Classes
class	Hdf5Util::H5Base
	Base class for all scoped Hdf5 util classes. More...
class	Hdf5Util::H5ScopedAget_space
	Scoped object - opens an attribute data space on creation and closes it on destruction. More...
class	Hdf5Util::H5ScopedAget_type
	Scoped object - opens an attribute data type on creation and closes it on destruction. More...
class	Hdf5Util::H5ScopedAopen
	Scoped object - Opens attribute by name and closes it on destruction. More...
class	Hdf5Util::H5ScopedAopenIdx
	Scoped object - Opens attribute by index and closes it on destruction. More...
class	Hdf5Util::H5ScopedDcreate
	Scoped object - creates a dataset on creation and closes it on destruction. More...
class	Hdf5Util::H5ScopedDget_space
	Scoped object - opens a dataset on creation and closes it on destruction. More...
class	Hdf5Util::H5ScopedDget_type
	Scoped object - opens a dataset on creation and closes it on destruction. More...
class	Hdf5Util::H5ScopedDopen
	Scoped object - opens a dataset on creation and closes it on destruction. More...
class	Hdf5Util::H5ScopedGcreate
	Scoped object - creates a group on creation and closes it on destruction. More...
class	Hdf5Util::H5ScopedGopen
	Scoped object - opens a group on creation and closes it on destruction. More...
class	Hdf5Util::H5ScopedScreate
	Scoped object - creates a dataspace on creation and closes it on destruction. More...
class	Hdf5Util::H5ScopedTget_native_type
	Scoped object - opens an native type id on creation and closes it on destruction. More...
Namespaces
namespace	Hdf5Util
	Contains utility functions and classes for Hdf5 files.
Functions
bool	Hdf5Util::checkHdf5Gzip ()
	Checks whether gzip is available in the current hdf5 library.
Read/write simple data to hdf5 location
template<typename T >
void	Hdf5Util::writeSimpleData (hid_t location, const std::string &name, const std::vector< T > &data)
	Writes a simple linear data set to the given location.
template<typename T >
void	Hdf5Util::readSimpleData (hid_t location, const std::string &name, std::vector< T > &data)
	Reads a simple linear data set from the given location.
Attribute reading
bool	Hdf5Util::readAttribute (hid_t location, const std::string &attrName, std::string &value)
	Reads a string attribute.
bool	Hdf5Util::readAttribute (hid_t location, const std::string &attrName, unsigned int attrSize, int &value)
	Reads an int attribute of arbitrary size.
bool	Hdf5Util::readAttribute (hid_t location, const std::string &attrName, unsigned int attrSize, float &value)
	Reads a float attribute of arbitrary size.
bool	Hdf5Util::readAttribute (hid_t location, const std::string &attrName, unsigned int attrSize, double &value)
	Reads a double attribute of arbitrary size.
bool	Hdf5Util::readAttribute (hid_t location, const std::string &attrName, std::vector< unsigned int > &attrSize, int &value)
	Reads a int attribute of arbitrary size and rank.
bool	Hdf5Util::readAttribute (hid_t location, const std::string &attrName, std::vector< unsigned int > &attrSize, float &value)
	Reads a float attribute of arbitrary size and rank.
bool	Hdf5Util::readAttribute (hid_t location, const std::string &attrName, std::vector< unsigned int > &attrSize, double &value)
	Reads a double attribute of arbitrary size and rank.
Attribute writing
bool	Hdf5Util::writeAttribute (hid_t location, const std::string &attrName, const std::string &value)
	Writes a string attribute.
bool	Hdf5Util::writeAttribute (hid_t location, const std::string &attrName, unsigned int attrSize, const int &value)
	Writes an int attribute of arbitrary size.
bool	Hdf5Util::writeAttribute (hid_t location, const std::string &attrName, unsigned int attrSize, const float &value)
	Writes a float attribute of arbitrary size.
bool	Hdf5Util::writeAttribute (hid_t location, const std::string &attrName, unsigned int attrSize, const double &value)
	Writes a double attribute of arbitrary size.
bool	Hdf5Util::writeAttribute (hid_t location, const std::string &attrName, std::vector< unsigned int > &attrSize, const int &value)
	Writes a float attribute of arbitrary size and rank.
bool	Hdf5Util::writeAttribute (hid_t location, const std::string &attrName, std::vector< unsigned int > &attrSize, const float &value)
	Writes a float attribute of arbitrary size and rank.
bool	Hdf5Util::writeAttribute (hid_t location, const std::string &attrName, std::vector< unsigned int > &attrSize, const double &value)
	Writes a double attribute of arbitrary size and rank.

