Read NIfTI-1 and NIfTI-2 medical image files. More...

#include <vtkNIFTIImageReader.h>

Inheritance diagram for vtkNIFTIImageReader:

Collaboration diagram for vtkNIFTIImageReader:

Public Member Functions
virtual void	PrintSelf (ostream &os, vtkIndent indent)

int	CanReadFile (const char *filename)

double	GetQFac ()

vtkMatrix4x4 *	GetQFormMatrix ()

vtkMatrix4x4 *	GetSFormMatrix ()

vtkNIFTIImageHeader *	GetNIFTIHeader ()


virtual const char *	GetFileExtensions ()


virtual const char *	GetDescriptiveName ()


virtual bool	GetTimeAsVector ()

virtual void	SetTimeAsVector (bool)

virtual void	TimeAsVectorOn ()

virtual void	TimeAsVectorOff ()


int	GetTimeDimension ()

double	GetTimeSpacing ()


double	GetRescaleSlope ()

double	GetRescaleIntercept ()


virtual bool	GetPlanarRGB ()

virtual void	SetPlanarRGB (bool)

virtual void	PlanarRGBOn ()

virtual void	PlanarRGBOff ()

Public Member Functions inherited from vtkImageReader2
vtkImageReader2 *	NewInstance () const

virtual void	SetHeaderSize (unsigned long size)

ifstream *	GetFile ()

virtual unsigned long *	GetDataIncrements ()

virtual void	GetDataIncrements (unsigned long data[4])

virtual int	OpenFile ()

virtual void	SeekFile (int i, int j, int k)

virtual void	SetFileName (const char *)

virtual char *	GetFileName ()

virtual void	SetFileNames (vtkStringArray *)

virtual vtkStringArray *	GetFileNames ()

virtual void	SetFilePrefix (const char *)

virtual char *	GetFilePrefix ()

virtual void	SetFilePattern (const char *)

virtual char *	GetFilePattern ()

virtual void	SetMemoryBuffer (void *)

virtual void *	GetMemoryBuffer ()

virtual void	SetMemoryBufferLength (vtkIdType buflen)

vtkIdType	GetMemoryBufferLength ()

virtual void	SetDataScalarType (int type)

virtual void	SetDataScalarTypeToFloat ()

virtual void	SetDataScalarTypeToDouble ()

virtual void	SetDataScalarTypeToInt ()

virtual void	SetDataScalarTypeToUnsignedInt ()

virtual void	SetDataScalarTypeToShort ()

virtual void	SetDataScalarTypeToUnsignedShort ()

virtual void	SetDataScalarTypeToChar ()

virtual void	SetDataScalarTypeToSignedChar ()

virtual void	SetDataScalarTypeToUnsignedChar ()

virtual int	GetDataScalarType ()

virtual void	SetNumberOfScalarComponents (int)

virtual int	GetNumberOfScalarComponents ()

virtual void	SetDataExtent (int, int, int, int, int, int)

virtual void	SetDataExtent (int[6])

virtual int *	GetDataExtent ()

virtual void	GetDataExtent (int &, int &, int &, int &, int &, int &)

virtual void	GetDataExtent (int[6])

virtual void	SetFileDimensionality (int)

int	GetFileDimensionality ()

virtual void	SetDataSpacing (double, double, double)

virtual void	SetDataSpacing (double[3])

virtual double *	GetDataSpacing ()

virtual void	GetDataSpacing (double &, double &, double &)

virtual void	GetDataSpacing (double[3])

virtual void	SetDataOrigin (double, double, double)

virtual void	SetDataOrigin (double[3])

virtual double *	GetDataOrigin ()

virtual void	GetDataOrigin (double &, double &, double &)

virtual void	GetDataOrigin (double[3])

unsigned long	GetHeaderSize ()

unsigned long	GetHeaderSize (unsigned long slice)

virtual void	SetDataByteOrderToBigEndian ()

virtual void	SetDataByteOrderToLittleEndian ()

virtual int	GetDataByteOrder ()

virtual void	SetDataByteOrder (int)

virtual const char *	GetDataByteOrderAsString ()

virtual void	SetFileNameSliceOffset (int)

virtual int	GetFileNameSliceOffset ()

virtual void	SetFileNameSliceSpacing (int)

virtual int	GetFileNameSliceSpacing ()

virtual void	SetSwapBytes (int)

virtual int	GetSwapBytes ()

virtual void	SwapBytesOn ()

virtual void	SwapBytesOff ()

virtual void	FileLowerLeftOn ()

virtual void	FileLowerLeftOff ()

virtual int	GetFileLowerLeft ()

virtual void	SetFileLowerLeft (int)

virtual void	ComputeInternalFileName (int slice)

virtual char *	GetInternalFileName ()

virtual int	CanReadFile (const char *vtkNotUsed(fname))

