eprop = self.new_edge_property("bool") eprop.a = not inverted_edges if vprop is None: vprop = self.new_vertex_property("bool") vprop.a = not inverted_vertices self.__graph.SetVertexFilterProperty(_prop("v", self, vprop), inverted_vertices) self.__filter_state["vertex_filter"] = (vprop, inverted_vertices) self.__graph.SetEdgeFilterProperty(_prop("e", self, eprop), inverted_edges) self.__filter_state["edge_filter"] = (eprop, inverted_edges) def set_vertex_filter(self, prop, inverted=False): """Set the vertex boolean filter property. Only the vertices with value different than ``False`` are kept in the filtered graph. If the ``inverted`` option is supplied with value ``True``, only the vertices with value ``False`` are kept. If the supplied property is ``None``, the filter is replaced by an uniform filter allowing all vertices.""" if prop is not None and prop.value_type() != "bool": raise ValueError("filter property map must have 'bool' type") vfilt = prop efilt = None eprop = self.get_edge_filter() if eprop[0] is None and vfilt is not None: efilt = self.new_edge_property("bool") efilt.a = True if eprop[0] is not None and vfilt is None: vfilt = self.new_vertex_property("bool") vfilt.a = not inverted self.__graph.SetVertexFilterProperty(_prop("v", self, vfilt), inverted) self.__filter_state["vertex_filter"] = (vfilt, inverted) if efilt is not None: self.set_edge_filter(efilt) def get_vertex_filter(self): """Return a tuple with the vertex filter property and bool value indicating whether or not it is inverted.""" return self.__filter_state["vertex_filter"] def set_edge_filter(self, prop, inverted=False): """Set the edge boolean filter property. Only the edges with value different than ``False`` are kept in the filtered graph. If the ``inverted`` option is supplied with value ``True``, only the edges with value ``False`` are kept. If the supplied property is ``None``, the filter is replaced by an uniform filter allowing all edges.""" if prop is not None and prop.value_type() != "bool": raise ValueError("filter property map must have 'bool' type") efilt = prop vfilt = None vprop = self.get_vertex_filter() if vprop[0] is None and efilt is not None: vfilt = self.new_vertex_property("bool") vfilt.a = True if vprop[0] is not None and efilt is None: efilt = self.new_edge_property("bool") efilt.a = not inverted self.__graph.SetEdgeFilterProperty(_prop("e", self, efilt), inverted) self.__filter_state["edge_filter"] = (efilt, inverted) if vfilt is not None: self.set_vertex_filter(vfilt) def get_edge_filter(self): """Return a tuple with the edge filter property and bool value indicating whether or not it is inverted.""" return self.__filter_state["edge_filter"] def clear_filters(self): """Remove vertex and edge filters, and set the graph to the unfiltered state.""" self.__graph.SetVertexFilterProperty(_prop("v", self, None), False) self.__filter_state["vertex_filter"] = (None, False) self.__graph.SetEdgeFilterProperty(_prop("e", self, None), False) self.__filter_state["edge_filter"] = (None, False) def purge_vertices(self, in_place=False): """Remove all vertices of the graph which are currently being filtered out, and return it to the unfiltered state. This operation is not reversible. If the option ``in_place == True`` is given, the algorithm will remove the filtered vertices and re-index all property maps which are tied with the graph. This is a slow operation which has an :math:`O(N^2)` complexity. If ``in_place == False``, the graph and its vertex and edge property maps are temporarily copied to a new unfiltered graph, which will replace the contents of the original graph. This is a fast operation with an :math:`O(N + E)` complexity. This is the default behaviour if no option is given. """ if in_place: old_indexes = self.vertex_index.copy("int64_t") self.__graph.PurgeVertices(_prop("v", self, old_indexes)) self.set_vertex_filter(None) for pmap in self.__known_properties.values(): if (pmap() is not None and pmap().key_type() == "v" and pmap().is_writable() and pmap() not in [self.vertex_index, self.edge_index]): self.__graph.ReIndexVertexProperty(pmap()._PropertyMap__map.get_map(), _prop("v", self, old_indexes)) else: stamp = id(self) pmaps = [] for pmap in self.