/*=========================================================================

  Program:   Visualization Toolkit
  Module:    vtkXdmfHeavyData.cxx

  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
  All rights reserved.
  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notice for more information.

=========================================================================*/
#include "vtkXdmfHeavyData.h"

#include "vtkCellArray.h"
#include "vtkCellData.h"
#include "vtkCellTypes.h"
#include "vtkDataObjectTypes.h"
#include "vtkDoubleArray.h"
#include "vtkExtractSelectedIds.h"
#include "vtkFloatArray.h"
#include "vtkInformation.h"
#include "vtkMath.h"
#include "vtkMergePoints.h"
#include "vtkMultiBlockDataSet.h"
#include "vtkObjectFactory.h"
#include "vtkPointData.h"
#include "vtkPolyData.h"
#include "vtkRectilinearGrid.h"
#include "vtkSelection.h"
#include "vtkSelectionNode.h"
#include "vtkSmartPointer.h"
#include "vtkStructuredData.h"
#include "vtkStructuredGrid.h"
#include "vtkUniformGrid.h"
#include "vtkUnstructuredGrid.h"
#include "vtkXdmfDataArray.h"
#include "vtkXdmfReader.h"
#include "vtkXdmfReaderInternal.h"

#include <deque>
#include <cassert>

#include <libxml/tree.h>

using namespace xdmf2;

static void vtkScaleExtents(int in_exts[6], int out_exts[6], int stride[3])
{
  out_exts[0] = in_exts[0] / stride[0];
  out_exts[1] = in_exts[1] / stride[0];
  out_exts[2] = in_exts[2] / stride[1];
  out_exts[3] = in_exts[3] / stride[1];
  out_exts[4] = in_exts[4] / stride[2];
  out_exts[5] = in_exts[5] / stride[2];
}

static void vtkGetDims(int exts[6], int dims[3])
{
  dims[0] = exts[1] - exts[0] + 1;
  dims[1] = exts[3] - exts[2] + 1;
  dims[2] = exts[5] - exts[4] + 1;
}

//----------------------------------------------------------------------------
vtkXdmfHeavyData::vtkXdmfHeavyData(vtkXdmfDomain* domain,
  vtkAlgorithm* reader)
{
  this->Reader = reader;
  this->Piece = 0;
  this->NumberOfPieces = 0;
  this->GhostLevels = 0;
  this->Extents[0] = this->Extents[2] = this->Extents[4] = 0;
  this->Extents[1] = this->Extents[3] = this->Extents[5] = -1;
  this->Domain = domain;
  this->Stride[0] = this->Stride[1] = this->Stride[2] = 1;
}

//----------------------------------------------------------------------------
vtkXdmfHeavyData::~vtkXdmfHeavyData()
{
}

//----------------------------------------------------------------------------
vtkDataObject* vtkXdmfHeavyData::ReadData()
{
  if (this->Domain->GetNumberOfGrids() == 1)
    {
    // There's just 1 grid. Now in serial, this is all good. In parallel, we
    // need to be care:
    // 1. If the data is structured, we respect the update-extent and read
    //    accordingly.
    // 2. If the data is unstructrued, we read only on the root node. The user
    //    can apply D3 or something to repartition the data.
    return this->ReadData(this->Domain->GetGrid(0));
    }

  // this code is similar to ReadComposite() however we cannot use the same code
  // since the API for getting the children differs on the domain and the grid.

  bool distribute_leaf_nodes = this->NumberOfPieces > 1;
  XdmfInt32 numChildren = this->Domain->GetNumberOfGrids();
  int number_of_leaf_nodes = 0;

  vtkMultiBlockDataSet* mb = vtkMultiBlockDataSet::New();
  mb->SetNumberOfBlocks(numChildren);

  for (XdmfInt32 cc=0; cc < numChildren; cc++)
    {
    XdmfGrid* xmfChild = this->Domain->GetGrid(cc);
    mb->GetMetaData(cc)->Set(vtkCompositeDataSet::NAME(),
      xmfChild->GetName());
    bool child_is_leaf = (xmfChild->IsUniform() != 0);
    if (!child_is_leaf || !distribute_leaf_nodes ||
      (number_of_leaf_nodes % this->NumberOfPieces) == this->Piece)
      {
      // it's possible that the data has way too many blocks, in which case the
      // reader didn't present the user with capabilities to select the actual
      // leaf node blocks as is the norm, instead only top-level grids were
      // shown. In that case we need to ensure that we skip grids the user
      // wanted us to skip explicitly.
      if (!this->Domain->GetGridSelection()->ArrayIsEnabled(xmfChild->GetName()))
        {
        continue;
        }
      vtkDataObject* childDO = this->ReadData(xmfChild);
      if (childDO)
        {
        mb->SetBlock(cc, childDO);
        childDO->Delete();
        }
      }
    number_of_leaf_nodes += child_is_leaf? 1 : 0;
    }

  return mb;
}

//----------------------------------------------------------------------------
vtkDataObject* vtkXdmfHeavyData::ReadData(XdmfGrid* xmfGrid, int blockId)
{
  if (!xmfGrid || xmfGrid->GetGridType() == XDMF_GRID_UNSET)
    {
    // sanity check-ensure that the xmfGrid is valid.
    return 0;
    }

  XdmfInt32 gridType = (xmfGrid->GetGridType() & XDMF_GRID_MASK);
  if (gridType == XDMF_GRID_COLLECTION &&
    xmfGrid->GetCollectionType() == XDMF_GRID_COLLECTION_TEMPORAL)
    {
    // grid is a temporal collection, pick the sub-grid with matching time and
    // process that.
    return this->ReadTemporalCollection(xmfGrid, blockId);
    }
  else if (gridType == XDMF_GRID_COLLECTION ||
    gridType == XDMF_GRID_TREE)
    {
    return this->ReadComposite(xmfGrid);
    }

  // grid is a primitive grid, so read the data.
  return this->ReadUniformData(xmfGrid, blockId);
}

//----------------------------------------------------------------------------
vtkDataObject* vtkXdmfHeavyData::ReadComposite(XdmfGrid* xmfComposite)
{
  assert((
      (xmfComposite->GetGridType() & XDMF_GRID_COLLECTION &&
       xmfComposite->GetCollectionType() != XDMF_GRID_COLLECTION_TEMPORAL) ||
      (xmfComposite->GetGridType() & XDMF_GRID_TREE))
    && "Input must be a spatial collection or a tree");

  vtkMultiBlockDataSet* multiBlock = vtkMultiBlockDataSet::New();
  XdmfInt32 numChildren = xmfComposite->GetNumberOfChildren();
  multiBlock->SetNumberOfBlocks(numChildren);

  bool distribute_leaf_nodes = (xmfComposite->GetGridType() & XDMF_GRID_COLLECTION &&
     this->NumberOfPieces > 1);

  int number_of_leaf_nodes = 0;
  for (XdmfInt32 cc=0; cc < numChildren; cc++)
    {
    XdmfGrid* xmfChild = xmfComposite->GetChild(cc);
    multiBlock->GetMetaData(cc)->Set(vtkCompositeDataSet::NAME(),
      xmfChild->GetName());
    bool child_is_leaf = (xmfChild->IsUniform() != 0);
    if (!child_is_leaf || !distribute_leaf_nodes ||
      (number_of_leaf_nodes % this->NumberOfPieces) == this->Piece)
      {
      vtkDataObject* childDO = this->ReadData(xmfChild, cc);
      if (childDO)
        {
        multiBlock->SetBlock(cc, childDO);
        childDO->Delete();
        }
      }
    number_of_leaf_nodes += child_is_leaf? 1 : 0;
    }

  return multiBlock;
}

//----------------------------------------------------------------------------
vtkDataObject* vtkXdmfHeavyData::ReadTemporalCollection(
  XdmfGrid* xmfTemporalCollection, int blockId)
{
  assert(xmfTemporalCollection->GetGridType() & XDMF_GRID_COLLECTION &&
    xmfTemporalCollection->GetCollectionType() == XDMF_GRID_COLLECTION_TEMPORAL
    && "Input must be a temporal collection");

  // Find the children that are valid for the requested time (this->Time) and
  // read only those.

