The class for 64b unsigned integers (indices). It is used for linear and cuboid corners masks to get the address of sampled voxels. More...

#include <IndexMatrix.h>

Inheritance diagram for IndexMatrix:

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Collaboration diagram for IndexMatrix:

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Public Member Functions
	IndexMatrix ()=delete
	Default constructor not allowed.

	IndexMatrix (const DimensionSizes &dimensionSizes)
	Constructor. More...

	IndexMatrix (const IndexMatrix &)=delete
	Copy constructor not allowed.

virtual	~IndexMatrix ()
	Destructor. More...

IndexMatrix &	operator= (const IndexMatrix &)
	Operator= is not allowed.

virtual void	readData (Hdf5File &file, MatrixName &matrixName)
	Read matrix from HDF5 file. More...

virtual void	writeData (Hdf5File &file, MatrixName &matrixName, const size_t compressionLevel)
	Write data into HDF5 file. More...

size_t &	operator[] (const size_t &index)
	operator []. More...

const size_t &	operator[] (const size_t &index) const
	operator [], constant version. More...

DimensionSizes	getTopLeftCorner (const size_t &index) const
	Get the top left corner of the index-th cuboid. More...

DimensionSizes	getBottomRightCorner (const size_t &index) const
	Get the top bottom right of the index-th cuboid. More...

void	recomputeIndicesToCPP ()
	Recompute indices MATALAB->C++. More...

void	recomputeIndicesToMatlab ()
	Recompute indices C++ -> MATLAB. More...

size_t	getSizeOfAllCuboids () const
	Get total number of elements in all cuboids to be able to allocate output file. More...

Public Member Functions inherited from BaseIndexMatrix
	BaseIndexMatrix ()
	Default constructor. More...

	BaseIndexMatrix (const BaseIndexMatrix &)=delete
	Copy constructor is not allowed.

virtual	~BaseIndexMatrix ()
	Destructor.

BaseIndexMatrix &	operator= (const BaseIndexMatrix &)=delete
	operator= is not allowed.

virtual const DimensionSizes &	getDimensionSizes () const
	Get dimension sizes of the matrix. More...

virtual size_t	size () const
	Size of the matrix. More...

virtual size_t	capacity () const
	The capacity of the matrix (this may differ from size due to padding, etc.). More...

virtual void	zeroMatrix ()
	Zero all elements of the matrix (NUMA first touch). More...

virtual size_t *	getData ()
	Get raw data out of the class (for direct kernel access). More...

virtual const size_t *	getData () const
	Get raw data out of the class (for direct kernel access), const version. More...

Public Member Functions inherited from BaseMatrix
	BaseMatrix ()
	Default constructor.

	BaseMatrix (const BaseMatrix &)=delete
	Copy constructor is not allowed.

virtual	~BaseMatrix ()
	Destructor.

BaseMatrix &	operator= (const BaseMatrix &)=delete
	Operator= is not allowed.

Private Member Functions
void	initDimensions (const DimensionSizes &dimensionSizes)
	Init dimension. More...

Static Private Attributes
static constexpr size_t	kChunkSize1D4MB = 1048576
	Number of elements to get 4MB block of data.

static constexpr size_t	kChunkSize1D1MB = 262144
	Number of elements to get 1MB block of data.

static constexpr size_t	kChunkSize1D256kB = 65536
	Number of elements to get 256KB block of data.

Additional Inherited Members
Protected Member Functions inherited from BaseIndexMatrix
virtual void	allocateMemory ()
	Aligned memory allocation (both on CPU and GPU). More...

virtual void	freeMemory ()
	Memory deallocation (both on CPU and GPU) More...

Protected Attributes inherited from BaseIndexMatrix
size_t	mSize
	Total number of elements.

size_t	mCapacity
	Total number of allocated elements (in terms of size_t).

DimensionSizes	mDimensionSizes
	Dimension sizes.

size_t	mRowSize
	Size of 1D row in X dimension.

size_t	mSlabSize
	Size of a XY slab.

size_t *	mData
	Raw matrix data.

Detailed Description

The class for 64b unsigned integers (indices). It is used for linear and cuboid corners masks to get the get the address of sampled voxels.

Definition at line 47 of file IndexMatrix.h.

