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HDF5IOHelper Class Reference

Public Member Functions

 HDF5IOHelper (const std::string &file_name, bool overwrite=false)
 
template<typename T >
void store_scalar (const std::string &dset_name, const T &val)
 Store scalar data to a data set.
 
void store_scalar (const std::string &dset_name, const String &val)
 Store string scalar data to a data set.
 
template<typename T >
void store_vector (const std::string &dset_name, const std::vector< T > &array) const
 Store vector (1D) information to a dataset.
 
template<typename T >
void store_vector (const std::string &dset_name, const Teuchos::SerialDenseVector< int, T > &vec)
 Store vector (1D) information to a dataset.
 
void store_vector (const std::string &dset_name, const StringMultiArrayConstView &vec)
 Store vector (1D) information to a dataset.
 
void store_vector (const std::string &dset_name, const SizetMultiArrayConstView &vec)
 Store vector (1D) information to a dataset.
 
template<typename T >
void store_matrix (const std::string &dset_name, const Teuchos::SerialDenseMatrix< int, T > &matrix, const bool &transpose=false) const
 Store matrix (2D) information to a dataset.
 
template<typename T >
void store_matrix (const std::string &dset_name, const std::vector< T > &buf, const int &num_cols, const bool &transpose=false) const
 Store matrix (2D) information to a dataset.
 
void store_matrix (const std::string &dset_name, const std::vector< String > &buf, const int &num_cols, const bool &transpose=false) const
 Store matrix (2D) information to a dataset.
 
template<typename T >
void set_scalar (const String &dset_name, const T &data, const int &index)
 Set a scalar in a 1D dataset at index using its name.
 
template<typename T >
void set_scalar (const String &dset_name, H5::DataSet &ds, const T &data, const int &index)
 Set a scalar in a 1D dataset at index using the dataset object.
 
void set_scalar (const String &dset_name, H5::DataSet &ds, const String &data, const int &index)
 Set a scalar in a 1D dataset at index using the dataset object. More...
 
template<typename T >
void set_vector (const String &dset_name, const T &data, const int &index, const bool &row=true)
 Set a row or column in a 2D dataset at index using its name.
 
void set_vector (const String &dset_name, H5::DataSet &ds, const StringMultiArrayConstView &data, const int &index, const bool &row=true)
 Set a row or column of Strings in a 2D dataset at index using the dataset object.
 
void set_vector (const String &dset_name, H5::DataSet &ds, const std::vector< String > &data, const int &index, const bool &row=true)
 Set a row or column of Strings in a 2D dataset at index using the dataset object.
 
template<typename T >
void set_vector (const String &dset_name, H5::DataSet &ds, const T &data, const int &index, const bool &row=true)
 Set a row or column in a 2D dataset at index using the dataset object.
 
template<typename T >
void set_matrix (const String &dset_name, const Teuchos::SerialDenseMatrix< int, T > &data, const int &index, const bool &transpose=false)
 Set a matrix in a 3D dataset at the index into the 0th dimension by name. Dims of matrix must match those of the trailing dimensions of the dataset.
 
template<typename T >
void set_matrix (const String &dset_name, H5::DataSet &ds, const Teuchos::SerialDenseMatrix< int, T > &data, const int &index, const bool &transpose=false)
 Set a matrix in a 3D dataset at the index into the 0th dimension using a dataset object. Dims of matrix must match those of the trailing dimensions of the dataset.
 
template<typename T >
void set_vector_matrix (const String &dset_name, const std::vector< Teuchos::SerialDenseMatrix< int, T > > &data, const int &index, const bool &transpose=false)
 Set a 3D slab in a 4D dataset at the index into the 0th dimension by name. The length of the vector must match the 1st dimension of the dataset, and the dimensions of the matrices must all match the 2nd and 3rd dimensions.
 
template<typename T >
void set_vector_matrix (const String &dset_name, H5::DataSet &ds, const std::vector< Teuchos::SerialDenseMatrix< int, T > > &data, const int &index, const bool &transpose=false)
 Set a 3D slab in a 4D dataset at the index into the 0th dimension using a dataset object. The length of the vector must match the 1st dimension of the dataset, and the dimensions of the matrices must all match the 2nd and 3rd dimensions.
 
template<typename T >
void set_vector_scalar_field (const String &dset_name, const T &data, const String &field_name)
 Set a scalar field on all elements of a 1D dataset of compound type using a ds name.
 
