GraphProcessing#

Module providing tools to create and manipulate graphs. Functions include graph construction from skeletons, simplification, reduction and clean-up of graphs.

clean_graph(graph, remove_self_loops=True, remove_isolated_vertices=True, vertex_mappings={'coordinates': <function mean_vertex_coordinates>, 'radii': <function max>}, verbose=False)[source]#

Remove all cliques to get pure branch structure of a graph.

Arguments

graphGraph: The graph to clean up.
verbosebool: If True, prin progress information.

Returns

graphGraph: A graph removed of all cliques.

Note

cliques are replaced by a single vertex connecting to all non-clique neighbours The center coordinate is used for that vertex as the coordinate.

expand_graph(graph)[source]#

expand_graph_length(graph, length='length', return_edge_mapping=False)[source]#: Expand a reduced graph to a full graph.

graph_from_skeleton(skeleton, points=None, radii=None, vertex_coordinates=True, check_border=True, delete_border=False, verbose=False)[source]#

Converts a binary skeleton image to a graph-tool graph.

Arguments

skeletonarray: Source with 2d/3d binary skeleton.
pointsarray: List of skeleton points as 1d indices of flat skeleton array (optional to save processing time).
radiiarray: List of radii associated with each vertex.
vertex_coordinatesbool: If True, store coordiantes of the vertices / edges.
check_borderbool: If True, check if the boder is empty. The algorithm reuqires this.
delete_borderbool: If True, delete the border.
verbosebool: If True, print progress information.

Returns

graphGraph class: The graph corresponding to the skeleton.

Note

Edges are detected between neighbouring foreground pixels using 26-connectivty.

graph_to_skeleton(graph, sink=None, dtype=<class 'bool'>, values=True)[source]#: Create a binary skeleton from a graph.

mean_vertex_coordinates(coordinates)[source]#

reduce_graph(graph, vertex_to_edge_mappings={'radii': <function max>}, edge_to_edge_mappings={'length': <function sum>}, edge_geometry=True, edge_length=None, edge_geometry_vertex_properties=['coordinates', 'radii'], edge_geometry_edge_properties=None, return_maps=False, verbose=False)[source]#: Reduce graph by replacing all vertices with degree two.

trace_edge_label(graph, edge_label, condition, max_iterations=None, dilation_steps=1, pass_label=False, **condition_args)[source]#

Traces label within a graph.

Arguments

edge_labelarray: Start label.
conditionfunction(graph, vertex): A function determining if the vertex should be added to the labels.
stepsint: Number edges to jump to find new neighbours. Default is 1.

Returns

edge_labelarray: The traced label.

trace_vertex_label(graph, vertex_label, condition, dilation_steps=1, max_iterations=None, pass_label=False, **condition_args)[source]#

Traces label within a graph.

Arguments

vertex_labelarray: Start label.
conditionfunction(graph, vertex): A function determining if the vertex should be added to the labels.
stepsint: Number edges to jump to find new neighbours. Default is 1.

Returns

vertex_labelarray: The traced label.