graph_tool.GraphView

graph_tool.GraphView#

class graph_tool.GraphView(g, vfilt=None, efilt=None, directed=None, reversed=False, skip_properties=False, skip_vfilt=False, skip_efilt=False)[source]#

Bases: Graph

A view of selected vertices or edges of another graph.

This class uses shared data from another Graph instance, but allows for local filtering of vertices and/or edges, edge directionality or reversal. See Graph views for more details and examples.

The existence of a 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 PropertyMap can be used interchangeably with a graph and its views.

The argument g must be an instance of a Graph class. If specified, vfilt and efilt select which vertices and edges are filtered, respectively. These parameters can either be a boolean-valued PropertyMap or numpy.ndarray, which specify which vertices/edges are selected, or an unary function that 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 is 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 PropertyMap instance, the instantiation running time is \(O(V)\) and \(O(E)\), respectively. Otherwise, the running time is \(O(1)\).

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.

Methods

`add_edge`(source, target[, add_missing])	Add a new edge from `source` to `target` to the graph, and return it.
`add_edge_list`(edge_list[, hashed, ...])	Add a list of edges to the graph, given by `edge_list`, which can be an iterator of `(source, target)` pairs where both `source` and `target` are vertex indices (or can be so converted), or a `numpy.ndarray` of shape `(E,2)`, where `E` is the number of edges, and each line specifies a `(source, target)` pair.
`add_vertex`([n])	Add a vertex to the graph, and return it.
`clear`()	Remove all vertices and edges from the graph.
`clear_edges`()	Remove all edges from the graph.
`clear_filters`()	Remove vertex and edge filters, and set the graph to the unfiltered state.
`clear_vertex`(vertex)	Remove all in and out-edges from the given vertex.
`copy`()	Return a deep copy of self.
`copy_property`(src[, tgt, value_type, g, full])	Copy contents of `src` property to `tgt` property.
`degree_property_map`(deg[, weight])	Create and return a vertex property map containing the degree type given by `deg`, which can be any of `"in"`, `"out"`, or `"total"`.
`edge`(s, t[, all_edges, add_missing])	Return the edge from vertex `s` to `t`, if it exists.
`edges`()	Return an `iterator` over the edges.
`get_all_edges`(v[, eprops])	Return a `numpy.ndarray` containing the in- and out-edges of vertex v, and optional edge properties list `eprops`.
`get_all_neighbors`(v[, vprops])	Return a `numpy.ndarray` containing the in-neighbors and out-neighbors of vertex `v`, and optional vertex properties list `vprops`.
`get_all_neighbours`(v[, vprops])	Return a `numpy.ndarray` containing the in-neighbors and out-neighbors of vertex `v`, and optional vertex properties list `vprops`.
`get_edge_filter`()	Return a tuple with the edge filter property and bool value indicating whether or not it is inverted.
`get_edges`([eprops])	Return a `numpy.ndarray` containing the edges, and optional edge properties list `eprops`.
`get_fast_edge_removal`()	Return whether the fast \(O(1)\) removal of edges is currently enabled.
`get_filter_state`()	Return a copy of the filter state of the graph.
`get_in_degrees`(vs[, eweight])	Return a `numpy.ndarray` containing the in-degrees of vertex list `vs`.
`get_in_edges`(v[, eprops])	Return a `numpy.ndarray` containing the in-edges of vertex `v`, and optional edge properties list `eprops`.
`get_in_neighbors`(v[, vprops])	Return a `numpy.ndarray` containing the in-neighbors of vertex `v`, and optional vertex properties list `vprops`.
`get_in_neighbours`(v[, vprops])	Return a `numpy.ndarray` containing the in-neighbors of vertex `v`, and optional vertex properties list `vprops`.
`get_out_degrees`(vs[, eweight])	Return a `numpy.ndarray` containing the out-degrees of vertex list `vs`.
`get_out_edges`(v[, eprops])	Return a `numpy.ndarray` containing the out-edges of vertex `v`, and optional edge properties list `eprops`.
`get_out_neighbors`(v[, vprops])	Return a `numpy.ndarray` containing the out-neighbors of vertex `v`, and optional vertex properties list `vprops`.
`get_out_neighbours`(v[, vprops])	Return a `numpy.ndarray` containing the out-neighbors of vertex `v`, and optional vertex properties list `vprops`.
`get_total_degrees`(vs[, eweight])	Return a `numpy.ndarray` containing the total degrees (i.e. in- plus out-degree) of vertex list `vs`.
