Field3D
SparseDataReader< Data_T > Class Template Reference

This class gets used by SparseFieldIO and SparseFileManager to read the block data. On creation it will open the data set and not close it until the object is destroyed. More...

#include <SparseDataReader.h>

List of all members.

Public Member Functions

void readBlock (int idx, Data_T &result)
 Reads a block, storing the data in result, which is assumed to contain enough room for m_valuesPerBlock entries.
void readBlockList (int idx, const std::vector< Data_T * > &memoryList)
 Reads a series of blocks, storing each block of data in memoryList, which is assumed to contain enough room for m_valuesPerBlock entries.
 SparseDataReader (hid_t location, int valuesPerBlock, int occupiedBlocks)
 Constructor. Requires knowledge of the Hdf5 location where data is stored.

Private Attributes

const std::string k_dataStr
Hdf5Util::H5ScopedDopen m_dataSet
Hdf5Util::H5ScopedDget_type m_dataType
Hdf5Util::H5ScopedDget_space m_fileDataSpace
Hdf5Util::H5ScopedScreate m_memDataSpace
int m_valuesPerBlock

Detailed Description

template<class Data_T>
class SparseDataReader< Data_T >

This class gets used by SparseFieldIO and SparseFileManager to read the block data. On creation it will open the data set and not close it until the object is destroyed.

Definition at line 68 of file SparseDataReader.h.


Constructor & Destructor Documentation

template<class Data_T >
SparseDataReader< Data_T >::SparseDataReader ( hid_t  location,
int  valuesPerBlock,
int  occupiedBlocks 
)

Constructor. Requires knowledge of the Hdf5 location where data is stored.

Definition at line 107 of file SparseDataReader.h.

References Hdf5Util::H5ScopedScreate::create(), Hdf5Util::H5Base::id(), SparseDataReader< Data_T >::k_dataStr, SparseDataReader< Data_T >::m_dataSet, SparseDataReader< Data_T >::m_dataType, SparseDataReader< Data_T >::m_fileDataSpace, SparseDataReader< Data_T >::m_memDataSpace, SparseDataReader< Data_T >::m_valuesPerBlock, Hdf5Util::H5ScopedDget_type::open(), Hdf5Util::H5ScopedDget_space::open(), and Hdf5Util::H5ScopedDopen::open().

  : m_valuesPerBlock(valuesPerBlock), 
    k_dataStr("data")
{
  using namespace Hdf5Util;
  using namespace Exc;

  hsize_t dims[2];
  hsize_t memDims[1];

  // Open the data set
  m_dataSet.open(location, k_dataStr, H5P_DEFAULT);
  if (m_dataSet.id() < 0) 
    throw OpenDataSetException("Couldn't open data set: " + k_dataStr);
    
  // Get the space and type
  m_fileDataSpace.open(m_dataSet.id());
  m_dataType.open(m_dataSet.id());
  if (m_fileDataSpace.id() < 0) 
    throw GetDataSpaceException("Couldn't get data space");
  if (m_dataType.id() < 0)
    throw GetDataTypeException("Couldn't get data type");

  // Make the memory data space
  memDims[0] = m_valuesPerBlock;
  m_memDataSpace.create(H5S_SIMPLE);
  H5Sset_extent_simple(m_memDataSpace.id(), 1, memDims, NULL);

  // Get the dimensions and check they match
  H5Sget_simple_extent_dims(m_fileDataSpace.id(), dims, NULL);
  if (dims[1] != static_cast<hsize_t>(m_valuesPerBlock)) {
    throw FileIntegrityException("Block length mismatch in "
                                 "SparseDataReader");
  }
  if (dims[0] != static_cast<hsize_t>(occupiedBlocks)) 
    throw FileIntegrityException("Block count mismatch in "
                                 "SparseDataReader");
}

Member Function Documentation

template<class Data_T >
void SparseDataReader< Data_T >::readBlock ( int  idx,
Data_T &  result 
)

Reads a block, storing the data in result, which is assumed to contain enough room for m_valuesPerBlock entries.

Definition at line 150 of file SparseDataReader.h.

References Hdf5Util::H5Base::id(), SparseDataReader< Data_T >::m_dataSet, SparseDataReader< Data_T >::m_fileDataSpace, SparseDataReader< Data_T >::m_memDataSpace, and SparseDataReader< Data_T >::m_valuesPerBlock.

