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use crate::mesh::Mesh;
use crate::Real;
use nalgebra::{DefaultAllocator, DimName, Scalar};
use vtkio::model::{Attribute, CellType, Cells, DataSet, UnstructuredGridPiece, VertexNumbers};
use crate::connectivity::{
Connectivity, Hex20Connectivity, Hex27Connectivity, Hex8Connectivity, Quad4d2Connectivity, Quad9d2Connectivity,
Segment2d2Connectivity, Segment2d3Connectivity, Tet10Connectivity, Tet20Connectivity, Tet4Connectivity,
Tri3d2Connectivity, Tri3d3Connectivity, Tri6d2Connectivity,
};
use nalgebra::allocator::Allocator;
use std::convert::TryInto;
// TODO: This is kind of a dirty hack to get around the fact that some VTK things are in
// the geometry crate and some are in this crate. Need to clean this up!
use crate::vtkio::model::{Attributes, ByteOrder, DataArray, Piece, Version, Vtk};
// TODO: We've currently disabled all vtkio impls, might have to re-enable/re-implement some of them in the future
//pub use fenris_geometry::vtkio::*;
use num::{ToPrimitive, Zero};
use std::fs::create_dir_all;
use std::path::Path;
/// Represents connectivity that is supported by VTK.
pub trait VtkCellConnectivity: Connectivity {
fn num_nodes(&self) -> usize {
self.vertex_indices().len()
}
fn cell_type(&self) -> vtkio::model::CellType;
/// Write connectivity and return number of nodes.
///
/// Panics if `connectivity.len() != self.num_nodes()`.
fn write_vtk_connectivity(&self, connectivity: &mut [usize]) {
assert_eq!(connectivity.len(), self.vertex_indices().len());
connectivity.clone_from_slice(self.vertex_indices());
}
}
impl VtkCellConnectivity for Segment2d2Connectivity {
fn cell_type(&self) -> CellType {
CellType::Line
}
}
impl VtkCellConnectivity for Segment2d3Connectivity {
fn cell_type(&self) -> CellType {
CellType::Line
}
}
impl VtkCellConnectivity for Tri3d2Connectivity {
fn cell_type(&self) -> CellType {
CellType::Triangle
}
}
impl VtkCellConnectivity for Tri6d2Connectivity {
fn cell_type(&self) -> CellType {
CellType::QuadraticTriangle
}
}
impl VtkCellConnectivity for Quad4d2Connectivity {
fn cell_type(&self) -> CellType {
CellType::Quad
}
}
impl VtkCellConnectivity for Quad9d2Connectivity {
fn cell_type(&self) -> CellType {
CellType::QuadraticQuad
}
}
impl VtkCellConnectivity for Tet4Connectivity {
fn cell_type(&self) -> CellType {
CellType::Tetra
}
}
impl VtkCellConnectivity for Hex8Connectivity {
fn cell_type(&self) -> CellType {
CellType::Hexahedron
}
}
impl VtkCellConnectivity for Tri3d3Connectivity {
fn cell_type(&self) -> CellType {
CellType::Triangle
}
}
impl VtkCellConnectivity for Tet10Connectivity {
fn cell_type(&self) -> CellType {
CellType::QuadraticTetra
}
fn write_vtk_connectivity(&self, connectivity: &mut [usize]) {
assert_eq!(connectivity.len(), self.vertex_indices().len());
connectivity.clone_from_slice(self.vertex_indices());
// Gmsh ordering and ParaView have different conventions for quadratic tets,
// so we must adjust for that. In particular, nodes 8 and 9 are switched
connectivity.swap(8, 9);
}
}
impl VtkCellConnectivity for Tet20Connectivity {
fn num_nodes(&self) -> usize {
4
}
fn cell_type(&self) -> CellType {
CellType::Tetra
}
fn write_vtk_connectivity(&self, connectivity: &mut [usize]) {
// TODO: As a stop-gap solution, we just export to linear tets,
// but we should try to support LagrangeTetrahedra instead,
// though this is probably only available for the XML-based format
assert_eq!(connectivity.len(), 4); //self.vertex_indices().len());
connectivity[0..4].copy_from_slice(&self.0[0..4]);
}
}
impl VtkCellConnectivity for Hex20Connectivity {
fn cell_type(&self) -> CellType {
CellType::QuadraticHexahedron
}
fn write_vtk_connectivity(&self, connectivity: &mut [usize]) {
assert_eq!(connectivity.len(), self.num_nodes());
let v = self.vertex_indices();
// The first 8 entries are the same
connectivity[0..8].clone_from_slice(&v[0..8]);
connectivity[8] = v[8];
connectivity[9] = v[11];
connectivity[10] = v[13];
connectivity[11] = v[9];
connectivity[12] = v[16];
connectivity[13] = v[18];
connectivity[14] = v[19];
connectivity[15] = v[17];
connectivity[16] = v[10];
connectivity[17] = v[12];
connectivity[18] = v[14];
connectivity[19] = v[15];
}
}
impl VtkCellConnectivity for Hex27Connectivity {
