kspaceFirstOrder3D-CUDA  1.1
The CUDA/C++ implementation of the k-wave toolbox for the time-domain simulation of acoustic wave fields in 3D
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THDF5_File Class Reference

Class wrapping the HDF5 routines. More...

#include <HDF5_File.h>

Collaboration diagram for THDF5_File:

Public Types

enum  TMatrixDataType { FLOAT = 0, LONG = 1 }
 HDF5 matrix data type (float or uint64). More...
 
enum  TMatrixDomainType { REAL = 0, COMPLEX = 1 }
 HDF5 Matrix domain type (real or complex). More...
 

Public Member Functions

 THDF5_File ()
 Constructor of the class. More...
 
virtual ~THDF5_File ()
 Destructor. More...
 
void Create (const std::string &fileName, unsigned int flags=H5F_ACC_TRUNC)
 Create a file. More...
 
void Open (const std::string &fileName, unsigned int flags=H5F_ACC_RDONLY)
 Open a file. More...
 
bool IsOpen () const
 Is the file opened? More...
 
void Close ()
 Close file. More...
 
hid_t CreateGroup (const hid_t parentGroup, TMatrixName &groupName)
 Create a HDF5 group at a specified place in the file tree. More...
 
hid_t OpenGroup (const hid_t parentGroup, TMatrixName &groupName)
 Open a HDF5 group at a specified place in the file tree. More...
 
void CloseGroup (const hid_t group)
 Close group. More...
 
hid_t GetRootGroup () const
 Get handle to the root group. More...
 
hid_t OpenDataset (const hid_t parentGroup, TMatrixName &datasetName)
 Open the HDF5 dataset at a specified place in the file tree. More...
 
hid_t CreateFloatDataset (const hid_t parentGroup, TMatrixName &datasetName, const TDimensionSizes &dimensionSizes, const TDimensionSizes &chunkSizes, const size_t compressionLevel)
 Create a float HDF5 dataset at a specified place in the file tree (3D/4D). More...
 
hid_t CreateIndexDataset (const hid_t parentGroup, TMatrixName &datasetName, const TDimensionSizes &dimensionSizes, const TDimensionSizes &chunkSizes, const size_t compressionLevel)
 Create an index HDF5 dataset at a specified place in the file tree (3D only). More...
 
void CloseDataset (const hid_t dataset)
 Close the HDF5 dataset. More...
 
void WriteHyperSlab (const hid_t dataset, const TDimensionSizes &position, const TDimensionSizes &size, const float *data)
 Write a hyper-slab into the dataset - float dataset. More...
 
void WriteHyperSlab (const hid_t dataset, const TDimensionSizes &position, const TDimensionSizes &size, const size_t *data)
 Write a hyper-slab into the dataset - long dataset. More...
 
void WriteCuboidToHyperSlab (const hid_t dataset, const TDimensionSizes &hyperslabPosition, const TDimensionSizes &cuboidPosition, const TDimensionSizes &cuboidSize, const TDimensionSizes &matrixDimensions, const float *mMatrixData)
 Write a cuboid selected within the matrixData into a hyperslab. More...
 
void WriteDataByMaskToHyperSlab (const hid_t dataset, const TDimensionSizes &hyperslabPosition, const size_t indexSensorSize, const size_t *indexSensorData, const TDimensionSizes &matrixDimensions, const float *matrixData)
 Write sensor data selected by the sensor mask - Occasionally very slow, do not use! More...
 
void WriteScalarValue (const hid_t parentGroup, TMatrixName &datasetName, const float value)
 Write the scalar value under a specified group, float value. More...
 
void WriteScalarValue (const hid_t parentGroup, TMatrixName &datasetName, const size_t value)
 Write the scalar value under a specified group, index value. More...
 
void ReadScalarValue (const hid_t parentGroup, TMatrixName &datasetName, float &value)
 Read the scalar value under a specified group, float value. More...
 
void ReadScalarValue (const hid_t parentGroup, TMatrixName &datasetName, size_t &value)
 Read the scalar value under a specified group, index value. More...
 
void ReadCompleteDataset (const hid_t parentGroup, TMatrixName &datasetName, const TDimensionSizes &dimensionSizes, float *data)
 Read data from the dataset under a specified group, float dataset. More...
 
void ReadCompleteDataset (const hid_t parentGroup, TMatrixName &datasetName, const TDimensionSizes &dimensionSizes, size_t *data)
 Read data from the dataset under a specified group, index dataset. More...
 
