TimeSeriesDatabase transforms a series of images stored on disk into a high performance database. More...

#include <Libs/vtkITK/itkTimeSeriesDatabase.h>

Inheritance diagram for itk::TimeSeriesDatabase< TPixel >:

Collaboration diagram for itk::TimeSeriesDatabase< TPixel >:

Classes
struct	CacheBlock
	our cache More...

Public Types
typedef Array< TPixel >	ArrayType

typedef SmartPointer< const Self >	ConstPointer

typedef WeakPointer< const Self >	ConstWeakPointer

typedef Image< TPixel, 3 >	OutputImageType

typedef OutputImageType::Pointer	OutputImageTypePointer

typedef Image< TPixel, 2 >	OutputSliceType

typedef OutputSliceType::Pointer	OutputSliceTypePointer

typedef SmartPointer< Self >	Pointer

typedef TimeSeriesDatabase	Self

typedef ImageSource< Image< TPixel, 3 > >	Superclass

Public Member Functions
void	Connect (const char *filename)

void	Disconnect ()

virtual void	GenerateData (void) ITK_OVERRIDE

virtual void	GenerateOutputInformation (void) ITK_OVERRIDE

float	GetCacheSizeInMiB ()

int	GetNumberOfVolumes ()

void	GetVoxelTimeSeries (typename OutputImageType::IndexType idx, ArrayType &array)

	itkGetMacro (CurrentImage, unsigned int)

	itkGetMacro (OutputSpacing, typename OutputImageType::SpacingType)

	itkGetMacro (OutputRegion, typename OutputImageType::RegionType)

	itkGetMacro (OutputOrigin, typename OutputImageType::PointType)

	itkGetMacro (OutputDirection, typename OutputImageType::DirectionType)

	itkNewMacro (Self)

	itkSetMacro (CurrentImage, unsigned int)

	itkTypeMacro (TimeSeriesDatabase, ImageSource)

void	SetCacheSizeInMiB (float sz)

Static Public Member Functions
static void	CreateFromFileArchetype (const char filename, const char archetype)

static void	CreateFromFileArchetype (const char filename, const char archetype, unsigned long BlocksPerFile)

Protected Types
typedef itk::TimeSeriesDatabaseHelper::counted_ptr< std::fstream >	StreamPtr

Protected Member Functions
unsigned int	CalculateFileIndex (unsigned long Index)

unsigned long	CalculateIndex (Size< 3 > Position, int ImageCount)

bool	CalculateIntersection (Size< 3 > BlockIndex, typename OutputImageType::RegionType RequestedRegion, typename OutputImageType::RegionType &BlockRegion, typename OutputImageType::RegionType &ImageRegion)
	Return true if this is a full block, false otherwise. Assumes there is overlap! More...

CacheBlock *	GetCacheBlock (unsigned long index)

bool	IsOpen () const

virtual void	PrintSelf (std::ostream &os, Indent indent) const ITK_OVERRIDE

	TimeSeriesDatabase ()

	~TimeSeriesDatabase ()

Static Protected Member Functions
static unsigned int	CalculateFileIndex (unsigned long Index, unsigned long BlocksPerFile)

static unsigned long	CalculateIndex (Size< 3 > Position, int ImageCount, unsigned int BlocksPerImage[3])

static std::streampos	CalculatePosition (unsigned long index, unsigned long BlocksPerFile)

Protected Attributes
unsigned long	m_BlocksPerFile

Array< unsigned int >	m_BlocksPerImage

TimeSeriesDatabaseHelper::LRUCache< unsigned long, CacheBlock >	m_Cache

unsigned int	m_CurrentImage

std::vector< std::string >	m_DatabaseFileNames

std::vector< StreamPtr >	m_DatabaseFiles

Array< unsigned int >	m_Dimensions

std::string	m_Filename

OutputImageType::DirectionType	m_OutputDirection

OutputImageType::PointType	m_OutputOrigin

OutputImageType::RegionType	m_OutputRegion

OutputImageType::SpacingType	m_OutputSpacing

Array< unsigned int >	m_PixelRemainder
	How many pixels are in the last block? More...

