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vtkHDFReader::Implementation Class Reference

Implementation for the vtkHDFReader. More...

#include <vtkHDFReaderImplementation.h>

Classes

struct  TypeDescription
 Used to store HDF native types in a map. More...
 

Public Member Functions

 Implementation (vtkHDFReader *reader)
 
virtual ~Implementation ()
 
bool Open (VTK_FILEPATH const char *fileName)
 Opens this VTK HDF file and checks if it is valid. More...
 
void Close ()
 Closes the VTK HDF file and releases any allocated resources. More...
 
int GetDataSetType ()
 Type of vtkDataSet stored by the HDF file, such as VTK_IMAGE_DATA or VTK_UNSTRUCTURED_GRID, from vtkTypes.h. More...
 
const std::array< int, 2 > & GetVersion ()
 Returns the version of the VTK HDF implementation. More...
 
template<typename T >
bool GetAttribute (const char *attributeName, size_t numberOfElements, T *value)
 Reads an attribute from the /VTKHDF group. More...
 
template<typename T >
bool GetAttribute (hid_t group, const char *attributeName, size_t numberOfElements, T *value)
 Reads an attribute from the group passed to it. More...
 
int GetNumberOfPieces (vtkIdType step=-1)
 Returns the number of partitions for this dataset at the time step step if applicable. More...
 
bool GetPartitionExtent (hsize_t partitionIndex, int *extent)
 For an ImageData, sets the extent for 'partitionIndex'. More...
 
std::vector< std::string > GetArrayNames (int attributeType)
 Returns the names of arrays for 'attributeType' (point or cell). More...
 
std::vector< std::string > GetOrderedChildrenOfGroup (const std::string &path)
 Return the name of all children of an HDF group given its path. More...
 
std::vector< hsize_t > GetDimensions (const char *dataset)
 Returns the dimensions of a HDF dataset. More...
 
bool IsPathSoftLink (const std::string &path)
 Return true if current root path is a soft link. More...
 
bool FillAMR (vtkOverlappingAMR *data, unsigned int maximumLevelsToReadByDefault, double origin[3], vtkDataArraySelection *dataArraySelection[3])
 Fills the given AMR data with the content of the opened HDF file. More...
 
vtkIdType GetArrayOffset (vtkIdType step, int attributeType, std::string name)
 Methods to query for array offsets when steps are present. More...
 
bool OpenGroupAsVTKGroup (const std::string &groupPath)
 Open a sub group of the current file and consider it as the new root file. More...
 
bool RetrieveHDFInformation (const std::string &rootName)
 Initialize meta information of the implementation based on root name specified. More...
 
vtkDataArrayNewArray (int attributeType, const char *name, const std::vector< hsize_t > &fileExtent)
 Reads and returns a new vtkDataArray. More...
 
vtkDataArrayNewArray (int attributeType, const char *name, hsize_t offset, hsize_t size)
 Reads and returns a new vtkDataArray. More...
 
vtkAbstractArrayNewFieldArray (const char *name, vtkIdType offset=-1, vtkIdType size=-1)
 Reads and returns a new vtkDataArray. More...
 
vtkDataArrayNewMetadataArray (const char *name, hsize_t offset, hsize_t size)
 Reads a 1D metadata array in a DataArray or a vector of vtkIdType. More...
 
std::vector< vtkIdTypeGetMetadata (const char *name, hsize_t size, hsize_t offset=0)
 Reads a 1D metadata array in a DataArray or a vector of vtkIdType. More...
 
bool FillAssembly (vtkDataAssembly *data)
 Fills the given Assembly with the content of the opened HDF file. More...
 
bool FillAssembly (vtkDataAssembly *data, hid_t assemblyHandle, int assemblyID, std::string path)
 Fills the given Assembly with the content of the opened HDF file. More...
 
std::size_t GetNumberOfSteps ()
 Read the number of steps from the opened file. More...
 
std::size_t GetNumberOfSteps (hid_t group)
 Read the number of steps from the opened file. More...
 
vtkDataArrayGetStepValues ()
 Read the values of the steps from the open file. More...
 
vtkDataArrayGetStepValues (hid_t group)
 Read the values of the steps from the open file. More...
 

Protected Member Functions

hid_t OpenDataSet (hid_t group, const char *name, hid_t *nativeType, std::vector< hsize_t > &dims)
 Opens the hdf5 dataset given the 'group' and 'name'. More...
 
template<typename T >
hid_t TemplateTypeToHdfNativeType ()
 Convert C++ template type T to HDF5 native type this can be constexpr in C++17 standard. More...
 
template<typename T >
vtkDataArrayNewVtkDataArray ()
 Create a vtkDataArray based on the C++ template type T. More...
 
void BuildTypeReaderMap ()
 Builds a map between native types and GetArray routines for that type. More...
 
