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updating GUI for reliable connections and parameters
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‎docs/api/domain.html‎

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@@ -99,6 +99,7 @@ <h4 class="sidebar-title">Contents</h4>
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<li><a href="#constructor"><i class="fas fa-hammer"></i> Constructor</a></li>
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<li><a href="#attributes"><i class="fas fa-database"></i> Attributes</a></li>
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<li><a href="#methods"><i class="fas fa-cogs"></i> Methods</a></li>
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<li><a href="#persistence"><i class="fas fa-save"></i> Persistence</a></li>
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<li><a href="#operators"><i class="fas fa-calculator"></i> Operators</a></li>
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<li><a href="#examples"><i class="fas fa-code"></i> Examples</a></li>
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<li><a href="#notes"><i class="fas fa-info-circle"></i> Notes</a></li>
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</div>
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</section>
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<!-- Persistence Section -->
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<section id="persistence" class="api-section">
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<h2>Persistence (Save/Load)</h2>
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<p>Domains can be saved to and loaded from <code>.dmn</code> files, allowing you to preserve
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expensive implicit function computations and share domain configurations.</p>
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<div class="api-method">
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<div class="api-method-signature">
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<code>save(path, include_boundary=False, include_mesh=False, include_patch_normals=True)</code>
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</div>
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<p>Save the domain to a <code>.dmn</code> file.</p>
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<div class="api-method-params">
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<h4>Parameters</h4>
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<ul>
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<li><code>path</code> (str): Output filename. If no extension is provided, <code>.dmn</code> is appended.</li>
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<li><code>include_boundary</code> (bool): Persist the boundary mesh for visualization without recomputation. Default is False.</li>
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<li><code>include_mesh</code> (bool): Persist the interior mesh for sampling without recomputation. Default is False.</li>
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<li><code>include_patch_normals</code> (bool): Include per-patch normals to fully restore Patch objects. Default is True.</li>
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</ul>
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<h4>Notes</h4>
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<p>The saved file contains the implicit function coefficients and patch data needed to
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reconstruct the domain. Including boundary and mesh data increases file size but
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speeds up subsequent operations.</p>
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</div>
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</div>
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<div class="api-method">
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<div class="api-method-signature">
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<code>Domain.load(path)</code> <span class="api-badge">classmethod</span>
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</div>
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<p>Load a domain from a <code>.dmn</code> file.</p>
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<div class="api-method-params">
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<h4>Parameters</h4>
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<ul>
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<li><code>path</code> (str): Path to a <code>.dmn</code> file.</li>
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</ul>
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<h4>Returns</h4>
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<ul>
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<li><code>Domain</code>: Fully initialized Domain instance ready for fast evaluation.</li>
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</ul>
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<h4>Notes</h4>
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<p>The loaded domain has its <code>function_tree</code> rebuilt and is ready for use
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with <code>__call__</code> (fast evaluation). Patches are reconstructed from stored
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arrays, enabling you to call <code>build()</code> again if needed.</p>
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</div>
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</div>
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<div class="api-example">
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<h4>Save/Load Example</h4>
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<pre data-copy><code class="language-python">from svv.domain.domain import Domain
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import pyvista as pv
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# Create domain from a complex mesh
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mesh = pv.read("heart_ventricle.stl")
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domain = Domain(mesh)
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domain.create() # Creates patches (can be slow for complex meshes)
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domain.solve() # Solves RBF system (expensive)
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domain.build() # Builds boundary and mesh
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# Save domain for later use
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domain.save("ventricle.dmn", include_boundary=True, include_mesh=True)
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# Later, load the domain instantly
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loaded_domain = Domain.load("ventricle.dmn")
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# Use immediately - no need to call create/solve/build
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point = [[0.5, 0.5, 0.5]]
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inside = loaded_domain(point) < 0 # Fast evaluation works immediately
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# Or call build() if you need fresh boundary/mesh
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loaded_domain.build()</code></pre>
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</div>
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<div class="callout tip">
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<strong>Performance Tip:</strong> For complex domains, saving with <code>include_boundary=True</code>
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and <code>include_mesh=True</code> significantly speeds up subsequent loads at the cost of
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larger file sizes. This is especially useful when iterating on tree generation with the same domain.
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</div>
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</section>
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<!-- Operators Section -->
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<section id="operators" class="api-section">
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<h2>Operators</h2>

