/usr/include/dune/grid/io/file/amiramesh/amirameshwriter.cc is in libdune-grid-dev 2.2.1-2.
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The actual contents of the file can be viewed below.
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#include <algorithm>
#include <fstream>
#include <limits>
#include <dune/common/stdstreams.hh>
#include <dune/grid/common/virtualrefinement.hh>
template<class GridView>
void Dune::AmiraMeshWriter<GridView>::addGrid(const GridView& gridView,
bool splitAll)
{
typedef typename GridView::Grid::ctype ct;
typedef typename GridView::template Codim<dim>::Iterator VertexIterator;
typedef typename GridView::template Codim<0>::Iterator ElementIterator;
typedef Dune::VirtualRefinement<dim, ct> Refinement;
typedef typename Refinement::VertexIterator vIterator;
typedef typename Refinement::ElementIterator eIterator;
typedef typename Refinement::VertexIterator::CoordVector Coordinate;
typedef typename Refinement::ElementIterator::IndexVector IndexVector;
const typename GridView::IndexSet& indexSet = gridView.indexSet();
if ((dim!=2 && dim!=3) || int(dim) != int(GridView::dimensionworld))
DUNE_THROW(IOError, "You can only write grids as AmiraMesh if dim==dimworld==2"
<< " or dim==dimworld==3.");
// Set the appropriate content type
if (dim==2)
amiramesh_.parameters.set("ContentType", "HxTriangularGrid");
// ///////////////////////////////////////////
// Write grid vertices
// ///////////////////////////////////////////
int noOfNodes = indexSet.size(dim);
int noOfElements;
AmiraMesh::Location* geo_nodes = new AmiraMesh::Location("Nodes", noOfNodes);
amiramesh_.insert(geo_nodes);
AmiraMesh::Data* geo_node_data = new AmiraMesh::Data("Coordinates", geo_nodes,
McPrimType::mc_float, dim);
amiramesh_.insert(geo_node_data);
VertexIterator vertex = gridView.template begin<dim>();
VertexIterator endvertex = gridView.template end<dim>();
//needed later to compare indices of refinement and indexset
std::vector<Coordinate> vertices_coords(noOfNodes);
for (; vertex!=endvertex; ++vertex) {
int index = indexSet.template index<dim>(*vertex);
vertices_coords[index]=vertex->geometry().corner(0);
// Copy coordinates
for (int i=0; i<dim; i++)
((float*)geo_node_data->dataPtr())[dim*index+i] = vertex->geometry().corner(0)[i];
}
/* write element section to file */
AmiraMesh::Location* elementLocation = NULL;
// ////////////////////////////////////////////////////////////////////
// Split up all elements into simplices, if requested, because
// Amira doesn't support all kind of grids.
// ////////////////////////////////////////////////////////////////////
if (splitAll) {
Dune::GeometryType coerceTo(Dune::GeometryType::simplex,dim);
noOfElements = 0;
int count=0;
for (size_t i=0;i<indexSet.geomTypes(0).size();i++){
if (indexSet.geomTypes(0)[i].isSimplex())
count=1;
else {
Refinement & refinement = Dune::buildRefinement<dim, ct>(indexSet.geomTypes(0)[i],coerceTo);
count = refinement.nElements(0);
}
noOfElements += count * indexSet.size(indexSet.geomTypes(0)[i]);
}
// write element section to file
int VerticesPerElement = dim + 1;
if (dim==2)
elementLocation = new AmiraMesh::Location("Triangles", noOfElements);
else
elementLocation = new AmiraMesh::Location("Tetrahedra", noOfElements);
amiramesh_.insert(elementLocation);
AmiraMesh::Data* element_data = new AmiraMesh::Data("Nodes", elementLocation, McPrimType::mc_int32, VerticesPerElement);
amiramesh_.insert(element_data);
int *dPtr = (int*)element_data->dataPtr();
ElementIterator eIt = gridView.template begin<0>();
ElementIterator eEndIt = gridView.template end<0>();
for (int i=0; eIt!=eEndIt; ++eIt) {
if (eIt->type().isSimplex()) {
for (int j=0; j<VerticesPerElement; j++)
// The +1 is added because AmiraMesh numbers vertices starting from 1
dPtr[i*VerticesPerElement+j] = indexSet.subIndex(*eIt,j,dim)+1;
i++;
}
else {
Refinement & refinement = Dune::buildRefinement<dim, ct>(eIt->type(),coerceTo);
eIterator eSubEnd = refinement.eEnd(0);
eIterator eSubIt = refinement.eBegin(0);
IndexVector vertexIds;
//Have to do this, because Refinement indices of corners don't match indexSet indices of the corners of that entity
//So we have to check equality of two indices by checking equality of the coordinates of the corners
//coordinates of nodes using refinement indices
std::vector<Coordinate> vertices(refinement.nVertices(0));
vIterator vEnd = refinement.vEnd(0);
for(vIterator vIt = refinement.vBegin(0); vIt != vEnd; ++vIt)
vertices[vIt.index()]=(eIt->geometry().global(vIt.coords()));
for( ;eSubIt != eSubEnd;++eSubIt) {
vertexIds = eSubIt.vertexIndices();
for (int j=0; j<VerticesPerElement; j++) {
//better way to do the comparison ?