Detailed Description

template<class TPixel>
class itk::TimeSeriesDatabase< TPixel >

TimeSeriesDatabase transforms a series of images stored on disk into a high performance database.

The main idea behind TimeSeriesDatabase is to have a representation of a 4 dimensional dataset that is larger than main memory, but may still be accessed in a rapid manner. Though not strictly ITK conforming, this initial pass is strictly 4 dimensional datasets.

Definition at line 28 of file itkTimeSeriesDatabase.h.

Member Typedef Documentation

◆ ArrayType

template<class TPixel >

typedef Array<TPixel> itk::TimeSeriesDatabase< TPixel >::ArrayType

Definition at line 47 of file itkTimeSeriesDatabase.h.

◆ ConstPointer

template<class TPixel >

typedef SmartPointer<const Self> itk::TimeSeriesDatabase< TPixel >::ConstPointer

Definition at line 34 of file itkTimeSeriesDatabase.h.

◆ ConstWeakPointer

template<class TPixel >

typedef WeakPointer<const Self> itk::TimeSeriesDatabase< TPixel >::ConstWeakPointer

Definition at line 35 of file itkTimeSeriesDatabase.h.

◆ OutputImageType

template<class TPixel >

typedef Image<TPixel, 3> itk::TimeSeriesDatabase< TPixel >::OutputImageType

Definition at line 43 of file itkTimeSeriesDatabase.h.

◆ OutputImageTypePointer

template<class TPixel >

typedef OutputImageType::Pointer itk::TimeSeriesDatabase< TPixel >::OutputImageTypePointer

Definition at line 44 of file itkTimeSeriesDatabase.h.

◆ OutputSliceType

template<class TPixel >

typedef Image<TPixel, 2> itk::TimeSeriesDatabase< TPixel >::OutputSliceType

Definition at line 45 of file itkTimeSeriesDatabase.h.

◆ OutputSliceTypePointer

template<class TPixel >

typedef OutputSliceType::Pointer itk::TimeSeriesDatabase< TPixel >::OutputSliceTypePointer

Definition at line 46 of file itkTimeSeriesDatabase.h.

◆ Pointer

template<class TPixel >

typedef SmartPointer<Self> itk::TimeSeriesDatabase< TPixel >::Pointer

Definition at line 33 of file itkTimeSeriesDatabase.h.

◆ Self

template<class TPixel >

typedef TimeSeriesDatabase itk::TimeSeriesDatabase< TPixel >::Self

Definition at line 31 of file itkTimeSeriesDatabase.h.

◆ StreamPtr

template<class TPixel >

typedef itk::TimeSeriesDatabaseHelper::counted_ptr<std::fstream> itk::TimeSeriesDatabase< TPixel >::StreamPtr

protected

Definition at line 118 of file itkTimeSeriesDatabase.h.

◆ Superclass

template<class TPixel >

typedef ImageSource<Image<TPixel,3> > itk::TimeSeriesDatabase< TPixel >::Superclass

Definition at line 32 of file itkTimeSeriesDatabase.h.

Constructor & Destructor Documentation

◆ TimeSeriesDatabase()

template<class TPixel >

itk::TimeSeriesDatabase< TPixel >::TimeSeriesDatabase ( )

protected

◆ ~TimeSeriesDatabase()

template<class TPixel >

itk::TimeSeriesDatabase< TPixel >::~TimeSeriesDatabase ( )

protected

Member Function Documentation

◆ CalculateFileIndex() [1/2]

template<class TPixel >

unsigned int itk::TimeSeriesDatabase< TPixel >::CalculateFileIndex ( unsigned long Index )

protected

◆ CalculateFileIndex() [2/2]

