itk::TimeSeriesDatabase< TPixel > Class Template Reference

#include <Libs/vtkITK/itkTimeSeriesDatabase.h>

Collaboration diagram for itk::TimeSeriesDatabase< TPixel >:

List of all members.

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)
virtual void	GenerateOutputInformation (void)
float	GetCacheSizeInMiB ()
int	GetNumberOfVolumes ()
void	GetVoxelTimeSeries (typename OutputImageType::IndexType idx, ArrayType &array)
	itkGetMacro (OutputSpacing, typename OutputImageType::SpacingType)
	itkGetMacro (OutputRegion, typename OutputImageType::RegionType)
	itkGetMacro (OutputOrigin, typename OutputImageType::PointType)
	itkGetMacro (OutputDirection, typename OutputImageType::DirectionType)
	itkGetMacro (CurrentImage, unsigned int)
	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!
CacheBlock *	GetCacheBlock (unsigned long index)
bool	IsOpen () const
virtual void	PrintSelf (std::ostream &os, Indent indent) const
	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?

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Detailed Description

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

Definition at line 28 of file itkTimeSeriesDatabase.h.

---

Member Typedef Documentation

template<class TPixel >

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

Definition at line 47 of file itkTimeSeriesDatabase.h.

template<class TPixel >

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

Definition at line 34 of file itkTimeSeriesDatabase.h.

template<class TPixel >

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

Definition at line 35 of file itkTimeSeriesDatabase.h.

template<class TPixel >

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

Definition at line 43 of file itkTimeSeriesDatabase.h.

template<class TPixel >

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

Definition at line 44 of file itkTimeSeriesDatabase.h.

template<class TPixel >

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

Definition at line 45 of file itkTimeSeriesDatabase.h.

template<class TPixel >

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

Definition at line 46 of file itkTimeSeriesDatabase.h.

template<class TPixel >

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

Definition at line 33 of file itkTimeSeriesDatabase.h.

template<class TPixel >

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

Definition at line 31 of file itkTimeSeriesDatabase.h.

template<class TPixel >

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

Definition at line 116 of file itkTimeSeriesDatabase.h.

template<class TPixel >

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

Definition at line 32 of file itkTimeSeriesDatabase.h.

---

Constructor & Destructor Documentation

template<class TPixel >

itk::TimeSeriesDatabase< TPixel >::TimeSeriesDatabase

(

)

[protected]

template<class TPixel >

itk::TimeSeriesDatabase< TPixel >::~TimeSeriesDatabase

(

)

[protected]

---

Member Function Documentation

template<class TPixel >

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

(

unsigned long

Index

)

[protected]

template<class TPixel >

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

template<class TPixel >

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

template<class TPixel >

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

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!

template<class TPixel >

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

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.

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.

template<class TPixel >

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

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.

template<class TPixel >

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

(

void

)

[virtual]

template<class TPixel >

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

(

void

)

[virtual]

Standard method for a ImageSource object

template<class TPixel >

CacheBlock* itk::TimeSeriesDatabase< TPixel >::GetCacheBlock

(

unsigned long

index

)

[protected]

template<class TPixel >

float itk::TimeSeriesDatabase< TPixel >::GetCacheSizeInMiB

(

)

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

template<class TPixel >

int itk::TimeSeriesDatabase< TPixel >::GetNumberOfVolumes

(

)

[inline]

Return information about the TimeSeriesDatabase file

Definition at line 81 of file itkTimeSeriesDatabase.h.

template<class TPixel >

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

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

template<class TPixel >

bool itk::TimeSeriesDatabase< TPixel >::IsOpen

(

)

const [protected]

template<class TPixel >

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

template<class TPixel >

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

template<class TPixel >

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

template<class TPixel >

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

template<class TPixel >

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

template<class TPixel >

itk::TimeSeriesDatabase< TPixel >::itkNewMacro

(

Self

)

Method for creation through the object factory.

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.

template<class TPixel >

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

Run-time type information (and related methods).

template<class TPixel >

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

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

template<class TPixel >

unsigned long itk::TimeSeriesDatabase< TPixel >::m_BlocksPerFile [protected]

Definition at line 138 of file itkTimeSeriesDatabase.h.

template<class TPixel >

Array<unsigned int> itk::TimeSeriesDatabase< TPixel >::m_BlocksPerImage [protected]

Definition at line 110 of file itkTimeSeriesDatabase.h.

template<class TPixel >

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

Definition at line 145 of file itkTimeSeriesDatabase.h.

template<class TPixel >

unsigned int itk::TimeSeriesDatabase< TPixel >::m_CurrentImage [protected]

Definition at line 134 of file itkTimeSeriesDatabase.h.

template<class TPixel >

std::vector<std::string> itk::TimeSeriesDatabase< TPixel >::m_DatabaseFileNames [protected]

Definition at line 137 of file itkTimeSeriesDatabase.h.

template<class TPixel >

std::vector<StreamPtr> itk::TimeSeriesDatabase< TPixel >::m_DatabaseFiles [protected]

Definition at line 136 of file itkTimeSeriesDatabase.h.

template<class TPixel >

Array<unsigned int> itk::TimeSeriesDatabase< TPixel >::m_Dimensions [protected]

Definition at line 109 of file itkTimeSeriesDatabase.h.

template<class TPixel >

std::string itk::TimeSeriesDatabase< TPixel >::m_Filename [protected]

Definition at line 133 of file itkTimeSeriesDatabase.h.

template<class TPixel >

OutputImageType::DirectionType itk::TimeSeriesDatabase< TPixel >::m_OutputDirection [protected]

Definition at line 115 of file itkTimeSeriesDatabase.h.

template<class TPixel >

OutputImageType::PointType itk::TimeSeriesDatabase< TPixel >::m_OutputOrigin [protected]

Definition at line 114 of file itkTimeSeriesDatabase.h.

template<class TPixel >

OutputImageType::RegionType itk::TimeSeriesDatabase< TPixel >::m_OutputRegion [protected]

Definition at line 113 of file itkTimeSeriesDatabase.h.

template<class TPixel >

OutputImageType::SpacingType itk::TimeSeriesDatabase< TPixel >::m_OutputSpacing [protected]

Definition at line 112 of file itkTimeSeriesDatabase.h.

template<class TPixel >

Array<unsigned int> itk::TimeSeriesDatabase< TPixel >::m_PixelRemainder [protected]

How many pixels are in the last block?

Definition at line 132 of file itkTimeSeriesDatabase.h.

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

• Libs/vtkITK/itkTimeSeriesDatabase.h