TypeDescription GetTypeDescription (hid_t type)
 Associates a struct of three integers with HDF type. More...
 
vtkDataArrayNewArrayForGroup (hid_t group, const char *name, const std::vector< hsize_t > &fileExtent)
 Reads a vtkDataArray of type T from the attributeType, dataset The array has type 'T' and 'numberOfComponents'. More...
 
vtkDataArrayNewArrayForGroup (hid_t dataset, hid_t nativeType, const std::vector< hsize_t > &dims, const std::vector< hsize_t > &fileExtent)
 Reads a vtkDataArray of type T from the attributeType, dataset The array has type 'T' and 'numberOfComponents'. More...
 
template<typename T >
vtkDataArrayNewArray (hid_t dataset, const std::vector< hsize_t > &fileExtent, hsize_t numberOfComponents)
 Reads a vtkDataArray of type T from the attributeType, dataset The array has type 'T' and 'numberOfComponents'. More...
 
template<typename T >
bool NewArray (hid_t dataset, const std::vector< hsize_t > &fileExtent, hsize_t numberOfComponents, T *data)
 Reads a vtkDataArray of type T from the attributeType, dataset The array has type 'T' and 'numberOfComponents'. More...
 
vtkStringArrayNewStringArray (hid_t dataset, hsize_t size)
 Reads a vtkDataArray of type T from the attributeType, dataset The array has type 'T' and 'numberOfComponents'. More...
 

Detailed Description

Implementation for the vtkHDFReader.

Opens, closes and reads information from a VTK HDF file.

Definition at line 30 of file vtkHDFReaderImplementation.h.

Constructor & Destructor Documentation

◆ Implementation()

vtkHDFReader::Implementation::Implementation ( vtkHDFReader reader)

◆ ~Implementation()

virtual vtkHDFReader::Implementation::~Implementation ( )
virtual

Member Function Documentation

◆ Open()

bool vtkHDFReader::Implementation::Open ( VTK_FILEPATH const char *  fileName)

Opens this VTK HDF file and checks if it is valid.

◆ Close()

void vtkHDFReader::Implementation::Close ( )

Closes the VTK HDF file and releases any allocated resources.

◆ GetDataSetType()

int vtkHDFReader::Implementation::GetDataSetType ( )
inline

Type of vtkDataSet stored by the HDF file, such as VTK_IMAGE_DATA or VTK_UNSTRUCTURED_GRID, from vtkTypes.h.

Definition at line 47 of file vtkHDFReaderImplementation.h.

◆ GetVersion()

const std::array<int, 2>& vtkHDFReader::Implementation::GetVersion ( )
inline

Returns the version of the VTK HDF implementation.

Definition at line 51 of file vtkHDFReaderImplementation.h.

◆ GetAttribute() [1/2]

template<typename T >
bool vtkHDFReader::Implementation::GetAttribute ( const char *  attributeName,
size_t  numberOfElements,
T *  value 
)

Reads an attribute from the /VTKHDF group.

◆ GetAttribute() [2/2]

template<typename T >
bool vtkHDFReader::Implementation::GetAttribute ( hid_t  group,
const char *  attributeName,
size_t  numberOfElements,
T *  value 
)

Reads an attribute from the group passed to it.

◆ GetNumberOfPieces()

int vtkHDFReader::Implementation::GetNumberOfPieces ( vtkIdType  step = -1)

Returns the number of partitions for this dataset at the time step step if applicable.

◆ GetPartitionExtent()

bool vtkHDFReader::Implementation::GetPartitionExtent ( hsize_t  partitionIndex,
int *  extent 
)

For an ImageData, sets the extent for 'partitionIndex'.

Returns true for success and false otherwise.

◆ GetArrayNames()

std::vector<std::string> vtkHDFReader::Implementation::GetArrayNames ( int  attributeType)

Returns the names of arrays for 'attributeType' (point or cell).

◆ GetOrderedChildrenOfGroup()

std::vector<std::string> vtkHDFReader::Implementation::GetOrderedChildrenOfGroup ( const std::string &  path)

Return the name of all children of an HDF group given its path.

◆ NewArray() [1/4]

vtkDataArray* vtkHDFReader::Implementation::NewArray ( int  attributeType,
const char *  name,
const std::vector< hsize_t > &  fileExtent 
)

Reads and returns a new vtkDataArray.

The actual type of the array depends on the type of the HDF array. The array is read from the PointData or CellData groups depending on the 'attributeType' parameter. There are two versions: a first one that reads from a 3D array using a fileExtent, and a second one that reads from a linear array using an offset and size. The array has to be deleted by the user.