__known_properties.values(): if (pmap() is not None and pmap().key_type() in ["v", "e"] and pmap() not in [self.vertex_index, self.edge_index]): pmaps.append(pmap()) pname = "__tmp_purge_vertices_%d_%d" % (stamp, id(pmaps[-1])) self.properties[(pmaps[-1].key_type(), pname)] = pmaps[-1] new_g = Graph(self, prune=(True, False, False)) self.__graph = new_g.__graph self.set_vertex_filter(None) for pmap in pmaps: pname = "__tmp_purge_vertices_%d_%d" % (stamp, id(pmap)) new_pmap = new_g.properties[(pmap.key_type(), pname)] pmap._PropertyMap__map = new_pmap._PropertyMap__map del self.properties[(pmap.key_type(), pname)] # update edge filter if set efilt = self.get_edge_filter() if efilt[0] is not None: self.set_edge_filter(efilt[0], efilt[1]) def purge_edges(self): """Remove all edges of the graph which are currently being filtered out, and return it to the unfiltered state. This operation is not reversible.""" self.__graph.PurgeEdges() self.set_edge_filter(None) def get_filter_state(self): """Return a copy of the filter state of the graph.""" self.__filter_state["directed"] = self.is_directed() self.__filter_state["reversed"] = self.is_reversed() return copy.copy(self.__filter_state) def set_filter_state(self, state): """Set the filter state of the graph.""" if libcore.graph_filtering_enabled(): self.set_vertex_filter(state["vertex_filter"][0], state["vertex_filter"][1]) self.set_edge_filter(state["edge_filter"][0], state["edge_filter"][1]) self.set_directed(state["directed"]) self.set_reversed(state["reversed"]) # Basic graph statistics # ====================== def num_vertices(self): """Get the number of vertices. .. note:: If the vertices are being filtered, this operation is :math:`O(N)`. Otherwise it is :math:`O(1)`. """ return self.__graph.GetNumberOfVertices(True) def num_edges(self): """Get the number of edges. .. note:: If the edges are being filtered, this operation is :math:`O(E)`. Otherwise it is :math:`O(1)`. """ return self.__graph.GetNumberOfEdges(True) # Pickling support # ================ def __getstate__(self): state = dict() if sys.version_info < (3,): sio = StringIO.StringIO() else: sio = io.BytesIO() stream = gzip.GzipFile(fileobj=sio, mode="wb") self.save(stream, "gt") stream.close() state["blob"] = sio.getvalue() return state def __setstate__(self, state): self.__init__() blob = state["blob"] if blob != "": try: if sys.version_info < (3,): sio = StringIO.StringIO(blob) else: sio = io.BytesIO(blob) stream = gzip.GzipFile(fileobj=sio, mode="rb") self.load(stream, "gt") except OSError: if sys.version_info < (3,): sio = StringIO.StringIO(blob) else: sio = io.BytesIO(blob) stream = gzip.GzipFile(fileobj=sio, mode="rb") self.load(stream, "xml") def load_graph(file_name, fmt="auto", ignore_vp=None, ignore_ep=None, ignore_gp=None): """Load a graph from ``file_name`` (which can be either a string or a file-like object). The format is guessed from ``file_name``, or can be specified by ``fmt``, which can be either "gt", "graphml", "xml", "dot" or "gml". (Note that "graphml" and "xml" are synonyms). If provided, the parameters ``ignore_vp``, ``ignore_ep`` and ``ignore_gp``, should contain a list of property names (vertex, edge or graph, respectively) which should be ignored when reading the file. .. warning:: The only file formats which are capable of perfectly preserving the internal property maps are "gt" and "graphml". Because of this, they should be preferred over the other formats whenever possible. """ g = Graph() g.load(file_name, fmt, ignore_vp, ignore_ep, ignore_gp) return g class GraphView(Graph): """ A view of selected vertices or edges of another graph. This class uses shared data from another :class:`~graph_tool.Graph` instance, but allows for local filtering of vertices and/or edges, edge directionality or reversal. See :ref:`sec_graph_views` for more details and examples. The existence of a :class:`~graph_tool.GraphView` object does not affect the original graph, except if the graph view is modified (addition or removal of vertices or edges), in which case the modification is directly reflected in the original graph (and vice-versa), since they both point to the same underlying data. Because of this, instances of :class:`~graph_tool.PropertyMap` can be used interchangeably with a graph and its views. The argument ``g`` must be an instance of a :class:`~graph_tool.Graph` class. If specified, ``vfilt`` and ``efilt`` select which vertices and edges are filtered, respectively. These parameters can either be a boolean-valued :class:`~graph_tool.PropertyMap` or