  // FIXME: I am tempted to remove support for supporting multiple matching
  // sub-grids for a time-step since that changes the composite data hierarchy
  // over time which makes it hard to use filters such as vtkExtractBlock etc.

  std::deque<XdmfGrid*> valid_children;
  for (XdmfInt32 cc=0; cc < xmfTemporalCollection->GetNumberOfChildren(); cc++)
    {
    XdmfGrid* child = xmfTemporalCollection->GetChild(cc);
    if (child)
      {
      // ensure that we set correct epsilon for comparison
      // BUG #0013766.
      child->GetTime()->SetEpsilon(VTK_DBL_EPSILON);
      if (child->GetTime()->IsValid(this->Time, this->Time))
        {
        valid_children.push_back(child);
        }
      }
    }
  // if no child matched this timestep, handle the case where the user didn't
  // specify any <Time /> element for the temporal collection.
  for (XdmfInt32 cc=0;
    valid_children.size() == 0 &&
    cc < xmfTemporalCollection->GetNumberOfChildren(); cc++)
    {
    XdmfGrid* child = xmfTemporalCollection->GetChild(cc);
    if (child && child->GetTime()->GetTimeType() == XDMF_TIME_UNSET)
      {
      valid_children.push_back(child);
      }
    }

  if (valid_children.size() == 0)
    {
    return 0;
    }

  std::deque<vtkSmartPointer<vtkDataObject> > child_data_objects;
  std::deque<XdmfGrid*>::iterator iter;
  for (iter = valid_children.begin(); iter != valid_children.end(); ++iter)
    {
    vtkDataObject* childDO = this->ReadData(*iter, blockId);
    if (childDO)
      {
      child_data_objects.push_back(childDO);
      childDO->Delete();
      }
    }

  if (child_data_objects.size() == 1)
    {
    vtkDataObject* dataObject = child_data_objects[0];
    dataObject->Register(NULL);
    return dataObject;
    }
  else if (child_data_objects.size() > 1)
    {
    vtkMultiBlockDataSet* mb = vtkMultiBlockDataSet::New();
    mb->SetNumberOfBlocks(static_cast<unsigned int>(child_data_objects.size()));
    for (unsigned int cc=0;
      cc < static_cast<unsigned int>(child_data_objects.size()); cc++)
      {
      mb->SetBlock(cc, child_data_objects[cc]);
      }
    return mb;
    }

  return 0;
}

//----------------------------------------------------------------------------
// Read a non-composite grid. Note here uniform has nothing to do with
// vtkUniformGrid but to what Xdmf's GridType="Uniform".
vtkDataObject* vtkXdmfHeavyData::ReadUniformData(XdmfGrid* xmfGrid, int blockId)
{
  assert(xmfGrid->IsUniform() && "Input must be a uniform xdmf grid.");

  int vtk_data_type = this->Domain->GetVTKDataType(xmfGrid);

  if (!this->Domain->GetGridSelection()->ArrayIsEnabled(xmfGrid->GetName()))
    {
    // simply create an empty data-object of the correct type and return it.
    return vtkDataObjectTypes::NewDataObject(vtk_data_type);
    }

  // Read heavy data for grid geometry/topology. This does not read any
  // data-arrays. They are read explicitly.
  XdmfTopology* topo = xmfGrid->GetTopology();
  XdmfGeometry* geom = xmfGrid->GetGeometry();
  xmlChar* filePtr;

  bool caching = true;
  XdmfDOM* topoDom = topo->GetDOM();
  XdmfXmlNode topoNode = topo->GetElement();
  XdmfXmlNode topoNodeDataItem = topoDom->FindElement("DataItem", 0, topoNode);
  std::string topoFilename = "NULL";
  if (topoNodeDataItem && caching)
    {
    filePtr = topoNodeDataItem->children->content;
    if (filePtr != NULL)
      {
      topoFilename = reinterpret_cast<char*>(filePtr);
      }
    else
      {
      vtkErrorWithObjectMacro(this->Reader, << "Cannot find DataItem element in topology xml, no caching possible");
      caching = false;
      }
    }
  else
    {
    caching = false;
    }

  XdmfDOM* geomDom = geom->GetDOM();
  XdmfXmlNode geomNode = geom->GetElement();
  XdmfXmlNode geomNodeDataItem = geomDom->FindElement("DataItem", 0, geomNode);
  std::string geomFilename = "NULL";
  if (geomNodeDataItem && caching)
    {
    filePtr =  geomNodeDataItem->children->content;
    if (filePtr != NULL)
      {
      geomFilename = reinterpret_cast<char*>(filePtr);
      }
    else
      {
      vtkErrorWithObjectMacro(this->Reader, << "Cannot find DataItem element in geometry xml, no caching possible");
      caching = false;
      }
    }
  else
    {
    caching = false;
    }

  vtkXdmfReader::XdmfReaderCachedData& cache =
    vtkXdmfReader::SafeDownCast(this->Reader)->GetDataSetCache();
  vtkXdmfReader::XdmfDataSetTopoGeoPath& cachedData = cache[blockId];
  if (caching &&
    (cachedData.topologyPath == topoFilename) && (cachedData.geometryPath == geomFilename))
    {
    vtkDataSet* ds = vtkDataSet::SafeDownCast(
      vtkDataObjectTypes::NewDataObject(cachedData.dataset->GetDataObjectType()));
    ds->ShallowCopy(cachedData.dataset);
    this->ReadAttributes(ds, xmfGrid);
    return ds;
    }

  if (caching)
    {
    cachedData.topologyPath = topoFilename;
    cachedData.geometryPath = geomFilename;
    if (cache[blockId].dataset != NULL)
      {
      cache[blockId].dataset->Delete();
      cache[blockId].dataset = NULL;
      }
    }

  XdmfInt32 status = xmfGrid->Update();
  if (status == XDMF_FAIL)
    {
    return 0;
    }

  vtkDataObject* dataObject = 0;

  switch (vtk_data_type)
    {
  case VTK_UNIFORM_GRID:
    dataObject = this->RequestImageData(xmfGrid, true);
    break;

  case VTK_IMAGE_DATA:
    dataObject = this->RequestImageData(xmfGrid, false);
    break;

  case VTK_STRUCTURED_GRID:
    dataObject = this->RequestStructuredGrid(xmfGrid);
    break;

  case VTK_RECTILINEAR_GRID:
    dataObject = this->RequestRectilinearGrid(xmfGrid);
    break;

  case VTK_UNSTRUCTURED_GRID:
    dataObject = this->ReadUnstructuredGrid(xmfGrid);
    break;

  default:
    // un-handled case.
    return 0;
    }

  if (caching)
    {
    cache[blockId].dataset = vtkDataSet::SafeDownCast(dataObject);
    dataObject->Register(0);
    }
  return dataObject;
}

