Merge pull request #32 from zasexton/main

simplifying imports and improving face extraction

Author: zasexton

.gitignore

@@ -27,3 +27,17 @@ svZeroDSolver*
 
 # Sample artifacts
 cube.dmn
+
+# Local GUI docs and scripts (ignored)
+CAD_GUI_DOCUMENTATION.md
+CAD_GUI_SUMMARY.md
+FIX_LLVM_MISMATCH.sh
+GUI_FEATURES.md
+GUI_IMPROVEMENTS.md
+GUI_QUICK_START.md
+GUI_UPGRADE_SUMMARY.md
+OPENGL_FIX_SUMMARY.md
+OPENGL_TROUBLESHOOTING.md
+STYLE_COMPARISON.md
+UBUNTU_20.04_SETUP.md
+launch_gui_system_mesa.sh

docs/api/domain.html

@@ -68,7 +68,7 @@ <h1><code>svv.domain.Domain</code></h1>
             <h2>Quick Example</h2>
             <pre data-copy><code class="language-python">import numpy as np
 import pyvista as pv
-from svv.domain import Domain
+from svv.domain.domain import Domain
 
 # Create domain from PyVista mesh
 mesh = pv.read('vessel_geometry.stl')
@@ -460,7 +460,7 @@ <h2>Examples</h2>
                     <div class="api-example">
                         <h3>Creating a Domain from STL File</h3>
                         <pre data-copy><code class="language-python">import pyvista as pv
-from svv.domain import Domain
+from svv.domain.domain import Domain
 
 # Load STL file
 mesh = pv.read('vessel.stl')
@@ -559,8 +559,8 @@ <h2>Notes</h2>
                     <h2>See Also</h2>
                     <ul>
                         <li><a href="patch.html"><code>svv.domain.Patch</code></a> - Individual patch for RBF interpolation</li>
-                        <li><a href="../tree/tree.html"><code>svv.tree.Tree</code></a> - Vascular tree generation using domains</li>
-                        <li><a href="../forest/forest.html"><code>svv.forest.Forest</code></a> - Collection of trees within a domain</li>
+                        <li><a href="tree.html"><code>svv.tree.Tree</code></a> - Vascular tree generation using domains</li>
+                        <li><a href="forest.html"><code>svv.forest.Forest</code></a> - Collection of trees within a domain</li>
                     </ul>
                 </section>
             </main>

docs/api/forest.html

@@ -66,8 +66,8 @@ <h1><code>svv.forest.Forest</code></h1>
         <!-- Quick Example -->
         <div class="api-quick-example">
             <h2>Quick Example</h2>
-            <pre data-copy><code class="language-python">from svv.forest import Forest
-from svv.domain import Domain
+            <pre data-copy><code class="language-python">from svv.forest.forest import Forest
+from svv.domain.domain import Domain
 import numpy as np
 import pyvista as pv
 
@@ -394,9 +394,10 @@ <h2>Examples</h2>
 
                     <div class="api-example">
                         <h3>Arterial-Venous Network</h3>
-                        <pre data-copy><code class="language-python">from svv.forest import Forest
-from svv.domain import Domain
+                        <pre data-copy><code class="language-python">from svv.forest.forest import Forest
+from svv.domain.domain import Domain
 import numpy as np
+import pyvista as pv
 
 # Create organ domain
 organ = pv.read('liver.stl')
@@ -438,7 +439,9 @@ <h3>Arterial-Venous Network</h3>
 
                     <div class="api-example">
                         <h3>Multi-Tree Network with Connections</h3>
-                        <pre data-copy><code class="language-python"># Create forest with multiple trees per network
+                        <pre data-copy><code class="language-python">from svv.forest.forest import Forest
+import numpy as np
+# Create forest with multiple trees per network
 forest = Forest(
     n_networks=1,
     n_trees_per_network=[4],  # 4 trees in single network
@@ -468,13 +471,17 @@ <h3>Multi-Tree Network with Connections</h3>
 if forest.connections:
     print(f"Tree connections solved: {len(forest.connections.tree_connections)}")
 
