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// SPDX-FileCopyrightText: Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
// SPDX-License-Identifier: BSD-3-Clause
#include "vtkConduitToDataObject.h"
#include "vtkAMRBox.h"
#include "vtkArrayDispatch.h"
#include "vtkCellArrayIterator.h"
#include "vtkCellData.h"
#include "vtkConduitArrayUtilities.h"
#include "vtkDataArray.h"
#include "vtkDataSet.h"
#include "vtkDataSetAttributes.h"
#include "vtkImageData.h"
#include "vtkInformation.h"
#include "vtkLogger.h"
#include "vtkMultiProcessController.h"
#include "vtkOverlappingAMR.h"
#include "vtkParallelAMRUtilities.h"
#include "vtkPartitionedDataSet.h"
#include "vtkRectilinearGrid.h"
#include "vtkStringArray.h"
#include "vtkStructuredGrid.h"
#include "vtkUniformGrid.h"
#include "vtkUnstructuredGrid.h"
#include <catalyst_conduit.hpp>
#include <catalyst_conduit_blueprint.hpp>
#include <numeric>
#include <set>
namespace vtkConduitToDataObject
{
VTK_ABI_NAMESPACE_BEGIN
//----------------------------------------------------------------------------
bool FillPartionedDataSet(vtkPartitionedDataSet* output, const conduit_cpp::Node& node)
{
conduit_cpp::Node info;
if (!conduit_cpp::BlueprintMesh::verify(node, info))
{
vtkLogF(ERROR, "Mesh blueprint verification failed!");
return false;
}
std::map<std::string, vtkSmartPointer<vtkDataSet>> datasets;
// process "topologies".
auto topologies = node["topologies"];
conduit_index_t nchildren = topologies.number_of_children();
for (conduit_index_t i = 0; i < nchildren; ++i)
{
auto child = topologies.child(i);
try
{
if (auto ds = CreateMesh(child, node["coordsets"]))
{
auto idx = output->GetNumberOfPartitions();
output->SetPartition(idx, ds);
output->GetMetaData(idx)->Set(vtkCompositeDataSet::NAME(), child.name().c_str());
datasets[child.name()] = ds;
}
}
catch (std::exception& e)
{
vtkLogF(ERROR, "failed to process '../topologies/%s'.", child.name().c_str());
vtkLogF(ERROR, "ERROR: \n%s\n", e.what());
return false;
}
}
// add field data at leaf level
if (node.has_path("state/fields"))
{
for (const auto& dataset : datasets)
{
AddFieldData(dataset.second.Get(), node["state/fields"]);
}
}
// process "fields"
if (!node.has_path("fields"))
{
return true;
}
auto fields = node["fields"];
nchildren = fields.number_of_children();
for (conduit_index_t i = 0; i < nchildren; ++i)
{
auto fieldNode = fields.child(i);
const auto& fieldname = fieldNode.name();
try
{
auto dataset = datasets.at(fieldNode["topology"].as_string());
const auto vtk_association = GetAssociation(fieldNode["association"].as_string());
auto dsa = dataset->GetAttributes(vtk_association);
auto values = fieldNode["values"];
size_t dataset_size;
if (values.number_of_children() == 0)
{
dataset_size = values.dtype().number_of_elements();
}
else
{
dataset_size = values.child(0).dtype().number_of_elements();
}
if (dataset_size > 0)
{
vtkSmartPointer<vtkDataArray> array;
if (fieldname == "ascent_ghosts")
{
// convert ascent ghost information into VTK ghost information
// the VTK array is named vtkDataSetAttributes::GhostArrayName()
// and has different values.