//----------------------------------------------------------------------------
int vtkXdmfHeavyData::GetNumberOfPointsPerCell(int vtk_cell_type)
{
  switch (vtk_cell_type)
    {
  case VTK_POLY_VERTEX:
    return 0;
  case VTK_POLY_LINE:
    return 0;
  case VTK_POLYGON:
    return 0;

  case VTK_TRIANGLE:
    return 3;
  case VTK_QUAD:
    return 4;
  case VTK_TETRA:
    return 4;
  case VTK_PYRAMID:
    return 5;
  case VTK_WEDGE:
    return 6;
  case VTK_HEXAHEDRON:
    return 8;
  case VTK_QUADRATIC_EDGE:
    return 3;
  case VTK_QUADRATIC_TRIANGLE:
    return 6;
  case VTK_QUADRATIC_QUAD:
    return 8;
  case VTK_BIQUADRATIC_QUAD:
    return 9;
  case VTK_QUADRATIC_TETRA:
    return 10;
  case VTK_QUADRATIC_PYRAMID:
    return 13;
  case VTK_QUADRATIC_WEDGE:
    return 15;
  case VTK_BIQUADRATIC_QUADRATIC_WEDGE:
    return 18;
  case VTK_QUADRATIC_HEXAHEDRON:
    return 20;
  case VTK_BIQUADRATIC_QUADRATIC_HEXAHEDRON:
    return 24;
  case VTK_TRIQUADRATIC_HEXAHEDRON:
    return 24;
    }
  return -1;
}
//----------------------------------------------------------------------------
int vtkXdmfHeavyData::GetVTKCellType(XdmfInt32 topologyType)
{
  switch (topologyType)
    {
  case  XDMF_POLYVERTEX :
    return VTK_POLY_VERTEX;
  case  XDMF_POLYLINE :
    return VTK_POLY_LINE;
  case  XDMF_POLYGON :
    return VTK_POLYGON; // FIXME: should this not be treated as mixed?
  case  XDMF_TRI :
    return VTK_TRIANGLE;
  case  XDMF_QUAD :
    return VTK_QUAD;
  case  XDMF_TET :
    return VTK_TETRA;
  case  XDMF_PYRAMID :
    return VTK_PYRAMID;
  case  XDMF_WEDGE :
    return VTK_WEDGE;
  case  XDMF_HEX :
    return VTK_HEXAHEDRON;
  case  XDMF_EDGE_3 :
    return VTK_QUADRATIC_EDGE ;
  case  XDMF_TRI_6 :
    return VTK_QUADRATIC_TRIANGLE ;
  case  XDMF_QUAD_8 :
    return VTK_QUADRATIC_QUAD ;
  case  XDMF_QUAD_9 :
    return VTK_BIQUADRATIC_QUAD ;
  case  XDMF_TET_10 :
    return VTK_QUADRATIC_TETRA ;
  case  XDMF_PYRAMID_13 :
    return VTK_QUADRATIC_PYRAMID ;
  case  XDMF_WEDGE_15 :
    return VTK_QUADRATIC_WEDGE ;
  case  XDMF_WEDGE_18 :
    return VTK_BIQUADRATIC_QUADRATIC_WEDGE ;
  case  XDMF_HEX_20 :
    return VTK_QUADRATIC_HEXAHEDRON ;
  case  XDMF_HEX_24 :
    return VTK_BIQUADRATIC_QUADRATIC_HEXAHEDRON ;
  case  XDMF_HEX_27 :
    return VTK_TRIQUADRATIC_HEXAHEDRON ;
  case XDMF_MIXED :
    return VTK_NUMBER_OF_CELL_TYPES;
    }
  // XdmfErrorMessage("Unknown Topology Type = "
  //  << xmfGrid->GetTopology()->GetTopologyType());
  return VTK_EMPTY_CELL;
}

//----------------------------------------------------------------------------
vtkDataObject* vtkXdmfHeavyData::ReadUnstructuredGrid(XdmfGrid* xmfGrid)
{
  vtkSmartPointer<vtkUnstructuredGrid> ugData =
    vtkSmartPointer<vtkUnstructuredGrid>::New();

  // BUG #12527. For non-partitioned data, don't read unstructured grid on
  // process id > 0.
  if (this->Piece != 0 &&
    this->Domain->GetNumberOfGrids() == 1 &&
    this->Domain->GetVTKDataType() == VTK_UNSTRUCTURED_GRID &&
    this->Domain->GetSetsSelection()->GetNumberOfArrays() == 0)
    {
    ugData->Register(NULL);
    return ugData;
    }

  XdmfTopology* xmfTopology = xmfGrid->GetTopology();
  XdmfArray* xmfConnectivity = xmfTopology->GetConnectivity();

  int vtk_cell_type = vtkXdmfHeavyData::GetVTKCellType(
      xmfTopology->GetTopologyType());

  if (vtk_cell_type == VTK_EMPTY_CELL)
    {
    // invalid topology.
    return NULL;
    }

  if (vtk_cell_type != VTK_NUMBER_OF_CELL_TYPES)
    // i.e. topologyType != XDMF_MIXED
    {
    // all cells are of the same type.
    XdmfInt32 numPointsPerCell= xmfTopology->GetNodesPerElement();

    // FIXME: is this needed, shouldn't xmfTopology->GetNodesPerElement()
    // return the correct value always?
    if (xmfConnectivity->GetRank() == 2)
      {
      numPointsPerCell = xmfConnectivity->GetDimension(1);
      }

    /* Create Cell Type Array */
    XdmfInt64 conn_length = xmfConnectivity->GetNumberOfElements();
    XdmfInt64* xmfConnections = new XdmfInt64[conn_length];
    xmfConnectivity->GetValues(0, xmfConnections, conn_length);

    vtkIdType numCells = xmfTopology->GetShapeDesc()->GetNumberOfElements();
    int *cell_types = new int[numCells];

    /* Create Cell Array */
    vtkCellArray* cells = vtkCellArray::New();

    /* Get the pointer */
    vtkIdType* cells_ptr = cells->WritePointer(
      numCells, numCells * (1 + numPointsPerCell));

    /* xmfConnections: N p1 p2 ... pN */
    /* i.e. Triangles : 3 0 1 2    3 3 4 5   3 6 7 8 */
    vtkIdType index = 0;
    for(vtkIdType cc = 0 ; cc < numCells; cc++ )
      {
      cell_types[cc] = vtk_cell_type;
      *cells_ptr++ = numPointsPerCell;
      for (vtkIdType i = 0 ; i < numPointsPerCell; i++ )
        {
        *cells_ptr++ = xmfConnections[index++];
        }
      }
    ugData->SetCells(cell_types, cells);
    cells->Delete();
    delete [] xmfConnections;
    delete [] cell_types;
    }
  else
    {
    // We have cells with mixed types.
    XdmfInt64 conn_length = xmfGrid->GetTopology()->GetConnectivity()->GetNumberOfElements();
    XdmfInt64* xmfConnections = new XdmfInt64[conn_length];
    xmfConnectivity->GetValues(0, xmfConnections, conn_length);

    vtkIdType numCells = xmfTopology->GetShapeDesc()->GetNumberOfElements();
    int *cell_types = new int[numCells];

    /* Create Cell Array */
    vtkCellArray* cells = vtkCellArray::New();

    /* Get the pointer. Make it Big enough ... too big for now */
    vtkIdType* cells_ptr = cells->WritePointer(numCells, conn_length);

    /* xmfConnections : N p1 p2 ... pN */
    /* i.e. Triangles : 3 0 1 2    3 3 4 5   3 6 7 8 */
    vtkIdType index = 0;
    int sub = 0;
    for(vtkIdType cc = 0 ; cc < numCells; cc++ )
      {
      int vtk_cell_typeI = this->GetVTKCellType(xmfConnections[index++]);
      XdmfInt32 numPointsPerCell =
        this->GetNumberOfPointsPerCell(vtk_cell_typeI);
      if (numPointsPerCell==-1)
        {
        // encountered an unknown cell.
        cells->Delete();
        delete [] cell_types;
        delete [] xmfConnections;
        return NULL;
        }

      if (numPointsPerCell==0)
        {
        // cell type does not have a fixed number of points in which case the
        // next entry in xmfConnections tells us the number of points.
        numPointsPerCell = xmfConnections[index++];
        sub++; // used to shrink the cells array at the end.
        }

      cell_types[cc] = vtk_cell_typeI;
      *cells_ptr++ = numPointsPerCell;
      for(vtkIdType i = 0 ; i < numPointsPerCell; i++ )
        {
        *cells_ptr++ = xmfConnections[index++];
        }
      }
    // Resize the Array to the Proper Size
    cells->GetData()->Resize(index-sub);
    ugData->SetCells(cell_types, cells);
    cells->Delete();
    delete [] cell_types;
    delete [] xmfConnections;
    }