TDimensionSizes GetDatasetDimensionSizes (const hid_t parentGroup, TMatrixName &datasetName)
 Get dimension sizes of the dataset under a specified group. More...
 
size_t GetDatasetNumberOfDimensions (const hid_t parentGroup, TMatrixName &datasetName)
 Get number of dimensions of the dataset under a specified group. More...
 
size_t GetDatasetElementCount (const hid_t parentGroup, TMatrixName &datasetName)
 Get dataset element count under a specified group. More...
 
void WriteMatrixDataType (const hid_t parentGroup, TMatrixName &datasetName, const TMatrixDataType &matrixDataType)
 Write matrix data type into the dataset under a specified group. More...
 
void WriteMatrixDomainType (const hid_t parentGroup, TMatrixName &datasetName, const TMatrixDomainType &matrixDomainType)
 Write matrix domain type into the dataset under the root group. More...
 
THDF5_File::TMatrixDataType ReadMatrixDataType (const hid_t parentGroup, TMatrixName &datasetName)
 Read matrix data type from the dataset. More...
 
THDF5_File::TMatrixDomainType ReadMatrixDomainType (const hid_t parentGroup, TMatrixName &datasetName)
 Read matrix domain type from the dataset under a specified group. More...
 
void WriteStringAttribute (const hid_t parentGroup, TMatrixName &datasetName, TMatrixName &attributeName, const std::string &value)
 Write string attribute into the dataset under the root group. More...
 
std::string ReadStringAttribute (const hid_t parentGroup, TMatrixName &datasetName, TMatrixName &attributeName)
 Read string attribute from the dataset under the root group. More...
 

Static Public Member Functions

static bool IsHDF5 (const std::string &fileName)
 Does the file exist? More...
 

Protected Member Functions

 THDF5_File (const THDF5_File &src)
 Copy constructor is not allowed for public.
 
THDF5_Fileoperator= (const THDF5_File &src)
 Operator = is not allowed for public.
 

Private Attributes

hid_t file
 HDF file handle.
 
std::string fileName
 File name.
 

Static Private Attributes

static const std::string matrixDomainTypeName = "domain_type"
 String representation of the Domain type in the HDF5 file.
 
static const std::string matrixDataTypeName = "data_type"
 String representation of the Data type in the HDF5 file.
 
static const std::string matrixDomainTypeNames [] = {"real","complex"}
 String representation of different domain types.
 
static const std::string matrixDataTypeNames [] = {"float","long"}
 String representation of different data types.
 

Detailed Description

This class is responsible for working with HDF5 files. It offers routines to manage files (create, open, close) as well as creating, reading and modifying the contents (groups and datasets).

Definition at line 500 of file HDF5_File.h.

Member Enumeration Documentation

HDF5 matrix data type (float or uint64).

Definition at line 509 of file HDF5_File.h.

HDF5 Matrix domain type (real or complex).

Definition at line 520 of file HDF5_File.h.

Constructor & Destructor Documentation

THDF5_File::THDF5_File ( )

Constructor.

Definition at line 82 of file HDF5_File.cpp.

THDF5_File::~THDF5_File ( )
virtual

Destructor.

Definition at line 193 of file HDF5_File.cpp.

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Member Function Documentation

void THDF5_File::Close ( )

Close the HDF5 file.

Exceptions
ios::failure

Definition at line 175 of file HDF5_File.cpp.

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void THDF5_File::CloseDataset ( const hid_t  dataset)

Close dataset.

Parameters
[in]dataset- Dataset to close

Definition at line 457 of file HDF5_File.cpp.

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void THDF5_File::CloseGroup ( const hid_t  group)

Close a group.

Parameters
[in]group- Group to close

Definition at line 254 of file HDF5_File.cpp.

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void THDF5_File::Create ( const std::string &  fileName,
unsigned int  flags = H5F_ACC_TRUNC 
)

Create the HDF5 file.

Parameters
[in]fileName- File name
[in]flags- Flags for the HDF5 runtime
Exceptions
ios:failureif error happened.