fn num_nodes(&self) -> usize {
20
}
// There is no tri-quadratic Hex in legacy VTK, so use Hex20 instead
fn cell_type(&self) -> CellType {
CellType::QuadraticHexahedron
}
fn write_vtk_connectivity(&self, connectivity: &mut [usize]) {
assert_eq!(connectivity.len(), self.num_nodes());
let v = self.vertex_indices();
// The first 8 entries are the same
connectivity[0..8].clone_from_slice(&v[0..8]);
connectivity[8] = v[8];
connectivity[9] = v[11];
connectivity[10] = v[13];
connectivity[11] = v[9];
connectivity[12] = v[16];
connectivity[13] = v[18];
connectivity[14] = v[19];
connectivity[15] = v[17];
connectivity[16] = v[10];
connectivity[17] = v[12];
connectivity[18] = v[14];
connectivity[19] = v[15];
}
}
// impl<'a, T, D, C> From<&'a Mesh<T, D, C>> for DataSet
// where
// T: Scalar + Zero,
// D: DimName,
// C: VtkCellConnectivity,
// DefaultAllocator: Allocator<T, D>,
// {
// fn from(mesh: &'a Mesh<T, D, C>) -> Self {
// // TODO: Create a "SmallDim" trait or something for this case...?
// // Or just implement the trait directly for U1/U2/U3?
// assert!(D::dim() <= 3, "Unable to support dimensions larger than 3.");
// let points: Vec<_> = {
// let mut points: Vec<T> = Vec::new();
// for v in mesh.vertices() {
// points.extend_from_slice(v.coords.as_slice());
//
// for _ in v.coords.len()..3 {
// points.push(T::zero());
// }
// }
// points
// };
//
// // Vertices is laid out as follows: N, i_1, i_2, ... i_N,
// // so for quads this becomes 4 followed by the four indices making up the quad
// let mut vertices = Vec::new();
// let mut cell_types = Vec::new();
// let mut vertex_indices = Vec::new();
// for cell in mesh.connectivity() {
// // TODO: Return Result or something
// vertices.push(cell.num_nodes() as u32);
//
// vertex_indices.clear();
// vertex_indices.resize(cell.num_nodes(), 0);
// cell.write_vtk_connectivity(&mut vertex_indices);
//
// // TODO: Safer cast? How to handle this? TryFrom instead of From?
// vertices.extend(vertex_indices.iter().copied().map(|i| i as u32));
// cell_types.push(cell.cell_type());
// }
//
// DataSet::UnstructuredGrid {
// points: points.into(),
// cells: Cells {
// num_cells: mesh.connectivity().len() as u32,
// vertices,
// },
// cell_types,
// data: Attributes::new(),
// }
// }
// }
// pub fn create_vtk_data_set_from_quadratures<T, C, D>(
// vertices: &[OPoint<T, D>],
// connectivity: &[C],
// quadrature_rules: impl IntoIterator<Item = impl Quadrature<T, C::ReferenceDim>>,
// ) -> DataSet
// where
// T: Real,
// D: DimName + DimMin<D, Output = D>,
// C: ElementConnectivity<T, GeometryDim = D, ReferenceDim = D>,
// DefaultAllocator: Allocator<T, D> + ElementConnectivityAllocator<T, C>,
// {
// let quadrature_rules = quadrature_rules.into_iter();
//
// // Quadrature weights and points mapped to physical domain
// let mut physical_weights = Vec::new();
// let mut physical_points = Vec::new();
// // Cell indices map each individual quadrature point to its original cell
// let mut cell_indices = Vec::new();
//
// for ((cell_idx, conn), quadrature) in zip_eq(connectivity.iter().enumerate(), quadrature_rules)
// {
// let element = conn.element(vertices).unwrap();
// for (w_ref, xi) in zip_eq(quadrature.weights(), quadrature.points()) {
// let j = element.reference_jacobian(xi);
// let x = element.map_reference_coords(xi);
// let w_physical = j.determinant().abs() * *w_ref;
// physical_points.push(OPoint::from(x));
// physical_weights.push(w_physical);
// cell_indices.push(cell_idx as u64);
// }
// }
//
// let mut dataset = create_vtk_data_set_from_points(&physical_points);
// let weight_point_attributes = Attribute::Scalars {
// num_comp: 1,
// lookup_table: None,
// data: physical_weights.into(),
// };
//
// let cell_idx_point_attributes = Attribute::Scalars {
// num_comp: 1,
// lookup_table: None,
// data: cell_indices.into(),
// };
//
// match dataset {
// DataSet::PolyData { ref mut data, .. } => {
// data.point
// .push(("weight".to_string(), weight_point_attributes));
// data.point
// .push(("cell_index".to_string(), cell_idx_point_attributes));
// }
// _ => panic!("Unexpected enum variant from data set."),
// }
//
// dataset
// }
//
// /// Convenience function for writing meshes to VTK files.