  // Read the geometry.
  vtkPoints* points = this->ReadPoints(xmfGrid->GetGeometry());
  if (!points)
    {
    // failed to read points.
    return NULL;
    }
  ugData->SetPoints(points);
  points->Delete();

  this->ReadAttributes(ugData, xmfGrid);

  // Read ghost cell/point information.
  this->ReadGhostSets(ugData, xmfGrid);

  // If this grid has sets defined on it, then we need to read those as well
  vtkMultiBlockDataSet* sets = this->ReadSets(ugData, xmfGrid);
  if (sets)
    {
    return sets;
    }

  ugData->Register(NULL);
  return ugData;
}

inline bool vtkExtentsAreValid(int exts[6])
{
  return exts[1] >= exts[0] && exts[3] >= exts[2] && exts[5] >= exts[4];
}

inline bool vtkExtentsAreEqual(int *exts1, int *exts2)
{
  if (!exts1 && !exts2)
    {
    return true;
    }
  if (!exts1 || !exts2)
    {
    return false;
    }
  return (exts1[0] == exts2[0] &&
    exts1[1] == exts2[1] &&
    exts1[2] == exts2[2] &&
    exts1[3] == exts2[3] &&
    exts1[4] == exts2[4] &&
    exts1[5] == exts2[5]);
}

//-----------------------------------------------------------------------------
vtkRectilinearGrid* vtkXdmfHeavyData::RequestRectilinearGrid(XdmfGrid* xmfGrid)
{
  vtkSmartPointer<vtkRectilinearGrid> rg =
    vtkSmartPointer<vtkRectilinearGrid>::New();
  int whole_extents[6];
  int update_extents[6];
  this->Domain->GetWholeExtent(xmfGrid, whole_extents);

  if (!vtkExtentsAreValid(this->Extents))
    {
    // if this->Extents are not valid, then simply read the whole image.
    memcpy(update_extents, whole_extents, sizeof(int)*6);
    }
  else
    {
    memcpy(update_extents, this->Extents, sizeof(int)*6);
    }

  // convert to stridden update extents.
  int scaled_extents[6];
  vtkScaleExtents(update_extents, scaled_extents, this->Stride);

  int scaled_dims[3];
  vtkGetDims(scaled_extents, scaled_dims);

  rg->SetExtent(scaled_extents);

  // Now read rectilinear geometry.
  XdmfGeometry* xmfGeometry = xmfGrid->GetGeometry();

  vtkSmartPointer<vtkDoubleArray> xarray =
    vtkSmartPointer<vtkDoubleArray>::New();
  xarray->SetNumberOfTuples(scaled_dims[0]);

  vtkSmartPointer<vtkDoubleArray> yarray =
    vtkSmartPointer<vtkDoubleArray>::New();
  yarray->SetNumberOfTuples(scaled_dims[1]);

  vtkSmartPointer<vtkDoubleArray> zarray =
    vtkSmartPointer<vtkDoubleArray>::New();
  zarray->SetNumberOfTuples(scaled_dims[2]);

  rg->SetXCoordinates(xarray);
  rg->SetYCoordinates(yarray);
  rg->SetZCoordinates(zarray);

  switch (xmfGeometry->GetGeometryType())
    {
  case XDMF_GEOMETRY_ORIGIN_DXDY:
  case XDMF_GEOMETRY_ORIGIN_DXDYDZ:
      {
      XdmfFloat64* origin = xmfGeometry->GetOrigin();
      XdmfFloat64* dxdydz = xmfGeometry->GetDxDyDz();
      for (int cc= scaled_extents[0]; cc <= scaled_extents[1]; cc++)
        {
        xarray->GetPointer(0)[cc - scaled_extents[0]] =
          origin[0] + (dxdydz[0] * cc * this->Stride[0]);
        }
      for (int cc= scaled_extents[2]; cc <= scaled_extents[3]; cc++)
        {
        yarray->GetPointer(0)[cc - scaled_extents[2]] =
          origin[1] + (dxdydz[1] * cc * this->Stride[1]);
        }
      for (int cc= scaled_extents[4]; cc <= scaled_extents[5]; cc++)
        {
        zarray->GetPointer(0)[cc - scaled_extents[4]] =
          origin[2] + (dxdydz[2] * cc * this->Stride[2]);
        }
      }
    break;


  case XDMF_GEOMETRY_VXVY:
      {
      xarray->FillComponent(0, 0);
      xmfGeometry->GetVectorY()->GetValues(update_extents[2],
        yarray->GetPointer(0), scaled_dims[1], this->Stride[1]);
      xmfGeometry->GetVectorX()->GetValues(update_extents[4],
        zarray->GetPointer(0), scaled_dims[2], this->Stride[2]);
      }
    break;

  case XDMF_GEOMETRY_VXVYVZ:
      {
      xmfGeometry->GetVectorX()->GetValues(update_extents[0],
        xarray->GetPointer(0), scaled_dims[0], this->Stride[0]);
      xmfGeometry->GetVectorY()->GetValues(update_extents[2],
        yarray->GetPointer(0), scaled_dims[1], this->Stride[1]);
      xmfGeometry->GetVectorZ()->GetValues(update_extents[4],
        zarray->GetPointer(0), scaled_dims[2], this->Stride[2]);
      }
    break;

  default:
    vtkErrorWithObjectMacro(this->Reader,
      "Geometry type : "
      << xmfGeometry->GetGeometryTypeAsString() << " is not supported for "
      << xmfGrid->GetTopology()->GetTopologyTypeAsString());
    return NULL;
    }

  this->ReadAttributes(rg, xmfGrid, update_extents);
  rg->Register(NULL);
  return rg;
}

//-----------------------------------------------------------------------------
vtkStructuredGrid* vtkXdmfHeavyData::RequestStructuredGrid(XdmfGrid* xmfGrid)
{
  vtkStructuredGrid* sg = vtkStructuredGrid::New();

  int whole_extents[6];
  int update_extents[6];
  this->Domain->GetWholeExtent(xmfGrid, whole_extents);

  if (!vtkExtentsAreValid(this->Extents))
    {
    // if this->Extents are not valid, then simply read the whole image.
    memcpy(update_extents, whole_extents, sizeof(int)*6);
    }
  else
    {
    memcpy(update_extents, this->Extents, sizeof(int)*6);
    }

  int scaled_extents[6];
  vtkScaleExtents(update_extents, scaled_extents, this->Stride);
  sg->SetExtent(scaled_extents);

  vtkPoints* points = this->ReadPoints(xmfGrid->GetGeometry(),
    update_extents, whole_extents);
  sg->SetPoints(points);
  points->Delete();

  this->ReadAttributes(sg, xmfGrid, update_extents);
  return sg;
}

//-----------------------------------------------------------------------------
vtkImageData* vtkXdmfHeavyData::RequestImageData(XdmfGrid* xmfGrid,
  bool use_uniform_grid)
{
  vtkImageData* imageData = use_uniform_grid?
    static_cast<vtkImageData*>(vtkUniformGrid::New()) :
    vtkImageData::New();

  int whole_extents[6];
  this->Domain->GetWholeExtent(xmfGrid, whole_extents);

  int update_extents[6];

  if (!vtkExtentsAreValid(this->Extents))
    {
    // if this->Extents are not valid, then simply read the whole image.
    memcpy(update_extents, whole_extents, sizeof(int)*6);
    }
  else
    {
    memcpy(update_extents, this->Extents, sizeof(int)*6);
    }

  int scaled_extents[6];
  vtkScaleExtents(update_extents, scaled_extents, this->Stride);
  imageData->SetExtent(scaled_extents);

  double origin[3], spacing[3];
  if (!this->Domain->GetOriginAndSpacing(xmfGrid, origin, spacing))
    {
    vtkErrorWithObjectMacro(this->Reader,
      "Could not determine image-data origin and spacing. "
      "Required geometry type is ORIGIN_DXDY or ORIGIN_DXDYDZ. "
      "The specified geometry type is : " <<
      xmfGrid->GetGeometry()->GetGeometryTypeAsString());
    // release image data.
    imageData->Delete();
    return NULL;
    }
  imageData->SetOrigin(origin);
  imageData->SetSpacing(
    spacing[0] * this->Stride[0],
    spacing[1] * this->Stride[1],
    spacing[2] * this->Stride[2]);
  this->ReadAttributes(imageData, xmfGrid, update_extents);
  return imageData;
}