`get_vertex_filter`()	Return a tuple with the vertex filter property and bool value indicating whether or not it is inverted.
`get_vertices`([vprops])	Return a `numpy.ndarray` containing the vertex indices, and optional vertex properties list `vprops`.
`is_directed`()	Get the directedness of the graph.
`is_reversed`()	Return `True` if the edges are reversed, and `False` otherwise.
`iter_all_edges`(v[, eprops])	Return an iterator over the in- and out-edge `(source, target) pairs for vertex `v`, and optional edge properties list `eprops`.
`iter_all_neighbors`(v[, vprops])	Return an iterator over the in- and out-neighbors of vertex `v`, and optional vertex properties list `vprops`.
`iter_all_neighbours`(v[, vprops])	Return an iterator over the in- and out-neighbors of vertex `v`, and optional vertex properties list `vprops`.
`iter_edges`([eprops])	Return an iterator over the edge `(source, target) pairs, and optional edge properties list `eprops`.
`iter_in_edges`(v[, eprops])	Return an iterator over the in-edge `(source, target) pairs for vertex `v`, and optional edge properties list `eprops`.
`iter_in_neighbors`(v[, vprops])	Return an iterator over the in-neighbors of vertex `v`, and optional vertex properties list `vprops`.
`iter_in_neighbours`(v[, vprops])	Return an iterator over the in-neighbors of vertex `v`, and optional vertex properties list `vprops`.
`iter_out_edges`(v[, eprops])	Return an iterator over the out-edge `(source, target) pairs for vertex `v`, and optional edge properties list `eprops`.
`iter_out_neighbors`(v[, vprops])	Return an iterator over the out-neighbors of vertex `v`, and optional vertex properties list `vprops`.
`iter_out_neighbours`(v[, vprops])	Return an iterator over the out-neighbors of vertex `v`, and optional vertex properties list `vprops`.
`iter_vertices`([vprops])	Return an iterator over the vertex indices, and optional vertex properties list `vprops`.
`list_properties`()	Print a list of all internal properties.
`load`(file_name[, fmt, ignore_vp, ignore_ep, ...])	Load graph from `file_name` (which can be either a string or a file-like object).
`new_edge_property`(value_type[, vals, val])	Create a new edge property map of type `value_type`, and return it.
`new_ep`(value_type[, vals, val])	Alias to `new_edge_property()`.
`new_gp`(value_type[, val])	Alias to `new_graph_property()`.
`new_graph_property`(value_type[, val])	Create a new graph property map of type `value_type`, and return it.
`new_property`(key_type, value_type[, vals])	Create a new (uninitialized) vertex property map of key type `key_type` (`v`, `e` or `g`), value type `value_type`, and return it.
`new_vertex_property`(value_type[, vals, val])	Create a new vertex property map of type `value_type`, and return it.
`new_vp`(value_type[, vals, val])	Alias to `new_vertex_property()`.
`num_edges`([ignore_filter])	Get the number of edges.
`num_vertices`([ignore_filter])	Get the number of vertices.
`own_property`(prop)	Return a version of the property map 'prop' (possibly belonging to another graph) which is owned by the current graph.
`purge_edges`()	Remove all edges of the graph which are currently being filtered out.
`purge_vertices`([in_place])	Remove all vertices of the graph which are currently being filtered out.
`reindex_edges`()	Reset the edge indices so that they lie in the [0, `num_edges()` - 1] range.
`remove_edge`(edge)	Remove an edge from the graph.
`remove_vertex`(vertex[, fast])	Remove a vertex from the graph.
`save`(file_name[, fmt])	Save graph to `file_name` (which can be either a string or a file-like object).
`set_directed`(is_directed)	Set the directedness of the graph.
`set_edge_filter`(prop[, inverted])	Set the edge boolean filter property.
`set_fast_edge_removal`([fast])	If `fast == True` the fast \(O(1)\) removal of edges will be enabled.
`set_filter_state`(state)	Set the filter state of the graph.
`set_filters`(eprop, vprop[, inverted_edges, ...])	Set the boolean properties for edge and vertex filters, respectively.
`set_reversed`(is_reversed)	Reverse the direction of the edges, if `is_reversed` is `True`, or maintain the original direction otherwise.
`set_vertex_filter`(prop[, inverted])	Set the vertex boolean filter property.
`shrink_to_fit`()	Force the physical capacity of the underlying containers to match the graph's actual size, potentially freeing memory back to the system.
`vertex`(i[, use_index, add_missing])	Return the vertex with index `i`.
`vertices`()	Return an `iterator` over the vertices.