array = vtkConduitArrayUtilities::MCGhostArrayToVTKGhostArray(
conduit_cpp::c_node(&values), dsa->IsA("vtkCellData"));
}
else
{
array =
vtkConduitArrayUtilities::MCArrayToVTKArray(conduit_cpp::c_node(&values), fieldname);
if (array->GetNumberOfTuples() != dataset->GetNumberOfElements(vtk_association))
{
throw std::runtime_error("mismatched tuple count!");
}
}
dsa->AddArray(array);
}
}
catch (std::exception& e)
{
vtkLogF(ERROR, "failed to process '../fields/%s'.", fieldname.c_str());
vtkLogF(ERROR, "ERROR: \n%s\n", e.what());
return false;
}
}
return true;
}
//----------------------------------------------------------------------------
bool FillAMRMesh(vtkOverlappingAMR* amr, const conduit_cpp::Node& node)
{
const int default_refinement_ratio = 2;
int nprocs = 1;
int rank = 0;
vtkMultiProcessController* controller = vtkMultiProcessController::GetGlobalController();
if (controller)
{
// if VTK was initialized properly controller should be non-null but that's not always
// the case so safer to check if controller is available
nprocs = controller->GetNumberOfProcesses();
rank = controller->GetLocalProcessId();
}
// pre-allocate the levels
const auto leaves_on_node = node.number_of_children();
std::vector<int> blocksPerLevelLocal(1);
std::map<int, std::pair<int, int>> domainID2LvlID;
vtkIdType blocks_local = 0;
vtkIdType blocks_global = 0;
double local_origin[3] = { vtkMath::Inf(), vtkMath::Inf(), vtkMath::Inf() };
double origin[3] = { 0, 0, 0 };
double spacing[3] = { 0, 0, 0 };
for (conduit_index_t cc = 0; cc < leaves_on_node; ++cc)
{
const auto child = node.child(cc);
if (child.has_path("state"))
{
const int level = child["state/level"].to_int32();
const int domain_id = child["state/domain_id"].to_int32();
if (size_t(level) >= blocksPerLevelLocal.size())
{
blocksPerLevelLocal.resize(level + 1);
blocksPerLevelLocal[level] = 0;
}
domainID2LvlID[domain_id] = { level, blocksPerLevelLocal[level] };
blocksPerLevelLocal[level]++;
origin[0] = child["coordsets/coords/origin/x"].to_float64();
origin[1] = child["coordsets/coords/origin/y"].to_float64();
origin[2] = child["coordsets/coords/origin/z"].to_float64();
// check global origin
if (origin[0] <= local_origin[0] && origin[1] <= local_origin[1] &&
origin[2] <= local_origin[2])
{
local_origin[0] = origin[0];
local_origin[1] = origin[1];
local_origin[2] = origin[2];
}
}
}
const vtkIdType levels_local = vtkIdType(blocksPerLevelLocal.size());
vtkIdType levels_global = 0;
double global_origin[3] = { vtkMath::Inf(), vtkMath::Inf(), vtkMath::Inf() };
if (nprocs == 1)
{
levels_global = levels_local;
std::copy(local_origin, local_origin + 3, global_origin);
}
else if (controller)
{
controller->AllReduce(&levels_local, &levels_global, 1, vtkCommunicator::MAX_OP);
controller->AllReduce(local_origin, global_origin, 3, vtkCommunicator::MIN_OP);
}
// need the total number of blocks across all processes
blocksPerLevelLocal.resize(levels_global, 0); // set the extra values created to 0
// globalBlockCount has block information for each process separated
std::vector<int> globalBlockCount(levels_global * nprocs);
// the ordering of the blocks for AMR is first all level 0 blocks, then all level 1 blocks, ...
// at each level we order based on proc rank first and then local id
if (nprocs == 1)
{
globalBlockCount = blocksPerLevelLocal;
}
else if (controller)
{
controller->AllGather(blocksPerLevelLocal.data(), globalBlockCount.data(), levels_global);
}
blocks_local = vtkIdType(domainID2LvlID.size());
blocks_global = std::accumulate(globalBlockCount.begin(), globalBlockCount.end(), 0);
// the offset for the start of each block at each level
std::vector<vtkIdType> offset_local(levels_global, 0);
if (nprocs > 1)
{
for (vtkIdType l = 0; l < levels_global; l++)
{
vtkIdType offset(0);
for (int p = 0; p < rank; p++)
{
offset += globalBlockCount[l + p * levels_global];
}
offset_local[l] = offset;
}
}
std::vector<int> blocksPerLevelGlobal(levels_global, 0);
for (vtkIdType l = 0; l < levels_global; l++)
{
for (int p = 0; p < nprocs; p++)
{
blocksPerLevelGlobal[l] += globalBlockCount[l + p * levels_global];
}
}
amr->Initialize(levels_global, blocksPerLevelGlobal.data());
