Initial commit
This commit is contained in:
redclawsystems
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//! FE Model data structures.
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//!
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//! This module defines the core data structures for representing
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//! finite element models created from MRI data.
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use nalgebra::Point3;
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use rtx_materials::PronyCoefficients;
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use rtx_mesh_gen::TetrahedralMesh;
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use serde::{Deserialize, Serialize};
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use std::collections::HashMap;
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/// A region in the FE model with associated material properties.
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#[derive(Debug, Clone, Serialize, Deserialize)]
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pub struct ModelRegion {
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/// Region identifier (typically from segmentation label).
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pub id: usize,
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/// Human-readable name for the region.
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pub name: String,
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/// Element indices belonging to this region.
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pub element_ids: Vec<usize>,
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/// Material model for this region.
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pub material: RegionMaterial,
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}
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/// Material assignment for a region.
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#[derive(Debug, Clone, Serialize, Deserialize)]
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pub enum RegionMaterial {
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/// Linear elastic material.
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Elastic {
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/// Young's modulus (Pa).
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young_modulus: f64,
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/// Poisson's ratio.
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poisson_ratio: f64,
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/// Density (kg/m³).
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density: f64,
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},
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/// Viscoelastic material with Prony series.
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Viscoelastic {
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/// Instantaneous shear modulus (Pa).
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g0: f64,
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/// Bulk modulus (Pa).
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bulk_modulus: f64,
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/// Prony series coefficients.
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prony_coeffs: PronyCoefficients,
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/// Density (kg/m³).
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density: f64,
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},
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/// Spatially varying MRE-derived properties.
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MreDerived {
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/// Base material (elastic or viscoelastic).
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base_material: Box<RegionMaterial>,
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/// MRE property values mapped to element nodes.
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mre_values: MrePropertyMap,
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},
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}
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/// MRE property mapping to mesh elements.
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#[derive(Debug, Clone, Serialize, Deserialize)]
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pub struct MrePropertyMap {
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/// Storage modulus G' (Pa) at each node.
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pub storage_modulus: Vec<f64>,
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/// Loss modulus G'' (Pa) at each node.
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pub loss_modulus: Vec<f64>,
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/// Frequency at which MRE was measured (Hz).
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pub frequency: f64,
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}
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/// Boundary condition definition.
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#[derive(Debug, Clone, Serialize, Deserialize)]
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pub enum BoundaryCondition {
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/// Fixed displacement (Dirichlet).
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Displacement {
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/// Node indices with this constraint.
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node_ids: Vec<usize>,
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/// Fixed displacement vector (None for fixed DOF).
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value: Option<[f64; 3]>,
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/// Which DOFs are constrained (x, y, z).
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constrained: [bool; 3],
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},
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/// Applied force (Neumann).
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Force {
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/// Node indices with applied force.
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node_ids: Vec<usize>,
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/// Force vector (N).
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value: [f64; 3],
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},
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/// Applied pressure on surface.
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Pressure {
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/// Surface element faces (element_id, face_id).
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faces: Vec<(usize, usize)>,
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/// Pressure value (Pa).
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value: f64,
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},
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}
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/// A complete finite element model for MRI2FE workflow.
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#[derive(Debug, Clone)]
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pub struct Mri2FeModel {
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/// Model name.
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pub name: String,
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/// Model description.
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pub description: String,
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/// The tetrahedral mesh.
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pub mesh: TetrahedralMesh,
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/// Regions with material assignments.
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pub regions: Vec<ModelRegion>,
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/// Boundary conditions.
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pub boundary_conditions: Vec<BoundaryCondition>,
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/// Model metadata.
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pub metadata: ModelMetadata,
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}
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/// Model metadata.
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#[derive(Debug, Clone, Default, Serialize, Deserialize)]
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pub struct ModelMetadata {
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/// Source image path.
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pub source_image: Option<String>,
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/// MRE image paths.
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pub mre_images: Vec<String>,
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/// Registration transforms applied.
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pub transforms: Vec<String>,
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/// Creation timestamp.
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pub created: Option<String>,
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/// Additional properties.
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pub properties: HashMap<String, String>,
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}
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impl Mri2FeModel {
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/// Create a new empty FE model.
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pub fn new(name: impl Into<String>, description: impl Into<String>) -> Self {
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Self {
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name: name.into(),
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description: description.into(),
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mesh: TetrahedralMesh::new(),
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regions: Vec::new(),
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boundary_conditions: Vec::new(),
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metadata: ModelMetadata::default(),
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}
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}
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/// Get the total number of nodes.
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pub fn node_count(&self) -> usize {
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self.mesh.vertices.len()
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}
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/// Get the total number of elements.
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pub fn element_count(&self) -> usize {
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self.mesh.tetrahedra.len()
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}
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/// Get a node position by index.
