geometry_utils¶

Graph-based geometry helpers. The package uses networkx directed graphs to represent the vascular tree. Each edge stores attributes such as length, radius, resistance, edge_id and strahler.

Main responsibilities¶

Building the initial directed graph from node and element lists
(create_geometry()).
Adding a venous mesh based on arterial topology
(create_venous_mesh()).
Computing Strahler ordering for radii assignment
(update_strahlers()).
Utility helpers to compute lengths, branching angles and to add
anastomoses (calcLength(), calculate_branching_angles(), create_anastomosis()).

create_geometry(nodes, elements, inlet_radius, strahler_ratio_arteries, …)

Construct a networkx.DiGraph from raw node and element data, set per-edge defaults, compute Strahler ordering and assign radii.

nodesdict: Mapping node_id -> [x, y, z] (0-based indices). Produced by file_parsing_utils.read_nodes().
elementslist of tuple: Connectivity list [(node_from, node_to), ...] (0-based indices).
inlet_radiusfloat: Radius (m) used for the root/inlet arterial vessels.
strahler_ratio_arteriesfloat: Scaling factor between Strahler orders used to set vessel radii.
arteries_onlybool, optional: When True do not create a venous mesh; only arterial graph is returned. Default is False.
outlet_vein_radiusfloat, optional: Outlet vein radius (m) used when building the venous mesh. Required if arteries_only is False.
strahler_ratio_veinsfloat, optional: Strahler scaling factor used for veins. Required when building venous mesh.
fieldsdict, optional: Optional per-edge fields (for example radius or resistance) as produced by file_parsing_utils.define_fields_from_files().
default_mufloat, optional: Default dynamic viscosity (Pa.s) assigned to edges.
default_hematocritfloat, optional: Default hematocrit value assigned to edges.

networkx.DiGraph: Directed graph with nodes and edges annotated with attributes such as length, radius, edge_id, strahler and vessel_type.

create_venous_mesh(), update_strahlers(), create_anastomosis()

>>> from FetoFlow.file_parsing_utils import read_nodes, read_elements
>>> nodes = read_nodes('placenta.ipnode')
>>> elements = read_elements('placenta.ipelem')
>>> G = create_geometry(nodes, elements, inlet_radius=0.002, strahler_ratio_arteries=0.79)

create_venous_mesh(…)

Build a venous graph by copying and relabelling the arterial graph, applying vein radii and reversing edge directions.

update_strahlers(G, node_in, node_out)

Recursive Strahler calculation used during geometry construction.

create_anastomosis(G, node_from, node_to, radius=None, mu=…)

Add a connecting edge (anastomosis) between two nodes and compute an approximate resistance for it. Input indices are in the external (1-based) IPNODE indexing and converted to internal 0-based indices.

Examples¶

G = create_geometry(nodes, elements, inlet_radius=0.002, strahler_ratio_arteries=0.79)
G = create_anastomosis(G, node_from=12, node_to=34, radius=0.1)

API reference¶

Function arguments¶

create_geometry

nodesdict: Mapping node_id -> [x, y, z] (0-based indices). Produced by file_parsing_utils.read_nodes().
elementslist of tuple: Connectivity list [(node_from, node_to), ...] (0-based indices).
inlet_radiusfloat: Radius (m) used for the root/inlet arterial vessels.
strahler_ratio_arteriesfloat: Scaling factor between Strahler orders used to set vessel radii.
arteries_onlybool, optional: When True do not create a venous mesh; only arterial graph is returned. Default is False.
outlet_vein_radiusfloat, optional: Outlet vein radius (m) used when building the venous mesh. Required if arteries_only is False.
strahler_ratio_veinsfloat, optional: Strahler scaling factor used for veins. Required when building venous mesh.
fieldsdict, optional: Optional per-edge fields (for example radius or resistance) as produced by file_parsing_utils.define_fields_from_files().
default_mufloat, optional: Default dynamic viscosity (Pa.s) assigned to edges.
default_hematocritfloat, optional: Default hematocrit value assigned to edges.

networkx.DiGraph

Directed graph with nodes and edges annotated with attributes such as length, radius, edge_id, strahler and vessel_type.

The function will compute Strahler numbers for each edge and assign radii by scaling from the inlet radius. If a fields dict is provided and contains a radius field that value is used where specified and Strahler scaling applied elsewhere.

Use FetoFlow.file_parsing_utils.read_nodes() and FetoFlow.file_parsing_utils.read_elements() to produce the nodes and elements inputs to this function.

create_venous_mesh

Gnetworkx.DiGraph: The arterial graph to copy and relabel into a venous mesh.

networkx.DiGraph: Venous mesh graph with relabelled nodes and vein attributes.

The venous mesh is generated by copying the arterial topology, relabelling node ids (offset by num_artery_nodes) and reversing edges. The function is usually called internally by create_geometry() when arteries_only=False.

update_strahlers

Gnetworkx.DiGraph: Graph to update in-place.
node_in, node_outint: Edge endpoints describing the arc for which Strahler ordering should be computed. This function is recursive and intended to be used during geometry building.

networkx.DiGraph: The graph with updated strahler attributes.

create_anastomosis

Gnetworkx.DiGraph: Graph to modify.
node_fromint: 1-based ipnode index identifying the anastomosis start node.
node_toint: 1-based ipnode index identifying the anastomosis end node.
radiusfloat, optional: Radius of the anastomosis (mm in calling code; will be converted to m).
mufloat, optional: Viscosity used to compute an approximate resistance for the new edge.

networkx.DiGraph: The modified graph with the new anastomosis edge and attributes set.

# build graph first from parsed files
G = create_geometry(nodes, elements, inlet_radius=0.002, strahler_ratio_arteries=0.79)
# add a small anastomosis between ipnode indices 12 and 34
G = create_anastomosis(G, node_from=12, node_to=34, radius=0.05)