-# Export connected network
-forest.export_solid(outdir='connected_network')</code></pre>
+# Export connected network: save each tree as STL
+for i in range(forest.n_networks):
+    for j in range(forest.n_trees_per_network[i]):
+        model = forest.networks[i][j].export_solid(watertight=True)
+        model.save(f'connected_network_{i}_{j}.stl')</code></pre>
                     </div>
 
                     <div class="api-example">
                         <h3>Competitive Growth Pattern</h3>
                         <pre data-copy><code class="language-python"># Enable competition between networks
+from svv.forest.forest import Forest
 import numpy as np
 forest = Forest(
     domain=domain,

docs/api/index_api.html

@@ -85,10 +85,10 @@ <h2>Quick Start</h2>
 
             <h3>Basic Import</h3>
             <pre data-copy><code class="language-python">import svv
-from svv.domain import Domain
-from svv.forest import Forest
-from svv.tree import Tree
-from svv.simulation import Simulation
+from svv.domain.domain import Domain
+from svv.forest.forest import Forest
+from svv.tree.tree import Tree
+from svv.simulation.simulation import Simulation
 
 # Create a domain
 domain = Domain()
@@ -190,7 +190,7 @@ <h4>Main Classes</h4>
                         </div>
                         <div class="api-example">
                             <h4>Example Usage</h4>
-                            <pre data-copy><code class="language-python">from svv.domain import Domain
+                            <pre data-copy><code class="language-python">from svv.domain.domain import Domain
 
 # Create a domain from a mesh
 import pyvista as pv
@@ -268,8 +268,8 @@ <h4>Main Classes</h4>
                         <div class="api-example">
                             <h4>Example Usage</h4>
                             <pre data-copy><code class="language-python">import pyvista as pv
-from svv.domain import Domain
-from svv.forest import Forest
+from svv.domain.domain import Domain
+from svv.forest.forest import Forest
 
 # Prepare a domain and build its implicit representation
 domain = Domain(pv.Cube())
@@ -399,7 +399,7 @@ <h4>Main Classes</h4>
 
                         <div class="api-example">
                             <h4>Example Usage</h4>
-                            <pre data-copy><code class="language-python">from svv.simulation import Simulation
+                            <pre data-copy><code class="language-python">from svv.simulation.simulation import Simulation
 from svv.simulation.fluid.rom.zero_d.zerod_tree import export_0d_simulation
 
 # Wrap a generated tree in a Simulation container
@@ -490,8 +490,8 @@ <h2>Common Examples</h2>
                 <div class="api-example-card">
                     <h3>Generate a Vascular Tree</h3>
                     <pre data-copy><code class="language-python">import pyvista as pv
-from svv.domain import Domain
-from svv.tree import Tree
+from svv.domain.domain import Domain
+from svv.tree.tree import Tree
 
 domain = Domain(pv.Cube())
 domain.create()
@@ -504,7 +504,8 @@ <h3>Generate a Vascular Tree</h3>
 tree.n_add(100)
 
 # Export watertight geometry for printing or meshing
-tree.export_solid(outdir='vascular_tree')</code></pre>
+solid_model = tree.export_solid(watertight=True)
+solid_model.save('vascular_tree.stl')</code></pre>
                 </div>
 
                 <div class="api-example-card">

docs/api/simulation.html

@@ -68,8 +68,8 @@ <h1><code>svv.simulation.Simulation</code></h1>
         <!-- Quick Example -->
         <div class="api-quick-example">
             <h2>Quick Example</h2>
-            <pre data-copy><code class="language-python">from svv.simulation import Simulation
-from svv.tree import Tree
+            <pre data-copy><code class="language-python">from svv.simulation.simulation import Simulation
+# Assumes `tree` is an existing svv.tree.Tree built as in the Quickstart
 
 # Create simulation from tree
 sim = Simulation(tree, name="coronary_sim", directory="./simulations")
@@ -425,9 +425,9 @@ <h2>Examples</h2>
 
                     <div class="api-example">
                         <h3>Complete 3D CFD Simulation Setup</h3>
-                        <pre data-copy><code class="language-python">from svv.simulation import Simulation
-from svv.tree import Tree
-from svv.domain import Domain
+                        <pre data-copy><code class="language-python">from svv.simulation.simulation import Simulation
+from svv.tree.tree import Tree
+from svv.domain.domain import Domain
 import pyvista as pv
 
 # Generate vascular tree
@@ -492,7 +492,8 @@ <h3>Multi-Scale Simulation (3D + 1D)</h3>
 
 # Write both simulations
 sim.write_3d_fluid_simulation()
-sim.write_1d_fluid_simulation()
+# Note: writing 1-D files is not yet automated.
+# Use the returned centerlines/mesh/params to invoke the SimVascular 1-D tools.
 