// pub fn write_vtk_mesh<'a, T, Connectivity>(
// mesh: &'a Mesh2d<T, Connectivity>,
// filename: &str,
// title: &str,
// ) -> Result<(), Error>
// where
// T: Scalar + Zero,
// &'a Mesh2d<T, Connectivity>: Into<DataSet>,
// {
// let data = mesh.into();
// write_vtk(data, filename, title)
// }
pub struct FiniteElementMeshDataSetBuilder<'a, T, D, C>
where
T: Scalar,
D: DimName,
DefaultAllocator: Allocator<T, D>,
{
mesh: &'a Mesh<T, D, C>,
attributes: Attributes,
// Only used for exporting directly to file
title: Option<String>, // TODO: How to represent attributes?
}
impl<'a, T, D, C> FiniteElementMeshDataSetBuilder<'a, T, D, C>
where
T: Scalar,
D: DimName,
DefaultAllocator: Allocator<T, D>,
{
pub fn from_mesh(mesh: &'a Mesh<T, D, C>) -> Self {
Self {
mesh,
attributes: Attributes::new(),
title: None,
}
}
}
impl<'a, T, D, C> FiniteElementMeshDataSetBuilder<'a, T, D, C>
where
T: Real + ToPrimitive,
D: DimName,
DefaultAllocator: Allocator<T, D>,
{
pub fn with_title(self, title: impl Into<String>) -> Self {
Self {
mesh: self.mesh,
title: Some(title.into()),
attributes: self.attributes,
}
}
/// Adds the given attribute data as vector point attributes.
///
/// The size of each vector is inferred from the size of the attributes array. For example, if the number of
/// elements in the attributes array is 20 and the number of points is 10, each vector will be interpreted as
/// two-dimensional.
///
/// # Panics
/// Panics if the number of entries in the attribute vector is not equal to the
/// product of the vertex count in the mesh and the number of components,
///
/// Panics if there are more than 3 components per vector.
pub fn with_point_vector_attributes<S: Scalar + Zero + ToPrimitive>(
self,
name: impl Into<String>,
num_components: usize,
attributes: &[S],
) -> Self {
let num_points = self.mesh.vertices().len();
assert_eq!(
attributes.len(),
num_components * num_points,
"Number of attribute entries incompatible with mesh and number of components."
);
assert!(num_components <= 3, "Each vector must not have more than 3 components.");
let mut attribute_vec = Vec::new();
// Vectors are always 3-dimensional in VTK
attribute_vec.reserve(3 * num_points);
for i in 0..num_points {
for j in 0..num_components {
attribute_vec.push(attributes[num_components * i + j].clone());
}
for _ in num_components..3 {
// Pad with zeros for remaining dimensions
attribute_vec.push(S::zero());
}
}
let mut attribs = self.attributes;
let data_array = DataArray::vectors(name).with_data(attribute_vec);
attribs.point.push(Attribute::DataArray(data_array));
Self {
mesh: self.mesh,
attributes: attribs,
title: self.title,
}
}
/// Adds the given attribute data as scalar point attributes.
///
/// # Panics
/// Panics if the number of entries in the attribute vector is not equal to the
/// product of the vertex count in the mesh and the number of components.
pub fn with_point_scalar_attributes<S: Scalar + ToPrimitive>(
self,
name: impl Into<String>,
num_components: usize,
attributes: &[S],
) -> Self {
let num_points = self.mesh.vertices().len();
assert_eq!(
attributes.len(),
num_components * num_points,
"Number of attribute entries incompatible with mesh and number of components."