for (int m=0;m<noOfNodes;m++){
if (vertices[vertexIds[j]]==vertices_coords[m]){
dPtr[i*VerticesPerElement+j]=m+1;
break;
}
}
}
i++;
}
}
}
} else {
// Find out whether the grid contains only tetrahedra. If yes, then
// it is written in TetraGrid format. If not, it is written in
// hexagrid format.
bool containsOnlySimplices =
(indexSet.geomTypes(0).size()==1)
&& (indexSet.geomTypes(0)[0].isSimplex());
int maxVerticesPerElement = (dim==3)
? ((containsOnlySimplices) ? 4 : 8)
: ((containsOnlySimplices) ? 3 : 4);
noOfElements = indexSet.size(0);
// write element section to file
if (dim==3) {
if (containsOnlySimplices)
elementLocation = new AmiraMesh::Location("Tetrahedra", noOfElements);
else
elementLocation = new AmiraMesh::Location("Hexahedra", noOfElements);
} else {
if (containsOnlySimplices)
elementLocation = new AmiraMesh::Location("Triangles", noOfElements);
else
elementLocation = new AmiraMesh::Location("Quadrilaterals", noOfElements);
}
amiramesh_.insert(elementLocation);
AmiraMesh::Data* element_data = new AmiraMesh::Data("Nodes", elementLocation,
McPrimType::mc_int32, maxVerticesPerElement);
amiramesh_.insert(element_data);
int *dPtr = (int*)element_data->dataPtr();
ElementIterator eIt = gridView.template begin<0>();
ElementIterator eEndIt = gridView.template end<0>();
if (dim==3) {
// //////////////////////////////////////////////////
// Write elements of a 3D-grid
// //////////////////////////////////////////////////
if (containsOnlySimplices) {
for (int i=0; eIt!=eEndIt; ++eIt, i++) {
for (int j=0; j<4; j++)
dPtr[i*4+j] = indexSet.subIndex(*eIt,j,dim)+1;
}
} else {
for (int i=0; eIt!=eEndIt; ++eIt, i++) {
GeometryType type = eIt->type();
if (type.isHexahedron()) {
const int hexaReordering[8] = {0, 1, 3, 2, 4, 5, 7, 6};
for (int j=0; j<8; j++)
dPtr[8*i + j] = indexSet.subIndex(*eIt, hexaReordering[j],dim)+1;
} else if (type.isPrism()) {
const int prismReordering[8] = {0, 1, 1, 2, 3, 4, 4, 5};
for (int j=0; j<8; j++)
dPtr[8*i + j] = indexSet.subIndex(*eIt, prismReordering[j],dim)+1;
} else if (type.isPyramid()) {
const int pyramidReordering[8] = {0, 1, 3, 2, 4, 4, 4, 4};
for (int j=0; j<8; j++)
dPtr[8*i + j] = indexSet.subIndex(*eIt, pyramidReordering[j], dim)+1;
} else if (type.isTetrahedron()) {
const int tetraReordering[8] = {0, 1, 2, 2, 3, 3, 3, 3};
for (int j=0; j<8; j++)
dPtr[8*i + j] = indexSet.subIndex(*eIt, tetraReordering[j],dim)+1;
} else
DUNE_THROW(NotImplemented, "Unknown element type encountered");
}
}
} else {
for (int i=0; eIt!=eEndIt; ++eIt, i++) {
GeometryType type = eIt->type();
if (type.isQuadrilateral()) {
dPtr[i*4+0] = indexSet.subIndex(*eIt, 0, dim)+1;
dPtr[i*4+1] = indexSet.subIndex(*eIt, 1, dim)+1;
dPtr[i*4+2] = indexSet.subIndex(*eIt, 3, dim)+1;
dPtr[i*4+3] = indexSet.subIndex(*eIt, 2, dim)+1;
} else if (type.isTriangle()) {
for (int j=0; j<3; j++)
dPtr[i*maxVerticesPerElement+j] = indexSet.subIndex(*eIt, j, dim)+1;
// If 4 vertices are expected per element use the last value
// to fill up the remaining slots
if (maxVerticesPerElement==4)
dPtr[i*4+3] = dPtr[i*4+2];
} else {
DUNE_THROW(IOError, "Elements of type " << type
<< " cannot be written to 2d AmiraMesh files!");
}
}
}
}
// write material section to grid file