Public Member Functions inherited from vtkImageAlgorithm
vtkImageAlgorithm *	NewInstance () const

vtkImageData *	GetOutput ()

vtkImageData *	GetOutput (int)

virtual void	SetOutput (vtkDataObject *d)

virtual int	ProcessRequest (vtkInformation , vtkInformationVector , vtkInformationVector )

void	SetInputData (vtkDataObject *)

void	SetInputData (int, vtkDataObject *)

vtkDataObject *	GetInput (int port)

vtkDataObject *	GetInput ()

vtkImageData *	GetImageDataInput (int port)

virtual void	AddInputData (vtkDataObject *)

virtual void	AddInputData (int, vtkDataObject *)

Public Member Functions inherited from vtkAlgorithm
vtkAlgorithm *	NewInstance () const

int	HasExecutive ()

vtkExecutive *	GetExecutive ()

virtual void	SetExecutive (vtkExecutive *executive)

virtual int	ModifyRequest (vtkInformation *request, int when)

vtkInformation *	GetInputPortInformation (int port)

vtkInformation *	GetOutputPortInformation (int port)

int	GetNumberOfInputPorts ()

int	GetNumberOfOutputPorts ()

void	UpdateProgress (double amount)

vtkInformation *	GetInputArrayInformation (int idx)

void	RemoveAllInputs ()

vtkDataObject *	GetOutputDataObject (int port)

virtual void	RemoveInputConnection (int port, vtkAlgorithmOutput *input)

virtual void	RemoveInputConnection (int port, int idx)

virtual void	RemoveAllInputConnections (int port)

int	GetNumberOfInputConnections (int port)

int	GetTotalNumberOfInputConnections ()

vtkAlgorithmOutput *	GetInputConnection (int port, int index)

vtkAlgorithm *	GetInputAlgorithm (int port, int index, int &algPort)

vtkAlgorithm *	GetInputAlgorithm (int port, int index)

vtkExecutive *	GetInputExecutive (int port, int index)

vtkInformation *	GetInputInformation (int port, int index)

vtkInformation *	GetOutputInformation (int port)

virtual void	UpdateInformation ()

virtual void	UpdateDataObject ()

virtual void	PropagateUpdateExtent ()

virtual void	UpdateWholeExtent ()

void	ConvertTotalInputToPortConnection (int ind, int &port, int &conn)

int	SetUpdateExtentToWholeExtent (int port)

int	SetUpdateExtentToWholeExtent ()

void	SetUpdateExtent (int port, int extent[6])

int	ProcessRequest (vtkInformation request, vtkCollection inInfo, vtkInformationVector *outInfo)

virtual int	ComputePipelineMTime (vtkInformation request, vtkInformationVector inInfoVec, vtkInformationVector outInfoVec, int requestFromOutputPort, unsigned long *mtime)

virtual vtkInformation *	GetInformation ()

virtual void	SetInformation (vtkInformation *)

virtual void	Register (vtkObjectBase *o)

virtual void	UnRegister (vtkObjectBase *o)

virtual void	SetAbortExecute (int)

virtual int	GetAbortExecute ()

virtual void	AbortExecuteOn ()

virtual void	AbortExecuteOff ()

virtual void	SetProgress (double)

virtual double	GetProgress ()

void	SetProgressText (const char *ptext)

virtual char *	GetProgressText ()

virtual unsigned long	GetErrorCode ()

virtual void	SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, const char *name)

virtual void	SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, int fieldAttributeType)

virtual void	SetInputArrayToProcess (int idx, vtkInformation *info)

virtual void	SetInputArrayToProcess (int idx, int port, int connection, const char fieldAssociation, const char attributeTypeorName)

vtkDataObject *	GetInputDataObject (int port, int connection)

virtual void	SetInputConnection (int port, vtkAlgorithmOutput *input)

virtual void	SetInputConnection (vtkAlgorithmOutput *input)

virtual void	AddInputConnection (int port, vtkAlgorithmOutput *input)

