cellcomplex.graph.temporal_property_graph module

This module provide a class that extends the PropertyGraph with different types of edges

class cellcomplex.graph.temporal_property_graph.TemporalPropertyGraph(graph=None, **kwds)

Bases: cellcomplex.graph.property_graph.PropertyGraph

Simple implementation of PropertyGraph using dict as properties and two dictionaries to maintain these properties

STRUCTURAL = 's'

TEMPORAL = 't'

ancestors(vids, n=None)

Return the 0, 1, …, nth ancestors of the vertex vid

Parameters

• vids : a set of vertex id

:Returns

• anestors_list : the set of the 0, 1, …, nth ancestors of the vertex vid

append(graph, mapping=None, disable_lineage_checking=False)

Append a (spatial) graph to the tpg structure with respect to a given temporal mapping.

children(vid)

Return children of the vertex vid

Parameters

• vid : a vertex id

:Returns

• children_list : the set of the children of the vertex vid

clear()

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

descendants(vids, n=None)

Return the 0, 1, …, nth descendants of the vertex vid

Parameters

• vids : a set of vertex id

:Returns

• descendant_list : the set of the 0, 1, …, nth descendant of the vertex vid

edge_property_at_time(edge_property, time_point)

Return a subpart of graph.edge_property(edge_property) with relabelled key-pair into “images labelpairs” thanks to the dictionary graph.vertex_property(‘old_labels’).

Parameters

• vertex_property : str a string refering to an existing ‘graph.edge_property’ to extract;

• time_point : int time-point for which to return the edge_property;

Examples

graph.edge_property_with_image_labelpairs(‘wall_area’, 0)

edge_property_with_image_labelpairs(edge_property, time_point)

Return a subpart of graph.edge_property(edge_property) with relabelled key-pair into “images labelpairs” thanks to the dictionary graph.vertex_property(‘old_labels’).

Parameters

• vertex_property : str a string refering to an existing ‘graph.edge_property’ to extract;

• time_point : int time-point for which to return the edge_property;

Examples

graph.edge_property_with_image_labelpairs(‘wall_area’, 0)

extend(graphs, mappings, time_steps=None, disable_lineage_checking=True)

Extend the structure with graphs and mappings. Each graph contains structural edges. Mapping define dynamic edges between two graphs.

Parameters

• graphs - a list of PropertyGraph

• mappings - a list defining the dynamic or temporal edges between two graphs.

• time_steps - time corresponding to each graph

Warning:

len(graphs) == len(mappings)-1

has_ancestors(vid, rank=1)

Return True if the vid vid has at least an ancestor at rank.

has_children(vid)

Return True if the vid vid has a child or children.

has_descendants(vid, rank=1)

Return True if the vid vid has at least a descendant at rank.

has_parent(vid)

Return True if the vid vid has a parent.

iter_ancestors(vids, n)

Return the 0, 1, …, nth ancestors of the vertex vid

Parameters

• vids : a set of vertex id

:Returns

• iterator : an iterator on the set of the 0, 1, …, nth ancestors of the vertex vid

iter_children(vid)

Return children of the vertex vid

Parameters

• vid : a vertex id

:Returns

• iterator : an iterator on the set of the children of the vertex vid

iter_descendants(vids, n=None)

Return the 0, 1, …, nth descendants of the vertex vid

Parameters

• vids : a set of vertex id

:Returns

• iterator : an iterator on the set of the 0, 1, …, nth descendants of the vertex vid

iter_parent(vid)

Return parents of the vertex vid

Parameters

• vid : a vertex id

:Returns

• iterator : the set of the children of the vertex vid

iter_sibling(vid)

Return of the vertex vid

Parameters

• vid : a vertex id

:Returns

• iterator : an iterator on the set of sibling of the vertex vid

lineaged_vertex(fully_lineaged=False, as_ancestor=False, as_descendant=False, lineage_rank=1)

Return ids of lineaged vertices, with differents type of lineage possible:

• a full lineage, i.e. only vids with a lineage from the first to the last time-point (fully_lineaged=True);

• a lineage over several ranks, i.e. only vids with a lineage from the vid to the vid+lineage_rank time-point (fully_lineaged=False, lineage_rank=int);

• an ‘ancestors’ based lineage (as_ancestor = True), i.e. only vids lineaged as ancestor (over lineage_rank if not None);

• an ‘descendants’ based lineage (as_ancestor = True), i.e. only vids lineaged as descendants (over lineage_rank if not None).