template<class TPixel >

static unsigned int itk::TimeSeriesDatabase< TPixel >::CalculateFileIndex	(	unsigned long	Index,
		unsigned long	BlocksPerFile
	)

staticprotected

◆ CalculateIndex() [1/2]

template<class TPixel >

unsigned long itk::TimeSeriesDatabase< TPixel >::CalculateIndex	(	Size< 3 >	Position,
		int	ImageCount
	)

protected

◆ CalculateIndex() [2/2]

template<class TPixel >

static unsigned long itk::TimeSeriesDatabase< TPixel >::CalculateIndex	(	Size< 3 >	Position,
		int	ImageCount,
		unsigned int	BlocksPerImage[3]
	)

staticprotected

◆ CalculateIntersection()

template<class TPixel >

bool itk::TimeSeriesDatabase< TPixel >::CalculateIntersection	(	Size< 3 >	BlockIndex,
		typename OutputImageType::RegionType	RequestedRegion,
		typename OutputImageType::RegionType &	BlockRegion,
		typename OutputImageType::RegionType &	ImageRegion
	)

protected

Return true if this is a full block, false otherwise. Assumes there is overlap!

◆ CalculatePosition()

template<class TPixel >

static std::streampos itk::TimeSeriesDatabase< TPixel >::CalculatePosition	(	unsigned long	index,
		unsigned long	BlocksPerFile
	)

staticprotected

◆ Connect()

template<class TPixel >

void itk::TimeSeriesDatabase< TPixel >::Connect ( const char * filename )

Connect to an existing TimeSeriesDatabase file on disk The idea behind the Connect method is to associate this class with a pre-existing self-describing file containing a 4-dimensional dataset that is indexed for rapid retrieval.

◆ CreateFromFileArchetype() [1/2]

template<class TPixel >

static void itk::TimeSeriesDatabase< TPixel >::CreateFromFileArchetype	(	const char *	filename,
		const char *	archetype
	)

static

Create a new TimeSeriesDatabase from an Archetype filename Find all the volumes matching the archetype pattern, loading and checking that they are all the same size. Write the data into a series of files. The default filesize is 1 GiB, but may be changed using the overloaded method. A call to Connect in required to open the newly created TimeSeriesDatabase.

◆ CreateFromFileArchetype() [2/2]

template<class TPixel >

static void itk::TimeSeriesDatabase< TPixel >::CreateFromFileArchetype	(	const char *	filename,
		const char *	archetype,
		unsigned long	BlocksPerFile
	)

static

◆ Disconnect()

template<class TPixel >

void itk::TimeSeriesDatabase< TPixel >::Disconnect ( )

Disconnect from a TimeSeriesDatabase file Essentially closes the file and returns the object to its original state.

◆ GenerateData()

template<class TPixel >

virtual void itk::TimeSeriesDatabase< TPixel >::GenerateData ( void )

virtual

◆ GenerateOutputInformation()

template<class TPixel >

virtual void itk::TimeSeriesDatabase< TPixel >::GenerateOutputInformation ( void )

virtual

Standard method for a ImageSource object

◆ GetCacheBlock()

template<class TPixel >

CacheBlock* itk::TimeSeriesDatabase< TPixel >::GetCacheBlock ( unsigned long index )

protected

◆ GetCacheSizeInMiB()

template<class TPixel >

float itk::TimeSeriesDatabase< TPixel >::GetCacheSizeInMiB ( )

Get the size of the cache in MiB (1 MiB = 2^20 bytes)

◆ GetNumberOfVolumes()

template<class TPixel >

int itk::TimeSeriesDatabase< TPixel >::GetNumberOfVolumes ( )

inline

Return information about the TimeSeriesDatabase file

Definition at line 81 of file itkTimeSeriesDatabase.h.