◆ NewArray() [2/4]

vtkDataArray* vtkHDFReader::Implementation::NewArray ( int  attributeType,
const char *  name,
hsize_t  offset,
hsize_t  size 
)

Reads and returns a new vtkDataArray.

The actual type of the array depends on the type of the HDF array. The array is read from the PointData or CellData groups depending on the 'attributeType' parameter. There are two versions: a first one that reads from a 3D array using a fileExtent, and a second one that reads from a linear array using an offset and size. The array has to be deleted by the user.

◆ NewFieldArray()

vtkAbstractArray* vtkHDFReader::Implementation::NewFieldArray ( const char *  name,
vtkIdType  offset = -1,
vtkIdType  size = -1 
)

Reads and returns a new vtkDataArray.

The actual type of the array depends on the type of the HDF array. The array is read from the PointData or CellData groups depending on the 'attributeType' parameter. There are two versions: a first one that reads from a 3D array using a fileExtent, and a second one that reads from a linear array using an offset and size. The array has to be deleted by the user.

◆ NewMetadataArray()

vtkDataArray* vtkHDFReader::Implementation::NewMetadataArray ( const char *  name,
hsize_t  offset,
hsize_t  size 
)

Reads a 1D metadata array in a DataArray or a vector of vtkIdType.

We read either the whole array for the vector version or a slice specified with (offset, size). For an error we return nullptr or an empty vector.

◆ GetMetadata()

std::vector<vtkIdType> vtkHDFReader::Implementation::GetMetadata ( const char *  name,
hsize_t  size,
hsize_t  offset = 0 
)

Reads a 1D metadata array in a DataArray or a vector of vtkIdType.

We read either the whole array for the vector version or a slice specified with (offset, size). For an error we return nullptr or an empty vector.

◆ GetDimensions()

std::vector<hsize_t> vtkHDFReader::Implementation::GetDimensions ( const char *  dataset)

Returns the dimensions of a HDF dataset.

◆ IsPathSoftLink()

bool vtkHDFReader::Implementation::IsPathSoftLink ( const std::string &  path)

Return true if current root path is a soft link.

◆ FillAMR()

bool vtkHDFReader::Implementation::FillAMR ( vtkOverlappingAMR data,
unsigned int  maximumLevelsToReadByDefault,
double  origin[3],
vtkDataArraySelection dataArraySelection[3] 
)

Fills the given AMR data with the content of the opened HDF file.

The number of level to read is limited by the maximumLevelsToReadByDefault argument. maximumLevelsToReadByDefault == 0 means to read all levels (no limit). Only the selected data array in dataArraySelection are added to the AMR data. Returns true on success.

◆ FillAssembly() [1/2]

bool vtkHDFReader::Implementation::FillAssembly ( vtkDataAssembly data)

Fills the given Assembly with the content of the opened HDF file.

Return true on success, false if the HDF File isn't a composite or the 'Assembly' is missing.

◆ FillAssembly() [2/2]

bool vtkHDFReader::Implementation::FillAssembly ( vtkDataAssembly data,
hid_t  assemblyHandle,
int  assemblyID,
std::string  path 
)

Fills the given Assembly with the content of the opened HDF file.

Return true on success, false if the HDF File isn't a composite or the 'Assembly' is missing.

◆ GetNumberOfSteps() [1/2]

std::size_t vtkHDFReader::Implementation::GetNumberOfSteps ( )

Read the number of steps from the opened file.

◆ GetNumberOfSteps() [2/2]

std::size_t vtkHDFReader::Implementation::GetNumberOfSteps ( hid_t  group)

Read the number of steps from the opened file.

◆ GetStepValues() [1/2]

vtkDataArray* vtkHDFReader::Implementation::GetStepValues ( )

Read the values of the steps from the open file.

◆ GetStepValues() [2/2]

vtkDataArray* vtkHDFReader::Implementation::GetStepValues ( hid_t  group)

Read the values of the steps from the open file.

◆ GetArrayOffset()

vtkIdType vtkHDFReader::Implementation::GetArrayOffset ( vtkIdType  step,
int  attributeType,
std::string  name 
)

Methods to query for array offsets when steps are present.

◆ OpenGroupAsVTKGroup()

bool vtkHDFReader::Implementation::OpenGroupAsVTKGroup ( const std::string &  groupPath)

Open a sub group of the current file and consider it as the new root file.

◆ RetrieveHDFInformation()

bool vtkHDFReader::Implementation::RetrieveHDFInformation ( const std::string &  rootName)

Initialize meta information of the implementation based on root name specified.

◆ OpenDataSet()

hid_t vtkHDFReader::Implementation::OpenDataSet ( hid_t  group,
const char *  name,
hid_t nativeType,
std::vector< hsize_t > &  dims 
)
protected

Opens the hdf5 dataset given the 'group' and 'name'.