Attributes

`base`	Base graph.
`edge_index`	Edge index map.
`edge_index_range`	The size of the range of edge indices.
`edge_properties`	Dictionary of internal edge properties.
`ep`	Alias to `edge_properties`.
`gp`	Alias to `graph_properties`.
`graph_properties`	Dictionary of internal graph properties.
`properties`	Dictionary of internal properties.
`vertex_index`	Vertex index map.
`vertex_properties`	Dictionary of internal vertex properties.
`vp`	Alias to `vertex_properties`.

add_edge(source, target, add_missing=True)#

Add a new edge from source to target to the graph, and return it. This operation is \(O(1)\).

If add_missing == True, the source and target vertices are included in the graph if they don’t yet exist.

add_edge_list(edge_list, hashed=False, hash_type='string', eprops=None)#

Add a list of edges to the graph, given by edge_list, which can be an iterator of (source, target) pairs where both source and target are vertex indices (or can be so converted), or a 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.

Optionally, if hashed == True, the vertex values in the edge list are not assumed to correspond to vertex indices directly. In this case they will be mapped to vertex indices according to the order in which they are encountered, and a vertex property map with the vertex values is returned. The option hash_type will determine the expected type used by the hash keys, and they can be any property map value type (see PropertyMap), unless edge_list is a numpy.ndarray, in which case the value of this option is ignored, and the type is determined automatically.

If hashed == False and the target value of an edge corresponds to the maximum interger value (sys.maxsize, or the maximum integer type of the numpy.ndarray object), or is a numpy.nan or numpy.inf value, then only the source vertex will be added to the graph.

If hashed == True, and the target value corresponds to None, then only the source vertex will be added to the graph.

If given, eprops should specify an iterable containing edge property maps that will be filled with the remaining values at each row, if there are more than two. Alternatively, eprops can contain a list of (name, value_type) pairs, in which case new internal dege property maps will be created with the corresponding name name and value type.

Note

If edge_list is a numpy.ndarray object, the execution of this function will be done entirely in C++, and hence much faster.

Examples

>>> edge_list = [(0, 1, .3, 10), (2, 3, .1, 0), (2, 0, .4, 42)]
>>> g = gt.Graph()
>>> eweight = g.new_ep("double")
>>> elayer = g.new_ep("int")
>>> g.add_edge_list(edge_list, eprops=[eweight, elayer])
>>> print(eweight.fa)
[0.3 0.1 0.4]
>>> g.get_edges()
array([[0, 1],
       [2, 3],
       [2, 0]])

add_vertex(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 \(O(n)\).

clear()#: Remove all vertices and edges from the graph.

clear_edges()#: Remove all edges from the graph.

clear_filters()#: Remove vertex and edge filters, and set the graph to the unfiltered state.

Note

This is a \(O(1)\) operation that does not modify the storage of the graph.