a :class:`~numpy.ndarray`, which specify which vertices/edges are selected, or an unary function which returns ``True`` if a given vertex/edge is to be selected, or ``False`` otherwise. The boolean parameter ``directed`` can be used to set the directionality of the graph view. If ``directed = None``, the directionality is inherited from ``g``. If ``reversed = True``, the direction of the edges is reversed. If ``vfilt`` or ``efilt`` is anything other than a :class:`~graph_tool.PropertyMap` instance, the instantiation running time is :math:`O(V)` and :math:`O(E)`, respectively. Otherwise, the running time is :math:`O(1)`. If either ``skip_properties``, ``skip_vfilt`` or ``skip_efilt`` is ``True``, then the internal properties, vertex filter or edge filter of the original graph are ignored, respectively. """ def __init__(self, g, vfilt=None, efilt=None, directed=None, reversed=False, skip_properties=False, skip_vfilt=False, skip_efilt=False): self.__base = g if not isinstance(g, GraphView) else g.base Graph.__init__(self) # copy graph reference self._Graph__graph = libcore.GraphInterface(g._Graph__graph, True, [], [], _prop("v", g, g.vertex_index)) if not skip_properties: for k, v in g.properties.items(): self.properties[k] = self.own_property(v) # set already existent filters if not skip_vfilt: vf = g.get_vertex_filter() if vf[0] is not None: self.set_vertex_filter(vf[0], vf[1]) if not skip_efilt: ef = g.get_edge_filter() if ef[0] is not None: self.set_edge_filter(ef[0], ef[1]) if vfilt is not None: if type(vfilt) is PropertyMap: self.set_vertex_filter(vfilt) else: vmap = self.new_vertex_property("bool") if issubclass(type(vfilt), numpy.ndarray): vmap.fa = vfilt else: for v in g.vertices(): vmap[v] = vfilt(v) self.set_vertex_filter(vmap) if efilt is not None: if type(efilt) is PropertyMap: self.set_edge_filter(efilt) else: emap = self.new_edge_property("bool") if issubclass(type(efilt), numpy.ndarray): emap.fa = efilt else: for e in g.edges(): emap[e] = efilt(e) self.set_edge_filter(emap) if directed is not None: self.set_directed(directed) if reversed: self.set_reversed(not g.is_reversed()) def __get_base(self): return self.__base base = property(__get_base, doc="Base graph.") # pickling support def __getstate__(self): return Graph.__getstate__(self) def __setstate__(self, state): g = Graph() g.__setstate__(state) self.__init__(g) def value_types(): """Return a list of possible properties value types.""" return libcore.get_property_types() # Vertex and Edge Types # ===================== from .libgraph_tool_core import Vertex, Edge, EdgeBase Vertex.__doc__ = """Vertex descriptor. This class represents a vertex in a :class:`~graph_tool.Graph` instance. :class:`~graph_tool.Vertex` instances are hashable, and are convertible to integers, corresponding to its index (see :attr:`~graph_tool.Graph.vertex_index`). """ def _out_neighbours(self): """Return an iterator over the out-neighbours.""" for e in self.out_edges(): yield e.target() Vertex.out_neighbours = _out_neighbours def _in_neighbours(self): """Return an iterator over the in-neighbours.""" for e in self.in_edges(): yield e.source() Vertex.in_neighbours = _in_neighbours def _all_edges(self): """Return an iterator over all edges (both in or out).""" for e in self.out_edges(): yield e for e in self.in_edges(): yield e Vertex.all_edges = _all_edges def _all_neighbours(self): """Return an iterator over all neighbours (both in or out).""" for v in self.out_neighbours(): yield v for v in self.in_neighbours(): yield v Vertex.all_neighbours = _all_neighbours def _in_degree(self, weight=None): """Return the in-degree of the vertex. If provided, ``weight`` should be a scalar edge property map, and the in-degree will correspond to the sum of the weights of the in-edges. """ if weight is None: return self.__in_degree() else: return self.__weighted_in_degree(_prop("e", self.get_graph(), weight)) Vertex.in_degree = _in_degree def _out_degree(self, weight=None): """Return the out-degree of the vertex. If provided, ``weight`` should be a scalar edge property map, and the out-degree will correspond to the sum of the weights of the out-edges. """ if weight is None: return self.__out_degree() else: return self.__weighted_out_degree(_prop("e", self.get_graph(), weight)) Vertex.out_degree = _out_degree def _vertex_repr(self): if not self.is_valid(): return "" % (id(self)) return "" % (int(self), id(self)) Vertex.