AmiraMesh::Data* element_materials = new AmiraMesh::Data("Materials", elementLocation, McPrimType::mc_uint8, 1);
amiramesh_.insert(element_materials);
for(int i=0; i<noOfElements; i++)
((unsigned char*)element_materials->dataPtr())[i] = 0;
}
template<class GridView>
template<class GridType2>
void Dune::AmiraMeshWriter<GridView>::addLevelGrid(const GridType2& grid,
int level,
bool splitAll)
{
addGrid(grid.levelView(level), splitAll);
}
template<class GridView>
template<class GridType2>
void Dune::AmiraMeshWriter<GridView>::addLeafGrid(const GridType2& grid, bool splitAll)
{
addGrid(grid.leafView(), splitAll);
}
template<class GridView>
template<class DataContainer>
void Dune::AmiraMeshWriter<GridView>::addCellData(const DataContainer& data,
const GridView& gridView,
bool gridSplitUp)
{
typedef typename GridView::template Codim<0>::Iterator ElementIterator;
typedef typename GridView::Grid::ctype ct;
typedef Dune::VirtualRefinement<dim, ct> Refinement;
const typename GridView::IndexSet& indexSet = gridView.indexSet();
//gridSplitUp tells programm that Amira "thinks" that all elements are tethraheda
// Find out whether the grid contains only tetrahedra. If yes, then
// it is written in TetraGrid format. If not, it is written in
// hexagrid format (if gridSplitUp=false).
bool containsOnlyTetrahedra =
(indexSet.geomTypes(0).size()==1)
&& (indexSet.geomTypes(0)[0].isSimplex());
// Get number of components
const int ncomp = DataContainer::block_type::dimension;
// Set the appropriate content type for 2D grid data, if no other
// content type hasn't been set already
if (dim==2 and amiramesh_.parameters.findBase("ContentType")==NULL)
amiramesh_.parameters.set("ContentType", "HxTriangularData");
if (!containsOnlyTetrahedra and dim==3 and !gridSplitUp)
{
AmiraMesh::Location* hexa_loc = new AmiraMesh::Location("Hexahedra", indexSet.size(0));
amiramesh_.insert(hexa_loc);
}
AmiraMesh::Location* amLocation;
if (data.size()==indexSet.size(0))
{
if (gridSplitUp || containsOnlyTetrahedra)
{
Dune::GeometryType coerceTo(Dune::GeometryType::simplex,dim);
int noOfElements = 0;
int count;
for (size_t i=0;i<indexSet.geomTypes(0).size();i++)
{
if (indexSet.geomTypes(0)[i].isSimplex())
count=1;
else
{
Refinement & refinement = Dune::buildRefinement<dim, ct>(indexSet.geomTypes(0)[i],coerceTo);
count = refinement.nElements(0);
}
noOfElements += count * indexSet.size(indexSet.geomTypes(0)[i]);
}
amLocation = new AmiraMesh::Location((dim==2) ? "Triangles" : "Tetrahedra", noOfElements);
}
else
amLocation = new AmiraMesh::Location("Hexahedra", data.size());
}
else
DUNE_THROW(IOError, "AmiraMeshWriter::addCellData: BlockVector doesn't match the grid! For vertex based data use addVertexData");
amiramesh_.insert(amLocation);
// \todo Auto-detect data type
AmiraMesh::Data* nodeData = new AmiraMesh::Data("Data", amLocation, McPrimType::mc_double, ncomp);
amiramesh_.insert(nodeData);
AmiraMesh::Field* nodeField;
nodeField = new AmiraMesh::Field("sol", ncomp, McPrimType::mc_double, AmiraMesh::t_constant, nodeData);
amiramesh_.insert(nodeField);
// write the data into the AmiraMesh object
typedef typename DataContainer::ConstIterator Iterator;
Iterator dit = data.begin();
Iterator ditend = data.end();
int i=0;
if (gridSplitUp)
{
ElementIterator eIt = gridView.template begin<0>();