//-----------------------------------------------------------------------------
vtkPoints* vtkXdmfHeavyData::ReadPoints(XdmfGeometry* xmfGeometry,
  int *update_extents /*=NULL*/, int *whole_extents /*=NULL*/)
{
  XdmfInt32 geomType = xmfGeometry->GetGeometryType();

  if (geomType != XDMF_GEOMETRY_X_Y_Z && geomType != XDMF_GEOMETRY_XYZ &&
    geomType != XDMF_GEOMETRY_X_Y && geomType != XDMF_GEOMETRY_XY)
    {
    return NULL;
    }

  XdmfArray* xmfPoints = xmfGeometry->GetPoints();
  if (!xmfPoints)
    {
    XdmfErrorMessage("No Points to Set");
    return NULL;
    }

  vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();

  if (xmfPoints->GetNumberType() == XDMF_FLOAT32_TYPE)
    {
    vtkFloatArray* da = vtkFloatArray::New();
    da->SetNumberOfComponents(3);
    points->SetData(da);
    da->Delete();
    }
  else // means == XDMF_FLOAT64_TYPE
    {
    vtkDoubleArray* da = vtkDoubleArray::New();
    da->SetNumberOfComponents(3);
    points->SetData(da);
    da->Delete();
    }

  XdmfInt64 numGeometryPoints = xmfGeometry->GetNumberOfPoints();
  vtkIdType numPoints = numGeometryPoints;
  bool structured_data = false;
  if (update_extents && whole_extents)
    {
    // we are reading a sub-extent.
    structured_data = true;
    int scaled_extents[6];
    int scaled_dims[3];
    vtkScaleExtents(update_extents, scaled_extents, this->Stride);
    vtkGetDims(scaled_extents, scaled_dims);
    numPoints = (scaled_dims[0] * scaled_dims[1] * scaled_dims[2]);
    }
  points->SetNumberOfPoints(numPoints);

  if (!structured_data)
    {
    // read all the points.
    switch (points->GetData()->GetDataType())
      {
    case VTK_DOUBLE:
      xmfPoints->GetValues(0, reinterpret_cast<double*>(
          points->GetVoidPointer(0)), numPoints*3);
      break;

    case VTK_FLOAT:
      xmfPoints->GetValues(0, reinterpret_cast<float*>(
          points->GetVoidPointer(0)), numPoints*3);
      break;

    default:
      return NULL;
      }
    }
  else
    {
    // treating the points as structured points
    XdmfFloat64* tempPoints = new XdmfFloat64[numGeometryPoints*3];
    xmfPoints->GetValues(0, tempPoints, numGeometryPoints*3);
    vtkIdType pointId=0;
    int xdmf_dims[3];
    vtkGetDims(whole_extents, xdmf_dims);

    for (int z = update_extents[4]; z <= update_extents[5]; z++)
      {
      if ((z-update_extents[4]) % this->Stride[2])
        {
        continue;
        }

      for (int y = update_extents[2]; y <= update_extents[3]; y++)
        {
        if ((y-update_extents[2]) % this->Stride[1])
          {
          continue;
          }

        for (int x = update_extents[0]; x <= update_extents[1]; x++)
          {
          if ((x-update_extents[0]) % this->Stride[0])
            {
            continue;
            }

          int xdmf_index[3] = {x,y,z};
          XdmfInt64 offset = vtkStructuredData::ComputePointId(xdmf_dims, xdmf_index);
          points->SetPoint(pointId, tempPoints[3*offset],
            tempPoints[3*offset+1], tempPoints[3*offset+2]);
          pointId++;
          }
        }
      }
    delete [] tempPoints;
    }

  points->Register(0);
  return points;
}

//-----------------------------------------------------------------------------
bool vtkXdmfHeavyData::ReadAttributes(
  vtkDataSet* dataSet, XdmfGrid* xmfGrid, int* update_extents)
{
  int data_dimensionality = this->Domain->GetDataDimensionality(xmfGrid);

  int numAttributes = xmfGrid->GetNumberOfAttributes();
  for (int cc=0; cc < numAttributes; cc++)
    {
    XdmfAttribute* xmfAttribute = xmfGrid->GetAttribute(cc);
    const char* attrName = xmfAttribute->GetName();
    int attrCenter = xmfAttribute->GetAttributeCenter();
    if (!attrName)
      {
      vtkWarningWithObjectMacro(this->Reader,
        "Skipping unnamed attributes.");
      continue;
      }

    vtkFieldData * fieldData = 0;
    // skip disabled arrays.
    switch (attrCenter)
      {
    case XDMF_ATTRIBUTE_CENTER_GRID:
      fieldData = dataSet->GetFieldData();
      break;

    case XDMF_ATTRIBUTE_CENTER_CELL:
      if (!this->Domain->GetCellArraySelection()->ArrayIsEnabled(attrName))
        {
        continue;
        }
      fieldData = dataSet->GetCellData();
      break;

    case XDMF_ATTRIBUTE_CENTER_NODE:
      if (!this->Domain->GetPointArraySelection()->ArrayIsEnabled(attrName))
        {
        continue;
        }
      fieldData = dataSet->GetPointData();
      break;

    case XDMF_ATTRIBUTE_CENTER_FACE:
    case XDMF_ATTRIBUTE_CENTER_EDGE:
    default:
      vtkWarningWithObjectMacro(this->Reader,
        "Skipping attribute " << attrName << " at " <<
        xmfAttribute->GetAttributeCenterAsString());
      continue; // unhandled.
      }

    vtkDataArray* array = this->ReadAttribute(xmfAttribute,
      data_dimensionality, update_extents);
    if (array)
      {
      array->SetName(attrName);
      fieldData->AddArray(array);
      bool is_active = xmfAttribute->GetActive() != 0;
      vtkDataSetAttributes* attributes =
        vtkDataSetAttributes::SafeDownCast(fieldData);
      if (attributes)
        {
        // make attribute active.
        switch (xmfAttribute->GetAttributeType())
          {
        case XDMF_ATTRIBUTE_TYPE_SCALAR:
          if (is_active || attributes->GetScalars() == NULL)
            {
            attributes->SetActiveScalars(attrName);
            }
          break;

        case XDMF_ATTRIBUTE_TYPE_VECTOR:
          if (is_active || attributes->GetVectors() == NULL)
            {
            attributes->SetActiveVectors(attrName);
            }
          break;

        case XDMF_ATTRIBUTE_TYPE_TENSOR:
        case XDMF_ATTRIBUTE_TYPE_TENSOR6:
          if (is_active || attributes->GetTensors() == NULL)
            {
            attributes->SetActiveTensors(attrName);
            }
          break;

        case XDMF_ATTRIBUTE_TYPE_GLOBALID:
          if (is_active || attributes->GetGlobalIds() == NULL)
            {
            attributes->SetActiveGlobalIds(attrName);
            }
          }
        }
      array->Delete();
      }
    }
  return true;
}