__repr__ = _vertex_repr Vertex.__eq__ = lambda v1, v2 : int(v1) == (int(v2) if isinstance(v2, Vertex) else v2) Vertex.__ne__ = lambda v1, v2 : int(v1) != (int(v2) if isinstance(v2, Vertex) else v2) Vertex.__lt__ = lambda v1, v2 : int(v1) < (int(v2) if isinstance(v2, Vertex) else v2) Vertex.__gt__ = lambda v1, v2 : int(v1) > (int(v2) if isinstance(v2, Vertex) else v2) Vertex.__le__ = lambda v1, v2 : int(v1) <= (int(v2) if isinstance(v2, Vertex) else v2) Vertex.__ge__ = lambda v1, v2 : int(v1) >= (int(v2) if isinstance(v2, Vertex) else v2) _edge_doc = """Edge descriptor. This class represents an edge in a :class:`~graph_tool.Graph`. :class:`~graph_tool.Edge` instances are hashable, and are convertible to a tuple, which contains the source and target vertices. """ def _edge_cmp(e1, e2): te1, te2 = tuple(e1), tuple(e2) g1 = e1.get_graph() g2 = e2.get_graph() if not g1.is_directed(): te1 = sorted(te1) if not g2.is_directed(): te2 = sorted(te2) te1 = (te1, g1.edge_index[e1]) te2 = (te2, g2.edge_index[e2]) if te1 < te2: return -1 if te1 > te2: return 1 return 0 def _edge_iter(self): """Iterate over the source and target""" for v in [self.source(), self.target()]: yield v def _edge_repr(self): if not self.is_valid(): return "" % (id(self)) return ("") % (int(self.source()), int(self.target()), id(self)) # There are several edge classes... me must cycle through them all to modify # them. def init_edge_classes(): for directed in [True, False]: for e_reversed in [True, False]: for e_filtered in [True, False]: for v_filtered in [True, False]: g = Graph(directed=directed) g.set_reversed(e_reversed) v = g.add_vertex() g.add_edge(v, v) if e_filtered: e_filter = g.new_edge_property("bool") e_filter.a = [1] g.set_edge_filter(e_filter) if v_filtered: v_filter = g.new_vertex_property("bool") v_filter.a = [1] g.set_vertex_filter(v_filter) e = next(g.edges()) e.__class__.__repr__ = _edge_repr e.__class__.__iter__ = _edge_iter e.__class__.__doc__ = _edge_doc e.__class__.__eq__ = lambda e1, e2 : _edge_cmp(e1, e2) == 0 e.__class__.__ne__ = lambda e1, e2 : _edge_cmp(e1, e2) != 0 e.__class__.__lt__ = lambda e1, e2 : _edge_cmp(e1, e2) < 0 e.__class__.__gt__ = lambda e1, e2 : _edge_cmp(e1, e2) > 0 e.__class__.__le__ = lambda e1, e2 : _edge_cmp(e1, e2) <= 0 e.__class__.__ge__ = lambda e1, e2 : _edge_cmp(e1, e2) >= 0 init_edge_classes() # some shenanigans to make it seem there is only a single edge class EdgeBase.__doc__ = Edge.__doc__ EdgeBase.source = Edge.source EdgeBase.target = Edge.target EdgeBase.is_valid = Edge.is_valid EdgeBase.get_graph = Edge.get_graph Edge = EdgeBase Edge.__name__ = "Edge" # Add convenience function to vector classes def _get_array_view(self): return self.get_array()[:] def _set_array_view(self, v): self.get_array()[:] = v vector_types = [Vector_bool, Vector_int16_t, Vector_int32_t, Vector_int64_t, Vector_double, Vector_long_double] for vt in vector_types: vt.a = property(_get_array_view, _set_array_view, doc=r"""Shortcut to the `get_array` method as an attribute.""") vt.__repr__ = lambda self: self.a.__repr__() Vector_string.a = None Vector_string.get_array = lambda self: None Vector_string.__repr__ = lambda self: repr(list(self)) # Global RNG _rng = libcore.get_rng((numpy.random.randint(0, sys.maxsize) + os.getpid()) % sys.maxsize) def seed_rng(seed): "Seed the random number generator used by graph-tool's algorithms." import graph_tool graph_tool._rng = libcore.get_rng(int(seed)) def _get_rng(): global _rng return _rng # OpenMP Setup def openmp_enabled(): """Return `True` if OpenMP was enabled during compilation.""" return libcore.openmp_enabled() def openmp_get_num_threads(): """Return the number of OpenMP threads.""" return libcore.openmp_get_num_threads() def openmp_set_num_threads(n): """Set the number of OpenMP threads.""" return libcore.openmp_set_num_threads(n) def openmp_get_schedule(): """Return the runtime OpenMP schedule and chunk size. The schedule can by any of: `"static"`, `"dynamic"`, `"guided"`, `"auto"`.""" return libcore.openmp_get_schedule() def openmp_set_schedule(schedule, chunk=0): """Set the runtime OpenMP schedule and chunk size. The schedule can by any of: `"static"`, `"dynamic"`, `"guided"`, `"auto"`.""" return libcore.openmp_set_schedule(schedule, chunk) if openmp_enabled() and os.environ.get("OMP_SCHEDULE") is None: openmp_set_schedule("static", 0)