HDF5DealWriter Class Reference

#include <hdf5dealwriter.h>

Inheritance diagram for HDF5DealWriter:

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Collaboration diagram for HDF5DealWriter:

[legend]

List of all members.

Public Member Functions
void	writeTriangulation (string triaName, Triangulation< 2 > &tria)
void	writeScalarField_ (const VecDouble &vec, std::string fieldName, std::string triaId="")
void	writeTriangulation (string triaName, Triangulation< 3 > &tria)
Static Public Member Functions
static HDF5DealWriter &	getHDF5DealWriter ()
Protected Member Functions
	HDF5DealWriter ()
	~HDF5DealWriter ()
void	registerTriangulation (string triaId, Triangulation< 3 > &tria)
void	registerTriangulation (string triaId, Triangulation< 2 > &tria)
void	sortVerticesValuesToStructuredGrid (Triangulation< 3 > &tria, const VecDouble &vOrig, VecDouble &vDest)
Static Protected Attributes
static HDF5DealWriter *	ptr = NULL

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Detailed Description

This is the class to output data in hdf5 format. HDF5 was created by the HDF group and is designed to store cientific data in one large file or multiple files. It gives a hierarchal structural of datasets very similar to directories and the database can be constructed with contributions of many concurrent processes and in fact it was designed with this objective in mind. To use this class you first specify one or more dealII triangulations that describe the mesh. The triangulations are referenced by a name that you give to the triangulation when you write it in the hdf5 file using the method writeTriangulation. Then we write the scalars values associated with the mesh's cells or vertices using the writeScalarField method. We can define attributes values using the mother class (DealWriter) methods. Attributes have a name and a value that is always a string. Every time we write a scalar field using the writeScalarField we create a DataSet and then write on the hdf5 file with all the attributes defined by the user using the methods DealWriter::setVariable since in HDF5 forma each DataSet can have one or more attributes. This class is a Singleton, to have a reference of it, use the method getHDF5DealWriter()

Definition at line 26 of file hdf5dealwriter.h.

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Constructor & Destructor Documentation

HDF5DealWriter::HDF5DealWriter

(

)

[protected]

Definition at line 10 of file hdf5dealwriter.cpp.

{
}

HDF5DealWriter::~HDF5DealWriter

(

)

[protected]

Definition at line 344 of file hdf5dealwriter.cpp.

{

}

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Member Function Documentation

HDF5DealWriter & HDF5DealWriter::getHDF5DealWriter

(

)

[static]

Definition at line 237 of file hdf5dealwriter.cpp.

{
   if (ptr == NULL)
     ptr = new HDF5DealWriter();
   return *ptr;
}

void HDF5DealWriter::registerTriangulation	(	string	triaId,
		Triangulation< 2 > &	tria
	)			[protected]

Register a triangulation

Parameters:

	triaId	Name of the new triangulation
	tria	The deal triangulation object

Definition at line 334 of file hdf5dealwriter.cpp.

{
  struct TriaInformation inf(tria.n_vertices(),tria.n_active_cells());
  appendMeshInfo(triaId,inf);

}

void HDF5DealWriter::registerTriangulation	(	string	triaId,
		Triangulation< 3 > &	tria
	)			[protected]

Register a triangulation

Parameters:

	triaId	Name of the new triangulation
	tria	The deal triangulation object

Definition at line 321 of file hdf5dealwriter.cpp.

{
  struct TriaInformation inf(tria.n_vertices(),tria.n_active_cells());
  appendMeshInfo(triaId,inf);


}

void HDF5DealWriter::sortVerticesValuesToStructuredGrid	(	Triangulation< 3 > &	tria,
		const VecDouble &	vOrig,
		VecDouble &	vDest
	)			[protected]

This function get a vector vOrig containing scalar values at vertices wich are indexed by the vertices numbers defined in a triangulation tria and change the order of the scalar values storing them at the vector vDes. In this new vector the indices of the vertices are changed such that the first vertice is at the bottom lower left corner of the mesh and the others are numbered growing in the X,Y,Z axis in that order.

Parameters:

	tria	Original triangulation
	vOrig	Vector containing scalar values indexed by the vertices numbering scheme defined in the triangulation.
	vDest	Vector to contain the permuted scalar values of the vOrig vector.

Returns:

Definition at line 363 of file hdf5dealwriter.cpp.