template<typename T >
void set_vector_scalar_field (const String &dset_name, H5::DataSet &ds, const std::vector< T > &data, const String &field_name)
 Set a scalar field on all elements of a 1D dataset of compound type using a ds object. More...
 
template<typename T >
void set_vector_vector_field (const String &dset_name, const T &data, const size_t length, const String &field_name)
 Set a vector field on all elements of a 1D dataset of compound type using a ds name.
 
template<typename T >
void set_vector_vector_field (const String &dset_name, H5::DataSet &ds, const std::vector< T > &data, const size_t length, const String &field_name)
 Set a vector field on all elements of a 1D dataset of compound type using a ds object. More...
 
void set_vector_vector_field (const String &dset_name, H5::DataSet &ds, const std::vector< String > &data, const size_t length, const String &field_name)
 Set a vector field on all elements of a 1D dataset of compound type using a ds object. More...
 
int append_empty (const String &dset_name)
 Append an empty "layer" to the 0th dimension and return its index.
 
template<typename T >
void append_scalar (const String &dset_name, const T &data)
 Append a scalar to a 1D dataset.
 
void append_scalar (const String &dset_name, const String &data)
 Append a scalar to a 1D dataset.
 
template<typename T >
void append_vector (const String &dset_name, const T &data, const bool &row=true)
 Append a vector as a row or column to a 2D dataset.
 
void append_vector (const String &dset_name, const std::vector< String > &data, const bool &row=true)
 Append a vector as a row or column to a 2D dataset.
 
void append_vector (const String &dset_name, const StringMultiArrayConstView &data, const bool &row=true)
 Append a vector as a row or column to a 2D dataset.
 
template<typename T >
void append_matrix (const String &dset_name, const Teuchos::SerialDenseMatrix< int, T > &data, const bool &transpose=false)
 Append a SerialDenseMatrix to a 3D dataset. The dataset will be expanded along the 0th dimension. By default, the shape of the matrix, (nrows, ncols), must match the size of the 1st and 2nd dimensions of the dataset. For transpose=true, the reverse must be true.
 
template<typename T >
void append_vector_matrix (const String &dset_name, const std::vector< Teuchos::SerialDenseMatrix< int, T > > &data, const bool &transpose=false)
 Append a std::vector of SerialDenseMatrix's to a 4D dataset. The dataset will be expanded along the 0th dimension. By default, the size of the vector must equal the size of the 1st dimension of the dataset, andthe shape of the SDMs (nrows, ncols), must match the sizes of the 2nd and 2nd dimensions of the dataset. For transpose=true, the reverse must be true of the SDMs.
 
template<typename T >
void read_scalar (const std::string &dset_name, T &val)
 Read scalar data from a dataset.
 
void read_scalar (const std::string &dset_name, String &val)
 Read scalar data from a dataset.
 
template<typename T >
void read_vector (const std::string &dset_name, T &array) const
 Read vector (1D) information from a dataset.
 
void read_vector (const std::string &dset_name, StringArray &array) const
 Read a vector of Strings from a dataset. More...
 
template<typename T >
void read_matrix (const std::string &dset_name, Teuchos::SerialDenseMatrix< int, T > &matrix, const bool &transpose=false) const
 Read matrix (2D) information from a dataset Currently this involves a wasteful copy to do the transpose and is intended only for purposes of testing.
 
template<typename T >
void get_matrix (const std::string &dset_name, Teuchos::SerialDenseMatrix< int, T > &matrix, const int &index, const bool &transpose=false) const
 Get the matrix (2D) at the index into the 0th dimension of the 3D dataset at dsetname. Currently this involves a wasteful copy to do the transpose and is intended only for purposes of testing.
 
template<typename T >
void get_vector_matrix (const std::string &dset_name, std::vector< Teuchos::SerialDenseMatrix< int, T > > &data, const int &index, const bool &transpose=false) const
 Read the 3D slice at the index into the 0th dimension of the 4D dataset at ds_name. Currently this involves a wasteful copy to do the transpose and is intended only for purposes of testing.
 
void report_num_open ()
 Report the number of open descriptors of each type; just for debugging.
 