‎docs/api/forest.html‎

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<li><a href="#growth-methods"><i class="fas fa-seedling"></i> Growth Methods</a></li>
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<li><a href="#connection-methods"><i class="fas fa-link"></i> Connection Methods</a></li>
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<li><a href="#export-methods"><i class="fas fa-file-export"></i> Export Methods</a></li>
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<li><a href="#persistence"><i class="fas fa-save"></i> Persistence</a></li>
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<li><a href="#examples"><i class="fas fa-code"></i> Examples</a></li>
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<li><a href="#algorithms"><i class="fas fa-brain"></i> Algorithms</a></li>
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</ul>
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</div>
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</section>
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<!-- Persistence Section -->
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<section id="persistence" class="api-section">
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<h2>Persistence (Save/Load)</h2>
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<p>Forests can be saved to and loaded from <code>.forest</code> files, enabling checkpointing during
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complex multi-tree growth processes and sharing of generated vascular networks.</p>
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<div class="api-method">
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<div class="api-method-signature">
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<code>save(path, include_timing=False)</code>
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</div>
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<p>Save the forest to a <code>.forest</code> file.</p>
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<div class="api-method-params">
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<h4>Parameters</h4>
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<ul>
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<li><code>path</code> (str): Output filename. If no extension is provided, <code>.forest</code> is appended.</li>
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<li><code>include_timing</code> (bool): Include generation timing data for each tree. Default is False.</li>
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</ul>
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<h4>Returns</h4>
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<ul>
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<li><code>pathlib.Path</code>: Path to the saved file.</li>
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</ul>
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<h4>Notes</h4>
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<p>The saved file contains all forest data, tree parameters, and connectivity information.
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If <code>connect()</code> has been called, connections are also saved. <strong>The domain
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is NOT saved</strong> and must be set separately after loading via <code>set_domain()</code>.</p>
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</div>
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</div>
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<div class="api-method">
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<div class="api-method-signature">
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<code>Forest.load(path)</code> <span class="api-badge">classmethod</span>
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</div>
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<p>Load a forest from a <code>.forest</code> file.</p>
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<div class="api-method-params">
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<h4>Parameters</h4>
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<ul>
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<li><code>path</code> (str): Path to a <code>.forest</code> file.</li>
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</ul>
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<h4>Returns</h4>
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<ul>
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<li><code>Forest</code>: Loaded forest instance with all trees and connections restored.</li>
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</ul>
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<h4>Notes</h4>
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<p>The loaded forest will NOT have a domain set. You must call <code>set_domain()</code>
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after loading to enable domain-dependent operations. If the forest was saved with
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connections (after calling <code>connect()</code>), those connections are restored.</p>
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</div>
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</div>
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<div class="api-example">
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<h4>Save/Load Example</h4>
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<pre data-copy><code class="language-python">from svv.forest.forest import Forest
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from svv.domain.domain import Domain
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import pyvista as pv
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# Create and grow a forest
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domain = Domain(pv.Cube())
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domain.create()
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domain.solve()
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domain.build()
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forest = Forest()
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forest.set_domain(domain)
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forest.set_roots() # Uses default opposing start points
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forest.add(50)
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forest.connect()
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# Save the complete forest (including connections)
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forest.save("vascular_network.forest")
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# Later, load it back
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loaded_forest = Forest.load("vascular_network.forest")
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# Re-attach the domain
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loaded_forest.set_domain(domain)
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# Connections are preserved - can visualize immediately
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loaded_forest.show(plot_domain=True)
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# Or continue growing
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loaded_forest.add(25)</code></pre>
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</div>
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<div class="callout info">
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<strong>Connections Preserved:</strong> Unlike trees, forests can include connection data when
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saved. If you saved after calling <code>connect()</code>, the connection geometry and parameters
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are restored on load.
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</div>
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</section>
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<!-- Examples Section -->
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<section id="examples" class="api-section">
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<h2>Examples</h2>

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