for (int l = 0; l < levels_global; ++l)
{
for (int b = 0; b < blocksPerLevelGlobal[l]; ++b)
{
amr->SetDataSet(l, b, nullptr);
}
}
// set origin
amr->SetOrigin(global_origin);
for (conduit_index_t cc = 0; cc < leaves_on_node; ++cc)
{
// set the spacing for each level via amr->SetSpacing();
const auto child = node.child(cc);
if (child.has_path("state"))
{
int pdims[3] = { 0, 0, 0 };
const int domain_id = child["state/domain_id"].to_int32();
const int level = child["state/level"].to_int32();
origin[0] = child["coordsets/coords/origin/x"].to_float64();
origin[1] = child["coordsets/coords/origin/y"].to_float64();
origin[2] = child["coordsets/coords/origin/z"].to_float64();
spacing[0] = child["coordsets/coords/spacing/dx"].to_float64();
spacing[1] = child["coordsets/coords/spacing/dy"].to_float64();
spacing[2] = child["coordsets/coords/spacing/dz"].to_float64();
pdims[0] = child["coordsets/coords/dims/i"].to_int32();
pdims[1] = child["coordsets/coords/dims/j"].to_int32();
pdims[2] = child["coordsets/coords/dims/k"].to_int32();
vtkNew<vtkUniformGrid> ug;
ug->Initialize();
ug->SetOrigin(origin);
ug->SetSpacing(spacing);
ug->SetDimensions(pdims);
const auto fields = child["fields"];
AddFieldData(ug, fields, true);
vtkAMRBox box(origin, pdims, spacing, global_origin, amr->GetGridDescription());
// set level spacing
amr->SetSpacing(level, spacing);
amr->SetAMRBox(domainID2LvlID[domain_id].first,
domainID2LvlID[domain_id].second + offset_local[domainID2LvlID[domain_id].first], box);
amr->SetDataSet(domainID2LvlID[domain_id].first,
domainID2LvlID[domain_id].second + offset_local[domainID2LvlID[domain_id].first], ug);
amr->SetRefinementRatio(level, default_refinement_ratio);
if (child.has_path("nestsets/nest/windows"))
{
const auto& windows = child["nestsets/nest/windows"];
const auto window_count = windows.number_of_children();
for (int i = 0; i < window_count; ++i)
{
const auto& window = windows.child(i);
if (window.has_path("ratio") && window.has_path("domain_type"))
{
amr->SetRefinementRatio(level, window["ratio/i"].to_int32());
break;
}
}
}
}
}
// distribute AMRBoxes to all processes
if (nprocs > 1 && controller)
{
std::vector<vtkIdType> boxBoundsOffsets(nprocs);
std::vector<vtkIdType> boxBoundsCounts(nprocs);
std::vector<int> boxExtentsLocal(8 * blocks_local, 0);
std::vector<int> boxExtentsGlobal(8 * blocks_global, 0);
for (int p = 0; p < nprocs; ++p)
{
int num_blocks = 0;
for (int l = 0; l < levels_global; l++)
{
num_blocks += globalBlockCount[l + p * levels_global];
}
boxBoundsCounts[p] = num_blocks * 8;
if (p > 0)
{
boxBoundsOffsets[p] = num_blocks * 8 + boxBoundsOffsets[p - 1];
}
}
int local_index = 0;
for (std::map<int, std::pair<int, int>>::const_iterator it = domainID2LvlID.begin();
it != domainID2LvlID.end(); ++it)
{
int level = it->second.first;
int id = it->second.second + offset_local[level];
vtkAMRBox box = amr->GetAMRBox(level, id);
const int* loCorner = box.GetLoCorner();
const int* hiCorner = box.GetHiCorner();
boxExtentsLocal[8 * local_index + 0] = level;
boxExtentsLocal[8 * local_index + 1] = id;
boxExtentsLocal[8 * local_index + 2] = loCorner[0];
boxExtentsLocal[8 * local_index + 3] = loCorner[1];
boxExtentsLocal[8 * local_index + 4] = loCorner[2];
boxExtentsLocal[8 * local_index + 5] = hiCorner[0];
boxExtentsLocal[8 * local_index + 6] = hiCorner[1];
boxExtentsLocal[8 * local_index + 7] = hiCorner[2];
++local_index;
}
controller->AllGatherV(boxExtentsLocal.data(), boxExtentsGlobal.data(), boxExtentsLocal.size(),
boxBoundsCounts.data(), boxBoundsOffsets.data());
for (int i = 0; i < blocks_global; ++i)
{
int level = boxExtentsGlobal[8 * i + 0];
int id = boxExtentsGlobal[8 * i + 1];
int* dims = &boxExtentsGlobal[8 * i + 2];
vtkAMRBox box(dims[0], dims[1], dims[2], dims[3], dims[4], dims[5]);
amr->SetAMRBox(level, id, box);
}
}
if (nprocs == 1)
{
vtkAMRUtilities::BlankCells(amr);
}
else if (controller)
{
vtkParallelAMRUtilities::BlankCells(amr, controller);
}
return true;
}
//----------------------------------------------------------------------------
vtkSmartPointer<vtkDataSet> CreateMesh(
const conduit_cpp::Node& topology, const conduit_cpp::Node& coordsets)
{
// get the coordset for this topology element.
