void MeshBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>::WriteVtkResultsToFile(const std::string& rDirectory)
{
#ifdef CHASTE_VTK
// Store the present time as a string
unsigned num_timesteps = SimulationTime::Instance()->GetTimeStepsElapsed();
std::stringstream time;
time << num_timesteps;
// Store the number of cells for which to output data to VTK
unsigned num_cells_from_mesh = GetNumNodes();
if (!mWriteVtkAsPoints && (mpVoronoiTessellation != NULL))
{
num_cells_from_mesh = mpVoronoiTessellation->GetNumElements();
}
// When outputting any CellData, we assume that the first cell is representative of all cells
unsigned num_cell_data_items = this->Begin()->GetCellData()->GetNumItems();
std::vector<std::string> cell_data_names = this->Begin()->GetCellData()->GetKeys();
std::vector<std::vector<double> > cell_data;
for (unsigned var=0; var<num_cell_data_items; var++)
{
std::vector<double> cell_data_var(num_cells_from_mesh);
cell_data.push_back(cell_data_var);
}
if (mOutputMeshInVtk)
{
// Create mesh writer for VTK output
VtkMeshWriter<ELEMENT_DIM, SPACE_DIM> mesh_writer(rDirectory, "mesh_"+time.str(), false);
mesh_writer.WriteFilesUsingMesh(rGetMesh());
}
if (mWriteVtkAsPoints)
{
// Create mesh writer for VTK output
VtkMeshWriter<SPACE_DIM, SPACE_DIM> cells_writer(rDirectory, "results_"+time.str(), false);
// Iterate over any cell writers that are present
unsigned num_cells = this->GetNumAllCells();
for (typename std::vector<boost::shared_ptr<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> > >::iterator cell_writer_iter = this->mCellWriters.begin();
cell_writer_iter != this->mCellWriters.end();
++cell_writer_iter)
{
// Create vector to store VTK cell data
std::vector<double> vtk_cell_data(num_cells);
// Loop over cells
for (typename AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>::Iterator cell_iter = this->Begin();
cell_iter != this->End();
++cell_iter)
{
// Get the node index corresponding to this cell
unsigned node_index = this->GetLocationIndexUsingCell(*cell_iter);
// Populate the vector of VTK cell data
vtk_cell_data[node_index] = (*cell_writer_iter)->GetCellDataForVtkOutput(*cell_iter, this);
}
cells_writer.AddPointData((*cell_writer_iter)->GetVtkCellDataName(), vtk_cell_data);
}
// Loop over cells
for (typename AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>::Iterator cell_iter = this->Begin();
cell_iter != this->End();
++cell_iter)
{
// Get the node index corresponding to this cell
unsigned node_index = this->GetLocationIndexUsingCell(*cell_iter);
for (unsigned var=0; var<num_cell_data_items; var++)
{
cell_data[var][node_index] = cell_iter->GetCellData()->GetItem(cell_data_names[var]);
}
}
for (unsigned var=0; var<num_cell_data_items; var++)
{
cells_writer.AddPointData(cell_data_names[var], cell_data[var]);
}
// Make a copy of the nodes in a disposable mesh for writing
{
std::vector<Node<SPACE_DIM>* > nodes;
for (unsigned index=0; index<this->mrMesh.GetNumNodes(); index++)
{
Node<SPACE_DIM>* p_node = this->mrMesh.GetNode(index);
nodes.push_back(p_node);
}
NodesOnlyMesh<SPACE_DIM> mesh;
mesh.ConstructNodesWithoutMesh(nodes, 1.5); // Arbitrary cut off as connectivity not used.