// used to convert a symmetric tensor to a regular tensor.
template <class T>
void vtkConvertTensor6(T* source, T* dest, vtkIdType numTensors)
{
  for (vtkIdType cc=0; cc < numTensors; cc++)
    {
    dest[cc*9 + 0] = source[cc*6 + 0];
    dest[cc*9 + 1] = source[cc*6 + 1];
    dest[cc*9 + 2] = source[cc*6 + 2];

    dest[cc*9 + 3] = source[cc*6 + 1];
    dest[cc*9 + 4] = source[cc*6 + 3];
    dest[cc*9 + 5] = source[cc*6 + 4];

    dest[cc*9 + 6] = source[cc*6 + 2];
    dest[cc*9 + 7] = source[cc*6 + 4];
    dest[cc*9 + 8] = source[cc*6 + 5];
    }
}

//-----------------------------------------------------------------------------
vtkDataArray* vtkXdmfHeavyData::ReadAttribute(XdmfAttribute* xmfAttribute,
  int data_dimensionality, int* update_extents/*=0*/)
{
  if (!xmfAttribute)
    {
    return NULL;
    }

  int attrType = xmfAttribute->GetAttributeType();
  int attrCenter = xmfAttribute->GetAttributeCenter();
  int numComponents = 1;

  switch (attrType)
    {
  case XDMF_ATTRIBUTE_TYPE_TENSOR :
    numComponents = 9;
    break;
  case XDMF_ATTRIBUTE_TYPE_TENSOR6:
    numComponents = 6;
    break;
  case XDMF_ATTRIBUTE_TYPE_VECTOR:
    numComponents = 3;
    break;
  default :
    numComponents = 1;
    break;
    }

  XdmfDataItem xmfDataItem;
  xmfDataItem.SetDOM(xmfAttribute->GetDOM());
  xmfDataItem.SetElement(xmfAttribute->GetDOM()->FindDataElement(0,
      xmfAttribute->GetElement()));
  xmfDataItem.UpdateInformation();

  XdmfInt64 data_dims[XDMF_MAX_DIMENSION];
  int data_rank = xmfDataItem.GetDataDesc()->GetShape(data_dims);

  if (update_extents && attrCenter != XDMF_ATTRIBUTE_CENTER_GRID)
    {
    // for hyperslab selection to work, the data shape must match the topology
    // shape.
    if (data_rank < 0)
      {
      vtkErrorWithObjectMacro(this->Reader,
        "Unsupported attribute rank: " << data_rank);
      return NULL;
      }
    if (data_rank > (data_dimensionality + 1))
      {
      vtkErrorWithObjectMacro(this->Reader,
        "The data_dimensionality and topology dimensionality mismatch");
      return NULL;
      }
    XdmfInt64 start[4] = { update_extents[4], update_extents[2], update_extents[0], 0 };
    XdmfInt64 stride[4] = {this->Stride[2], this->Stride[1], this->Stride[0], 1};
    XdmfInt64 count[4] = {0, 0, 0, 0};
    int scaled_dims[3];
    int scaled_extents[6];
    vtkScaleExtents(update_extents, scaled_extents, this->Stride);
    vtkGetDims(scaled_extents, scaled_dims);
    count[0] = (scaled_dims[2]-1);
    count[1] = (scaled_dims[1]-1);
    count[2] = (scaled_dims[0]-1);
    if (data_rank == (data_dimensionality+1))
      {
      // this refers the number of components in the attribute.
      count[data_dimensionality] = data_dims[data_dimensionality];
      }

    if (attrCenter == XDMF_ATTRIBUTE_CENTER_NODE)
      {
      // Point count is 1 + cell extent if not a single layer
      count[0] += (update_extents[5] - update_extents[4] > 0)? 1 : 1;
      count[1] += (update_extents[3] - update_extents[2] > 0)? 1 : 1;
      count[2] += (update_extents[1] - update_extents[0] > 0)? 1 : 1;
      }
    xmfDataItem.GetDataDesc()->SelectHyperSlab(start, stride, count);
    }

  if (xmfDataItem.Update()==XDMF_FAIL)
    {
    vtkErrorWithObjectMacro(this->Reader, "Failed to read attribute data");
    return 0;
    }

  vtkXdmfDataArray* xmfConvertor = vtkXdmfDataArray::New();
  vtkDataArray* dataArray = xmfConvertor->FromXdmfArray(
    xmfDataItem.GetArray()->GetTagName(), 1, data_rank, numComponents, 0);
  xmfConvertor->Delete();

  if (attrType == XDMF_ATTRIBUTE_TYPE_TENSOR6)
    {
    // convert Tensor6 to Tensor.
    vtkDataArray* tensor = dataArray->NewInstance();
    vtkIdType numTensors = dataArray->GetNumberOfTuples();
    tensor->SetNumberOfComponents(9);
    tensor->SetNumberOfTuples(numTensors);

    // Copy Symmetrical Tensor Values to Correct Positions in 3x3 matrix
    void* source = dataArray->GetVoidPointer(0);
    void* dest = tensor->GetVoidPointer(0);
    switch (tensor->GetDataType())
      {
      vtkTemplateMacro(
        vtkConvertTensor6(reinterpret_cast<VTK_TT*>(source),
          reinterpret_cast<VTK_TT*>(dest), numTensors)
      );
      }
    dataArray->Delete();
    return tensor;
    }
  return dataArray;
}

//-----------------------------------------------------------------------------
// Read ghost cell/point information. This is simply loaded info a
// vtkGhostType attribute array.
bool vtkXdmfHeavyData::ReadGhostSets(vtkDataSet* dataSet, XdmfGrid* xmfGrid,
  int *vtkNotUsed(update_extents)/*=0*/)
{
  //int data_dimensionality = this->Domain->GetDataDimensionality(xmfGrid);
  for (int cc=0; cc < xmfGrid->GetNumberOfSets(); cc++)
    {
    XdmfSet *xmfSet = xmfGrid->GetSets(cc);
    int ghost_value = xmfSet->GetGhost();
    if (ghost_value <= 0)
      {
      // not a ghost-set, simply continue.
      continue;
      }
    XdmfInt32 setCenter = xmfSet->GetSetType();
    vtkIdType numElems = 0;
    vtkDataSetAttributes* dsa = 0;
    unsigned char ghostFlag = 0;
    switch (setCenter)
      {
    case XDMF_SET_TYPE_NODE:
      dsa = dataSet->GetPointData();
      numElems = dataSet->GetNumberOfPoints();
      ghostFlag = vtkDataSetAttributes::DUPLICATEPOINT;
      break;

    case XDMF_SET_TYPE_CELL:
      dsa = dataSet->GetCellData();
      numElems = dataSet->GetNumberOfCells();
      ghostFlag = vtkDataSetAttributes::DUPLICATECELL;
      break;

    default:
      vtkWarningWithObjectMacro(this->Reader,
        "Only ghost-cells and ghost-nodes are currently supported.");
      continue;
      }

    vtkUnsignedCharArray* ghosts = vtkUnsignedCharArray::SafeDownCast(
      dsa->GetArray(vtkDataSetAttributes::GhostArrayName()));
    if (!ghosts)
      {
      ghosts = vtkUnsignedCharArray::New();
      ghosts->SetName(vtkDataSetAttributes::GhostArrayName());
      ghosts->SetNumberOfComponents(1);
      ghosts->SetNumberOfTuples(numElems);
      ghosts->FillComponent(0, 0);
      dsa->AddArray(ghosts);
      ghosts->Delete();
      }

    unsigned char* ptrGhosts = ghosts->GetPointer(0);

    // Read heavy data. We cannot do anything smart if update_extents or stride
    // is specified here. We have to read the entire set and then prune it.
    xmfSet->Update();