Definition at line 97 of file HDF5_File.cpp.

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hid_t THDF5_File::CreateFloatDataset ( const hid_t  parentGroup,
TMatrixName datasetName,
const TDimensionSizes dimensionSizes,
const TDimensionSizes chunkSizes,
const size_t  compressionLevel 
)

Create a float HDF5 dataset at a specified place in the file tree.

Parameters
[in]parentGroup- Parent group Id
[in]datasetName- Dataset name
[in]dimensionSizes- Dimension sizes
[in]chunkSizes- Chunk sizes
[in]compressionLevel- Compression level
Returns
A handle to the new dataset
Exceptions
ios::failure

Definition at line 296 of file HDF5_File.cpp.

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hid_t THDF5_File::CreateGroup ( const hid_t  parentGroup,
TMatrixName groupName 
)

Create a HDF5 group at a specified place in the file tree.

Parameters
[in]parentGroup- Where to link the group at
[in]groupName- Group name
Returns
A handle to the new group
Exceptions
ios::failure

Definition at line 208 of file HDF5_File.cpp.

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hid_t THDF5_File::CreateIndexDataset ( const hid_t  parentGroup,
TMatrixName datasetName,
const TDimensionSizes dimensionSizes,
const TDimensionSizes chunkSizes,
const size_t  compressionLevel 
)

Create an index HDF5 dataset at a specified place in the file tree (always 3D).

Parameters
[in]parentGroup- Parent group
[in]datasetName- Dataset name
[in]dimensionSizes- Dimension sizes
[in]chunkSizes- Chunk sizes
[in]compressionLevel- Compression level
Returns
A handle to the new dataset
Exceptions
ios::failure

Definition at line 392 of file HDF5_File.cpp.

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TDimensionSizes THDF5_File::GetDatasetDimensionSizes ( const hid_t  parentGroup,
TMatrixName datasetName 
)

Get dimension sizes of the dataset at a specified place in the file tree.

Parameters
[in]parentGroup- Where the dataset is
[in]datasetName- Dataset name
Returns
Dimension sizes of the dataset
Exceptions
ios::failure

Definition at line 949 of file HDF5_File.cpp.

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size_t THDF5_File::GetDatasetElementCount ( const hid_t  parentGroup,
TMatrixName datasetName 
)

Get dataset element count at a specified place in the file tree.

Parameters
[in]parentGroup- Where the dataset is
[in]datasetName- Dataset name
Returns
Number of elements
Exceptions
ios::failure

Definition at line 1006 of file HDF5_File.cpp.

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size_t THDF5_File::GetDatasetNumberOfDimensions ( const hid_t  parentGroup,
TMatrixName datasetName 
)

Get number of dimensions of the dataset under a specified group.

Parameters
[in]parentGroup- Where the dataset is
[in]datasetName- Dataset name
Returns
Number of dimensions
Exceptions
ios::failure

Definition at line 982 of file HDF5_File.cpp.

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hid_t THDF5_File::GetRootGroup ( ) const
inline

Get handle to the root group.

Returns
handle to the root group

Definition at line 573 of file HDF5_File.h.

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bool THDF5_File::IsHDF5 ( const std::string &  fileName)
static

Check if the file exist.

Parameters
[in]fileName
Returns
true if the file exists.

Is a HDF5 file (can I access it)

Parameters
[in]fileName- Filename
Returns
true if I can access the file

Definition at line 158 of file HDF5_File.cpp.

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bool THDF5_File::IsOpen ( ) const
inline

Is the file opened?

Returns
true if the file is opened.

Definition at line 545 of file HDF5_File.h.

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void THDF5_File::Open ( const std::string &  fileName,
unsigned int  flags = H5F_ACC_RDONLY 
)

Open the HDF5 file.

Parameters
[in]fileName- File name
[in]flags- Flags for the HDF5 runtime
Exceptions
ios:failureif error happened.

Definition at line 127 of file HDF5_File.cpp.

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hid_t THDF5_File::OpenDataset ( const hid_t  parentGroup,
TMatrixName datasetName 
)

Open a dataset at a specified place in the file tree.

Parameters
[in]parentGroup- Parent group Id (can be the file Id for root).
[in]datasetName- Dataset name
Returns
A handle to open dataset
Exceptions
ios::failure

Definition at line 268 of file HDF5_File.cpp.