);
let mut attribs = self.attributes;
let num_comp = num_components
.try_into()
.expect("Number of components is ridiculously huge, stop it!");
let data_array = DataArray::scalars(name, num_comp).with_data(attributes.to_vec());
attribs.point.push(Attribute::DataArray(data_array));
Self {
mesh: self.mesh,
attributes: attribs,
title: self.title,
}
}
/// Adds the given attribute data as scalar cell attributes.
///
/// # Panics
/// Panics if the number of entries in the attribute vector is not equal to the
/// product of the cell count in the mesh and the number of components.
pub fn with_cell_scalar_attributes<S: Scalar + ToPrimitive>(
self,
name: impl Into<String>,
num_components: usize,
attributes: &[S],
) -> Self {
let num_cells = self.mesh.connectivity().len();
assert_eq!(
attributes.len(),
num_components * num_cells,
"Number of attribute entries incompatible with mesh and number of components."
);
let mut attribs = self.attributes;
let num_comp = num_components
.try_into()
.expect("Number of components is ridiculously huge, stop it!");
let data_array = DataArray::scalars(name, num_comp).with_data(attributes.to_vec());
attribs.cell.push(Attribute::DataArray(data_array));
Self {
mesh: self.mesh,
attributes: attribs,
title: self.title,
}
}
// TODO: Different error type
pub fn try_build(&self) -> eyre::Result<DataSet>
where
C: VtkCellConnectivity,
{
// TODO: Create a "SmallDim" trait or something for this case...?
// Or just implement the trait directly for U1/U2/U3?
assert!(D::dim() <= 3, "Unable to support dimensions larger than 3.");
let points: Vec<_> = {
let mut points: Vec<T> = Vec::new();
for v in self.mesh.vertices() {
points.extend_from_slice(v.coords.as_slice());
for _ in v.coords.len()..3 {
points.push(T::zero());
}
}
points
};
// Vertices is laid out as follows: N, i_1, i_2, ... i_N,
// so for e.g. quads this becomes 4 followed by the four indices making up the quad
let mut vertices = Vec::new();
let mut cell_types = Vec::new();
let mut vertex_indices = Vec::new();
for cell in self.mesh.connectivity() {
// TODO: Return better error
vertices.push(cell.num_nodes().try_into()?);
vertex_indices.clear();
vertex_indices.resize(cell.num_nodes(), 0);
cell.write_vtk_connectivity(&mut vertex_indices);
for &idx in &vertex_indices {
// TODO: Return better error
vertices.push(idx.try_into()?);
}
cell_types.push(cell.cell_type());
}
let piece = UnstructuredGridPiece {
points: points.into(),
cells: Cells {
// TODO: Use XML instead of Legacy?
cell_verts: VertexNumbers::Legacy {
num_cells: self.mesh.connectivity().len() as u32,
vertices,
},
types: cell_types,
},
data: self.attributes.clone(),
};
Ok(DataSet::UnstructuredGrid {
meta: None,
pieces: vec![Piece::Inline(Box::new(piece))],
})
}
/// Convenience function for directly exporting the dataset to a file.
pub fn try_export(&self, filename: impl AsRef<Path>) -> eyre::Result<()>
where
C: VtkCellConnectivity,
{
let filepath = filename.as_ref();
let fallback_title = filepath
.file_stem()
.map(|os_str| os_str.to_string_lossy().to_string())
.unwrap_or_else(|| "untitled".to_string());
let dataset = self.try_build()?;
if let Some(parent) = filepath.parent() {
create_dir_all(parent)?;
}
// Set VTK format version depending on detected file extension
// Workaround for vtkio not setting version number automatically depending on format
// Issue: https://github.com/elrnv/vtkio/issues/12
let extension = filepath
.extension()
.map(|os_str| os_str.to_string_lossy().to_ascii_lowercase());
let version = match extension.as_ref().map(|s| s.as_str()) {
Some("vtu") => Version { major: 1, minor: 0 },
Some("vtk") | _ => Version { major: 4, minor: 1 },
};
Vtk {
version,
// If we don't have a title then just make the filepath the title
title: self.title.clone().unwrap_or(fallback_title),
byte_order: ByteOrder::BigEndian,
data: dataset,
file_path: None,
}
.export(filepath)?;
Ok(())
}
}