{
  using namespace Hdf5Util;
  using namespace Exc;

  hsize_t offset[2];
  hsize_t count[2];
  herr_t status;
    
  offset[0] = idx;             // Index of block
  offset[1] = 0;               // Index of first data in block. Always 0
  count[0] = 1;                // Number of columns to read. Always 1
  count[1] = m_valuesPerBlock; // Number of values in one column

  status = H5Sselect_hyperslab(m_fileDataSpace.id(), H5S_SELECT_SET, 
                               offset, NULL, count, NULL);
  if (status < 0) {
    throw ReadHyperSlabException("Couldn't select slab " + 
                                 boost::lexical_cast<std::string>(idx));
  }

  status = H5Dread(m_dataSet.id(), DataTypeTraits<Data_T>::h5type(), 
                   m_memDataSpace.id(), m_fileDataSpace.id(), 
                   H5P_DEFAULT, &result);
}
template<class Data_T >
void SparseDataReader< Data_T >::readBlockList ( int  idx,
const std::vector< Data_T * > &  memoryList 
)

Reads a series of blocks, storing each block of data in memoryList, which is assumed to contain enough room for m_valuesPerBlock entries.

Definition at line 180 of file SparseDataReader.h.

References Hdf5Util::H5Base::id(), SparseDataReader< Data_T >::m_dataSet, SparseDataReader< Data_T >::m_fileDataSpace, and SparseDataReader< Data_T >::m_valuesPerBlock.

Referenced by SparseFieldIO::readData().

{
  using namespace Hdf5Util;
  using namespace Exc;

  hsize_t offset[2];
  hsize_t count[2];
  herr_t status;

  offset[0] = idxLo;            // Index of block
  offset[1] = 0;                // Index of first data in block. Always 0
  count[0] = memoryList.size(); // Number of columns to read.
  count[1] = m_valuesPerBlock;  // Number of values in one column
  
  status = H5Sselect_hyperslab(m_fileDataSpace.id(), H5S_SELECT_SET, 
                               offset, NULL, count, NULL);
  if (status < 0) {
    throw ReadHyperSlabException("Couldn't select slab " + 
                                 boost::lexical_cast<std::string>(idxLo));
  }

  // Make the memory data space ---
 
  Hdf5Util::H5ScopedScreate localMemDataSpace;
  hsize_t memDims[2];  
  memDims[0] = memoryList.size();
  memDims[1] = m_valuesPerBlock;
  localMemDataSpace.create(H5S_SIMPLE);
  H5Sset_extent_simple(localMemDataSpace.id(), 2, memDims, NULL);

  // Setup the temporary memory region ---

  int bytesPerValue = 0;
  {
    hid_t t = DataTypeTraits<Data_T>::h5type();
    if (t == H5T_NATIVE_CHAR)
      bytesPerValue = 1;
    else if (t == H5T_NATIVE_SHORT)
      bytesPerValue = 2;
    else if (t == H5T_NATIVE_FLOAT)
      bytesPerValue = 4;
    else if (t == H5T_NATIVE_DOUBLE)
      bytesPerValue = 8;
  }

  int dim = sizeof(Data_T) / bytesPerValue;
  std::vector<Data_T> bigblock(memoryList.size() * m_valuesPerBlock/dim);

  status = H5Dread(m_dataSet.id(), 
                   DataTypeTraits<Data_T>::h5type(), 
                   localMemDataSpace.id(),
                   m_fileDataSpace.id(), 
                   H5P_DEFAULT, &bigblock[0]);

  if (status < 0) {
    throw Hdf5DataReadException("Couldn't read slab " + 
                                boost::lexical_cast<std::string>(idxLo));
  }

  // Distribute block data into memory slots ---
  for (size_t i = 0; i < memoryList.size(); ++i) {
    memcpy(memoryList[i], 
           &bigblock[i * m_valuesPerBlock / dim],
           bytesPerValue * m_valuesPerBlock);
  }
}

Member Data Documentation

template<class Data_T>
Hdf5Util::H5ScopedDget_type SparseDataReader< Data_T >::m_dataType [private]

Definition at line 94 of file SparseDataReader.h.

Referenced by SparseDataReader< Data_T >::SparseDataReader().

template<class Data_T>
const std::string SparseDataReader< Data_T >::k_dataStr [private]

Definition at line 99 of file SparseDataReader.h.

Referenced by SparseDataReader< Data_T >::SparseDataReader().


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