Function Documentation

template<typename T >

void Hdf5Util::writeSimpleData	(	hid_t	location,
		const std::string &	name,
		const std::vector< T > &	data
	)

Writes a simple linear data set to the given location.

Definition at line 530 of file Hdf5Util.h.

References Hdf5Util::H5Base::id().

{
  using namespace Exc;

  // Calculate the total number of entries. This factors in that
  // V3f uses 3 components per value, etc.
  hsize_t totalSize[1];
  int components = FieldTraits<T>::dataDims();
  totalSize[0] = data.size() * components;

  // Get the internal data type
  hid_t type = DataTypeTraits<T>::h5type();

  H5ScopedScreate dataSpace(H5S_SIMPLE);

  if (dataSpace.id() < 0)
    throw WriteSimpleDataException("Couldn't create data space");
  
  H5Sset_extent_simple(dataSpace.id(), 1, totalSize, NULL);

  H5ScopedDcreate dataSet(location, name.c_str(), type, dataSpace.id(), 
                          H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

  if (dataSet.id() < 0) 
    throw WriteSimpleDataException("Couldn't create data set");
    
  hid_t err = H5Dwrite(dataSet.id(), type, H5S_ALL, H5S_ALL, 
                       H5P_DEFAULT, &data[0]);

  if (err < 0) 
    throw WriteSimpleDataException("Couldn't write data");
}

template<typename T >

void Hdf5Util::readSimpleData	(	hid_t	location,
		const std::string &	name,
		std::vector< T > &	data
	)

Reads a simple linear data set from the given location.

Definition at line 567 of file Hdf5Util.h.

{
  using namespace Exc;

  int components = FieldTraits<T>::dataDims();
  hsize_t dims[1];

  H5ScopedDopen dataSet(location, name.c_str(), H5P_DEFAULT);

  if (dataSet.id() < 0) 
    throw OpenDataSetException("Couldn't open data set: " + name);
  
  H5ScopedDget_space dataSpace(dataSet.id());
  H5ScopedDget_type dataType(dataSet.id());
  H5Sget_simple_extent_dims(dataSpace.id(), dims, NULL);

  if (dataSpace.id() < 0) 
    throw GetDataSpaceException("Couldn't get data space");

  if (dataType.id() < 0)
    throw GetDataTypeException("Couldn't get data type");

  int reportedSize = dims[0] / components;

  // Resize target
  data.clear();
  data.resize(reportedSize);
  
  // Get the internal data type
  hid_t type = DataTypeTraits<T>::h5type();

  if (H5Dread(dataSet.id(), type, H5S_ALL, H5S_ALL, 
              H5P_DEFAULT, &data[0]) < 0) {
    throw Hdf5DataReadException("Couldn't read simple data");
  }
}

bool Hdf5Util::readAttribute	(	hid_t	location,
		const std::string &	attrName,
		std::string &	value
	)

Reads a string attribute.

Referenced by Field3DInputFile::parseLayer(), InputFile::parseLayers(), SparseFieldIO::read(), MACFieldIO::read(), FrustumFieldMappingIO::read(), MatrixFieldMappingIO::read(), NullFieldMappingIO::read(), DenseFieldIO::read(), SparseFieldIO::readData(), readFieldMapping(), Field3DInputFile::readGroupMembership(), Field3DInputFile::readLayer(), Field3DInputFile::readMetadata(), and Field3DInputFile::readProxyLayer().

bool Hdf5Util::readAttribute	(	hid_t	location,
		const std::string &	attrName,
		unsigned int	attrSize,
		int &	value
	)