virtual void	AddInputConnection (vtkAlgorithmOutput *input)

virtual void	SetInputDataObject (int port, vtkDataObject *data)

virtual void	SetInputDataObject (vtkDataObject *data)

virtual void	AddInputDataObject (int port, vtkDataObject *data)

virtual void	AddInputDataObject (vtkDataObject *data)

vtkAlgorithmOutput *	GetOutputPort (int index)

vtkAlgorithmOutput *	GetOutputPort ()

vtkAlgorithm *	GetInputAlgorithm ()

vtkExecutive *	GetInputExecutive ()

vtkInformation *	GetInputInformation ()

virtual void	Update (int port)

virtual void	Update ()

virtual void	SetReleaseDataFlag (int)

virtual int	GetReleaseDataFlag ()

void	ReleaseDataFlagOn ()

void	ReleaseDataFlagOff ()

int	UpdateExtentIsEmpty (vtkInformation pinfo, vtkDataObject output)

int	UpdateExtentIsEmpty (vtkInformation *pinfo, int extentType)

void	SetUpdateExtent (int port, int piece, int numPieces, int ghostLevel)

void	SetUpdateExtent (int piece, int numPieces, int ghostLevel)

void	SetUpdateExtent (int extent[6])

int *	GetUpdateExtent ()

int *	GetUpdateExtent (int port)

void	GetUpdateExtent (int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)

void	GetUpdateExtent (int port, int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)

void	GetUpdateExtent (int extent[6])

void	GetUpdateExtent (int port, int extent[6])

int	GetUpdatePiece ()

int	GetUpdatePiece (int port)

int	GetUpdateNumberOfPieces ()

int	GetUpdateNumberOfPieces (int port)

int	GetUpdateGhostLevel ()

int	GetUpdateGhostLevel (int port)

void	SetProgressObserver (vtkProgressObserver *)

virtual vtkProgressObserver *	GetProgressObserver ()

Public Member Functions inherited from vtkObject
vtkObject *	NewInstance () const

virtual void	DebugOn ()

virtual void	DebugOff ()

bool	GetDebug ()

void	SetDebug (bool debugFlag)

virtual void	Modified ()

virtual unsigned long	GetMTime ()

unsigned long	AddObserver (unsigned long event, vtkCommand *, float priority=0.0f)

unsigned long	AddObserver (const char event, vtkCommand , float priority=0.0f)

vtkCommand *	GetCommand (unsigned long tag)

void	RemoveObserver (vtkCommand *)

void	RemoveObservers (unsigned long event, vtkCommand *)

void	RemoveObservers (const char event, vtkCommand )

int	HasObserver (unsigned long event, vtkCommand *)

int	HasObserver (const char event, vtkCommand )

void	RemoveObserver (unsigned long tag)

void	RemoveObservers (unsigned long event)

void	RemoveObservers (const char *event)

void	RemoveAllObservers ()

int	HasObserver (unsigned long event)

int	HasObserver (const char *event)

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, void(T::*callback)(), float priority=0.0f)

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, void(T::callback)(vtkObject , unsigned long, void *), float priority=0.0f)

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, bool(T::callback)(vtkObject , unsigned long, void *), float priority=0.0f)

int	InvokeEvent (unsigned long event, void *callData)

int	InvokeEvent (const char event, void callData)

int	InvokeEvent (unsigned long event)

int	InvokeEvent (const char *event)

Public Member Functions inherited from vtkObjectBase
const char *	GetClassName () const

virtual void	Delete ()

virtual void	FastDelete ()

void	Print (ostream &os)

void	SetReferenceCount (int)

void	PrintRevisions (ostream &)

virtual void	PrintHeader (ostream &os, vtkIndent indent)

virtual void	PrintTrailer (ostream &os, vtkIndent indent)

int	GetReferenceCount ()

Protected Member Functions
	vtkNIFTIImageReader ()

	~vtkNIFTIImageReader ()


virtual int	RequestInformation (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)


virtual int	RequestData (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)

Protected Member Functions inherited from vtkImageReader2
virtual void	ExecuteInformation ()

virtual void	ExecuteDataWithInformation (vtkDataObject data, vtkInformation outInfo)

virtual void	ComputeDataIncrements ()

	vtkImageReader2 ()

	~vtkImageReader2 ()

Protected Member Functions inherited from vtkImageAlgorithm
	vtkImageAlgorithm ()