auto coords = coordsets[topology["coordset"].as_string()];
if (topology["type"].as_string() == "uniform" && coords["type"].as_string() == "uniform")
{
return CreateImageData(coords);
}
if (topology["type"].as_string() == "rectilinear" && coords["type"].as_string() == "rectilinear")
{
return CreateRectilinearGrid(coords);
}
if (topology["type"].as_string() == "structured" && coords["type"].as_string() == "explicit")
{
return CreateStructuredGrid(topology, coords);
}
if (coords["type"].as_string() == "explicit" && topology["type"].as_string() == "unstructured" &&
topology.has_path("elements/shape"))
{
std::string shape = topology["elements/shape"].as_string();
if (shape != "mixed")
{
return CreateMonoShapedUnstructuredGrid(topology, coords);
}
else if (topology.has_path("elements/shape_map") && topology.has_path("elements/shapes"))
{
return CreateMixedUnstructuredGrid(topology, coords);
}
// if there are no cells in the Conduit mesh, return an empty ug
return vtkSmartPointer<vtkUnstructuredGrid>::New();
}
throw std::runtime_error("unsupported topology or coordset");
}
//----------------------------------------------------------------------------
vtkSmartPointer<vtkImageData> CreateImageData(const conduit_cpp::Node& coordset)
{
auto image = vtkSmartPointer<vtkImageData>::New();
int dims[3] = { 1, 1, 1 };
const char* dims_paths[] = { "dims/i", "dims/j", "dims/k" };
double origin[3] = { 0, 0, 0 };
const char* origin_paths[] = { "origin/x", "origin/y", "origin/z" };
double spacing[3] = { 1, 1, 1 };
const char* spacing_paths[] = { "spacing/dx", "spacing/dy", "spacing/dz" };
for (int cc = 0; cc < 3; ++cc)
{
if (coordset.has_path(dims_paths[cc]))
{
dims[cc] = coordset[dims_paths[cc]].to_int32();
}
if (coordset.has_path(origin_paths[cc]))
{
origin[cc] = coordset[origin_paths[cc]].to_double();
}
if (coordset.has_path(spacing_paths[cc]))
{
spacing[cc] = coordset[spacing_paths[cc]].to_double();
}
}
image->SetOrigin(origin);
image->SetSpacing(spacing);
image->SetDimensions(dims);
return image;
}
//----------------------------------------------------------------------------
/**
* The "const" of values_xyz is necessary to avoid creating a new object.
* If value_xyz is not const, coordset["values/xyz"] must NOT be const either
* to call the correct copy constructor.
*/
vtkSmartPointer<vtkRectilinearGrid> CreateRectilinearGrid(const conduit_cpp::Node& coordset)
{
auto rectilinearGrid = vtkSmartPointer<vtkRectilinearGrid>::New();
const bool has_x_values = coordset.has_path("values/x");
const conduit_cpp::Node values_x = has_x_values ? coordset["values/x"] : conduit_cpp::Node();
const bool has_y_values = coordset.has_path("values/y");
const conduit_cpp::Node values_y = has_y_values ? coordset["values/y"] : conduit_cpp::Node();
const bool has_z_values = coordset.has_path("values/z");
const conduit_cpp::Node values_z = has_z_values ? coordset["values/z"] : conduit_cpp::Node();
vtkIdType x_dimension = 1;
vtkSmartPointer<vtkDataArray> xArray;
if (has_x_values)
{
xArray = vtkConduitArrayUtilities::MCArrayToVTKArray(conduit_cpp::c_node(&values_x), "xcoords");
x_dimension = xArray->GetNumberOfTuples();
}
vtkIdType y_dimension = 1;
vtkSmartPointer<vtkDataArray> yArray;
if (has_y_values)
{
yArray = vtkConduitArrayUtilities::MCArrayToVTKArray(conduit_cpp::c_node(&values_y), "ycoords");
y_dimension = yArray->GetNumberOfTuples();
}
vtkIdType z_dimension = 1;
vtkSmartPointer<vtkDataArray> zArray;
if (has_z_values)
{
zArray = vtkConduitArrayUtilities::MCArrayToVTKArray(conduit_cpp::c_node(&values_z), "zcoords");
z_dimension = zArray->GetNumberOfTuples();
}
rectilinearGrid->SetDimensions(x_dimension, y_dimension, z_dimension);
if (has_x_values)
{
rectilinearGrid->SetXCoordinates(xArray);
}
if (has_y_values)
{
rectilinearGrid->SetYCoordinates(yArray);
}