Warning

Clearing vertex and edge filters will invalidate existing vertex and edge descriptors.

clear_vertex(vertex)#: Remove all in and out-edges from the given vertex.

copy()#: Return a deep copy of self. All internal property maps are also copied.

copy_property(src, tgt=None, value_type=None, g=None, full=True)#: 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 source graph to copy properties from (defaults to the graph than owns src). If full == False, then in the case of filtered graphs only the unmasked values are copied (with the remaining ones taking the type-dependent default value).

Note

In case the source property map belongs to different graphs, this function behaves as follows.

For vertex properties, the source and target graphs must have the same number of vertices, and the properties are copied according to the index values.

For edge properties, the edge index is not important, and the properties are copied by matching edges between the different graphs according to the source and target vertex indices. In case the graph has parallel edges with the same source and target vertices, they are matched according to their iteration order. The edge sets do not have to be the same between source and target graphs, as the copying occurs only for edges that lie at their intersection.

degree_property_map(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 EdgePropertyMap containing the edge weights which should be summed.

edge(s, t, all_edges=False, add_missing=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.

If add_missing == True, a new edge is created and returned, if none currently exists.

This operation will take \(O(\min(k(s), k(t)))\) time, where \(k(s)\) and \(k(t)\) are the out-degree and in-degree (or out-degree if undirected) of vertices \(s\) and \(t\).

edges()#: Return an 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 edge_index property map. This will only happen after 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.

get_all_edges(v, eprops=[])#

Return a numpy.ndarray containing the in- and out-edges of vertex v, and optional edge properties list eprops. The shape of the array will be (E, 2 + len(eprops)), where E is the number of edges, and each line will contain the source, target and the edge property values.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> g.get_all_edges(66, [g.edge_index])
array([[    66,     63,   5266],
       [    66,  20369,   5267],
       [    66,  13980,   5268],
       [    66,   8687,   5269],
       [    66,  38674,   5270],
       [  8687,     66, 179681],
       [ 20369,     66, 255033],
       [ 38674,     66, 300230]])

get_all_neighbors(v, vprops=[])#

Return a numpy.ndarray containing the in-neighbors and out-neighbors of vertex v, and optional vertex properties list vprops. If vprops is not empty, the shape of the array will be (V, 1 + len(eprops)), where V is the number of vertices, and each line will contain a vertex and its property values.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> g.get_all_neighbors(66)
array([   63, 20369, 13980,  8687, 38674,  8687, 20369, 38674])

get_all_neighbours(v, vprops=[])#

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> g.get_all_neighbors(66)
array([   63, 20369, 13980,  8687, 38674,  8687, 20369, 38674])

get_edge_filter()#: Return a tuple with the edge filter property and bool value indicating whether or not it is inverted.

get_edges(eprops=[])#

Return a numpy.ndarray containing the edges, and optional edge properties list eprops. The shape of the array will be (E, 2 + len(eprops)), where E is the number of edges, and each line will contain the source, target and the edge property values.

Note

The order of the edges is identical to edges().

Examples

>>> g = gt.random_graph(6, lambda: 1, directed=False)
>>> g.get_edges([g.edge_index])
array([[0, 1, 2],
       [3, 4, 0],
       [5, 2, 1]])

get_fast_edge_removal()#: Return whether the fast \(O(1)\) removal of edges is currently enabled.

get_filter_state()#: Return a copy of the filter state of the graph.

get_in_degrees(vs, eweight=None)#

Return a numpy.ndarray containing the in-degrees of vertex list vs. If supplied, the degrees will be weighted according to the edge EdgePropertyMap eweight.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> g.get_in_degrees([42, 666])
array([20, 39], dtype=uint64)

get_in_edges(v, eprops=[])#

Return a numpy.ndarray containing the in-edges of vertex v, and optional edge properties list eprops. The shape of the array will be (E, 2 + len(eprops)), where E is the number of edges, and each line will contain the source, target and the edge property values.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> g.get_in_edges(66, [g.edge_index])
array([[  8687,     66, 179681],
       [ 20369,     66, 255033],
       [ 38674,     66, 300230]])