void create_empty_dataset (const String &dset_name, const IntArray &dims, ResultsOutputType stored_type, int chunk_size=0, const void *fill_val=NULL)
 Create an empty dataset. Setting the first element of dims to 0 makes the dataset unlimited in that dimension. DSs unlimited in other dimensions currently are unsupported.
 
void create_empty_dataset (const String &dset_name, const IntArray &dims, const std::vector< VariableParametersField > &fields)
 Create a dataset with compound type.
 
void attach_scale (const String &dset_name, const String &scale_name, const String &label, const int &dim) const
 attach a dimension scale to a dataset
 
template<typename T >
void add_attribute (const String &location, const String &label, const T &value)
 Add an attribute to a group or dataset.
 
void add_attribute (const String &location, const String &label, const String &value)
 Add an attribute to a group or dataset.
 
bool exists (const String location_name) const
 Does a group or dataset exist?
 
bool is_scale (const H5::DataSet dset) const
 Is the dataset a dimenions scale?
 
H5::Group create_groups (const std::string &name, bool includes_dset=true) const
 Create a group hierarchy (final token optionally a dataset name)
 
H5::DataSet create_dataset (const H5::H5Location &loc, const std::string &name, const H5::DataType &type, const H5::DataSpace &space, const H5::DSetCreatPropList &create_plist=H5::DSetCreatPropList(), const H5::DSetAccPropList &access_plist=H5::DSetAccPropList()) const
 Create a dataset with a custom CreatPropList.
 
H5::Group create_group (const H5::H5Location &loc, const std::string &name) const
 Create a group.
 
void create_softlink (const String &link_location, const String &source_location)
 Create a soft link.
 
void flush () const
 Flush cache to file.
 

Public Attributes

H5::LinkCreatPropList linkCreatePL
 Gobal link creation property list.
 
H5::DSetCreatPropList datasetCompactPL
 Gobal DataSet creation property list for compact datasets.
 
H5::DSetCreatPropList datasetContiguousPL
 Gobal DataSet creation property list for contiguous datasets.
 

Protected Member Functions

template<typename T >
H5::Attribute create_attribute (const String &location, const String &label, const T &data)
 create an attribute at the location and return it
 
template<typename T >
void store_vector (const String &dset_name, const T *data, const int &len) const
 Store vector data using a pointer to the first element and length.
 
void store_vector (const String &dset_name, const String *data, const int &len) const
 Store vector of Strings using a pointer to the first element and length.
 

Protected Attributes

std::string fileName
 Name of the HDF5 file.
 
H5::H5File h5File
 HDF5 file object.
 
std::map< String, H5::DataSet > datasetCache
 Cache open datasets that have unlimited dimension This is an optimization to prevent eval-related datasets being repeatedly flushed and reopened, which is very costly.
 

Detailed Description

This helper class provides wrapper functions that perform low-level access operations in HDF5 databases.

Authors: J. Adam Stephens, Russell Hooper, Elliott Ridgway

Member Function Documentation

void set_scalar ( const String &  dset_name,
H5::DataSet &  ds,
const String &  data,
const int &  index 
)

Set a scalar in a 1D dataset at index using the dataset object.

Set a scalar in a 1D dataset at index using an object.

void set_vector_scalar_field ( const String &  dset_name,
H5::DataSet &  ds,
const std::vector< T > &  data,
const String &  field_name 
)

Set a scalar field on all elements of a 1D dataset of compound type using a ds object.

Set a field on all elements of a 1D dataset of compound type using a ds object.

References Dakota::h5_mem_dtype().

void set_vector_vector_field ( const String &  dset_name,
H5::DataSet &  ds,
const std::vector< T > &  data,
const size_t  length,
const String &  field_name 
)

Set a vector field on all elements of a 1D dataset of compound type using a ds object.

Set a field on all elements of a 1D dataset of compound type using a ds object.

References Dakota::h5_mem_dtype().

void set_vector_vector_field ( const String &  dset_name,
H5::DataSet &  ds,
const std::vector< String > &  data,
const size_t  length,
const String &  field_name 
)

Set a vector field on all elements of a 1D dataset of compound type using a ds object.

Set a field on all elements of a 1D dataset of compound type using a ds object.

References Dakota::pointers_to_strings().

void read_vector ( const std::string &  dset_name,
StringArray &  array 
) const

Read a vector of Strings from a dataset.

Read vector (1D) String information from a dataset.

References Dakota::abort_handler(), and Dakota::h5_mem_dtype().


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