◆ GetVoxelTimeSeries()

template<class TPixel >

void itk::TimeSeriesDatabase< TPixel >::GetVoxelTimeSeries	(	typename OutputImageType::IndexType	idx,
		ArrayType &	array
	)

A convenience method for reading a voxel's time course Subsequent calls to voxels in the immediate region of this will be cached for quick access

◆ IsOpen()

template<class TPixel >

bool itk::TimeSeriesDatabase< TPixel >::IsOpen ( ) const

protected

◆ itkGetMacro() [1/5]

template<class TPixel >

itk::TimeSeriesDatabase< TPixel >::itkGetMacro	(	CurrentImage	,
		unsigned	int
	)

◆ itkGetMacro() [2/5]

template<class TPixel >

itk::TimeSeriesDatabase< TPixel >::itkGetMacro	(	OutputSpacing	,
		typename OutputImageType::SpacingType
	)

◆ itkGetMacro() [3/5]

template<class TPixel >

itk::TimeSeriesDatabase< TPixel >::itkGetMacro	(	OutputRegion	,
		typename OutputImageType::RegionType
	)

◆ itkGetMacro() [4/5]

template<class TPixel >

itk::TimeSeriesDatabase< TPixel >::itkGetMacro	(	OutputOrigin	,
		typename OutputImageType::PointType
	)

◆ itkGetMacro() [5/5]

template<class TPixel >

itk::TimeSeriesDatabase< TPixel >::itkGetMacro	(	OutputDirection	,
		typename OutputImageType::DirectionType
	)

◆ itkNewMacro()

template<class TPixel >

itk::TimeSeriesDatabase< TPixel >::itkNewMacro ( Self )

Method for creation through the object factory.

◆ itkSetMacro()

template<class TPixel >

itk::TimeSeriesDatabase< TPixel >::itkSetMacro	(	CurrentImage	,
		unsigned	int
	)

Set the image to be read when GenerateData is called. This method selects the image to be returned by an Update call. By changing the CurrentImage, a pipeline can process each image in the series one after another.

◆ itkTypeMacro()

template<class TPixel >

itk::TimeSeriesDatabase< TPixel >::itkTypeMacro	(	TimeSeriesDatabase< TPixel >	,
		ImageSource
	)

Run-time type information (and related methods).

◆ PrintSelf()

template<class TPixel >

virtual void itk::TimeSeriesDatabase< TPixel >::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)		const

protectedvirtual

◆ SetCacheSizeInMiB()

template<class TPixel >

void itk::TimeSeriesDatabase< TPixel >::SetCacheSizeInMiB ( float sz )

Set the size of the cache in MiB (1 MiB = 2^20 bytes)

Member Data Documentation

◆ m_BlocksPerFile

template<class TPixel >

unsigned long itk::TimeSeriesDatabase< TPixel >::m_BlocksPerFile

protected

Definition at line 141 of file itkTimeSeriesDatabase.h.

◆ m_BlocksPerImage

template<class TPixel >

Array<unsigned int> itk::TimeSeriesDatabase< TPixel >::m_BlocksPerImage

protected

Definition at line 111 of file itkTimeSeriesDatabase.h.

◆ m_Cache

template<class TPixel >

TimeSeriesDatabaseHelper::LRUCache<unsigned long, CacheBlock> itk::TimeSeriesDatabase< TPixel >::m_Cache

protected

Definition at line 148 of file itkTimeSeriesDatabase.h.

◆ m_CurrentImage

template<class TPixel >

unsigned int itk::TimeSeriesDatabase< TPixel >::m_CurrentImage

protected

Definition at line 137 of file itkTimeSeriesDatabase.h.

◆ m_DatabaseFileNames

template<class TPixel >

std::vector<std::string> itk::TimeSeriesDatabase< TPixel >::m_DatabaseFileNames

protected

Definition at line 140 of file itkTimeSeriesDatabase.h.