Returns the hdf dataset and sets 'nativeType' and 'dims'. The caller needs to close the returned hid_t manually using H5Dclose or a Scoped Handle if it is not an invalid hid.

◆ TemplateTypeToHdfNativeType()

template<typename T >
hid_t vtkHDFReader::Implementation::TemplateTypeToHdfNativeType ( )
protected

Convert C++ template type T to HDF5 native type this can be constexpr in C++17 standard.

◆ NewVtkDataArray()

template<typename T >
vtkDataArray* vtkHDFReader::Implementation::NewVtkDataArray ( )
protected

Create a vtkDataArray based on the C++ template type T.

For instance, for a float we create a vtkFloatArray. this can be constexpr in C++17 standard

◆ NewArrayForGroup() [1/2]

vtkDataArray* vtkHDFReader::Implementation::NewArrayForGroup ( hid_t  group,
const char *  name,
const std::vector< hsize_t > &  fileExtent 
)
protected

Reads a vtkDataArray of type T from the attributeType, dataset The array has type 'T' and 'numberOfComponents'.

We are reading fileExtent slab from the array. It returns the array or nullptr in case of an error. There are three cases for fileExtent: fileExtent.size() == 0 - in this case we expect a 1D array and we read the whole array. Used for field arrays. fileExtent.size()>>1 == ndims - in this case we read a scalar fileExtent.size()>>1 + 1 == ndims - in this case we read an array with the number of components > 1.

◆ NewArrayForGroup() [2/2]

vtkDataArray* vtkHDFReader::Implementation::NewArrayForGroup ( hid_t  dataset,
hid_t  nativeType,
const std::vector< hsize_t > &  dims,
const std::vector< hsize_t > &  fileExtent 
)
protected

Reads a vtkDataArray of type T from the attributeType, dataset The array has type 'T' and 'numberOfComponents'.

We are reading fileExtent slab from the array. It returns the array or nullptr in case of an error. There are three cases for fileExtent: fileExtent.size() == 0 - in this case we expect a 1D array and we read the whole array. Used for field arrays. fileExtent.size()>>1 == ndims - in this case we read a scalar fileExtent.size()>>1 + 1 == ndims - in this case we read an array with the number of components > 1.

◆ NewArray() [3/4]

template<typename T >
vtkDataArray* vtkHDFReader::Implementation::NewArray ( hid_t  dataset,
const std::vector< hsize_t > &  fileExtent,
hsize_t  numberOfComponents 
)
protected

Reads a vtkDataArray of type T from the attributeType, dataset The array has type 'T' and 'numberOfComponents'.

We are reading fileExtent slab from the array. It returns the array or nullptr in case of an error. There are three cases for fileExtent: fileExtent.size() == 0 - in this case we expect a 1D array and we read the whole array. Used for field arrays. fileExtent.size()>>1 == ndims - in this case we read a scalar fileExtent.size()>>1 + 1 == ndims - in this case we read an array with the number of components > 1.

◆ NewArray() [4/4]

template<typename T >
bool vtkHDFReader::Implementation::NewArray ( hid_t  dataset,
const std::vector< hsize_t > &  fileExtent,
hsize_t  numberOfComponents,
T *  data 
)
protected

Reads a vtkDataArray of type T from the attributeType, dataset The array has type 'T' and 'numberOfComponents'.

We are reading fileExtent slab from the array. It returns the array or nullptr in case of an error. There are three cases for fileExtent: fileExtent.size() == 0 - in this case we expect a 1D array and we read the whole array. Used for field arrays. fileExtent.size()>>1 == ndims - in this case we read a scalar fileExtent.size()>>1 + 1 == ndims - in this case we read an array with the number of components > 1.

◆ NewStringArray()

vtkStringArray* vtkHDFReader::Implementation::NewStringArray ( hid_t  dataset,
hsize_t  size 
)
protected

Reads a vtkDataArray of type T from the attributeType, dataset The array has type 'T' and 'numberOfComponents'.

We are reading fileExtent slab from the array. It returns the array or nullptr in case of an error. There are three cases for fileExtent: fileExtent.size() == 0 - in this case we expect a 1D array and we read the whole array. Used for field arrays. fileExtent.size()>>1 == ndims - in this case we read a scalar fileExtent.size()>>1 + 1 == ndims - in this case we read an array with the number of components > 1.

◆ BuildTypeReaderMap()

void vtkHDFReader::Implementation::BuildTypeReaderMap ( )
protected

Builds a map between native types and GetArray routines for that type.

◆ GetTypeDescription()

TypeDescription vtkHDFReader::Implementation::GetTypeDescription ( hid_t  type)
protected

Associates a struct of three integers with HDF type.

This can be used as key in a map.


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