{
  assert(tria.n_vertices() == vOrig.size());
  assert(vDest.size() == vOrig.size());
  

  Triangulation<3>::active_cell_iterator cellX,cellY,cellZ = tria.begin_active();
  //Walk first in X direction
  unsigned i=0;
  while (1)
  {
    cellY = cellZ;
    while(1)
    {
      //Run in X
      cellX = cellY;
      while(1)
      {
        vDest(i++)=vOrig(cellX->vertex_index(VERTEX_000));
        if (cellX->neighbor_index(RIGHT_CELL) == DealBase::INVALID_INDEX)
        {
          vDest(i++)=vOrig(cellX->vertex_index(VERTEX_100));
          break;
        }
        else
          cellX = cellX->neighbor(RIGHT_CELL);
      }
      if (cellY->neighbor_index(BACK_CELL) == DealBase::INVALID_INDEX)
      {
        cellX = cellY;
        while(1)
        {
          vDest(i++)=vOrig(cellX->vertex_index(VERTEX_010));
          if (cellX->neighbor_index(RIGHT_CELL) == DealBase::INVALID_INDEX)
          {
            vDest(i++)=vOrig(cellX->vertex_index(VERTEX_110));
            break;
          }
          else
            cellX = cellX->neighbor(RIGHT_CELL);
        }
        break;
      }
      else
        cellY=cellY->neighbor(BACK_CELL);
    }
    if (cellZ->neighbor_index(UP_CELL) == DealBase::INVALID_INDEX)
    {
      cellY = cellZ;
      while(1)
      {
        //Run in X
        cellX = cellY;
        while(1)
        {
          vDest(i++)=vOrig(cellX->vertex_index(VERTEX_001));
          if (cellX->neighbor_index(RIGHT_CELL) == DealBase::INVALID_INDEX)
          {
            vDest(i++)=vOrig(cellX->vertex_index(VERTEX_101));
            break;
          }
          else
            cellX = cellX->neighbor(RIGHT_CELL);
        }
        if (cellY->neighbor_index(BACK_CELL) == DealBase::INVALID_INDEX)
        {
          cellX = cellY;
          while(1)
          {
            vDest(i++)=vOrig(cellX->vertex_index(VERTEX_011));
            if (cellX->neighbor_index(RIGHT_CELL) == DealBase::INVALID_INDEX)
            {
              vDest(i++)=vOrig(cellX->vertex_index(VERTEX_111));
              break;
            }
            else
              cellX = cellX->neighbor(RIGHT_CELL);
          }
          break;
        }
        else
          cellY=cellY->neighbor(BACK_CELL);
      }
      break;
    }
    else
    {
      cellZ = cellZ->neighbor(UP_CELL);
    }
    
  }
}

void HDF5DealWriter::writeScalarField_	(	const VecDouble &	vec,
		std::string	fieldName,
		std::string	triaId = ""
	)

Write the scalar values associated with the vertices or cells of a triangulation. Given the name of a field, this method creates a dataset having the path /DataSets/<field name>="">/<field name>="">_0. If we call the method again using the the same name, it will create the dataset /DataSets/<field name>="">/<field name>="">_1 and so on.

Parameters:

	vec	The vector containing the scalar values at the vertices
	fieldName	The name of the field.
	triaId	The name of the triangulation, if none is specified, the last triangulation registered using the method writeTriangulation is used.

Definition at line 254 of file hdf5dealwriter.cpp.

{
 if (triaId == "")
 {
   triaId = this->getNameOfLastRegisteredTriangulation();
 }
  
    
  validateField(triaId,fieldName);
  assert(getFile() != -1);
  assert(getTriaInformation(triaId).n_vertices == vec.size() ||
         getTriaInformation(triaId).n_cells == vec.size());

  char str[2000];
  //Validation of the parameters.
  
