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‎docs/doc.html‎

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@@ -37,7 +37,7 @@ <h2>svVascularize Documentation</h2>
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<h3>Get Started</h3>
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<p>New to <code>svVascularize</code>? Begin with the quickstart tutorial that walks you through generating a vascular tree and running a 0‑D hemodynamic simulation in under five minutes.</p>
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<ul>
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<li><a href="tutorials/quickstart.html">🟢 Quickstart tutorial</a></li>
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<li><a href="quickstart.html">🟢 Quickstart tutorial</a></li>
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<li><a href="tutorials/pipeline.html">End‑to‑end pipeline (generation → 3‑D CFD)</a></li>
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</ul>
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‎docs/graphics/quickstart_forest_connected_orbit.gif‎

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‎docs/index.html‎

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<div class="container">
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<h3>About<code>svVascularize</code> </h3>
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<p><code>svVascularize</code> (svv) is an <strong>open-source</strong>, <strong>user-friendly</strong> toolkit that algorithmically grows physiologically realistic vascular trees when imaging data are unavailable or incomplete.</p>
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<p><strong>Why it matters:</strong></p>
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<p><strong>Capabilities:</strong></p>
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<ul>
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<li><em>Biofabrication &amp; 3D printing</em> — export watertight VTP/STL meshes ready for extrusion-based printing, <a href="https://doi.org/10.1126/sciadv.1500758">FRESH</a>/<a href="https://doi.org/10.1126/sciadv.aaw2459">SWIFT</a> bioprinting, or sacrificial templating. Radii, bifurcation angles, and tapering rules are tunable to match printer resolution and biomaterial rheology.</li>
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<li><em>Patient-specific cardiovascular modelling</em> — fill in unresolved distal vasculature to close boundary conditions for 0D, 1D, or full 3D <a href="https://simvascular.github.io/">SimVascular</a> flow simulations. Trees can be constrained to an anatomical mask or grown freely inside an organ ROI.</li>

