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// SPDX-FileCopyrightText: Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
// SPDX-License-Identifier: BSD-3-Clause
/**
* @class vtkHDFReaderImplementation
* @brief Implementation class for vtkHDFReader
*
*/
#ifndef vtkHDFReaderImplementation_h
#define vtkHDFReaderImplementation_h
#include "vtkHDFReader.h"
#include "vtk_hdf5.h"
#include <array>
#include <map>
#include <string>
#include <vector>
VTK_ABI_NAMESPACE_BEGIN
class vtkAbstractArray;
class vtkDataArray;
class vtkStringArray;
/**
* Implementation for the vtkHDFReader. Opens, closes and
* reads information from a VTK HDF file.
*/
class vtkHDFReader::Implementation
{
public:
Implementation(vtkHDFReader* reader);
virtual ~Implementation();
/**
* Opens this VTK HDF file and checks if it is valid.
*/
bool Open(VTK_FILEPATH const char* fileName);
/**
* Closes the VTK HDF file and releases any allocated resources.
*/
void Close();
/**
* Type of vtkDataSet stored by the HDF file, such as VTK_IMAGE_DATA or
* VTK_UNSTRUCTURED_GRID, from vtkTypes.h
*/
int GetDataSetType() { return this->DataSetType; }
/**
* Returns the version of the VTK HDF implementation.
*/
const std::array<int, 2>& GetVersion() { return this->Version; }
/**
* Reads an attribute from the /VTKHDF group
*/
template <typename T>
bool GetAttribute(const char* attributeName, size_t numberOfElements, T* value);
/**
* Reads an attribute from the group passed to it
*/
template <typename T>
bool GetAttribute(hid_t group, const char* attributeName, size_t numberOfElements, T* value);
/**
* Returns the number of partitions for this dataset at the time step
* `step` if applicable.
*/
int GetNumberOfPieces(vtkIdType step = -1);
/**
* For an ImageData, sets the extent for 'partitionIndex'. Returns
* true for success and false otherwise.
*/
bool GetPartitionExtent(hsize_t partitionIndex, int* extent);
/**
* Returns the names of arrays for 'attributeType' (point or cell).
*/
std::vector<std::string> GetArrayNames(int attributeType);
///@{
/**
* 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.
*/
vtkDataArray* NewArray(
int attributeType, const char* name, const std::vector<hsize_t>& fileExtent);
vtkDataArray* NewArray(int attributeType, const char* name, hsize_t offset, hsize_t size);
vtkAbstractArray* NewFieldArray(const char* name, vtkIdType offset = -1, vtkIdType size = -1);
///@}
///@{
/**
* 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.
*/
vtkDataArray* NewMetadataArray(const char* name, hsize_t offset, hsize_t size);
std::vector<vtkIdType> GetMetadata(const char* name, hsize_t size, hsize_t offset = 0);
///@}
/**
* Returns the dimensions of a HDF dataset.
*/
std::vector<hsize_t> GetDimensions(const char* dataset);
/**
* 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.
*/
bool FillAMR(vtkOverlappingAMR* data, unsigned int maximumLevelsToReadByDefault, double origin[3],
vtkDataArraySelection* dataArraySelection[3]);
///@{
/**
* Read the number of steps from the opened file
*/
std::size_t GetNumberOfSteps();
std::size_t GetNumberOfSteps(hid_t group);
///@}
///@{
/**
* Read the values of the steps from the open file
*/
vtkDataArray* GetStepValues();
vtkDataArray* GetStepValues(hid_t group);
///@}
/**
* Methods to query for array offsets when steps are present
*/
vtkIdType GetArrayOffset(vtkIdType step, int attributeType, std::string name);
protected:
/**
* Used to store HDF native types in a map
*/
struct TypeDescription
{
int Class;
size_t Size;
int Sign;
TypeDescription()
: Class(H5T_NO_CLASS)
, Size(0)
, Sign(H5T_SGN_ERROR)
{
}
bool operator<(const TypeDescription& other) const
{
return Class < other.Class || (Class == other.Class && Size < other.Size) ||
(Class == other.Class && Size == other.Size && Sign < other.Sign);
}
};
/**
* Opens the hdf5 dataset given the 'group'
* and 'name'.
* Returns the hdf dataset and sets 'nativeType' and 'dims'.
*/
hid_t OpenDataSet(hid_t group, const char* name, hid_t* nativeType, std::vector<hsize_t>& dims);
/**
* Convert C++ template type T to HDF5 native type
* this can be constexpr in C++17 standard
*/
template <typename T>
hid_t TemplateTypeToHdfNativeType();
/**
* 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
*/
template <typename T>
vtkDataArray* NewVtkDataArray();
///@{
/**
* 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.
*/
vtkDataArray* NewArrayForGroup(
hid_t group, const char* name, const std::vector<hsize_t>& fileExtent);
vtkDataArray* NewArrayForGroup(hid_t dataset, hid_t nativeType, const std::vector<hsize_t>& dims,
const std::vector<hsize_t>& fileExtent);
template <typename T>
vtkDataArray* NewArray(
hid_t dataset, const std::vector<hsize_t>& fileExtent, hsize_t numberOfComponents);
template <typename T>
bool NewArray(
hid_t dataset, const std::vector<hsize_t>& fileExtent, hsize_t numberOfComponents, T* data);
vtkStringArray* NewStringArray(hid_t dataset, hsize_t size);
///@}
/**
* Builds a map between native types and GetArray routines for that type.
*/
void BuildTypeReaderMap();
/**
* Associates a struc of three integers with HDF type. This can be used as
* key in a map.
*/
TypeDescription GetTypeDescription(hid_t type);
private:
std::string FileName;
hid_t File;
hid_t VTKGroup;
// in the same order as vtkDataObject::AttributeTypes: POINT, CELL, FIELD
std::array<hid_t, 3> AttributeDataGroup;
int DataSetType;
int NumberOfPieces;
std::array<int, 2> Version;
vtkHDFReader* Reader;
using ArrayReader = vtkDataArray* (vtkHDFReader::Implementation::*)(hid_t dataset,
const std::vector<hsize_t>& fileExtent, hsize_t numberOfComponents);
std::map<TypeDescription, ArrayReader> TypeReaderMap;
bool ReadDataSetType();
///@{
/**
* These methods are valid only with AMR data set type.
*/
bool ComputeAMRBlocksPerLevels(std::vector<int>& levels);
bool ReadLevelSpacing(hid_t levelGroupID, double* spacing);
bool ReadAMRBoxRawValues(hid_t levelGroupID, std::vector<int>& amrBoxRawData);
bool ReadLevelTopology(unsigned int level, const std::string& levelGroupName,
vtkOverlappingAMR* data, double origin[3]);
bool ReadLevelData(unsigned int level, const std::string& levelGroupName, vtkOverlappingAMR* data,
vtkDataArraySelection* dataArraySelection[3]);
///@}
};
VTK_ABI_NAMESPACE_END
#endif
// VTK-HeaderTest-Exclude: vtkHDFReaderImplementation.h
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