if (has_z_values)
{
rectilinearGrid->SetZCoordinates(zArray);
}
return rectilinearGrid;
}
//----------------------------------------------------------------------------
vtkSmartPointer<vtkStructuredGrid> CreateStructuredGrid(
const conduit_cpp::Node& topology, const conduit_cpp::Node& coordset)
{
auto sg = vtkSmartPointer<vtkStructuredGrid>::New();
sg->SetPoints(CreatePoints(coordset));
sg->SetDimensions(
topology.has_path("elements/dims/i") ? topology["elements/dims/i"].to_int32() + 1 : 1,
topology.has_path("elements/dims/j") ? topology["elements/dims/j"].to_int32() + 1 : 1,
topology.has_path("elements/dims/k") ? topology["elements/dims/k"].to_int32() + 1 : 1);
return sg;
}
//----------------------------------------------------------------------------
vtkSmartPointer<vtkDataSet> CreateMonoShapedUnstructuredGrid(
const conduit_cpp::Node& topologyNode, const conduit_cpp::Node& coordset)
{
auto unstructured = vtkSmartPointer<vtkUnstructuredGrid>::New();
conduit_cpp::Node connectivity = topologyNode["elements/connectivity"];
const conduit_cpp::DataType dtype0 = connectivity.dtype();
const auto nb_cells = dtype0.number_of_elements();
unstructured->SetPoints(CreatePoints(coordset));
const auto vtk_cell_type = GetCellType(topologyNode["elements/shape"].as_string());
if (nb_cells > 0)
{
if (vtk_cell_type == VTK_POLYHEDRON)
{
// polyhedra uses O2M and not M2C arrays, so need to process it
// differently.
conduit_cpp::Node t_elements = topologyNode["elements"];
conduit_cpp::Node t_subelements = topologyNode["subelements"];
auto elements = vtkConduitArrayUtilities::O2MRelationToVTKCellArray(
conduit_cpp::c_node(&t_elements), "connectivity");
auto subelements = vtkConduitArrayUtilities::O2MRelationToVTKCellArray(
conduit_cpp::c_node(&t_subelements), "connectivity");
// currently, this is an ugly deep-copy. Once vtkUnstructuredGrid is modified
// as proposed here (vtk/vtk#18190), this will get simpler.
SetPolyhedralCells(unstructured, elements, subelements);
}
else if (vtk_cell_type == VTK_POLYGON)
{
// polygons use O2M and not M2C arrays, so need to process it
// differently.
conduit_cpp::Node t_elements = topologyNode["elements"];
auto cellArray = vtkConduitArrayUtilities::O2MRelationToVTKCellArray(
conduit_cpp::c_node(&t_elements), "connectivity");
unstructured->SetCells(vtk_cell_type, cellArray);
}
else
{
const auto cell_size = GetNumberOfPointsInCellType(vtk_cell_type);
auto cellArray = vtkConduitArrayUtilities::MCArrayToVTKCellArray(
cell_size, conduit_cpp::c_node(&connectivity));
unstructured->SetCells(vtk_cell_type, cellArray);
}
}
return unstructured;
}
/**
* Internal struct to be passed to a worker.
* See CreateMixedUnstructuredGrid.
*/
struct MixedPolyhedralCells
{
conduit_cpp::Node* ElementShapes;
conduit_cpp::Node* ElementSizes;
conduit_cpp::Node* ElementOffsets;
conduit_cpp::Node* SubElementSizes;
conduit_cpp::Node* SubElementOffsets;
MixedPolyhedralCells(conduit_cpp::Node* elementShapes, conduit_cpp::Node* elementSizes,
conduit_cpp::Node* elementOffsets, conduit_cpp::Node* subElementSizes,
conduit_cpp::Node* subElementOffsets)
: ElementShapes(elementShapes)
, ElementSizes(elementSizes)
, ElementOffsets(elementOffsets)
, SubElementSizes(subElementSizes)
, SubElementOffsets(subElementOffsets)
{
}
template <typename ConnectivityArray, typename SubConnectivityArray>
void operator()(ConnectivityArray* elementConnectivity,
SubConnectivityArray* subElementConnectivity, vtkUnstructuredGrid* ug)
{
using ConnectivityArrayType = vtk::GetAPIType<ConnectivityArray>;
using SubConnectivityArrayType = vtk::GetAPIType<SubConnectivityArray>;
const auto elementShapesArray =
vtkConduitArrayUtilities::MCArrayToVTKArray(conduit_cpp::c_node(this->ElementShapes));
const auto elementSizesArray =
vtkConduitArrayUtilities::MCArrayToVTKArray(conduit_cpp::c_node(this->ElementSizes));