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hid_t THDF5_File::OpenGroup ( const hid_t  parentGroup,
TMatrixName groupName 
)

Open a HDF5 group at a specified place in the file tree.

Parameters
[in]parentGroup- Parent group
[in]groupName- Group name
Returns
A handle to the group
Exceptions
ios::failure

Definition at line 232 of file HDF5_File.cpp.

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void THDF5_File::ReadCompleteDataset ( const hid_t  parentGroup,
TMatrixName datasetName,
const TDimensionSizes dimensionSizes,
float *  data 
)

Read data from the dataset at a specified place in the file tree, float version.

Parameters
[in]parentGroup- Where is the dataset situated
[in]datasetName- Dataset name
[in]dimensionSizes- Dimension sizes
[out]data- Pointer to data
Exceptions
ios::failure

Definition at line 887 of file HDF5_File.cpp.

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void THDF5_File::ReadCompleteDataset ( const hid_t  parentGroup,
TMatrixName datasetName,
const TDimensionSizes dimensionSizes,
size_t *  data 
)

Read data from the dataset at a specified place in the file tree, index version.

Parameters
[in]parentGroup- Where is the dataset situated
[in]datasetName- Dataset name
[in]dimensionSizes- Dimension sizes
[out]data- Pointer to data
Exceptions
ios::failure

Definition at line 919 of file HDF5_File.cpp.

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THDF5_File::TMatrixDataType THDF5_File::ReadMatrixDataType ( const hid_t  parentGroup,
TMatrixName datasetName 
)

Read matrix data type from the dataset at a specified place in the file tree.

Parameters
[in]parentGroup- Where the dataset is
[in]datasetName- Dataset name
Returns
Matrix data type
Exceptions
ios::failure

Definition at line 1068 of file HDF5_File.cpp.

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THDF5_File::TMatrixDomainType THDF5_File::ReadMatrixDomainType ( const hid_t  parentGroup,
TMatrixName datasetName 
)

Read matrix dataset domain type at a specified place in the file tree.

Parameters
[in]parentGroup- Where the dataset is
[in]datasetName- Dataset name
Returns
Matrix domain type
Exceptions
ios::failure

Definition at line 1101 of file HDF5_File.cpp.

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void THDF5_File::ReadScalarValue ( const hid_t  parentGroup,
TMatrixName datasetName,
float &  value 
)

Read the scalar value under a specified group, float value.

Parameters
[in]parentGroup- Where to link the scalar dataset
[in]datasetName- HDF5 dataset name
[out]value- Data to be read

Definition at line 855 of file HDF5_File.cpp.

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void THDF5_File::ReadScalarValue ( const hid_t  parentGroup,
TMatrixName datasetName,
size_t &  value 
)

Read the scalar value under a specified group, index value.

Parameters
[in]parentGroup- Where to link the scalar dataset
[in]datasetName- HDF5 dataset name
[out]value- Data to be read

Definition at line 870 of file HDF5_File.cpp.

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string THDF5_File::ReadStringAttribute ( const hid_t  parentGroup,
TMatrixName datasetName,
TMatrixName attributeName 
)
inline

Read integer attribute at a specified place in the file tree.

Parameters
[in]parentGroup- Where the dataset is
[in]datasetName- Dataset name
[in]attributeName- Attribute name
Returns
Attribute value
Exceptions
ios::failure

Definition at line 1163 of file HDF5_File.cpp.

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void THDF5_File::WriteCuboidToHyperSlab ( const hid_t  dataset,
const TDimensionSizes hyperslabPosition,
const TDimensionSizes cuboidPosition,
const TDimensionSizes cuboidSize,
const TDimensionSizes matrixDimensions,
const float *  matrixData 
)

Write a cuboid selected within the matrixData into a hyperslab. The routine writes 3D cuboid into a 4D dataset (only intended for raw time series).

Parameters
[in]dataset- Dataset to write MatrixData into
[in]hyperslabPosition- Position in the dataset (hyperslab) - may be 3D/4D
[in]cuboidPosition- Position of the cuboid in MatrixData (what to sample) - must be 3D
[in]cuboidSize- Cuboid size (size of data being sampled) - must by 3D
[in]matrixDimensions- Size of the original matrix (the sampled one)
[in]matrixData- C array of MatrixData
Exceptions
ios::failure

Definition at line 618 of file HDF5_File.cpp.