  //Now get the counter of this field and increment it. 
  unsigned refCount = getFieldCount(fieldName);
  if (refCount == 0)
  {
     //This field is new, create a directory entry for the field name and initialize the counter
    sprintf(str,"/DataSets/%s",fieldName.c_str());
    H5Gclose(H5Gcreate1(getFile(),str,0));    
  }
    
    
    
    
  
  //Now write the dataset.
  //Create the dataset
  hsize_t dim[]={vec.size()};
  hid_t dataspace = H5Screate_simple(1,dim,NULL);
  hid_t datatype  = H5Tcopy(H5T_NATIVE_DOUBLE);
  H5Tset_order(datatype,H5T_ORDER_LE);
  sprintf(str,"/DataSets/%s/%s_%d",fieldName.c_str(),fieldName.c_str(),getFieldCount(fieldName));
  hid_t dataset = H5Dcreate1(getFile(), str, datatype, dataspace, H5P_DEFAULT);

  //Copy the data.
  H5Dwrite(dataset,H5T_NATIVE_DOUBLE,H5S_ALL,H5S_ALL,H5P_DEFAULT, vec.begin());
  
  //Set attributes
  H5LTset_attribute_string(getFile(),str,"Triangulation",triaId.c_str());
  this->writeContextVariables(str);

  //Close the resources.3
  H5Sclose(dataspace);
  H5Tclose(datatype);
  H5Dclose(dataset);

  //Increment the field count
  incFieldCount(fieldName);

}

void HDF5DealWriter::writeTriangulation	(	string	triaName,
		Triangulation< 3 > &	tria
	)

Definition at line 107 of file hdf5dealwriter.cpp.

{
  assert(getFile() != -1);
  double buff[HDF5_BUFF_SIZE][3];
  int buff_int[HDF5_BUFF_SIZE][8];
  
  this->registerTriangulation(triaName,tria);
  
  //Criar Grupo
  char strPath[500];
  sprintf(strPath,"/Triangulations/%s",triaName.c_str());
  hid_t triaGroup=H5Gcreate1(getFile(),strPath,0);

  H5LTset_attribute_string(getFile(),strPath,"Type","GRID_3D");

  
  
  hsize_t dim[]={tria.n_vertices(),3};
  hid_t dataspace = H5Screate_simple(2,dim,NULL);
  hid_t datatype  = H5Tcopy(H5T_NATIVE_DOUBLE);
  H5Tset_order(datatype,H5T_ORDER_LE);
  hid_t dataset = H5Dcreate1(triaGroup, "vertices", datatype, dataspace, H5P_DEFAULT);

  int nSteps = tria.n_vertices()/HDF5_BUFF_SIZE;
  hsize_t count[]={HDF5_BUFF_SIZE,3};
  hsize_t offset[]={0,0};
  unsigned k=0;
  for (int i=0;i<=nSteps;i++)
  {
    int MaxJ = (i==nSteps) ? (tria.n_vertices() % HDF5_BUFF_SIZE) : HDF5_BUFF_SIZE;
    count[0]=MaxJ;
    for (int j=0;j<MaxJ;j++)
    {
      buff[j][0]= tria.get_vertices()[k](0);
      buff[j][1]= tria.get_vertices()[k](1);
      buff[j][2]= tria.get_vertices()[k](2);
      k++;
    }
    writeInChunks(dataset,offset,count,buff);
    offset[0]+=MaxJ;
  }
  H5Sclose(dataspace);
  H5Tclose(datatype);
  H5Dclose(dataset);

  dim[0]=tria.n_active_cells();
  dim[1]=8;
  dataspace = H5Screate_simple(2,dim,NULL);
  datatype  = H5Tcopy(H5T_NATIVE_INT);
  H5Tset_order(datatype,H5T_ORDER_LE);
  dataset = H5Dcreate1(triaGroup, "connections", datatype, dataspace, H5P_DEFAULT);


  nSteps = tria.n_active_cells()/HDF5_BUFF_SIZE;
  count[1]=8;
  offset[0]=0;
  Triangulation<3>::active_cell_iterator cell = tria.begin_active(),
                                         endc = tria.end();

  for (int i=0;i<=nSteps;i++)
  {
    int MaxJ = (i==nSteps) ? (tria.n_active_cells() % HDF5_BUFF_SIZE) : HDF5_BUFF_SIZE;
    count[0]=MaxJ;
    //Write the cell points conectivity. The order of the cell vertex
    //is like vtkVOXEL 
    for (int j=0;j<MaxJ;j++)
    {
      buff_int[j][0]= cell->vertex_index(VERTEX_000);
      buff_int[j][1]= cell->vertex_index(VERTEX_100);
      buff_int[j][2]= cell->vertex_index(VERTEX_010);
      buff_int[j][3]= cell->vertex_index(VERTEX_110);
      buff_int[j][4]= cell->vertex_index(VERTEX_001);
      buff_int[j][5]= cell->vertex_index(VERTEX_101);
      buff_int[j][6]= cell->vertex_index(VERTEX_011);
      buff_int[j][7]= cell->vertex_index(VERTEX_111);
      cell++;
    }
    writeInChunks(dataset,offset,count,buff_int);
    offset[0]+=MaxJ;
  }
  H5Sclose(dataspace);
  H5Tclose(datatype);
  H5Dclose(dataset);
  H5Gclose(triaGroup);
  