get_in_neighbors(v, vprops=[])#

Return a numpy.ndarray containing the in-neighbors of vertex v, and optional vertex properties list vprops. If vprops is not empty, the shape of the array will be (V, 1 + len(eprops)), where V is the number of vertices, and each line will contain a vertex and its property values.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> g.get_in_neighbors(66)
array([ 8687, 20369, 38674])

get_in_neighbours(v, vprops=[])#

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> g.get_in_neighbors(66)
array([ 8687, 20369, 38674])

get_out_degrees(vs, eweight=None)#

Return a numpy.ndarray containing the out-degrees of vertex list vs. If supplied, the degrees will be weighted according to the edge EdgePropertyMap eweight.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> g.get_out_degrees([42, 666])
array([20, 38], dtype=uint64)

get_out_edges(v, eprops=[])#

Return a numpy.ndarray containing the out-edges of vertex v, and optional edge properties list eprops. The shape of the array will be (E, 2 + len(eprops)), where E is the number of edges, and each line will contain the source, target and the edge property values.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> g.get_out_edges(66, [g.edge_index])
array([[   66,    63,  5266],
       [   66, 20369,  5267],
       [   66, 13980,  5268],
       [   66,  8687,  5269],
       [   66, 38674,  5270]])

get_out_neighbors(v, vprops=[])#

Return a numpy.ndarray containing the out-neighbors of vertex v, and optional vertex properties list vprops. If vprops is not empty, the shape of the array will be (V, 1 + len(eprops)), where V is the number of vertices, and each line will contain a vertex and its property values.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> g.get_out_neighbors(66)
array([   63, 20369, 13980,  8687, 38674])

get_out_neighbours(v, vprops=[])#

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> g.get_out_neighbors(66)
array([   63, 20369, 13980,  8687, 38674])

get_total_degrees(vs, eweight=None)#

Return a numpy.ndarray containing the total degrees (i.e. in- plus out-degree) of vertex list vs. If supplied, the degrees will be weighted according to the edge EdgePropertyMap eweight.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> g.get_total_degrees([42, 666])
array([40, 77], dtype=uint64)

get_vertex_filter()#: Return a tuple with the vertex filter property and bool value indicating whether or not it is inverted.

get_vertices(vprops=[])#

Return a numpy.ndarray containing the vertex indices, and optional vertex properties list vprops. If vprops is not empty, the shape of the array will be (V, 1 + len(vprops)), where V is the number of vertices, and each line will contain the vertex and the vertex property values.

Note

The order of the vertices is identical to vertices().

Examples

>>> g = gt.Graph()
>>> g.add_vertex(5)
<...>
>>> g.get_vertices()
array([0, 1, 2, 3, 4])

is_directed()#: Get the directedness of the graph.

is_reversed()#: Return True if the edges are reversed, and False otherwise.

iter_all_edges(v, eprops=[])#

Return an iterator over the in- and out-edge `(source, target) pairs for vertex v, and optional edge properties list eprops.

Note

This mode of iteration is more efficient than using all_edges(), as descriptor objects are not created.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> for s, t, i in g.iter_all_edges(66, [g.edge_index]):
...     print(s, t, i)
63 5266
20369 5267
13980 5268
8687 5269
38674 5270
66 179681
66 255033
66 300230

iter_all_neighbors(v, vprops=[])#

Return an iterator over the in- and out-neighbors of vertex v, and optional vertex properties list vprops.