cells_writer.WriteFilesUsingMesh(mesh);
}
*(this->mpVtkMetaFile) << " <DataSet timestep=\"";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << ".vtu\"/>\n";
}
else if (mpVoronoiTessellation != NULL)
{
// Create mesh writer for VTK output
VertexMeshWriter<ELEMENT_DIM, SPACE_DIM> mesh_writer(rDirectory, "results", false);
std::vector<double> cell_volumes(num_cells_from_mesh);
// Iterate over any cell writers that are present
unsigned num_cells = this->GetNumAllCells();
for (typename std::vector<boost::shared_ptr<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> > >::iterator cell_writer_iter = this->mCellWriters.begin();
cell_writer_iter != this->mCellWriters.end();
++cell_writer_iter)
{
// Create vector to store VTK cell data
std::vector<double> vtk_cell_data(num_cells);
// Loop over elements of mpVoronoiTessellation
for (typename VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator elem_iter = mpVoronoiTessellation->GetElementIteratorBegin();
elem_iter != mpVoronoiTessellation->GetElementIteratorEnd();
++elem_iter)
{
// Get index of this element in mpVoronoiTessellation
unsigned elem_index = elem_iter->GetIndex();
// Get the cell corresponding to this element, via the index of the corresponding node in mrMesh
unsigned node_index = mpVoronoiTessellation->GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(elem_index);
CellPtr p_cell = this->GetCellUsingLocationIndex(node_index);
// Populate the vector of VTK cell data
vtk_cell_data[elem_index] = (*cell_writer_iter)->GetCellDataForVtkOutput(p_cell, this);
}
mesh_writer.AddCellData((*cell_writer_iter)->GetVtkCellDataName(), vtk_cell_data);
}
// Loop over elements of mpVoronoiTessellation
for (typename VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator elem_iter = mpVoronoiTessellation->GetElementIteratorBegin();
elem_iter != mpVoronoiTessellation->GetElementIteratorEnd();
++elem_iter)
{
// Get index of this element in mpVoronoiTessellation
unsigned elem_index = elem_iter->GetIndex();
// Get the cell corresponding to this element, via the index of the corresponding node in mrMesh
unsigned node_index = mpVoronoiTessellation->GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(elem_index);
CellPtr p_cell = this->GetCellUsingLocationIndex(node_index);
for (unsigned var=0; var<num_cell_data_items; var++)
{
cell_data[var][elem_index] = p_cell->GetCellData()->GetItem(cell_data_names[var]);
}
}
for (unsigned var=0; var<cell_data.size(); var++)
{
mesh_writer.AddCellData(cell_data_names[var], cell_data[var]);
}
mesh_writer.WriteVtkUsingMesh(*mpVoronoiTessellation, time.str());
*(this->mpVtkMetaFile) << " <DataSet timestep=\"";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << ".vtu\"/>\n";
}
#endif //CHASTE_VTK
}
void PottsBasedCellPopulation<DIM>::WriteVtkResultsToFile(const std::string& rDirectory)
{
#ifdef CHASTE_VTK
unsigned num_timesteps = SimulationTime::Instance()->GetTimeStepsElapsed();
std::stringstream time;
time << num_timesteps;
// Create mesh writer for VTK output
VtkMeshWriter<DIM, DIM> mesh_writer(rDirectory, "results_"+time.str(), false);
// Iterate over any cell writers that are present
unsigned num_nodes = GetNumNodes();
for (typename std::set<boost::shared_ptr<AbstractCellWriter<DIM, DIM> > >::iterator cell_writer_iter = this->mCellWriters.begin();
cell_writer_iter != this->mCellWriters.end();
++cell_writer_iter)
{
// Create vector to store VTK cell data
std::vector<double> vtk_cell_data(num_nodes);
// Iterate over nodes in the mesh
for (typename AbstractMesh<DIM,DIM>::NodeIterator iter = mpPottsMesh->GetNodeIteratorBegin();
iter != mpPottsMesh->GetNodeIteratorEnd();
++iter)
{
// Get the index of this node in the mesh and those elements (i.e. cells) that contain this node
unsigned node_index = iter->GetIndex();
std::set<unsigned> element_indices = iter->rGetContainingElementIndices();
// If there are no elements associated with this node, then we set the value of any VTK cell data to be -1 at this node...
if (element_indices.empty())
{
// Populate the vector of VTK cell data
vtk_cell_data[node_index] = -1.0;
}
else
{
// ... otherwise there should be exactly one element (i.e. cell) containing this node
assert(element_indices.size() == 1);
unsigned elem_index = *(element_indices.begin());
CellPtr p_cell = this->GetCellUsingLocationIndex(elem_index);
// Populate the vector of VTK cell data
vtk_cell_data[node_index] = (*cell_writer_iter)->GetCellDataForVtkOutput(p_cell, this);
}
}
mesh_writer.AddPointData((*cell_writer_iter)->GetVtkCellDataName(), vtk_cell_data);
}
// When outputting any CellData, we assume that the first cell is representative of all cells
unsigned num_cell_data_items = this->Begin()->GetCellData()->GetNumItems();
std::vector<std::string> cell_data_names = this->Begin()->GetCellData()->GetKeys();
std::vector<std::vector<double> > cell_data;
for (unsigned var=0; var<num_cell_data_items; var++)
{
std::vector<double> cell_data_var(num_nodes);
cell_data.push_back(cell_data_var);
}
for (typename AbstractMesh<DIM,DIM>::NodeIterator iter = mpPottsMesh->GetNodeIteratorBegin();
iter != mpPottsMesh->GetNodeIteratorEnd();
++iter)
{
// Get the index of this node in the mesh and those elements (i.e. cells) that contain this node
unsigned node_index = iter->GetIndex();
std::set<unsigned> element_indices = iter->rGetContainingElementIndices();
// If there are no elements associated with this node, then we set the value of any VTK cell data to be -1 at this node...
if (element_indices.empty())
{
for (unsigned var=0; var<num_cell_data_items; var++)
{
cell_data[var][node_index] = -1.0;
}
}
else
{
// ... otherwise there should be exactly one element (i.e. cell) containing this node
assert(element_indices.size() == 1);
unsigned elem_index = *(element_indices.begin());
CellPtr p_cell = this->GetCellUsingLocationIndex(elem_index);
for (unsigned var=0; var<num_cell_data_items; var++)
{
cell_data[var][node_index] = p_cell->GetCellData()->GetItem(cell_data_names[var]);
}
}
}
for (unsigned var=0; var<cell_data.size(); var++)
{
mesh_writer.AddPointData(cell_data_names[var], cell_data[var]);
}
/*
* The current VTK writer can only write things which inherit from AbstractTetrahedralMeshWriter.