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void THDF5_File::WriteDataByMaskToHyperSlab ( const hid_t  dataset,
const TDimensionSizes hyperslabPosition,
const size_t  indexSensorSize,
const size_t *  indexSensorData,
const TDimensionSizes matrixDimensions,
const float *  matrixData 
)

Write sensor data selected by the sensor mask. A routine pick elements from the MatixData based on the sensor data and store. them into a single hyperslab of size [Nsens, 1, 1].

Parameters
[in]dataset- Dataset to write MaatrixData into
[in]hyperslabPosition- 3D position in the dataset (hyperslab)
[in]indexSensorSize- Size of the index based sensor mask
[in]indexSensorData- Index based sensor mask
[in]matrixDimensions- Size of the sampled matrix
[in]matrixData- Matrix data
Warning
- Very slow at this version of HDF5 for orthogonal planes-> DO NOT USE
Exceptions
ios::failure

Definition at line 686 of file HDF5_File.cpp.

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void THDF5_File::WriteHyperSlab ( const hid_t  dataset,
const TDimensionSizes position,
const TDimensionSizes size,
const float *  data 
)

Write a hyperslab into the dataset, float version.

Parameters
[in]dataset- Dataset id
[in]position- Position in the dataset
[in]size- Size of the hyperslab
[in]data- Data to be written
Exceptions
ios::failure

Definition at line 473 of file HDF5_File.cpp.

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void THDF5_File::WriteHyperSlab ( const hid_t  dataset,
const TDimensionSizes position,
const TDimensionSizes size,
const size_t *  data 
)

Write a hyperslab into the dataset, index version.

Parameters
[in]dataset- Dataset id
[in]position- Position in the dataset
[in]size- Size of the hyperslab
[in]data- Data to be written
Exceptions
ios::failure

Definition at line 544 of file HDF5_File.cpp.

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void THDF5_File::WriteMatrixDataType ( const hid_t  parentGroup,
TMatrixName datasetName,
const TMatrixDataType matrixDataType 
)

Write matrix data type into the dataset at a specified place in the file tree.

Parameters
[in]parentGroup- Where the dataset is
[in]datasetName- Dataset name
[in]matrixDataType- Matrix data type in the file

Definition at line 1029 of file HDF5_File.cpp.

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void THDF5_File::WriteMatrixDomainType ( const hid_t  parentGroup,
TMatrixName datasetName,
const TMatrixDomainType matrixDomainType 
)

Write matrix data type into the dataset at a specified place in the file tree.

Parameters
[in]parentGroup- Where the dataset is
[in]datasetName- Dataset name
[in]matrixDomainType- Matrix domain type

Definition at line 1048 of file HDF5_File.cpp.

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void THDF5_File::WriteScalarValue ( const hid_t  parentGroup,
TMatrixName datasetName,
const float  value 
)

Write a scalar value at a specified place in the file tree (no chunks, no compression). Float value.

Parameters
[in]parentGroup- Where to link the scalar dataset
[in]datasetName- HDF5 dataset name
[in]value- data to be written
Exceptions
ios::failure

Definition at line 748 of file HDF5_File.cpp.

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void THDF5_File::WriteScalarValue ( const hid_t  parentGroup,
TMatrixName datasetName,
const size_t  value 
)

Write a scalar value at a specified place in the file tree (no chunks, no compression). Index value.

Parameters
[in]parentGroup- Where to link the scalar dataset
[in]datasetName- HDF5 dataset name
[in]value- Data to be written
Exceptions
ios::failure

Definition at line 803 of file HDF5_File.cpp.

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void THDF5_File::WriteStringAttribute ( const hid_t  parentGroup,
TMatrixName datasetName,
TMatrixName attributeName,
const std::string &  value 
)
inline

Write integer attribute at a specified place in the file tree.

Parameters
[in]parentGroup- Where the dataset is
[in]datasetName- Dataset name
[in]attributeName- Attribute name
[in]value- Data to write
Exceptions
ios::failure

Definition at line 1135 of file HDF5_File.cpp.

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