Note

This mode of iteration is more efficient than using all_neighbors(), as descriptor objects are not created.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> for u, i in g.iter_all_neighbors(66, [g.vp.uid]):
...     print(u, i)
['paul wilders <webmaster@wilders.org>']
['Zhen-Xjell <zhen-xjell@teamhelix.net>']
['Hooman <Hooman@iname.com>']
['H. Loeung (howe81) <howe81@unixque.com>', 'howe81 <howe81@bigpond.net.au>', 'Howie L (howe81) <howe81@bigpond.net.au>']
['Howie L (howe81) <howe81@bigpond.net.au>']
['H. Loeung (howe81) <howe81@unixque.com>', 'howe81 <howe81@bigpond.net.au>', 'Howie L (howe81) <howe81@bigpond.net.au>']
['Zhen-Xjell <zhen-xjell@teamhelix.net>']
['Howie L (howe81) <howe81@bigpond.net.au>']

iter_all_neighbours(v, vprops=[])#

Return an iterator over the in- and out-neighbors of vertex v, and optional vertex properties list vprops.

Note

This mode of iteration is more efficient than using all_neighbors(), as descriptor objects are not created.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> for u, i in g.iter_all_neighbors(66, [g.vp.uid]):
...     print(u, i)
['paul wilders <webmaster@wilders.org>']
['Zhen-Xjell <zhen-xjell@teamhelix.net>']
['Hooman <Hooman@iname.com>']
['H. Loeung (howe81) <howe81@unixque.com>', 'howe81 <howe81@bigpond.net.au>', 'Howie L (howe81) <howe81@bigpond.net.au>']
['Howie L (howe81) <howe81@bigpond.net.au>']
['H. Loeung (howe81) <howe81@unixque.com>', 'howe81 <howe81@bigpond.net.au>', 'Howie L (howe81) <howe81@bigpond.net.au>']
['Zhen-Xjell <zhen-xjell@teamhelix.net>']
['Howie L (howe81) <howe81@bigpond.net.au>']

iter_edges(eprops=[])#

Return an iterator over the edge `(source, target) pairs, and optional edge properties list eprops.

Note

This mode of iteration is more efficient than using edges(), as descriptor objects are not created.

Examples

>>> g = gt.collection.data["karate"]
>>> for s, t, i in g.iter_edges([g.edge_index]):
...     print(s, t, i)
...     if s == 5:
...         break
1 0 0
2 0 1
2 1 2
3 0 3
3 1 4
3 2 5
4 0 6
5 0 7

iter_in_edges(v, eprops=[])#

Return an iterator over the in-edge `(source, target) pairs for vertex v, and optional edge properties list eprops.

Note

This mode of iteration is more efficient than using in_edges(), as descriptor objects are not created.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> for s, t, i in g.iter_in_edges(66, [g.edge_index]):
...     print(s, t, i)
8687 66 179681
20369 66 255033
38674 66 300230

iter_in_neighbors(v, vprops=[])#

Return an iterator over the in-neighbors of vertex v, and optional vertex properties list vprops.

Note

This mode of iteration is more efficient than using in_neighbors(), as descriptor objects are not created.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> for u, i in g.iter_in_neighbors(66, [g.vp.uid]):
...     print(u, i)
8687 ['H. Loeung (howe81) <howe81@unixque.com>', 'howe81 <howe81@bigpond.net.au>', 'Howie L (howe81) <howe81@bigpond.net.au>']
20369 ['Zhen-Xjell <zhen-xjell@teamhelix.net>']
38674 ['Howie L (howe81) <howe81@bigpond.net.au>']

iter_in_neighbours(v, vprops=[])#

Return an iterator over the in-neighbors of vertex v, and optional vertex properties list vprops.

Note

This mode of iteration is more efficient than using in_neighbors(), as descriptor objects are not created.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> for u, i in g.iter_in_neighbors(66, [g.vp.uid]):
...     print(u, i)
8687 ['H. Loeung (howe81) <howe81@unixque.com>', 'howe81 <howe81@bigpond.net.au>', 'Howie L (howe81) <howe81@bigpond.net.au>']
20369 ['Zhen-Xjell <zhen-xjell@teamhelix.net>']
38674 ['Howie L (howe81) <howe81@bigpond.net.au>']

iter_out_edges(v, eprops=[])#

Return an iterator over the out-edge `(source, target) pairs for vertex v, and optional edge properties list eprops.