* For now, we do an explicit conversion to NodesOnlyMesh. This can be written to VTK then visualized as glyphs.
*/
NodesOnlyMesh<DIM> temp_mesh;
temp_mesh.ConstructNodesWithoutMesh(*mpPottsMesh, 1.5); // This cut-off is arbitrary, as node connectivity is not used here
mesh_writer.WriteFilesUsingMesh(temp_mesh);
*(this->mpVtkMetaFile) << " <DataSet timestep=\"";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << ".vtu\"/>\n";
#endif //CHASTE_VTK
}
void NodeBasedCellPopulation<DIM>::WriteVtkResultsToFile(const std::string& rDirectory)
{
#ifdef CHASTE_VTK
// Store the present time as a string
std::stringstream time;
time << SimulationTime::Instance()->GetTimeStepsElapsed();
// Make sure the nodes are ordered contiguously in memory
NodeMap map(1 + this->mpNodesOnlyMesh->GetMaximumNodeIndex());
this->mpNodesOnlyMesh->ReMesh(map);
// Store the number of cells for which to output data to VTK
unsigned num_nodes = GetNumNodes();
std::vector<double> rank(num_nodes);
unsigned num_cell_data_items = 0;
std::vector<std::string> cell_data_names;
// We assume that the first cell is representative of all cells
if (num_nodes > 0)
{
num_cell_data_items = this->Begin()->GetCellData()->GetNumItems();
cell_data_names = this->Begin()->GetCellData()->GetKeys();
}
std::vector<std::vector<double> > cell_data;
for (unsigned var=0; var<num_cell_data_items; var++)
{
std::vector<double> cell_data_var(num_nodes);
cell_data.push_back(cell_data_var);
}
// Create mesh writer for VTK output
VtkMeshWriter<DIM, DIM> mesh_writer(rDirectory, "results_"+time.str(), false);
mesh_writer.SetParallelFiles(*mpNodesOnlyMesh);
// Iterate over any cell writers that are present
for (typename std::vector<boost::shared_ptr<AbstractCellWriter<DIM, DIM> > >::iterator cell_writer_iter = this->mCellWriters.begin();
cell_writer_iter != this->mCellWriters.end();
++cell_writer_iter)
{
// Create vector to store VTK cell data
std::vector<double> vtk_cell_data(num_nodes);
// Loop over cells
for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->Begin();
cell_iter != this->End();
++cell_iter)
{
// Get the node index corresponding to this cell
unsigned global_index = this->GetLocationIndexUsingCell(*cell_iter);
unsigned node_index = this->rGetMesh().SolveNodeMapping(global_index);
// Populate the vector of VTK cell data
vtk_cell_data[node_index] = (*cell_writer_iter)->GetCellDataForVtkOutput(*cell_iter, this);
}
mesh_writer.AddPointData((*cell_writer_iter)->GetVtkCellDataName(), vtk_cell_data);
}
// Loop over cells
for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->Begin();
cell_iter != this->End();
++cell_iter)
{
// Get the node index corresponding to this cell
unsigned global_index = this->GetLocationIndexUsingCell(*cell_iter);
unsigned node_index = this->rGetMesh().SolveNodeMapping(global_index);
for (unsigned var=0; var<num_cell_data_items; var++)
{
cell_data[var][node_index] = cell_iter->GetCellData()->GetItem(cell_data_names[var]);
}
rank[node_index] = (PetscTools::GetMyRank());
}
mesh_writer.AddPointData("Process rank", rank);
if (num_cell_data_items > 0)
{
for (unsigned var=0; var<cell_data.size(); var++)
{
mesh_writer.AddPointData(cell_data_names[var], cell_data[var]);
}
}
mesh_writer.WriteFilesUsingMesh(*mpNodesOnlyMesh);
*(this->mpVtkMetaFile) << " <DataSet timestep=\"";
*(this->mpVtkMetaFile) << SimulationTime::Instance()->GetTimeStepsElapsed();
*(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
*(this->mpVtkMetaFile) << SimulationTime::Instance()->GetTimeStepsElapsed();
if (PetscTools::IsSequential())
{
*(this->mpVtkMetaFile) << ".vtu\"/>\n";
}
else
{
// Parallel vtu files .vtu -> .pvtu
*(this->mpVtkMetaFile) << ".pvtu\"/>\n";
}
#endif //CHASTE_VTK
}