    XdmfArray* xmfIds = xmfSet->GetIds();
    XdmfInt64 numIds = xmfIds->GetNumberOfElements();
    XdmfInt64 *ids = new XdmfInt64[numIds+1];
    xmfIds->GetValues(0, ids, numIds);

    // release the heavy data that was read.
    xmfSet->Release();

    for (vtkIdType kk=0; kk < numIds; kk++)
      {
      if (ids[kk] < 0 || ids[kk] > numElems)
        {
        vtkWarningWithObjectMacro(this->Reader,
          "No such cell or point exists: " << ids[kk]);
        continue;
        }
      ptrGhosts[ids[kk]] = ghostFlag;
      }
    delete []ids;
    }
  return true;
}


//-----------------------------------------------------------------------------
vtkMultiBlockDataSet* vtkXdmfHeavyData::ReadSets(
  vtkDataSet* dataSet, XdmfGrid* xmfGrid, int *vtkNotUsed(update_extents)/*=0*/)
{
  unsigned int number_of_sets = 0;
  for (int cc=0; cc < xmfGrid->GetNumberOfSets(); cc++)
    {
    XdmfSet *xmfSet = xmfGrid->GetSets(cc);
    int ghost_value = xmfSet->GetGhost();
    if (ghost_value != 0)
      {
      // skip ghost-sets.
      continue;
      }
    number_of_sets++;
    }
  if (number_of_sets == 0)
    {
    return NULL;
    }

  vtkMultiBlockDataSet* mb = vtkMultiBlockDataSet::New();
  mb->SetNumberOfBlocks(1+number_of_sets);
  mb->SetBlock(0, dataSet);
  mb->GetMetaData(static_cast<unsigned int>(0))->Set(vtkCompositeDataSet::NAME(), "Data");

  unsigned int current_set_index = 1;
  for (int cc=0; cc < xmfGrid->GetNumberOfSets(); cc++)
    {
    XdmfSet *xmfSet = xmfGrid->GetSets(cc);
    int ghost_value = xmfSet->GetGhost();
    if (ghost_value != 0)
      {
      // skip ghost-sets.
      continue;
      }

    const char* setName = xmfSet->GetName();
    mb->GetMetaData(current_set_index)->Set(vtkCompositeDataSet::NAME(),
      setName);
    if (!this->Domain->GetSetsSelection()->ArrayIsEnabled(setName))
      {
      continue;
      }

    // Okay now we have an enabled set. Create a new dataset for it
    vtkDataSet* set = 0;

    XdmfInt32 setType = xmfSet->GetSetType();
    switch (setType)
      {
    case XDMF_SET_TYPE_NODE:
      set = this->ExtractPoints(xmfSet, dataSet);
      break;

    case XDMF_SET_TYPE_CELL:
      set = this->ExtractCells(xmfSet, dataSet);
      break;

    case XDMF_SET_TYPE_FACE:
      set = this->ExtractFaces(xmfSet, dataSet);
      break;

    case XDMF_SET_TYPE_EDGE:
      set = this->ExtractEdges(xmfSet, dataSet);
      break;
      }

    if (set)
      {
      mb->SetBlock(current_set_index, set);
      set->Delete();
      }
    current_set_index++;
    }
  return mb;
}

//-----------------------------------------------------------------------------
vtkDataSet* vtkXdmfHeavyData::ExtractPoints(XdmfSet* xmfSet,
  vtkDataSet* dataSet)
{
  // TODO: How to handle structured datasets with update_extents/strides etc.
  // Do they too always produce vtkUniformGrid or do we want to produce
  // structured dataset

  // Read heavy data. We cannot do anything smart if update_extents or stride
  // is specified here. We have to read the entire set and then prune it.
  xmfSet->Update();

  XdmfArray* xmfIds = xmfSet->GetIds();
  XdmfInt64 numIds = xmfIds->GetNumberOfElements();
  XdmfInt64 *ids = new XdmfInt64[numIds+1];
  xmfIds->GetValues(0, ids, numIds);

  // release heavy data.
  xmfSet->Release();

  vtkUnstructuredGrid* output = vtkUnstructuredGrid::New();
  vtkPoints* outputPoints = vtkPoints::New();
  outputPoints->SetNumberOfPoints(numIds);
  output->SetPoints(outputPoints);
  outputPoints->Delete();

  vtkIdType numInPoints = dataSet->GetNumberOfPoints();
  for (vtkIdType kk=0; kk < numIds; kk++)
    {
    if (ids[kk] < 0 || ids[kk] > numInPoints)
      {
      vtkWarningWithObjectMacro(this->Reader,
        "No such cell or point exists: " << ids[kk]);
      continue;
      }
    double point_location[3];
    dataSet->GetPoint(ids[kk], point_location);
    outputPoints->SetPoint(kk, point_location);
    }
  delete []ids;
  ids = NULL;

  // Read node-centered attributes that may be defined on this set.
  int numAttributes = xmfSet->GetNumberOfAttributes();
  for (int cc=0; cc < numAttributes; cc++)
    {
    XdmfAttribute* xmfAttribute = xmfSet->GetAttribute(cc);
    const char* attrName = xmfAttribute->GetName();
    int attrCenter = xmfAttribute->GetAttributeCenter();
    if (attrCenter != XDMF_ATTRIBUTE_CENTER_NODE)
      {
      continue;
      }
    vtkDataArray* array = this->ReadAttribute(xmfAttribute,
      1, NULL);
    if (array)
      {
      array->SetName(attrName);
      output->GetPointData()->AddArray(array);
      array->Delete();
      }
    }

  vtkIdType *vtk_cell_ids = new vtkIdType[numIds];
  for (vtkIdType cc=0; cc < numIds; cc++)
    {
    vtk_cell_ids[cc] = cc;
    }
  output->InsertNextCell(VTK_POLY_VERTEX, numIds, vtk_cell_ids);
  delete []vtk_cell_ids;
  vtk_cell_ids = NULL;

  return output;
}

//-----------------------------------------------------------------------------
vtkDataSet* vtkXdmfHeavyData::ExtractCells(XdmfSet* xmfSet,
  vtkDataSet* dataSet)
{
  // TODO: How to handle structured datasets with update_extents/strides etc.
  // Do they too always produce vtkUniformGrid or do we want to produce
  // structured dataset

  // Read heavy data.
  xmfSet->Update();

  XdmfArray* xmfIds = xmfSet->GetIds();
  XdmfInt64 numIds = xmfIds->GetNumberOfElements();

  vtkIdTypeArray* ids = vtkIdTypeArray::New();
  ids->SetNumberOfComponents(1);
  ids->SetNumberOfTuples(numIds);
  xmfIds->GetValues(0, ids->GetPointer(0), numIds);

  // release heavy data.
  xmfSet->Release();

  // We directly use vtkExtractSelectedIds for extract cells since the logic to
  // extract cells it no trivial (like extracting points).
  vtkSelectionNode* selNode = vtkSelectionNode::New();
  selNode->SetContentType(vtkSelectionNode::INDICES);
  selNode->SetFieldType(vtkSelectionNode::CELL);
  selNode->SetSelectionList(ids);

  vtkSelection* sel = vtkSelection::New();
  sel->AddNode(selNode);
  selNode->Delete();

  vtkExtractSelectedIds* extractCells = vtkExtractSelectedIds::New();
  extractCells->SetInputData(0, dataSet);
  extractCells->SetInputData(1, sel);
  extractCells->Update();

  vtkDataSet* output = vtkDataSet::SafeDownCast(
    extractCells->GetOutput()->NewInstance());
  output->CopyStructure(vtkDataSet::SafeDownCast(extractCells->GetOutput()));

  sel->Delete();
  extractCells->Delete();
  ids->Delete();

