openalea.core.graph package

Subpackages

• openalea.core.graph.interface package
  • Submodules
  • openalea.core.graph.interface.graph module
    • GraphError
    • ICopyGraph
      • ICopyGraph.copy()
    • IEdgeListGraph
      • IEdgeListGraph.edges()
      • IEdgeListGraph.in_edges()
      • IEdgeListGraph.nb_edges()
      • IEdgeListGraph.nb_in_edges()
      • IEdgeListGraph.nb_out_edges()
      • IEdgeListGraph.out_edges()
    • IExtendGraph
      • IExtendGraph.extend()
    • IGraph
      • IGraph.edge()
      • IGraph.has_edge()
      • IGraph.has_vertex()
      • IGraph.is_valid()
      • IGraph.source()
      • IGraph.target()
    • IMutableEdgeGraph
      • IMutableEdgeGraph.add_edge()
      • IMutableEdgeGraph.clear_edges()
      • IMutableEdgeGraph.remove_edge()
    • IMutableVertexGraph
      • IMutableVertexGraph.add_vertex()
      • IMutableVertexGraph.clear()
      • IMutableVertexGraph.remove_vertex()
    • IVertexListGraph
      • IVertexListGraph.in_neighbors()
      • IVertexListGraph.nb_in_neighbors()
      • IVertexListGraph.nb_neighbors()
      • IVertexListGraph.nb_out_neighbors()
      • IVertexListGraph.nb_vertices()
      • IVertexListGraph.neighbors()
      • IVertexListGraph.out_neighbors()
      • IVertexListGraph.vertices()
    • InvalidEdge
    • InvalidVertex
  • openalea.core.graph.interface.graphconcept module
    • CopyConcept
      • CopyConcept.copy()
    • EdgeListGraphConcept
      • EdgeListGraphConcept.edges()
      • EdgeListGraphConcept.in_edges()
      • EdgeListGraphConcept.nb_edges()
      • EdgeListGraphConcept.nb_in_edges()
      • EdgeListGraphConcept.nb_out_edges()
      • EdgeListGraphConcept.out_edges()
    • ExtendConcept
      • ExtendConcept.extend()
    • GraphConcept
      • GraphConcept.edge()
      • GraphConcept.has_edge()
      • GraphConcept.has_vertex()
      • GraphConcept.is_valid()
      • GraphConcept.source()
      • GraphConcept.target()
    • GraphError
    • InexistingVertex
    • InvalidEdge
    • InvalidGraph
    • InvalidVertex
    • MutableEdgeGraphConcept
      • MutableEdgeGraphConcept.add_edge()
      • MutableEdgeGraphConcept.clear_edges()
      • MutableEdgeGraphConcept.edge_id()
      • MutableEdgeGraphConcept.remove_edge()
    • MutableVertexGraphConcept
      • MutableVertexGraphConcept.add_vertex()
      • MutableVertexGraphConcept.clear()
      • MutableVertexGraphConcept.remove_vertex()
      • MutableVertexGraphConcept.vertex_id()
    • VertexListGraphConcept
      • VertexListGraphConcept.in_neighbors()
      • VertexListGraphConcept.nb_in_neighbors()
      • VertexListGraphConcept.nb_neighbors()
      • VertexListGraphConcept.nb_out_neighbors()
      • VertexListGraphConcept.nb_vertices()
      • VertexListGraphConcept.neighbors()
      • VertexListGraphConcept.out_neighbors()
      • VertexListGraphConcept.vertices()
  • openalea.core.graph.interface.latticeconcept module
    • Container
      • Container.elements()
      • Container.has_element()
      • Container.nb_elements()
    • MultiscaleContainer
      • MultiscaleContainer.complex()
      • MultiscaleContainer.components()
      • MultiscaleContainer.container()
      • MultiscaleContainer.element()
      • MultiscaleContainer.nb_components()
      • MultiscaleContainer.scale()
    • MultiscaleTree
    • MutableMultiscaleContainer
    • MutableMultiscaleTree
    • MutableScaleLattice
      • MutableScaleLattice.add_scale()
      • MutableScaleLattice.remove_scale()
      • MutableScaleLattice.scale_id()
    • ScaleLattice
      • ScaleLattice.coarser()
      • ScaleLattice.coarsest()
      • ScaleLattice.finer()
      • ScaleLattice.finest()
      • ScaleLattice.max()
      • ScaleLattice.min()
      • ScaleLattice.nb_coarser()
      • ScaleLattice.nb_finer()
      • ScaleLattice.nb_scales()
      • ScaleLattice.scales()
  • openalea.core.graph.interface.port_graph module
    • IPortGraph
      • IPortGraph.add_in_port()
      • IPortGraph.add_out_port()
      • IPortGraph.capacity()
      • IPortGraph.connect()
      • IPortGraph.disconnect()
      • IPortGraph.in_port()
      • IPortGraph.in_ports()
      • IPortGraph.is_in_port()
      • IPortGraph.is_out_port()
      • IPortGraph.out_port()
      • IPortGraph.out_ports()
      • IPortGraph.port()
      • IPortGraph.port_edges()
      • IPortGraph.port_neighbors()
      • IPortGraph.ports()
      • IPortGraph.remove_port()
      • IPortGraph.set_capacity()
      • IPortGraph.source_port()
      • IPortGraph.target_port()
      • IPortGraph.vertex()
  • openalea.core.graph.interface.property_graph module
    • IPropertyGraph
      • IPropertyGraph.add_edge_property()
      • IPropertyGraph.add_vertex_property()
      • IPropertyGraph.edge_property()
      • IPropertyGraph.edge_property_names()
      • IPropertyGraph.remove_edge_property()
      • IPropertyGraph.remove_vertex_property()
      • IPropertyGraph.vertex_property()
      • IPropertyGraph.vertex_property_names()
    • PropertyError
  • openalea.core.graph.interface.treeconcept module
    • EditableTreeConcept
      • EditableTreeConcept.add_child_tree()
      • EditableTreeConcept.insert_sibling_tree()
      • EditableTreeConcept.sub_tree()
    • MutableTreeConcept
      • MutableTreeConcept.add_child()
      • MutableTreeConcept.insert_parent()
      • MutableTreeConcept.insert_sibling()
    • OrderedTreeConcept
      • OrderedTreeConcept.first_child()
      • OrderedTreeConcept.last_child()
      • OrderedTreeConcept.next_sibling()
      • OrderedTreeConcept.previous_sibling()
    • RootedTreeConcept
      • RootedTreeConcept.children()
      • RootedTreeConcept.get_root()
      • RootedTreeConcept.is_leaf()
      • RootedTreeConcept.nb_children()
      • RootedTreeConcept.nb_siblings()
      • RootedTreeConcept.parent()
      • RootedTreeConcept.root
      • RootedTreeConcept.set_root()
      • RootedTreeConcept.siblings()
    • Visitor
      • Visitor.post_order()
      • Visitor.pre_order()
    • traverse_tree()
  • Module contents