const auto elementOffsetsArray =
vtkConduitArrayUtilities::MCArrayToVTKArray(conduit_cpp::c_node(this->ElementOffsets));
vtkSmartPointer<vtkDataArray> subElementSizesArray(nullptr), subElementOffsetsArray(nullptr);
if (this->SubElementSizes != nullptr)
{
subElementSizesArray =
vtkConduitArrayUtilities::MCArrayToVTKArray(conduit_cpp::c_node(this->SubElementSizes));
}
if (this->SubElementOffsets != nullptr)
{
subElementOffsetsArray =
vtkConduitArrayUtilities::MCArrayToVTKArray(conduit_cpp::c_node(this->SubElementOffsets));
}
auto elementShapesRange = vtk::DataArrayValueRange(elementShapesArray);
auto elementSizesRange = vtk::DataArrayValueRange(elementSizesArray);
auto elementOffsetsRange = vtk::DataArrayValueRange(elementOffsetsArray);
assert(elementShapesRange.size() == elementSizesRange.size());
assert(elementShapesRange.size() == elementOffsetsRange.size());
auto elementSizesIterator = elementSizesRange.begin();
auto elementOffsetsIterator = elementOffsetsRange.begin();
const vtkNew<vtkUnsignedCharArray> cellTypes;
const vtkNew<vtkCellArray> connectivity;
const vtkNew<vtkCellArray> faces;
const vtkNew<vtkCellArray> faceLocations;
vtkIdType numFace = 0;
for (const auto& cellType : elementShapesRange)
{
auto type = static_cast<unsigned char>(cellType);
cellTypes->InsertNextValue(type);
if (type == VTK_POLYHEDRON)
{
assert(subElementSizesArray != nullptr);
assert(subElementOffsetsArray != nullptr);
std::set<vtkIdType> cellPointSet;
auto nCellFaces = static_cast<vtkIdType>(*elementSizesIterator++);
auto offset = static_cast<vtkIdType>(*elementOffsetsIterator++);
faceLocations->InsertNextCell(nCellFaces);
auto elementRange =
vtk::DataArrayValueRange(elementConnectivity, offset, offset + nCellFaces);
for (const ConnectivityArrayType faceId : elementRange)
{
const vtkIdType nFacePts = subElementSizesArray->GetVariantValue(faceId).ToLongLong();
const vtkIdType faceOffset = subElementOffsetsArray->GetVariantValue(faceId).ToLongLong();
faceLocations->InsertCellPoint(numFace++);
auto facePtRange =
vtk::DataArrayValueRange(subElementConnectivity, faceOffset, faceOffset + nFacePts);
faces->InsertNextCell(nFacePts);
for (const SubConnectivityArrayType ptId : facePtRange)
{
faces->InsertCellPoint(ptId);
cellPointSet.insert(ptId);
}
}
connectivity->InsertNextCell(static_cast<int>(cellPointSet.size()));
for (const vtkIdType cellPoint : cellPointSet)
{
connectivity->InsertCellPoint(cellPoint);
}
}
else
{
auto npts = static_cast<vtkIdType>(*elementSizesIterator++);
auto offset = static_cast<vtkIdType>(*elementOffsetsIterator++);
auto elementRange = vtk::DataArrayValueRange(elementConnectivity, offset, offset + npts);
connectivity->InsertNextCell(static_cast<int>(npts));
for (const ConnectivityArrayType item : elementRange)
{
connectivity->InsertCellPoint(static_cast<vtkIdType>(item));
}
faceLocations->InsertNextCell(0);
}
}
if (faces->GetNumberOfCells() > 0)
{
ug->SetPolyhedralCells(cellTypes, connectivity, faceLocations, faces);
}
else
{
ug->SetPolyhedralCells(cellTypes, connectivity, nullptr, nullptr);
}
}
};
//----------------------------------------------------------------------------
vtkSmartPointer<vtkDataSet> CreateMixedUnstructuredGrid(
const conduit_cpp::Node& topologyNode, const conduit_cpp::Node& coords)
{
auto unstructured = vtkSmartPointer<vtkUnstructuredGrid>::New();
// mixed shapes definition
conduit_cpp::Node shape_map = topologyNode["elements/shape_map"];
// check presence of polyhedra
bool hasPolyhedra(false);
conduit_index_t nCells = shape_map.number_of_children();
for (conduit_index_t i = 0; i < nCells; ++i)
{
auto child = shape_map.child(i);
int cellType = child.to_int32();
hasPolyhedra |= (cellType == VTK_POLYHEDRON);
}
// if polyhedra are present, the subelements should be present as well.
