svVascularize API Reference

`svv.domain`

Core Module

Core domain functionality for defining computational domains and geometric operations. Provides matrix operations, I/O capabilities, and solver implementations.

Submodules

Submodule	Description	Key Components
`domain.core`	Core matrix operations	a_matrix(), h_matrix(), m_matrix(), n_matrix()
`domain.io`	Input/output operations	read()
`domain.kernel`	Kernel functions and coordinate transforms	Kernel, cost(), cart2sph(), sph2cart()
`domain.routines`	Computational routines	allocate(), contour(), tetrahedralize(), boolean()
`domain.solver`	Domain-specific solvers	Solver class

Main Classes

Domain - Main domain class for defining spatial regions
Patch - Individual patches for RBF interpolation

Example Usage

from svv.domain import Domain

# Create a domain from a mesh
import pyvista as pv
mesh = pv.read('tissue_geometry.stl')
domain = Domain(mesh)

# Build implicit function
domain.create()
domain.solve()
domain.build()

# Export domain
boundary, _ = domain.get_boundary(resolution=30)

Performance Note: The domain.routines module includes Cython-optimized functions (c_allocate.pyx, c_sample.pyx) for enhanced performance.

`svv.forest`

Core Module

Forest structures for managing collections of vascular trees and their interconnections. Supports various connection algorithms and export formats.

Connection Methods

Class	Description	Use Case
`ForestConnection`	High-level connection manager	Builds connections for each network
`TreeConnection`	Per-network connection solver	Assigns and optimizes tree-to-tree links
`VesselConnection`	Single connection optimizer	Generates connecting vessel segments
`Curve`	Curve factory	Supports Bezier, Catmull-Rom, and NURBS shapes

Main Classes

Forest - Main class for building connected vascular structures.

Example Usage

import pyvista as pv
from svv.domain import Domain
from svv.forest import Forest

# Prepare a domain and build its implicit representation
domain = Domain(pv.Cube())
domain.create()
domain.solve()
domain.build()

# Initialize a forest with two trees in one network
trees_per_network = [2]
forest = Forest(domain=domain, n_networks=1, n_trees_per_network=trees_per_network)
forest.set_domain(domain)
forest.set_roots()  # Randomize root placement
forest.add(50)      # Grow 50 vessels per tree

# Connect the trees (starting with cubic curves)
forest.connect(3)

# Export watertight solids for downstream simulation or fabrication
forest.export_solid(outdir='forest_model')

`svv.tree`

Core Module

Tree structures and algorithms for vascular tree generation, manipulation, and analysis. Includes branching logic, collision detection, and optimization utilities.

Key Classes

Class	Module	Purpose
`Tree`	tree	Main tree structure
`Bifurcation`	tree.branch	Bifurcation point management
`TreeManager`	tree.utils	Tree lifecycle management
`TreeCollision`	tree.collision	Collision detection

Main Classes

Tree - Main class for building bifurcating vascular structures

Performance note: The tree.utils module contains several Cython-optimized functions (c_angle, c_basis, c_close, c_extend, c_local_optimize, c_obb, c_update) for performance-critical operations.

`svv.simulation`

Simulation

Comprehensive simulation framework for fluid dynamics and hemodynamic modeling. Supports both 0D and 1D reduced-order models.

Simulation Types

0D Models

Lumped parameter models for rapid system-level analysis

zerod_forest
zerod_tree
project_solution

1D Models

One-dimensional flow models for detailed hemodynamics

centerlines
generate_1d_mesh
parameters

Example Usage

from svv.simulation import Simulation
from svv.simulation.fluid.rom.zero_d.zerod_tree import export_0d_simulation

# Wrap a generated tree in a Simulation container
sim = Simulation(tree, name='example_sim')

# Build CFD-ready meshes and identify boundary faces
sim.build_meshes(fluid=True, tissue=False, boundary_layer=True)
sim.extract_faces(crease_angle=60.0)

# Construct and write an svFSI configuration
sim.construct_3d_fluid_simulation()
sim.write_3d_fluid_simulation()

# Export a matching 0D model for fast hemodynamic studies
export_0d_simulation(tree, outdir='tree_0d')

`svv.utils`

Utilities

Utility functions for mesh operations, spatial calculations, and cross-platform support.

Platform Support: The remeshing module includes platform-specific MMG binaries for Linux, macOS, and Windows. Ensure you have the correct binary for your system.

Available Utilities

remeshing.remesh_surface() - Remesh surface meshes with MMG
remeshing.remesh_volume() - Volume remeshing helpers
spatial.minimum_segment_distance() - Pairwise vessel distance checks
spatial.minimum_self_segment_distance() - Self-collision distance utility

`svv.visualize`

Visualization

Visualization tools for rendering vascular trees and forests.

Example Usage

from svv.visualize.tree.show import show as show_tree
from svv.visualize.forest.show import show as show_forest

# Visualize a single tree with the enclosing domain
show_tree(tree, color='crimson', plot_domain=True)

# Visualize an entire forest and save a screenshot
plotter = show_forest(forest, colors=['red', 'royalblue'], plot_domain=True, return_plotter=True)
plotter.screenshot('forest_viz.png')

svVascularize