Submodules

openalea.core.graph.graph module

This module provide a simple pure python implementation for a graph interface do not implement copy concept.

class openalea.core.graph.graph.Graph(graph=None)

Bases: IGraph, IVertexListGraph, IEdgeListGraph, IMutableVertexGraph, IMutableEdgeGraph, IExtendGraph

Directed graph with multiple links in this implementation: - vertices are tuple of edge_in, edge_out - edges are tuple of source,target

add_edge(edge=(None, None), eid=None)

add an edge to the graph, if eid is not provided create a new eid

Parameters:

• edge : a tuple (vertex source,vertex target)

• eid : the id of the created edge

Types:

• edge : (vid,vid)

• eid : eid

Returns:

the id of the newly created edge

Return type:

eid

add_vertex(vid=None)

add a vertex to the graph, if vid is not provided create a new vid

Parameters:

vid (vid) – the id of the vertex to add, default=None

Returns:

the id of the created vertex

Return type:

vid

clear()

remove all vertices and edges don’t change references to objects

clear_edges()

remove all the edges of the graph don’t change references to objects

edges(vid=None)

retrieve the edges linked to a specified vertex, all if vid is None

Parameters:

vid (vid) – id of the reference vertex, default=None

Return type:

iter of eid

extend(graph)

add the specified graph to self, create new vid and eid

Parameters:

graph (Graph) – the graph to add

Returns:

two dictionnary specifying correspondence between graph id and self id

Return type:

({vid:vid},{eid:eid})

has_edge(eid)

test wether an edge belong to the graph

Parameters:

eid (eid) – edge id to test

Return type:

bool

has_vertex(vid)

test wether a vertex belong to the graph

Parameters:

vid (vid) – vertex id to test

Return type:

bool

in_edges(vid)

retrieve the edges linked to a specified vertex, oriented inside the vertex

Parameters:

vid (vid) – id of the reference vertex, default=None

Return type:

iter of eid

in_neighbors(vid)

iterator on the neighbors of vid where edges are directed from neighbor to vid

Parameters:

vid (vid) – id of the reference vertex

Return type:

iter of vid

is_valid()

test the validity of the graph

Return type:

bool

nb_edges(vid=None)

number of edges linked to a specified vertex, total number if vid is None

Parameters:

vid (vid) – id of the reference vertex, default=None

Return type:

iter of eid

nb_in_edges(vid)

number of edges linked to a specified vertex, oriented inside vertex

Parameters:

vid (vid) – id of the reference vertex, default=None

Return type:

iter of eid

nb_in_neighbors(vid)

number of neighbors such as edges are directed from neighbor to vid

Parameters:

vid (vid) – id of the reference vertex

Return type:

int

nb_neighbors(vid)

number of neighbors regardless of the orientation of the edge

Parameters:

vid (vid) – id of the reference vertex

Return type:

int

nb_out_edges(vid)

number of edges linked to a specified vertex, oriented outside vertex

Parameters:

vid (vid) – id of the reference vertex, default=None

Return type:

iter of eid

nb_out_neighbors(vid)

number of neighbors such as edges are directed from vid to neighbor

Parameters:

vid (vid) – id of the reference vertex

Return type:

int

nb_vertices()

return the total number of vertices

Return type:

int

neighbors(vid)

iterator on the neighbors of vid regardless of the orientation of the edge

Parameters:

vid (vid) – id of the reference vertex

Return type:

iter of vid

out_edges(vid)

retrieve the edges linked to a specified vertex, oriented outside the vertex

Parameters:

vid (vid) – id of the reference vertex, default=None

Return type:

iter of eid

out_neighbors(vid)

iterator on the neighbors of vid where edges are directed from vid to neighbor

Parameters:

vid (vid) – id of the reference vertex

Return type:

iter of vid

remove_edge(eid)

remove a specified edge from the graph

Parameters:

eid (eid) – id of the edge to remove

remove_vertex(vid)

remove a specified vertex of the graph remove all the edges attached to it

Parameters:

vid (vid) – the id of the vertex to remove

source(eid)

retrieve the source of an edge

Parameters:

eid (eid) – id of the edge

Return type:

vid

target(eid)

retrieve the target of an edge

Parameters:

eid (eid) – id of the edge

Return type:

vid

vertices()

iterator on vertices

Return type:

iter of vid

openalea.core.graph.id_generator module

This module provide a generator for id numbers

class openalea.core.graph.id_generator.IdGenerator

Bases: object

get_id(id=None)

release_id(id)

openalea.core.graph.property_graph module

This module provide a set of concepts to add properties to graph elements

class openalea.core.graph.property_graph.PropertyGraph(graph=None)

Bases: IPropertyGraph, Graph

simple implementation of IPropertyGraph using dict as properties and two dictionaries to maintain these properties

add_edge_property(property_name)

add a new map between eid and a data do not fill this property for any edge

add_vertex_property(property_name)

add a new map between vid and a data do not fill this property for any vertex

clear()

remove all vertices and edges don’t change references to objects

clear_edges()

remove all the edges of the graph don’t change references to objects

edge_property(property_name)

return a map between eid and data for all edges where property_name is defined

Return type:

dict of {eid:data}

edge_property_names()

iter on names of all property maps defined on edge return iter of keys

extend(graph)

add the specified graph to self, create new vid and eid

Parameters:

graph (Graph) – the graph to add

Returns:

two dictionnary specifying correspondence between graph id and self id

Return type:

({vid:vid},{eid:eid})

remove_edge(eid)

remove a specified edge from the graph

Parameters:

eid (eid) – id of the edge to remove

remove_edge_property(property_name)

remove the map called property_name from the graph

remove_vertex(vid)

remove a specified vertex of the graph remove all the edges attached to it

Parameters:

vid (vid) – the id of the vertex to remove

remove_vertex_property(property_name)

remove the map called property_name from the graph

vertex_property(property_name)

return a map between vid and data for all vertices where property_name is defined

Return type:

dict of {vid:data}

vertex_property_names()

iter on names of all property maps defined on vertices return iter of keys

Module contents