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pub fn node(&self, index: usize) -> Option<Point3<f64>> {
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self.mesh.vertices.get(index).map(|v| v.position)
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}
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/// Get an element's node indices.
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pub fn element(&self, index: usize) -> Option<[usize; 4]> {
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self.mesh.tetrahedra.get(index).map(|t| t.vertices)
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}
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/// Find the region containing an element.
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pub fn region_for_element(&self, element_id: usize) -> Option<&ModelRegion> {
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self.regions
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.iter()
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.find(|r| r.element_ids.contains(&element_id))
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}
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/// Add a region to the model.
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pub fn add_region(&mut self, region: ModelRegion) {
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self.regions.push(region);
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}
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/// Add a boundary condition.
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pub fn add_boundary_condition(&mut self, bc: BoundaryCondition) {
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self.boundary_conditions.push(bc);
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}
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/// Validate the model for export.
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pub fn validate(&self) -> Result<(), Vec<String>> {
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let mut errors = Vec::new();
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if self.mesh.vertices.is_empty() {
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errors.push("Mesh has no nodes".to_string());
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}
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if self.mesh.tetrahedra.is_empty() {
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errors.push("Mesh has no elements".to_string());
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}
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// Check all elements reference valid nodes
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let node_count = self.mesh.vertices.len();
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for (i, tet) in self.mesh.tetrahedra.iter().enumerate() {
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for &node_id in &tet.vertices {
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if node_id >= node_count {
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errors.push(format!("Element {} references invalid node {}", i, node_id));
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}
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}
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}
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// Check region element assignments
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let elem_count = self.mesh.tetrahedra.len();
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for region in &self.regions {
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for &elem_id in ®ion.element_ids {
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if elem_id >= elem_count {
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errors.push(format!(
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"Region '{}' references invalid element {}",
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region.name, elem_id
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));
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}
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}
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}
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// Check boundary condition node references
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for (i, bc) in self.boundary_conditions.iter().enumerate() {
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let node_ids = match bc {
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BoundaryCondition::Displacement { node_ids, .. } => node_ids,
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BoundaryCondition::Force { node_ids, .. } => node_ids,
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BoundaryCondition::Pressure { .. } => continue,
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};
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for &node_id in node_ids {
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if node_id >= node_count {
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errors.push(format!(
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"Boundary condition {} references invalid node {}",
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i, node_id
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));
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}
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}
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}
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if errors.is_empty() {
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Ok(())
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} else {
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Err(errors)
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}
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}
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/// Get model bounding box.
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pub fn bounding_box(&self) -> Option<(Point3<f64>, Point3<f64>)> {
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if self.mesh.vertices.is_empty() {
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return None;
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}
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let points: Vec<Point3<f64>> = self.mesh.vertices.iter().map(|v| v.position).collect();
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rtx_segmentation::kdtree::bounding_box(&points)
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}
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/// Get model center of mass.
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pub fn center_of_mass(&self) -> Option<Point3<f64>> {
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if self.mesh.vertices.is_empty() {
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return None;
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}
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let points: Vec<Point3<f64>> = self.mesh.vertices.iter().map(|v| v.position).collect();
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rtx_segmentation::kdtree::center_of_mass(&points)
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}
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/// Convert to rtx-fem-export FEModel for export.
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pub fn to_fem_model(&self) -> rtx_fem_export::FEModel {
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use rtx_fem_export::{ElementType, FEModelBuilder, Material};
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use rtx_materials::LinearElastic;
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let mut builder = FEModelBuilder::new(&self.name, &self.description);
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// Add all nodes
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let node_ids: Vec<u64> = self
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.mesh
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.vertices
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.iter()
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.map(|v| builder.add_node(v.position.x, v.position.y, v.position.z))
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.collect();
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// Add materials and parts for each region
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for region in &self.regions {
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let mat_id = match ®ion.material {
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RegionMaterial::Elastic {
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young_modulus,
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poisson_ratio,
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density,
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} => {
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let elastic = LinearElastic::new(*young_modulus, *poisson_ratio, *density);
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builder.add_material(Material::Elastic(elastic))
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}
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RegionMaterial::Viscoelastic {
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g0: _,
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bulk_modulus,
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prony_coeffs,
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density,
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} => {
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let km = rtx_materials::KelvinMaxwell::from_prony(
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prony_coeffs,
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*density,
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*bulk_modulus,
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);
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builder.add_material(Material::KelvinMaxwell(km))
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}
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RegionMaterial::MreDerived { base_material, .. } => {
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// Use base material for export (MRE values are for analysis)
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if let RegionMaterial::Elastic {
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young_modulus,
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poisson_ratio,
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density,