◆ m_DatabaseFiles

template<class TPixel >

std::vector<StreamPtr> itk::TimeSeriesDatabase< TPixel >::m_DatabaseFiles

protected

Definition at line 139 of file itkTimeSeriesDatabase.h.

◆ m_Dimensions

template<class TPixel >

Array<unsigned int> itk::TimeSeriesDatabase< TPixel >::m_Dimensions

protected

Definition at line 110 of file itkTimeSeriesDatabase.h.

◆ m_Filename

template<class TPixel >

std::string itk::TimeSeriesDatabase< TPixel >::m_Filename

protected

Definition at line 136 of file itkTimeSeriesDatabase.h.

◆ m_OutputDirection

template<class TPixel >

OutputImageType::DirectionType itk::TimeSeriesDatabase< TPixel >::m_OutputDirection

protected

Definition at line 116 of file itkTimeSeriesDatabase.h.

◆ m_OutputOrigin

template<class TPixel >

OutputImageType::PointType itk::TimeSeriesDatabase< TPixel >::m_OutputOrigin

protected

Definition at line 115 of file itkTimeSeriesDatabase.h.

◆ m_OutputRegion

template<class TPixel >

OutputImageType::RegionType itk::TimeSeriesDatabase< TPixel >::m_OutputRegion

protected

Definition at line 114 of file itkTimeSeriesDatabase.h.

◆ m_OutputSpacing

template<class TPixel >

OutputImageType::SpacingType itk::TimeSeriesDatabase< TPixel >::m_OutputSpacing

protected

Definition at line 113 of file itkTimeSeriesDatabase.h.

◆ m_PixelRemainder

template<class TPixel >

Array<unsigned int> itk::TimeSeriesDatabase< TPixel >::m_PixelRemainder

protected

How many pixels are in the last block?

Definition at line 134 of file itkTimeSeriesDatabase.h.

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

Libs/vtkITK/itkTimeSeriesDatabase.h

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

template<class TPixel> class itk::TimeSeriesDatabase< TPixel >

Member Typedef Documentation

◆ ArrayType

◆ ConstPointer

◆ ConstWeakPointer

◆ OutputImageType

◆ OutputImageTypePointer

◆ OutputSliceType

◆ OutputSliceTypePointer

◆ Pointer

◆ Self

◆ StreamPtr

◆ Superclass

Constructor & Destructor Documentation

◆ TimeSeriesDatabase()

◆ ~TimeSeriesDatabase()

Member Function Documentation

◆ CalculateFileIndex() [1/2]

◆ CalculateFileIndex() [2/2]

◆ CalculateIndex() [1/2]

◆ CalculateIndex() [2/2]

◆ CalculateIntersection()

◆ CalculatePosition()

◆ Connect()

◆ CreateFromFileArchetype() [1/2]

◆ CreateFromFileArchetype() [2/2]

◆ Disconnect()

◆ GenerateData()

◆ GenerateOutputInformation()

◆ GetCacheBlock()

◆ GetCacheSizeInMiB()

◆ GetNumberOfVolumes()

◆ GetVoxelTimeSeries()

◆ IsOpen()

◆ itkGetMacro() [1/5]

◆ itkGetMacro() [2/5]

◆ itkGetMacro() [3/5]

◆ itkGetMacro() [4/5]

◆ itkGetMacro() [5/5]

◆ itkNewMacro()

◆ itkSetMacro()

◆ itkTypeMacro()

◆ PrintSelf()

◆ SetCacheSizeInMiB()

Member Data Documentation

◆ m_BlocksPerFile

◆ m_BlocksPerImage

◆ m_Cache

◆ m_CurrentImage

◆ m_DatabaseFileNames

◆ m_DatabaseFiles

◆ m_Dimensions

◆ m_Filename

◆ m_OutputDirection

◆ m_OutputOrigin

◆ m_OutputRegion

◆ m_OutputSpacing

◆ m_PixelRemainder

template<class TPixel>
class itk::TimeSeriesDatabase< TPixel >