  // Read cell-centered attributes that may be defined on this set.
  int numAttributes = xmfSet->GetNumberOfAttributes();
  for (int cc=0; cc < numAttributes; cc++)
    {
    XdmfAttribute* xmfAttribute = xmfSet->GetAttribute(cc);
    const char* attrName = xmfAttribute->GetName();
    int attrCenter = xmfAttribute->GetAttributeCenter();
    if (attrCenter != XDMF_ATTRIBUTE_CENTER_CELL)
      {
      continue;
      }
    vtkDataArray* array = this->ReadAttribute(xmfAttribute, 1, NULL);
    if (array)
      {
      array->SetName(attrName);
      output->GetCellData()->AddArray(array);
      array->Delete();
      }
    }

  return output;
}

//-----------------------------------------------------------------------------
vtkDataSet* vtkXdmfHeavyData::ExtractFaces(XdmfSet* xmfSet, vtkDataSet* dataSet)
{
  xmfSet->Update();

  XdmfArray* xmfIds = xmfSet->GetIds();
  XdmfArray* xmfCellIds = xmfSet->GetCellIds();

  XdmfInt64 numFaces = xmfIds->GetNumberOfElements();

  // ids is a 2 component array were each tuple is (cell-id, face-id).
  vtkIdTypeArray* ids = vtkIdTypeArray::New();
  ids->SetNumberOfComponents(2);
  ids->SetNumberOfTuples(numFaces);
  xmfCellIds->GetValues(0, ids->GetPointer(0), numFaces, 1, 2);
  xmfIds->GetValues(0, ids->GetPointer(1), numFaces, 1, 2);

  vtkPolyData* output = vtkPolyData::New();
  vtkCellArray* polys = vtkCellArray::New();
  output->SetPolys(polys);
  polys->Delete();

  vtkPoints* outPoints = vtkPoints::New();
  output->SetPoints(outPoints);
  outPoints->Delete();

  vtkMergePoints* mergePoints = vtkMergePoints::New();
  mergePoints->InitPointInsertion(outPoints,
    dataSet->GetBounds());

  for (vtkIdType cc=0; cc < numFaces; cc++)
    {
    vtkIdType cellId = ids->GetValue(cc*2);
    vtkIdType faceId = ids->GetValue(cc*2+1);
    vtkCell* cell = dataSet->GetCell(cellId);
    if (!cell)
      {
      vtkWarningWithObjectMacro(
        this->Reader, "Invalid cellId: " << cellId)
      continue;
      }
    vtkCell* face = cell->GetFace(faceId);
    if (!face)
      {
      vtkWarningWithObjectMacro(this->Reader,
        "Invalid faceId " << faceId << " on cell " << cellId);
      continue;
      }

    // Now insert this face a new cell in the output dataset.
    vtkIdType numPoints = face->GetNumberOfPoints();
    vtkPoints* facePoints = face->GetPoints();
    vtkIdType* outputPts = new vtkIdType[numPoints+1];
    for (vtkIdType kk=0; kk < numPoints; kk++)
      {
      mergePoints->InsertUniquePoint(
        facePoints->GetPoint(kk), outputPts[kk]);
      }
    polys->InsertNextCell(numPoints, outputPts);
    delete [] outputPts;
    }

  ids->Delete();
  xmfSet->Release();
  mergePoints->Delete();

  // Read face-centered attributes that may be defined on this set.
  int numAttributes = xmfSet->GetNumberOfAttributes();
  for (int cc=0; cc < numAttributes; cc++)
    {
    XdmfAttribute* xmfAttribute = xmfSet->GetAttribute(cc);
    const char* attrName = xmfAttribute->GetName();
    int attrCenter = xmfAttribute->GetAttributeCenter();
    if (attrCenter != XDMF_ATTRIBUTE_CENTER_FACE)
      {
      continue;
      }
    vtkDataArray* array = this->ReadAttribute(xmfAttribute, 1, NULL);
    if (array)
      {
      array->SetName(attrName);
      output->GetCellData()->AddArray(array);
      array->Delete();
      }
    }

  return output;
}

//-----------------------------------------------------------------------------
vtkDataSet* vtkXdmfHeavyData::ExtractEdges(XdmfSet* xmfSet, vtkDataSet* dataSet)
{
  xmfSet->Update();

  XdmfArray* xmfIds = xmfSet->GetIds();
  XdmfArray* xmfCellIds = xmfSet->GetCellIds();
  XdmfArray* xmfFaceIds = xmfSet->GetFaceIds();

  XdmfInt64 numEdges = xmfIds->GetNumberOfElements();

  // ids is a 3 component array were each tuple is (cell-id, face-id, edge-id).
  vtkIdTypeArray* ids = vtkIdTypeArray::New();
  ids->SetNumberOfComponents(3);
  ids->SetNumberOfTuples(numEdges);
  xmfCellIds->GetValues(0, ids->GetPointer(0), numEdges, 1, 3);
  xmfFaceIds->GetValues(0, ids->GetPointer(1), numEdges, 1, 3);
  xmfIds->GetValues(0, ids->GetPointer(2), numEdges, 1, 3);

  vtkPolyData* output = vtkPolyData::New();
  vtkCellArray* lines = vtkCellArray::New();
  output->SetLines(lines);
  lines->Delete();

  vtkPoints* outPoints = vtkPoints::New();
  output->SetPoints(outPoints);
  outPoints->Delete();

  vtkMergePoints* mergePoints = vtkMergePoints::New();
  mergePoints->InitPointInsertion(outPoints,
    dataSet->GetBounds());

  for (vtkIdType cc=0; cc < numEdges; cc++)
    {
    vtkIdType cellId = ids->GetValue(cc*3);
    vtkIdType faceId = ids->GetValue(cc*3+1);
    vtkIdType edgeId = ids->GetValue(cc*3+2);
    vtkCell* cell = dataSet->GetCell(cellId);
    if (!cell)
      {
      vtkWarningWithObjectMacro(this->Reader,
        "Invalid cellId: " << cellId);
      continue;
      }
    vtkCell* face = cell->GetFace(faceId);
    if (!face)
      {
      vtkWarningWithObjectMacro(this->Reader,
        "Invalid faceId " << faceId << " on cell " << cellId);
      continue;
      }
    vtkCell* edge = cell->GetEdge(edgeId);
    if (!edge)
      {
      vtkWarningWithObjectMacro(this->Reader,
        "Invalid edgeId " << edgeId << " on face "
        << faceId << " on cell " << cellId);
      continue;
      }

    // Now insert this edge as a new cell in the output dataset.
    vtkIdType numPoints = edge->GetNumberOfPoints();
    vtkPoints* edgePoints = edge->GetPoints();
    vtkIdType* outputPts = new vtkIdType[numPoints+1];
    for (vtkIdType kk=0; kk < numPoints; kk++)
      {
      mergePoints->InsertUniquePoint(
        edgePoints->GetPoint(kk), outputPts[kk]);
      }
    lines->InsertNextCell(numPoints, outputPts);
    delete [] outputPts;
    }

  ids->Delete();
  xmfSet->Release();
  mergePoints->Delete();

  // Read edge-centered attributes that may be defined on this set.
  int numAttributes = xmfSet->GetNumberOfAttributes();
  for (int cc=0; cc < numAttributes; cc++)
    {
    XdmfAttribute* xmfAttribute = xmfSet->GetAttribute(cc);
    const char* attrName = xmfAttribute->GetName();
    int attrCenter = xmfAttribute->GetAttributeCenter();
    if (attrCenter != XDMF_ATTRIBUTE_CENTER_EDGE)
      {
      continue;
      }
    vtkDataArray* array = this->ReadAttribute(xmfAttribute, 1, NULL);
    if (array)
      {
      array->SetName(attrName);
      output->GetCellData()->AddArray(array);
      array->Delete();
      }
    }

  return output;
}
