svZeroDTrees

Structured tree boundary condition modeling for svZeroD cardiovascular simulations.

Capabilities

• Generate structured tree boundary conditions for svZeroD outlets.
• Tune boundary conditions (impedance or RCR) to clinical targets.
• Adapt microvasculature using CWSS or Pries/Secomb models.
• Optional 3D coupling pipeline via SimVascular tools.

Requirements

• Python >= 3.8.
• Python packages (installed via pip install -e .): scipy, numpy, vtk, pandas, matplotlib, networkx, svsuperestimator, multiprocess, pysvzerod, pyyaml.
• External tools for 3D coupling only: SimVascular svpre, svsolver, svpost in PATH.
• Input data files:
• zerod_config.json (svZeroD config)
• clinical_targets.csv
• mesh-surfaces directory
• Optional inflow.csv for custom inflow

Install

git clone https://github.com/ncdorn/svZeroDTrees.git
cd svZeroDTrees
pip install -e .

Quickstart CLI (use the example config):

svzerodtrees pipeline examples/pipeline_example.yml

Generate a schema template:

svzerodtrees schema

Python API:

from svzerodtrees import load_config
from svzerodtrees.api import PipelineWorkflow

cfg = load_config("examples/pipeline_example.yml")
PipelineWorkflow.from_config(cfg).run()

Workflows

• pipeline: end-to-end run (0D setup, BC tuning, optional 3D, adaptation).
• tune_bcs: optimize impedance or RCR parameters only.
• construct_trees: assign impedance or RCR BCs to a svZeroD config.
• adapt: run microvascular adaptation using preop/postop results.
• postprocess: generate figures from saved tree pickles.

Outputs Typical outputs are written under paths.root and include:

• optimized_params.csv or optimized_rcr_params.csv from tuning.
• svzerod_config_with_bcs.json (or paths.output_config) from tree construction.
• preop, postop, adapted directories for pipeline/adaptation runs.
• Figures from postprocess workflow (PNG outputs you specify).

Examples

• YAML configs: examples/pipeline_example.yml, examples/tune_bcs_example.yml, examples/construct_tree/construct_trees_example.yml, examples/adapt_example.yml, examples/postprocess_example.yml.
• Narrative example: examples/construct_tree/README.md.

Reference

• Schema reference: docs/interface.md.
• User guide: docs/overview.md.