Dune::GeometryType coerceTo(Dune::GeometryType::simplex,dim);
for (; dit!=ditend; ++dit)
{
Refinement & refinement = Dune::buildRefinement<dim, ct>(eIt->type(),coerceTo);
int num_subsimplices=refinement.nElements(0);
//Have to copy data if gridSplitUp because number_elements != number_data;
for(int k=0;k<num_subsimplices;k++)
{
for (int j=0; j<ncomp; j++)
((double*)nodeData->dataPtr())[i++] = (*dit)[j];
}
++eIt;
}
} else {
// Write data directly
for (; dit!=ditend; ++dit)
for (int j=0; j<ncomp; j++)
((double*)nodeData->dataPtr())[i++] = (*dit)[j];
}
}
template<class GridView>
template<class DataContainer>
void Dune::AmiraMeshWriter<GridView>::addVertexData(const DataContainer& data,
const GridView& gridView,
bool gridSplitUp)
{
typedef typename GridView::Grid::ctype ct;
static const int dimworld = GridView::dimensionworld;
typedef Dune::VirtualRefinement<dim, ct> Refinement;
const typename GridView::IndexSet& indexSet = gridView.indexSet();
//gridSplitUp tells programm that Amira "thinks" that all elements are tethraheda
// Find out whether the grid contains only tetrahedra. If yes, then
// it is written in TetraGrid format. If not, it is written in
// hexagrid format (if gridSplitUp=false).
bool containsOnlyTetrahedra =
(indexSet.geomTypes(0).size()==1)
&& (indexSet.geomTypes(0)[0].isSimplex());
// Get number of components
const int ncomp = DataContainer::value_type::dimension;
// Set the appropriate content type for 2D grid data, if no other
// content type hasn't been set already
if (dim==2 and amiramesh_.parameters.findBase("ContentType")==NULL) {
if (dimworld==3)
amiramesh_.parameters.set("ContentType", "SurfaceField");
else
amiramesh_.parameters.set("ContentType", "HxTriangularData");
}
if (!containsOnlyTetrahedra and dim==3 and !gridSplitUp)
{
AmiraMesh::Location* hexa_loc = new AmiraMesh::Location("Hexahedra", indexSet.size(0));
amiramesh_.insert(hexa_loc);
}
AmiraMesh::Location* amLocation;
if (data.size()==indexSet.size(dim))
{
// P1 data
amLocation = new AmiraMesh::Location("Nodes", data.size());
}
else
DUNE_THROW(IOError, "AmiraMeshWriter::addVertexData: BlockVector doesn't match the grid! For element based data use addCellData");
amiramesh_.insert(amLocation);
// The primitive data type used to store the data in the file
// We are forced to use float for surface (i.e. 2d-in-3d) fields, because Amira
// can only read those in float precision
McPrimType primType = McPrimType::mc_double;
if (Dune::is_same<ct,float>::value or (dim==2 and dimworld==3))
primType = McPrimType::mc_float;
AmiraMesh::Data* nodeData = new AmiraMesh::Data("Data", amLocation, primType, ncomp);
amiramesh_.insert(nodeData);
AmiraMesh::Field* nodeField;
if (containsOnlyTetrahedra || dim==2 || gridSplitUp)
{
nodeField = new AmiraMesh::Field("sol", ncomp, primType, AmiraMesh::t_linear, nodeData);
}
else
{
nodeField = new AmiraMesh::Field("sol", ncomp, primType, AmiraMesh::t_trilinear, nodeData);
}
amiramesh_.insert(nodeField);
// write the data into the AmiraMesh object
typedef typename DataContainer::const_iterator Iterator;
Iterator dit = data.begin();
Iterator ditend = data.end();
int i=0;
if (Dune::is_same<ct,float>::value or (dim==2 and dimworld==3)) {
// Write double data