 # Access centerlines for coupling
 centerlines = sim.fluid_1d_simulations[0][0]

docs/api/tree.html

@@ -66,8 +66,8 @@ <h1><code>svv.tree.Tree</code></h1>
         <!-- Quick Example -->
         <div class="api-quick-example">
             <h2>Quick Example</h2>
-            <pre data-copy><code class="language-python">from svv.tree import Tree
-from svv.domain import Domain
+            <pre data-copy><code class="language-python">from svv.tree.tree import Tree
+from svv.domain.domain import Domain
 import pyvista as pv
 
 # Create domain from mesh
@@ -397,8 +397,8 @@ <h2>Examples</h2>
 
                     <div class="api-example">
                         <h3>Basic Tree Generation</h3>
-                        <pre data-copy><code class="language-python">from svv.tree import Tree
-from svv.domain import Domain
+                        <pre data-copy><code class="language-python">from svv.tree.tree import Tree
+from svv.domain.domain import Domain
 import numpy as np
 import pyvista as pv
 
@@ -457,7 +457,8 @@ <h3>Constrained Growth with Physical Clearance</h3>
 
                     <div class="api-example">
                         <h3>Export for Simulation</h3>
-                        <pre data-copy><code class="language-python"># Generate tree
+                        <pre data-copy><code class="language-python">import numpy as np
+# Generate tree
 tree = Tree()
 tree.set_domain(domain)
 tree.set_root([0, 0, 0])
@@ -509,7 +510,8 @@ <h2>Performance Considerations</h2>
 
                     <h3>Timing Analysis</h3>
                     <p>Access detailed timing information through the <code>times</code> attribute:</p>
-                    <pre data-copy><code class="language-python"># After growing tree
+                        <pre data-copy><code class="language-python"># After growing tree
+import numpy as np
 import pandas as pd
 
 # Convert timing data to DataFrame

svv/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.0.33"
+__version__ = "0.0.34"
 
 # If the optional companion package with compiled accelerators is installed
 # (svv-accelerated), prefer those modules transparently by aliasing them into

svv/simulation/boundary_conditions.py

@@ -16,7 +16,10 @@ def __str__(self):
         return str(vars(self))
 
     def __repr__(self):
-        return str(vars(self))
+        try:
+            return self.toxml().toprettyxml(indent="  ")
+        except Exception:
+            return str(vars(self))
 
     def __eq__(self, other):
         check = ["bc_type", "value", "time_varying", "time_varying_file", "impose_flux", "profile"]
@@ -37,7 +40,10 @@ def __str__(self):
         return self.toxml().toprettyxml()
 
     def __repr__(self):
-        return self.toxml().toprettyxml()
+        try:
+            return self.toxml().toprettyxml(indent="  ")
+        except Exception:
+            return str(vars(self))
 
     def set_type(self, bc_type):
         if bc_type not in ["Dirichlet", "Neumann", "Dir", "Neu"]:

svv/simulation/equation.py

@@ -51,7 +51,10 @@ def __str__(self):
         return self.toxml().toprettyxml()
 
     def __repr__(self):
-        return self.toxml().toprettyxml()
+        try:
+            return self.toxml().toprettyxml(indent="  ")
+        except Exception:
+            return str(vars(self))
 
     def set_type(self, equation_type):
         if equation_type not in ["fluid", "scalarTransport"]:

svv/simulation/fluid/fluid_equation.py

@@ -64,10 +64,12 @@ def add_wall(self, face, value=0.0, bc_type='Dirichlet', time_varying_file=None)
 
     def check_bcs(self):
         """
-        Check that all boundary conditions are set.
+        Check that all boundary conditions are set for caps.
         """
         for face in self.faces:
             found = False
+            if not 'cap' in face:
+                continue
             for bc in self.boundary_conditions:
                 if bc.name == face:
                     found = True