Note

This mode of iteration is more efficient than using out_edges(), as descriptor objects are not created.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> for s, t, i in g.iter_out_edges(66, [g.edge_index]):
...     print(s, t, i)
66 63 5266
66 20369 5267
66 13980 5268
66 8687 5269
66 38674 5270

iter_out_neighbors(v, vprops=[])#

Return an iterator over the out-neighbors of vertex v, and optional vertex properties list vprops.

Note

This mode of iteration is more efficient than using out_neighbors(), as descriptor objects are not created.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> for u, i in g.iter_out_neighbors(66, [g.vp.uid]):
...     print(u, i)
63 ['paul wilders <webmaster@wilders.org>']
20369 ['Zhen-Xjell <zhen-xjell@teamhelix.net>']
13980 ['Hooman <Hooman@iname.com>']
8687 ['H. Loeung (howe81) <howe81@unixque.com>', 'howe81 <howe81@bigpond.net.au>', 'Howie L (howe81) <howe81@bigpond.net.au>']
38674 ['Howie L (howe81) <howe81@bigpond.net.au>']

iter_out_neighbours(v, vprops=[])#

Return an iterator over the out-neighbors of vertex v, and optional vertex properties list vprops.

Note

This mode of iteration is more efficient than using out_neighbors(), as descriptor objects are not created.

Examples

>>> g = gt.collection.data["pgp-strong-2009"]
>>> for u, i in g.iter_out_neighbors(66, [g.vp.uid]):
...     print(u, i)
63 ['paul wilders <webmaster@wilders.org>']
20369 ['Zhen-Xjell <zhen-xjell@teamhelix.net>']
13980 ['Hooman <Hooman@iname.com>']
8687 ['H. Loeung (howe81) <howe81@unixque.com>', 'howe81 <howe81@bigpond.net.au>', 'Howie L (howe81) <howe81@bigpond.net.au>']
38674 ['Howie L (howe81) <howe81@bigpond.net.au>']

iter_vertices(vprops=[])#

Return an iterator over the vertex indices, and optional vertex properties list vprops.

Note

This mode of iteration is more efficient than using vertices(), as descriptor objects are not created.

Examples

>>> g = gt.Graph()
>>> g.add_vertex(5)
<...>
>>> for v in g.iter_vertices():
...     print(v)
0
1
2
3
4

list_properties()#

Print a list of all internal properties.

Examples

>>> g = gt.Graph()
>>> g.properties[("e", "foo")] = g.new_edge_property("vector<double>")
>>> 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<double>)

load(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.

new_edge_property(value_type, vals=None, val=None)#: Create a new edge property map of type value_type, and return it. If provided, the values will be initialized by vals, which should be sequence or by val which should be a single value.

new_ep(value_type, vals=None, val=None)#: Alias to new_edge_property().

new_gp(value_type, val=None)#: Alias to new_graph_property().

new_graph_property(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.

new_property(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.

new_vertex_property(value_type, vals=None, val=None)#: Create a new vertex property map of type value_type, and return it. If provided, the values will be initialized by vals, which should be sequence or by val which should be a single value.

new_vp(value_type, vals=None, val=None)#: Alias to new_vertex_property().

num_edges(ignore_filter=False)#

Get the number of edges.

If ignore_filter == True, edge filters are ignored.

Note

If the edges are being filtered, and ignore_filter == False, this operation is \(O(E)\). Otherwise it is \(O(1)\).

num_vertices(ignore_filter=False)#

Get the number of vertices.

If ignore_filter == True, vertex filters are ignored.

Note

If the vertices are being filtered, and ignore_filter == False, this operation is \(O(V)\). Otherwise it is \(O(1)\).

own_property(prop)#: Return a version of the property map ‘prop’ (possibly belonging to another graph) which is owned by the current graph.

purge_edges()#: Remove all edges of the graph which are currently being filtered out. This operation is not reversible.

purge_vertices(in_place=False)#

Remove all vertices of the graph which are currently being filtered out. 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 \(O(V^2)\) 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 \(O(V + E)\) complexity. This is the default behaviour if no option is given.

reindex_edges()#: Reset the edge indices so that they lie in the [0, num_edges() - 1] range. The index ordering will be compatible with the sequence returned by the 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 indices, and thus may become scrambled.

remove_edge(edge)#: Remove an edge from the graph.