‎docs/quickstart.html‎

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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>svVascularize Quickstart</title>
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<link href="https://fonts.googleapis.com/css?family=Montserrat:400,700" rel="stylesheet" />
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<link rel="stylesheet" href="style.css" />
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</head>
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<body>
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<header class="topnav">
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<div class="container">
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<h1><a href="../index.html">svVascularize</a></h1>
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<nav>
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<a href="index.html#about">About</a>
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<a href="install.html">Installation</a>
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<a href="doc.html">Documentation</a>
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<a href="index.html#simulation">Simulation</a>
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<a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
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<a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
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</nav>
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</div>
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</header>
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<main class="container content">
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<h2>Quickstart tutorial</h2>
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<p>This guide shows how to grow a small synthetic vascular objects and export 0‑D simulation files for a simple
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convex shape. For this example we will forgo including other build parameters such as starting points and
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additional hemodynamic constraints in order to focus on only the essential API for minimally viable
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vascular objects. Here we create a simple domain, grow a vascular tree and forest, visualising them in an interactive viewer, and
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export 0‑D hemodynamic simulation files for further analysis using <code>svzerodsolver</code> .</p>
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<h3>Generate and visualise a tree</h3>
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<pre data-copy><code class="language-python">import pyvista as pv
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from svv.domain.domain import Domain
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from svv.tree.tree import Tree
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# Creating the Tissue Domain
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cube = Domain(pv.Cube())
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cube.create()
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cube.solve()
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cube.build()
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# Creating the Vascular Tree Object
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t = Tree()
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t.set_domain(cube)
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t.set_root()
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t.n_add(50)
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# Visualizing the Tree and Domain
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t.show(plot_domain=True)</code></pre>
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<figure class="figure-center">
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<img src="graphics/quickstart_orbit.gif" alt="Orbit around vascular tree" width="300" />
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<figcaption> Rotating view of the generated vascular tree </figcaption>
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</figure>
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<h3>Export 0‑D simulation files</h3>
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<pre data-copy><code class="language-python">from svv.simulation.fluid.rom.zero_d.zerod_tree import export_0d_simulation
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export_0d_simulation(t, outdir="my_tree_0d")
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</code></pre>
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<p>This writes a 0-D solver input file, <code>solver_0d.in</code>, and geometric file, <code>geom.csv</code>, in
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the folder <code>my_tree_0d/</code>. The input file should contain all necessary parameters and inflow conditions to run
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the simulation. By default, 0-D simulations exported via this routine will simulate steady state flow through the
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vascular trees. Time-varying flows can be considered if additional arguments are applied to the
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<code>export_0d_simulation</code> function. Run the solver with <a href="https://simvascular.github.io/documentation/rom_simulation.html#0d-solver-user-guide"><code>svZeroDSolver</code></a>.</p>
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<h3>Generate and visualise a forest</h3>
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<p>Unlike <code>tree</code>, <code>forest</code> objects are composed by connecting synthetic vascular trees to form fluid circuits
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with a desired number of inlets and outlets. These are especially useful for fabrication and fluid routing problems in which
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control over the start/end points are critical.</p>
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<pre data-copy><code class="language-python">import pyvista as pv
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from svv.domain.domain import Domain
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from svv.forest.forest import Forest
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# Creating the Tissue Domain
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cube = Domain(pv.Cube())
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cube.create()
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cube.solve()
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cube.build()
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# Creating the Vascular Forest Object
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f = Forest()
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f.set_domain(cube)
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f.set_roots()
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f.add(50)
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# Visualizing the Forest and Domain
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f.show(plot_domain=True)</code></pre>
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<figure class="figure-center">
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<img src="graphics/quickstart_forest_orbit.gif" alt="Orbit around unconnected vascular forest" width="400" />
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<figcaption> Rotating view of the generated vascular forest </figcaption>
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</figure>
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<p>At this step our vascular forest object remains unconnected and should contain two non-intersecting trees.
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Because we have not specified any special build parameters, these trees adhere to the same default fluid constrains
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and are allowed to grow homogeneously within the tissue domain. Connections among multiple trees is accomplished via
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the <code>forest.connect()</code> method which automatically sets up a two-step optimization problem to form
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connections among sets of tree terminals. </p>
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<pre data-copy><code class="language-python"># Form connections
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f.connect()
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# Visualize the Connected Forest Object
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f.connections.tree_connections[0].show().show()</code></pre>
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<figure class="figure-center">
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<img src="graphics/quickstart_forest_connected_orbit.gif" alt="Orbit around connected vascular forest" width="400" />
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<figcaption> Rotating view of the connected vascular forest </figcaption>
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</figure>
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<h3>Export 0-D simulation files</h3>
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<p>Because a forest object may contain multiple fluid networks, it is important to specify which network a user wants
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to export for simulation as well as the inlet boundaries. These are the second and thrid positional arguments of the
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simulation exporting function, respectively. </p>
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<pre data-copy><code class="language-python">from svv.simulation.fluid.rom.zero_d.zerod_forest import export_0d_simulation
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export_0d_simulation(f, 0, [0], outdir="my_forest_0d") </code> </pre>
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<p>Similar to exporting the <code>tree</code> object for simulation, this function will write out a 0-D solver input
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file <code>solver_0d.in</code> as well as a geometric file, <code>geom.csv</code> for casting solutions back onto
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the 3D geometry for visualization. The inlet boundary conditions will be applied to the root vessel of the first tree
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since we specified this in the third argument of our function above. By default, this will be a steady flow simulation
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with a simple resistance outflow boundary condition. Solutions to the 0-D problem can be obtained using the same <code>svzerodsolver</code>
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workflow.</p>
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</main>
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<footer>
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<div class="container">
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<p>&copy; 2025 SimVascular, Stanford University, The Regents of the University of California, and others —
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<a href="https://opensource.org/license/BSD-3-Clause">BSD 3-Clause License</a><br></p>
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</div>
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</footer>
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<script defer src="script.js"></script>
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</body>
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</html>

‎docs/style.css‎

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.figure-center figcaption {
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font-size: 0.85rem;
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color: var(--clr-grey-500);
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}
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background: var(--clr-grey-100); /* light grey fill */

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