Reads an int attribute of arbitrary size.

bool Hdf5Util::readAttribute	(	hid_t	location,
		const std::string &	attrName,
		unsigned int	attrSize,
		float &	value
	)

Reads a float attribute of arbitrary size.

bool Hdf5Util::readAttribute	(	hid_t	location,
		const std::string &	attrName,
		unsigned int	attrSize,
		double &	value
	)

Reads a double attribute of arbitrary size.

bool Hdf5Util::readAttribute	(	hid_t	location,
		const std::string &	attrName,
		std::vector< unsigned int > &	attrSize,
		int &	value
	)

Reads a int attribute of arbitrary size and rank.

bool Hdf5Util::readAttribute	(	hid_t	location,
		const std::string &	attrName,
		std::vector< unsigned int > &	attrSize,
		float &	value
	)

Reads a float attribute of arbitrary size and rank.

bool Hdf5Util::readAttribute	(	hid_t	location,
		const std::string &	attrName,
		std::vector< unsigned int > &	attrSize,
		double &	value
	)

Reads a double attribute of arbitrary size and rank.

bool Hdf5Util::writeAttribute	(	hid_t	location,
		const std::string &	attrName,
		const std::string &	value
	)

Writes a string attribute.

Referenced by Field3DOutputFile::createNewPartition(), SparseFieldIO::write(), MACFieldIO::write(), FrustumFieldMappingIO::write(), MatrixFieldMappingIO::write(), NullFieldMappingIO::write(), DenseFieldIO::write(), writeField(), writeFieldMapping(), Field3DOutputFile::writeGroupMembership(), SparseFieldIO::writeInternal(), MACFieldIO::writeInternal(), DenseFieldIO::writeInternal(), Field3DOutputFile::writeLayer(), and Field3DOutputFile::writeMetadata().

bool Hdf5Util::writeAttribute	(	hid_t	location,
		const std::string &	attrName,
		unsigned int	attrSize,
		const int &	value
	)

Writes an int attribute of arbitrary size.

bool Hdf5Util::writeAttribute	(	hid_t	location,
		const std::string &	attrName,
		unsigned int	attrSize,
		const float &	value
	)

Writes a float attribute of arbitrary size.

bool Hdf5Util::writeAttribute	(	hid_t	location,
		const std::string &	attrName,
		unsigned int	attrSize,
		const double &	value
	)

Writes a double attribute of arbitrary size.

bool Hdf5Util::writeAttribute	(	hid_t	location,
		const std::string &	attrName,
		std::vector< unsigned int > &	attrSize,
		const int &	value
	)

Writes a float attribute of arbitrary size and rank.

bool Hdf5Util::writeAttribute	(	hid_t	location,
		const std::string &	attrName,
		std::vector< unsigned int > &	attrSize,
		const float &	value
	)

Writes a float attribute of arbitrary size and rank.

bool Hdf5Util::writeAttribute	(	hid_t	location,
		const std::string &	attrName,
		std::vector< unsigned int > &	attrSize,
		const double &	value
	)

Writes a double attribute of arbitrary size and rank.

bool Hdf5Util::checkHdf5Gzip ( )

Checks whether gzip is available in the current hdf5 library.

Definition at line 680 of file Hdf5Util.cpp.

Referenced by MACFieldIO::writeData(), SparseFieldIO::writeInternal(), and DenseFieldIO::writeInternal().

{
  htri_t avail = H5Zfilter_avail(H5Z_FILTER_DEFLATE);
  if (!avail)
    return false;

  unsigned int filter_info;
  herr_t status = H5Zget_filter_info (H5Z_FILTER_DEFLATE, &filter_info);

  if (status < 0)
    return false;

  if (!(filter_info & H5Z_FILTER_CONFIG_ENCODE_ENABLED) ||
      !(filter_info & H5Z_FILTER_CONFIG_DECODE_ENABLED)) {
    return false;
  }

  return true;
}

Classes

Namespaces

Functions

Read/write simple data to hdf5 location

Attribute reading

Attribute writing

Function Documentation