if (hasPolyhedra &&
!(topologyNode.has_path("subelements/shape") &&
topologyNode.has_path("subelements/shape_map") &&
topologyNode.has_path("subelements/shapes")))
{
throw std::runtime_error("no subelements found for polyhedral cell definition.");
}
if (nCells > 0)
{
unstructured->SetPoints(CreatePoints(coords));
conduit_cpp::Node t_elementShapes = topologyNode["elements/shapes"];
conduit_cpp::Node t_elementSizes = topologyNode["elements/sizes"];
conduit_cpp::Node t_elementOffsets = topologyNode["elements/offsets"];
conduit_cpp::Node t_elementConnectivity = topologyNode["elements/connectivity"];
auto elementConnectivity =
vtkConduitArrayUtilities::MCArrayToVTKArray(conduit_cpp::c_node(&t_elementConnectivity));
if (elementConnectivity == nullptr)
{
throw std::runtime_error("element/connectivity not available (nullptr)");
}
conduit_cpp::Node* p_subElementSizes(nullptr);
conduit_cpp::Node* p_subElementOffsets(nullptr);
vtkSmartPointer<vtkDataArray> subConnectivity(nullptr);
if (hasPolyhedra)
{
// get the face nodes for size, offset and connectivity
conduit_cpp::Node t_subElementSizes = topologyNode["subelements/sizes"];
conduit_cpp::Node t_subElementOffsets = topologyNode["subelements/offsets"];
conduit_cpp::Node t_subElementConnectivity = topologyNode["subelements/connectivity"];
p_subElementOffsets = &t_subElementOffsets;
p_subElementSizes = &t_subElementSizes;
subConnectivity =
vtkConduitArrayUtilities::MCArrayToVTKArray(conduit_cpp::c_node(&t_subElementConnectivity));
if (subConnectivity == nullptr)
{
throw std::runtime_error("subelements/connectivity not available (nullptr)");
}
}
// dispatch the mcarrays to create the mixed element grid
MixedPolyhedralCells worker(
&t_elementShapes, &t_elementSizes, &t_elementOffsets, p_subElementSizes, p_subElementOffsets);
if (!vtkArrayDispatch::Dispatch2::Execute(
elementConnectivity, subConnectivity, worker, unstructured))
{
worker(elementConnectivity.GetPointer(), subConnectivity.GetPointer(), unstructured);
}
}
return unstructured;
}
//----------------------------------------------------------------------------
bool AddFieldData(vtkDataObject* output, const conduit_cpp::Node& stateFields, bool isAMReX)
{
auto field_data = output->GetFieldData();
auto number_of_children = stateFields.number_of_children();
for (conduit_index_t child_index = 0; child_index < number_of_children; ++child_index)
{
auto field_node = stateFields.child(child_index);
const auto& field_name = field_node.name();
try
{
size_t dataset_size = 0;
if (field_node.number_of_children() == 0)
{
dataset_size = field_node.dtype().number_of_elements();
}
else
{
dataset_size = field_node.child(0).dtype().number_of_elements();
}
if (dataset_size > 0)
{
vtkSmartPointer<vtkAbstractArray> dataArray;
if (field_node.dtype().is_string())
{
auto stringArray = vtkSmartPointer<vtkStringArray>::New();
stringArray->SetNumberOfTuples(1);
stringArray->SetValue(0, field_node.as_string().c_str());
dataArray = stringArray;
dataArray->SetName(field_name.c_str());
}
else
{
dataArray = vtkConduitArrayUtilities::MCArrayToVTKArray(
conduit_cpp::c_node(&field_node), field_name);
}
if (dataArray)
{
if (isAMReX)
{
auto ug = vtkUniformGrid::SafeDownCast(output);
const auto vtk_association = GetAssociation(field_node["association"].as_string());
auto dsa = ug->GetAttributes(vtk_association);
dsa->AddArray(dataArray);
}
else
{
field_data->AddArray(dataArray);
}
}
if ((field_name == "time" || field_name == "TimeValue") && field_node.dtype().is_number())
{
// let's also set DATA_TIME_STEP.