Parameter

• fully_lineaged (bool) : if True (and lineage_rank is None), return vertices lineaged from the first to the last time-point (or from vid_time_point to vid_time_point + lineage_rank), otherwise return vertices having at least a parent or a child(ren);

• as_parent (bool) : if True, return vertices lineaged as parents;

• as_children (bool) : if True, return vertices lineaged as children;

• ‘lineage_rank’ : int usefull if you want to check the lineage for a different rank than the rank-1 temporal neighborhood.

parent(vid)

Return parents of the vertex vid

Parameters

• vid : a vertex id

:Returns

• parents_list : the set of the parents of the vertex vid

rank_ancestors(vid, rank=1)

Return the ancestor of the vertex vid only at a given rank

Parameters

• vid : a vertex id or a set of vertex id

:Returns

• descendant_list : the set of the rank-ancestor of the vertex vid or a list of set

rank_descendants(vid, rank=1)

Return the descendants of the vertex vid only at a given rank

Parameters

• vid : a vertex id or a set of vertex id

:Returns

• descendant_list : the set of the rank-descendant of the vertex vid or a list of set

region_vids(region_name)

Return a list of vids (TPG vertex id type) that belong to the region region_name according to graph. :Parameters:

• region_name (str) : the name of a region (e.g. from self.add_vertex_to_region())

sibling(vid)

Return sibling of the vertex vid

Parameters

• vid : a vertex id

:Returns

• sibling_list : the set of sibling of the vertex vid

vertex_at_time(time_point, lineaged=False, fully_lineaged=False, as_ancestor=False, as_descendant=False, lineage_rank=1)

Return vertices ids corresponding to a given time point in the TPG. Optional parameters can be used to filter the list of vertices ids returned.

Parameters

• time_point (int) : integer giving which time point should be considered;

• lineaged (bool) : if True, return vertices having at least a parent or a child(ren);

• ‘lineage_rank’ : int usefull if you want to check the lineage for a different rank than the rank-1 temporal neighborhood;

• fully_lineaged (bool) : if True, return vertices linked from the beginning to the end of the graph;

• as_parent (bool) : if True, return vertices lineaged as parents;

• as_children (bool) : if True, return vertices lineaged as children.

vertex_property_at_time(vertex_property, time_point, lineaged=False, fully_lineaged=False, as_ancestor=False, as_descendant=False, lineage_rank=1)

Return the vertex_property``for a given `time_point. May be conditionned by extra temporal property: lineaged, fully_lineaged, as_parent, as_children.

Parameters

• vertex_property : str a string refering to an existing ‘graph.vertex_property’ to extract;

• time_point (int) : integer giving which time point should be considered;

• lineaged (bool) : if True, return vertices having at least a parent or a child(ren);

• ‘lineage_rank’ : int usefull if you want to check the lineage for a different rank than the rank-1 temporal neighborhood;

• fully_lineaged (bool) : if True, return vertices linked from the beginning to the end of the graph;

• as_parent (bool) : if True, return vertices lineaged as parents;

• as_children (bool) : if True, return vertices lineaged as children.

vertex_property_with_image_labels(vertex_property, time_point, lineaged=False, fully_lineaged=False, as_ancestor=False, as_descendant=False, lineage_rank=1)

Return a subpart of graph.vertex_property(vertex_property) with relabelled keys into “images labels” thanks to the dictionary graph.vertex_property(‘old_labels’). Since “images labels” can be similar (not unique), it is mandatory to give a time_point. Additional parameters can be given and are related to the ‘self.vertex_property_at_time’ parameters.

Parameters

• vertex_property : str a string refering to an existing ‘graph.vertex_property’ to extract;

• time_point : int time-point for which to return the vertex_property;

• lineaged (bool) : if True, return vertices having at least a parent or a child(ren);

• ‘lineage_rank’ : int usefull if you want to check the lineage for a different rank than the rank-1 temporal neighborhood;

• fully_lineaged (bool) : if True, return vertices linked from the beginning to the end of the graph;

• as_parent (bool) : if True, return vertices lineaged as parents;

• as_children (bool) : if True, return vertices lineaged as children.

:Returns

• *key_ vertex/cell label, *values_ vertex_property

Examples

graph.vertex_property_with_image_labels(‘volume’, 0)

vertex_temporal_index(vid)

Return the temporal index of a vid self.vertex_property(‘index’)[vid].

cellcomplex.graph.temporal_property_graph.iterable(obj)