Note

This operation is normally \(O(k_s + k_t)\), where \(k_s\) and \(k_s\) are the total degrees of the source and target vertices, respectively. However, if set_fast_edge_removal() is set to True, this operation becomes \(O(1)\).

Warning

The relative ordering of the remaining edges in the graph is kept unchanged, unless set_fast_edge_removal() is set to True, in which case it can change.

remove_vertex(vertex, fast=False)#

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 \(O(V + E)\) (this is the default). Otherwise it is \(O(k + k_{\text{last}})\), where \(k\) is the (total) degree of the vertex being deleted, and \(k_{\text{last}}\) 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 \([0, N-1]\), 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:

# '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.

save(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.

set_directed(is_directed)#: Set the directedness of the graph.

Note

This is a \(O(1)\) operation that does not modify the storage of the graph.

Warning

Changing directedness will invalidate existing vertex and edge descriptors, which will still point to the original graph.

set_edge_filter(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.

Note

This is a \(O(1)\) operation that does not modify the storage of the graph.

Warning

Setting edge filters will invalidate existing vertex and edge descriptors, which will still point to the unfiltered graph.

set_fast_edge_removal(fast=True)#: If fast == True the fast \(O(1)\) removal of edges will be enabled. This requires an additional data structure of size \(O(E)\) to be kept at all times. If fast == False, this data structure is destroyed.

set_filter_state(state)#: Set the filter state of the graph.

set_filters(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 False 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.

Note

This is a \(O(1)\) operation that does not modify the storage of the graph.

Warning

Setting vertex or edge filters will invalidate existing vertex and edge descriptors, which will still point to the unfiltered graph.

set_reversed(is_reversed)#: Reverse the direction of the edges, if is_reversed is True, or maintain the original direction otherwise.

Note

This is a \(O(1)\) operation that does not modify the storage of the graph.

Warning

Reversing the graph will invalidate existing vertex and edge descriptors, which will still point to the original graph.

set_vertex_filter(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.

Note

This is a \(O(1)\) operation that does not modify the storage of the graph.

Warning

Setting vertex filters will invalidate existing vertex and edge descriptors, which will still point to the unfiltered graph.

shrink_to_fit()#: Force the physical capacity of the underlying containers to match the graph’s actual size, potentially freeing memory back to the system.

vertex(i, use_index=True, add_missing=False)#

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).

If add_missing == True, and the vertex does not exist in the graph, the necessary number of missing vertices are inserted, and the new vertex is returned.

vertices()#

Return an 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 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)

base#: Base graph.

edge_index#

Edge index map.

It maps for each edge in the graph an unique integer.

Note

Like vertex_index, this is a special instance of a EdgePropertyMap class, which is immutable, and cannot be accessed as an array.

Additionally, the indices may not necessarily lie in the range [0, num_edges() - 1]. However this will always happen whenever no edges are deleted from the graph.

edge_index_range#: The size of the range of edge indices.

edge_properties#: Dictionary of internal edge properties. The keys are the property names.

ep#: Alias to edge_properties.

gp#: Alias to graph_properties.

graph_properties#: Dictionary of internal graph properties. The keys are the property names.

properties#

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<double>")
>>> del g.properties[("e", "foo")]

vertex_index#

Vertex index map.

It maps for each vertex in the graph an unique integer in the range [0, num_vertices() - 1].

Note

Like edge_index, this is a special instance of a VertexPropertyMap class, which is immutable, and cannot be accessed as an array.

vertex_properties#: Dictionary of internal vertex properties. The keys are the property names.

vp#: Alias to vertex_properties.

graph_tool.GraphView

Contents

graph_tool.GraphView#