Constructor & Destructor Documentation

◆ IndexMatrix()

IndexMatrix::IndexMatrix ( const DimensionSizes & dimensionSizes )

Parameters

[in] dimensionSizes - Dimension sizes of the matrix.

Constructor allocating memory.

Definition at line 50 of file IndexMatrix.cpp.

◆ ~IndexMatrix()

IndexMatrix::~IndexMatrix ( )

virtual

Destructor.

Definition at line 61 of file IndexMatrix.cpp.

Member Function Documentation

◆ getBottomRightCorner()

DimensionSizes IndexMatrix::getBottomRightCorner ( const size_t & index ) const

Parameters

[in] index - Index of the cuboid

Returns: The bottom right corner

Get the top bottom right of the index-th cuboid. Cuboids are stored as 6-tuples (two 3D coordinates). This gives the first three coordinates. This routine works only on the CPU side.

Definition at line 156 of file IndexMatrix.cpp.

◆ getSizeOfAllCuboids()

size_t IndexMatrix::getSizeOfAllCuboids ( ) const

Returns: Total sampled grid points

Get total number of elements in all cuboids to be able to allocate output file.

Definition at line 195 of file IndexMatrix.cpp.

◆ getTopLeftCorner()

DimensionSizes IndexMatrix::getTopLeftCorner ( const size_t & index ) const

Parameters

[in] index - Index of the cuboid

Returns: The top left corner

Get the top left corner of the index-th cuboid. Cuboids are stored as 6-tuples (two 3D coordinates). This gives the first three coordinates.

Definition at line 142 of file IndexMatrix.cpp.

◆ initDimensions()

void IndexMatrix::initDimensions ( const DimensionSizes & dimensionSizes )

private

Set necessary dimensions and auxiliary variables.

Definition at line 218 of file IndexMatrix.cpp.

◆ operator[]() [1/2]

size_t& IndexMatrix::operator[] ( const size_t & index )

inline

Parameters

[in] index - 1D index into the matrix.

Returns: An element of the matrix.

Definition at line 92 of file IndexMatrix.h.

◆ operator[]() [2/2]

const size_t& IndexMatrix::operator[] ( const size_t & index ) const

inline

Parameters

[in] index - 1D index into the matrix.

Returns: An element of the matrix.

Definition at line 98 of file IndexMatrix.h.

◆ readData()

void IndexMatrix::readData	(	Hdf5File &	file,
		MatrixName &	matrixName
	)

virtual

Read matrix from HDF5 file.

Parameters

[in]	file	- Handle to the HDF5 file
[in]	matrixName	- HDF5 dataset name to read from

Exceptions

ios::failure - If error occurred.

Read data from HDF5 file (only from the root group).

Implements BaseMatrix.

Definition at line 70 of file IndexMatrix.cpp.

◆ recomputeIndicesToCPP()

void IndexMatrix::recomputeIndicesToCPP ( )

Recompute indeces, MATLAB -> C++.

Definition at line 169 of file IndexMatrix.cpp.

◆ recomputeIndicesToMatlab()

void IndexMatrix::recomputeIndicesToMatlab ( )

Recompute indeces, C++ -> MATLAB.

Definition at line 182 of file IndexMatrix.cpp.

◆ writeData()

void IndexMatrix::writeData	(	Hdf5File &	file,
		MatrixName &	matrixName,
		const size_t	compressionLevel
	)

virtual

Write data into HDF5 file.

Parameters

[in]	file	- Handle to the HDF5 file
[in]	matrixName	- HDF5 dataset name to write to
[in]	compressionLevel	- Compression level for the HDF5 dataset

Exceptions

ios::failure - If an error occurred.

Write data to HDF5 file.

Implements BaseMatrix.

Definition at line 94 of file IndexMatrix.cpp.

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

MatrixClasses/IndexMatrix.h
MatrixClasses/IndexMatrix.cpp

Public Member Functions

Private Member Functions

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ IndexMatrix()

◆ ~IndexMatrix()

Member Function Documentation

◆ getBottomRightCorner()

◆ getSizeOfAllCuboids()

◆ getTopLeftCorner()

◆ initDimensions()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ readData()

◆ recomputeIndicesToCPP()

◆ recomputeIndicesToMatlab()

◆ writeData()