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} = base_material.as_ref() {
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let elastic =
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LinearElastic::new(*young_modulus, *poisson_ratio, *density);
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builder.add_material(Material::Elastic(elastic))
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} else {
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let elastic = LinearElastic::new(1e6, 0.45, 1000.0);
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builder.add_material(Material::Elastic(elastic))
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}
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}
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};
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let part_id = builder.add_part(®ion.name, mat_id, ElementType::Tet4);
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// Add elements for this region
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for &elem_idx in ®ion.element_ids {
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if let Some(tet) = self.mesh.tetrahedra.get(elem_idx) {
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builder.add_tet4(
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part_id,
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node_ids[tet.vertices[0]],
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node_ids[tet.vertices[1]],
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node_ids[tet.vertices[2]],
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node_ids[tet.vertices[3]],
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);
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}
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}
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}
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// If no regions defined, add all elements to a default part
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if self.regions.is_empty() && !self.mesh.tetrahedra.is_empty() {
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let elastic = LinearElastic::new(1e6, 0.45, 1000.0);
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let mat_id = builder.add_material(Material::Elastic(elastic));
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let part_id = builder.add_part("Default", mat_id, ElementType::Tet4);
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for tet in &self.mesh.tetrahedra {
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builder.add_tet4(
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part_id,
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node_ids[tet.vertices[0]],
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node_ids[tet.vertices[1]],
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node_ids[tet.vertices[2]],
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node_ids[tet.vertices[3]],
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);
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}
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}
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builder.build()
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}
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}
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#[cfg(test)]
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mod tests {
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use super::*;
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use rtx_mesh_gen::Vertex;
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fn create_simple_mesh() -> TetrahedralMesh {
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let mut mesh = TetrahedralMesh::new();
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mesh.vertices = vec![
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Vertex::new(0.0, 0.0, 0.0),
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Vertex::new(1.0, 0.0, 0.0),
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Vertex::new(0.0, 1.0, 0.0),
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Vertex::new(0.0, 0.0, 1.0),
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];
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mesh.tetrahedra = vec![rtx_mesh_gen::Tetrahedron::new(0, 1, 2, 3)];
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mesh
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}
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#[test]
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fn test_new_model() {
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let model = Mri2FeModel::new("Test", "A test model");
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assert_eq!(model.name, "Test");
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assert_eq!(model.description, "A test model");
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assert_eq!(model.node_count(), 0);
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assert_eq!(model.element_count(), 0);
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}
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#[test]
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fn test_model_with_mesh() {
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let mut model = Mri2FeModel::new("Test", "Test model");
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model.mesh = create_simple_mesh();
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assert_eq!(model.node_count(), 4);
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assert_eq!(model.element_count(), 1);
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assert!(model.validate().is_ok());
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}
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#[test]
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fn test_region_material() {
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let elastic = RegionMaterial::Elastic {
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young_modulus: 1e9,
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poisson_ratio: 0.3,
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density: 1000.0,
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};
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let region = ModelRegion {
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id: 1,
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name: "Brain".to_string(),
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element_ids: vec![0],
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material: elastic,
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};
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assert_eq!(region.name, "Brain");
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assert_eq!(region.element_ids.len(), 1);
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}
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#[test]
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fn test_boundary_conditions() {
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let mut model = Mri2FeModel::new("Test", "Test");
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model.mesh = create_simple_mesh();
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model.add_boundary_condition(BoundaryCondition::Displacement {
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node_ids: vec![0],
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value: None,
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constrained: [true, true, true],
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});
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model.add_boundary_condition(BoundaryCondition::Force {
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node_ids: vec![3],
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value: [0.0, 0.0, -100.0],
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});
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assert_eq!(model.boundary_conditions.len(), 2);
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assert!(model.validate().is_ok());
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}
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#[test]
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fn test_invalid_element_reference() {
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let mut model = Mri2FeModel::new("Test", "Test");
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let mut mesh = TetrahedralMesh::new();
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mesh.vertices = vec![Vertex::new(0.0, 0.0, 0.0), Vertex::new(1.0, 0.0, 0.0)];
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// Invalid vertex references
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mesh.tetrahedra = vec![rtx_mesh_gen::Tetrahedron::new(0, 1, 10, 20)];
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model.mesh = mesh;
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let result = model.validate();
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assert!(result.is_err());
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}
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#[test]
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fn test_to_fem_model() {
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let mut model = Mri2FeModel::new("Test", "Test");
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model.mesh = create_simple_mesh();
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model.regions.push(ModelRegion {
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id: 1,
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name: "Default".to_string(),
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element_ids: vec![0],
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material: RegionMaterial::Elastic {
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young_modulus: 1e6,
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poisson_ratio: 0.3,
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density: 1000.0,
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},
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});
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let fem = model.to_fem_model();
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assert_eq!(fem.nodes.len(), 4);
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assert_eq!(fem.elements.len(), 1);
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}
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}
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