for (; dit!=ditend; ++dit)
for (int j=0; j<ncomp; j++)
((float*)nodeData->dataPtr())[i++] = (*dit)[j];
} else {
// Write float data
for (; dit!=ditend; ++dit)
for (int j=0; j<ncomp; j++)
((double*)nodeData->dataPtr())[i++] = (*dit)[j];
}
}
template<class GridView>
void Dune::AmiraMeshWriter<GridView>::write(const std::string& filename,
bool ascii) const
{
// Actually write the file
if(!amiramesh_.write(filename.c_str(), ascii))
DUNE_THROW(IOError, "Writing geometry file '" << filename << "' failed!");
Dune::dinfo << "Grid written successfully to: " << filename << std::endl;
}
template<class GridView>
template<class DataContainer>
void Dune::AmiraMeshWriter<GridView>::addUniformData(const GridView& gridView,
const array<unsigned int, dim>& n,
const DataContainer& data)
{
dune_static_assert(dim==2 || dim==3, "You can only write 2d and 3d uniform data to AmiraMesh");
// ///////////////////////////////////////////
// Detect grid bounding box
// ///////////////////////////////////////////
float bbox[2*dim];
for (int i=0; i<dim; i++) {
bbox[2*i ] = std::numeric_limits<double>::max();
bbox[2*i+1] = -std::numeric_limits<double>::max();
}
typename GridView::template Codim<dim>::Iterator vIt = gridView.template begin<dim>();
typename GridView::template Codim<dim>::Iterator vEndIt = gridView.template end<dim>();
for (; vIt!=vEndIt; ++vIt)
for (int i=0; i<dim; i++) {
bbox[2*i] = std::min((double)bbox[2*i], vIt->geometry().corner(0)[i]);
bbox[2*i+1] = std::max((double)bbox[2*i+1], vIt->geometry().corner(0)[i]);
}
// Set the appropriate content type
if (dim==2)
amiramesh_.parameters.set("ContentType", "HxField2d");
amiramesh_.parameters.set("BoundingBox", 2*dim, bbox);
amiramesh_.parameters.set("CoordType", "uniform");
AmiraMesh::Location* loc = amiramesh_.findLocation("Lattice");
int dims[dim];
for (int i=0; i<dim; i++)
dims[i] = n[i];
if (!loc) {
loc = new AmiraMesh::Location("Lattice", dim, dims);
amiramesh_.insert(loc);
}
// set up data
// we assume that at least the inner vector follows ISTL conventions
// unfortunately istl and std containers are not compatible
// in that it is not possible to extract the size
// of array and FieldVector by the same method
int numComponents = DataContainer::value_type::dimension;
AmiraMesh::Data* amData =
new AmiraMesh::Data("Data", loc, McPrimType::mc_double, numComponents);
amiramesh_.insert(amData);
// ////////////////////////////////////////////////////////
// Write the data
// ////////////////////////////////////////////////////////
typedef typename DataContainer::const_iterator iterator;
iterator it = data.begin();
iterator endIt = data.end();
int i=0;
for (; it!=endIt; ++it)
for (int j=0; j<numComponents; j++, i++)
((double*)amData->dataPtr())[i] = (*it)[j];
}
template <class GridView>
void Dune::AmiraMeshWriter<GridView>::writeSurfaceGrid(const GridView& gridView, const std::string& filename)
{
enum {dimworld = GridView::dimensionworld};
if (dim!=2 or dimworld!=3)
DUNE_THROW(Dune::NotImplemented, "writeSurfaceGrid is only implemented for 2D-grids in a 3D world!");
const typename GridView::IndexSet& indexSet = gridView.indexSet();
// ////////////////////////////////////////////
// Write header
// ////////////////////////////////////////////
std::ofstream outfile(filename.c_str());