output->GetInformation()->Set(vtkDataObject::DATA_TIME_STEP(), field_node.to_float64());
}
}
}
catch (std::exception& e)
{
vtkLogF(ERROR, "failed to process '../state/fields/%s'.", field_name.c_str());
vtkLogF(ERROR, "ERROR: \n%s\n", e.what());
return false;
}
}
return true;
}
//----------------------------------------------------------------------------
vtkSmartPointer<vtkPoints> CreatePoints(const conduit_cpp::Node& coords)
{
if (coords["type"].as_string() != "explicit")
{
throw std::runtime_error("invalid node!");
}
conduit_cpp::Node values = coords["values"];
auto array = vtkConduitArrayUtilities::MCArrayToVTKArray(conduit_cpp::c_node(&values), "coords");
if (array == nullptr)
{
throw std::runtime_error("failed to convert to VTK array!");
}
if (array->GetNumberOfComponents() < 3)
{
array = vtkConduitArrayUtilities::SetNumberOfComponents(array, 3);
}
else if (array->GetNumberOfComponents() > 3)
{
throw std::runtime_error("points cannot have more than 3 components!");
}
auto pts = vtkSmartPointer<vtkPoints>::New();
pts->SetData(array);
return pts;
}
//----------------------------------------------------------------------------
void SetPolyhedralCells(
vtkUnstructuredGrid* grid, vtkCellArray* elements, vtkCellArray* subelements)
{
vtkNew<vtkCellArray> connectivity;
vtkNew<vtkCellArray> faces;
vtkNew<vtkCellArray> faceLocations;
connectivity->AllocateEstimate(elements->GetNumberOfCells(), 10);
faces->AllocateExact(
subelements->GetNumberOfCells(), subelements->GetConnectivityArray()->GetNumberOfTuples());
faceLocations->AllocateExact(elements->GetNumberOfCells(), subelements->GetNumberOfCells());
auto eIter = vtk::TakeSmartPointer(elements->NewIterator());
auto seIter = vtk::TakeSmartPointer(subelements->NewIterator());
std::vector<vtkIdType> cellPoints;
vtkIdType faceNum = 0;
for (eIter->GoToFirstCell(); !eIter->IsDoneWithTraversal(); eIter->GoToNextCell())
{
// init;
cellPoints.clear();
// get cell from 'elements'.
vtkIdType size;
vtkIdType const* seIds;
eIter->GetCurrentCell(size, seIds);
faceLocations->InsertNextCell(size);
for (vtkIdType fIdx = 0; fIdx < size; ++fIdx)
{
faceLocations->InsertCellPoint(faceNum++);
seIter->GoToCell(seIds[fIdx]);
vtkIdType ptSize;
vtkIdType const* ptIds;
seIter->GetCurrentCell(ptSize, ptIds);
faces->InsertNextCell(ptSize, ptIds);
// accumulate pts from all faces in this cell to build the 'connectivity' array.
std::copy(ptIds, ptIds + ptSize, std::back_inserter(cellPoints));
}
connectivity->InsertNextCell(
static_cast<vtkIdType>(cellPoints.size()), cellPoints.empty() ? nullptr : cellPoints.data());
}
connectivity->Squeeze();
faces->Squeeze();
faceLocations->Squeeze();
vtkNew<vtkUnsignedCharArray> cellTypes;
cellTypes->SetNumberOfTuples(connectivity->GetNumberOfCells());
cellTypes->FillValue(static_cast<unsigned char>(VTK_POLYHEDRON));
grid->SetPolyhedralCells(cellTypes, connectivity, faceLocations, faces);
}
//----------------------------------------------------------------------------
vtkIdType GetNumberOfPointsInCellType(int vtk_cell_type)
{
switch (vtk_cell_type)
{
case VTK_VERTEX:
return 1;
case VTK_LINE:
return 2;
case VTK_TRIANGLE:
return 3;
case VTK_QUAD:
case VTK_TETRA:
return 4;
case VTK_HEXAHEDRON:
return 8;
default:
throw std::runtime_error("unsupported cell type " + std::to_string(vtk_cell_type));
}
}
//----------------------------------------------------------------------------
int GetCellType(const std::string& shape)
{
if (shape == "point")
{
return VTK_VERTEX;
}
else if (shape == "line")
{
return VTK_LINE;
}
else if (shape == "tri")
{
return VTK_TRIANGLE;
}
else if (shape == "quad")
{
return VTK_QUAD;
}
else if (shape == "tet")
{
return VTK_TETRA;
}
else if (shape == "hex")
{
return VTK_HEXAHEDRON;
}
else if (shape == "polyhedral")
{
return VTK_POLYHEDRON;
}
else if (shape == "polygonal")
{
return VTK_POLYGON;
}
else
{
throw std::runtime_error("unsupported shape " + shape);
}
}
//----------------------------------------------------------------------------
int GetAssociation(const std::string& assoc)
{
if (assoc == "element")
{
return vtkDataObject::CELL;
}
else if (assoc == "vertex")
{
return vtkDataObject::POINT;
}
throw std::runtime_error("unsupported association " + assoc);
}
VTK_ABI_NAMESPACE_END
} // vtkDataObjectToConduit namespace
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