Improve GUI .dmn loading and add advanced lumen detection for mesh face extraction #20
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…elpers - Integrate UnitSystem into TreeParameters with default CGS and mmHg - Convert viscosity, density, pressure, and flow to active unit system - Support set(..., unit=...) to accept alternate units - Add set_unit_system(convert_existing=...) to switch systems safely - Improve __str__ to include unit symbols and cleaner formatting
…ow injecting an existing parameters instance\n- Add optional unit_system for default parameters\n- Wire __init__ to set or convert unit system
…ella VTK import to avoid optional IO deps (e.g., NetCDF) at import time
- Create kernel on-demand in Patch.build() when loading from .dmn - Auto-rebuild domain boundary in GUI when not included in .dmn file - Resolves AttributeError when accessing kernel.d on loaded patches
…tection
This commit enhances the extract_faces function with multi-criteria surface
classification to accurately distinguish between caps, lumens, and walls.
Major changes:
1. Lumen Detection
- Added new 'lumen' surface category exported separately from caps
- Lumens are surfaces with 2+ boundary loops that exhibit boundary creases
- Boundary crease detection checks if face normals are perpendicular to
boundary loop plane normals (indicating clean separation from surroundings)
- Multi-criteria verification using circularity, separation, planarity, and
aspect ratio for 2-loop surfaces
- Support for multi-outlet lumens (3+ boundary loops with creases)
2. Boundary Overlap Classification
- Caps with boundary loops that share edges/vertices with other boundaries
are now reclassified as walls
- This correctly handles cases where flat endcaps connect to cylindrical
lumens via shared circular edges
3. Improved Normal Computation
- Switched to PyVista's auto-orientation with non-manifold traversal
- Correctly handles both outer surfaces and interior holes
- Removed manual normal correction that was causing issues
4. Graph-Based Wall Combination
- Replaced linear wall merging with graph-based connected components
- More robust handling of complex wall topologies
- Caps and lumens are never merged with walls or each other
Return value updated: now returns (faces, wall_surfaces, cap_surfaces,
lumen_surfaces, shared_boundaries) with lumens as a separate list.
Classification hierarchy:
- Caps: Single boundary loop, no overlap with other boundaries
- Lumens: 2+ boundary loops with boundary creases (perpendicular normals)
- Walls: All other surfaces (no boundary creases or overlapping boundaries)
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Current situation
This PR addresses critical usability issues in GUI workflow and
mesh processing:
data
surfaces as walls or merging them with caps
These improvements enable proper handling of vessel network
geometries and seamless GUI operation with persisted domain
files.
Breaking Changes
wall_surfaces, cap_surfaces, lumen_surfaces, shared_boundaries)
with lumens as a separate list (previously returned 4 values, now
returns 5)
New Features
cylindrical lumen surfaces separately from caps and walls
sharp separation from surroundings
planarity, aspect ratio)
share edges/vertices with other boundaries are now correctly
reclassified as walls
Bug Fixes
now load correctly
AttributeError
auto-orientation with non-manifold traversal for better handling
of surfaces with interior holes
Enhancements
surfaces using connected component analysis
Migration Guide
If your code uses extract_faces(), update to handle the new
return signature:
Before:
faces, walls, caps, shared_boundaries = extract_faces(surface,
mesh)
After:
faces, walls, caps, lumens, shared_boundaries =
extract_faces(surface, mesh)
Documentation
logic
hierarchy:
(perpendicular normals)
boundaries)
Testing
holes
cylindrical surfaces separate from 4 endcaps
overlap with lumens
patches
Files Modified:
detection, boundary overlap checks, graph-based wall merging)
boundaries)
Code of Conduct & Contributing Guidelines