if (!outfile)
DUNE_THROW(Dune::IOError, "Couldn't open '" << filename << "' for writing!");
outfile << "# HyperSurface 0.1 ASCII" << std::endl;
outfile << "" << std::endl;
outfile << "Parameters {" << std::endl;
outfile << " Materials {" << std::endl;
outfile << " outside {" << std::endl;
outfile << " Id 0" << std::endl;
outfile << " }" << std::endl;
outfile << " inside {" << std::endl;
outfile << " Id 1" << std::endl;
outfile << " }" << std::endl;
outfile << " }" << std::endl;
outfile << "" << std::endl;
outfile << "}" << std::endl;
outfile << std::endl;
// ////////////////////////////////////////////
// Write vertices
// ////////////////////////////////////////////
outfile << "Vertices " << indexSet.size(dim) << std::endl;
typedef typename GridView::template Codim<dim>::Iterator VertexIterator;
// write coordinates
// First we need to sort them to make sure they appear in the file in the proper order
VertexIterator vIt = gridView.template begin<dim>();
VertexIterator vEndIt = gridView.template end<dim>();
std::vector<Dune::FieldVector<double,dimworld> > coords(indexSet.size(dim));
for (; vIt!=vEndIt; ++vIt) {
typename GridView::IndexSet::IndexType idx = indexSet.index(*vIt);
coords[idx] = vIt->geometry().corner(0);
}
for (size_t i=0; i<coords.size(); i++)
outfile << coords[i] << std::endl;
// ////////////////////////////////////////////
// Write triangles
// ////////////////////////////////////////////
outfile << "NBranchingPoints 0" << std::endl;
outfile << "NVerticesOnCurves 0" << std::endl;
outfile << "BoundaryCurves 0" << std::endl;
outfile << "Patches 1" << std::endl;
outfile << "{" << std::endl;
outfile << "InnerRegion inside" << std::endl;
outfile << "OuterRegion outside" << std::endl;
outfile << "BoundaryID 0" << std::endl;
outfile << "BranchingPoints 0" << std::endl;
outfile << "" << std::endl;
// Count all boundary segments. We have to do this manually because
// quadrilaterals need to be transformed to two triangles because
// Amira doesn't know quadrilateral surfaces :-(((
int numFaces = 0;
// loop over all elements
typedef typename GridView::template Codim<0>::Iterator ElementIterator;
ElementIterator it = gridView.template begin<0>();
ElementIterator endIt = gridView.template end<0>();
for (; it!=endIt; ++it) {
switch (it->geometry().corners()) {
case 3:
numFaces++;
break;
case 4:
numFaces += 2;
break;
default:
DUNE_THROW(Dune::NotImplemented, "Unknown boundary segment type encountered!");
}
}
outfile << "Triangles " << numFaces << std::endl;
// loop over all elements again
it = gridView.template begin<0>();
for (; it!=endIt; ++it) {
const Dune::GenericReferenceElement<double,dim>& refElement =
Dune::GenericReferenceElements<double, dim>::general(it->type());
int n = refElement.size(dim);
outfile << indexSet.subIndex(*it, 0, dim) + 1
<< " " << indexSet.subIndex(*it, 1, dim) + 1
<< " " << indexSet.subIndex(*it, 2, dim) + 1
<< std::endl;
if (n==4)
outfile << indexSet.subIndex(*it, 2, dim) + 1
<< " " << indexSet.subIndex(*it, 1, dim) + 1
<< " " << indexSet.subIndex(*it, 3, dim) + 1
<< std::endl;
}
outfile << "}" << std::endl;
Dune::dinfo << "Surface successfully written to: " << filename << std::endl;
}
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