}

void HDF5DealWriter::writeTriangulation	(	string	triaName,
		Triangulation< 2 > &	tria
	)

Definition at line 23 of file hdf5dealwriter.cpp.

{
  assert(getFile() != -1);
  double buff[HDF5_BUFF_SIZE][2];
  int buff_int[HDF5_BUFF_SIZE][4];
  
  //Memorize a triangulacao.
  this->registerTriangulation(triaName,tria);


  //Criar Grupo
  char strPath[500];
  sprintf(strPath,"/Triangulations/%s",triaName.c_str());
  hid_t triaGroup=H5Gcreate1(getFile(),strPath,0);
  
  H5LTset_attribute_string(getFile(),strPath,"Type","GRID_2D");

  
  hsize_t dim[]={tria.n_vertices(),2};
  hid_t dataspace = H5Screate_simple(2,dim,NULL);
  hid_t datatype  = H5Tcopy(H5T_NATIVE_DOUBLE);
  H5Tset_order(datatype,H5T_ORDER_LE);
  hid_t dataset = H5Dcreate1(triaGroup, "vertices", datatype, dataspace, H5P_DEFAULT);

  int nSteps = tria.n_vertices()/HDF5_BUFF_SIZE;
  hsize_t count[]={HDF5_BUFF_SIZE,2};
  hsize_t offset[]={0,0};
  unsigned k=0;
  for (int i=0;i<=nSteps;i++)
  {
    int MaxJ = (i==nSteps) ? (tria.n_vertices() % HDF5_BUFF_SIZE) : HDF5_BUFF_SIZE;
    count[0]=MaxJ;
    for (int j=0;j<MaxJ;j++)
    {
      buff[j][0]= tria.get_vertices()[k](0);
      buff[j][1]= tria.get_vertices()[k](1);
      k++;
    }
    writeInChunks(dataset,offset,count,buff);
    offset[0]+=MaxJ;
  }
  H5Sclose(dataspace);
  H5Tclose(datatype);
  H5Dclose(dataset);

  dim[0]=tria.n_active_cells();
  dim[1]=4;
  dataspace = H5Screate_simple(2,dim,NULL);
  datatype  = H5Tcopy(H5T_NATIVE_INT);
  H5Tset_order(datatype,H5T_ORDER_LE);
  dataset = H5Dcreate1(triaGroup, "connections", datatype, dataspace, H5P_DEFAULT);


  nSteps = tria.n_active_cells()/HDF5_BUFF_SIZE;
  count[1]=4;
  offset[0]=0;
  Triangulation<2>::active_cell_iterator cell = tria.begin_active(),
                                         endc = tria.end();

  for (int i=0;i<=nSteps;i++)
  {
    int MaxJ = (i==nSteps) ? (tria.n_active_cells() % HDF5_BUFF_SIZE) : HDF5_BUFF_SIZE;
    count[0]=MaxJ;
    for (int j=0;j<MaxJ;j++)
    {
      buff_int[j][0]= cell->vertex_index(BL_VERTEX);
      buff_int[j][1]= cell->vertex_index(BR_VERTEX);
      buff_int[j][2]= cell->vertex_index(UR_VERTEX);
      buff_int[j][3]= cell->vertex_index(UL_VERTEX);
      cell++;
    }
    writeInChunks(dataset,offset,count,buff_int);
    offset[0]+=MaxJ;
  }
  H5Sclose(dataspace);
  H5Tclose(datatype);
  H5Dclose(dataset);
  H5Gclose(triaGroup);
  
}

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Member Data Documentation

HDF5DealWriter * HDF5DealWriter::ptr = NULL [static, protected]

Definition at line 31 of file hdf5dealwriter.h.

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The documentation for this class was generated from the following files:

• hdf5dealwriter.h
• hdf5dealwriter.cpp