	~vtkImageAlgorithm ()

virtual int	RequestUpdateExtent (vtkInformation , vtkInformationVector , vtkInformationVector )

virtual void	CopyInputArrayAttributesToOutput (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)

virtual void	ExecuteData (vtkDataObject *output)

virtual void	Execute ()

virtual void	AllocateOutputData (vtkImageData out, vtkInformation outInfo, int *uExtent)

virtual vtkImageData *	AllocateOutputData (vtkDataObject out, vtkInformation outInfo)

virtual void	CopyAttributeData (vtkImageData in, vtkImageData out, vtkInformationVector **inputVector)

virtual int	FillOutputPortInformation (int port, vtkInformation *info)

virtual int	FillInputPortInformation (int port, vtkInformation *info)

Protected Member Functions inherited from vtkAlgorithm
	vtkAlgorithm ()

	~vtkAlgorithm ()

virtual void	SetNumberOfInputPorts (int n)

virtual void	SetNumberOfOutputPorts (int n)

int	InputPortIndexInRange (int index, const char *action)

int	OutputPortIndexInRange (int index, const char *action)

int	GetInputArrayAssociation (int idx, vtkInformationVector **inputVector)

virtual vtkExecutive *	CreateDefaultExecutive ()

virtual void	ReportReferences (vtkGarbageCollector *)

virtual void	SetNumberOfInputConnections (int port, int n)

int	GetInputArrayAssociation (int idx, int connection, vtkInformationVector **inputVector)

int	GetInputArrayAssociation (int idx, vtkDataObject *input)

vtkDataArray *	GetInputArrayToProcess (int idx, vtkInformationVector **inputVector)

vtkDataArray *	GetInputArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)

vtkDataArray *	GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)

vtkDataArray *	GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)

vtkDataArray *	GetInputArrayToProcess (int idx, vtkDataObject *input)

vtkDataArray *	GetInputArrayToProcess (int idx, vtkDataObject *input, int &association)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkDataObject *input)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkDataObject *input, int &association)

vtkInformation *	GetInputArrayFieldInformation (int idx, vtkInformationVector **inputVector)

virtual void	SetNthInputConnection (int port, int index, vtkAlgorithmOutput *input)

void	SetInputDataInternal (int port, vtkDataObject *input)

void	AddInputDataInternal (int port, vtkDataObject *input)

virtual void	SetErrorCode (unsigned long)

Protected Member Functions inherited from vtkObject
	vtkObject ()

virtual	~vtkObject ()

virtual void	RegisterInternal (vtkObjectBase *, int check)

virtual void	UnRegisterInternal (vtkObjectBase *, int check)

void	InternalGrabFocus (vtkCommand mouseEvents, vtkCommand keypressEvents=NULL)

void	InternalReleaseFocus ()

Protected Member Functions inherited from vtkObjectBase
	vtkObjectBase ()

virtual	~vtkObjectBase ()

virtual void	CollectRevisions (ostream &)

	vtkObjectBase (const vtkObjectBase &)

void	operator= (const vtkObjectBase &)

Static Protected Member Functions
static bool	CheckExtension (const char fname, const char ext)

static int	CheckNIFTIVersion (const nifti_1_header *hdr)

static bool	CheckAnalyzeHeader (const nifti_1_header *hdr)


static char *	ReplaceExtension (const char fname, const char ext1, const char *ext2)

Static Protected Member Functions inherited from vtkAlgorithm
static vtkInformationIntegerKey *	PORT_REQUIREMENTS_FILLED ()

Protected Attributes
bool	TimeAsVector

double	QFac

int	Dim [8]

double	PixDim [8]

vtkNIFTIImageHeader *	NIFTIHeader

bool	PlanarRGB


double	RescaleIntercept

double	RescaleSlope


vtkMatrix4x4 *	QFormMatrix

vtkMatrix4x4 *	SFormMatrix

Protected Attributes inherited from vtkImageReader2
vtkStringArray *	FileNames

char *	InternalFileName

char *	FileName

char *	FilePrefix

char *	FilePattern

int	NumberOfScalarComponents

int	FileLowerLeft

void *	MemoryBuffer

vtkIdType	MemoryBufferLength

ifstream *	File

unsigned long	DataIncrements [4]

int	DataExtent [6]

int	SwapBytes

int	FileDimensionality

unsigned long	HeaderSize

int	DataScalarType

unsigned long	ManualHeaderSize

double	DataSpacing [3]

double	DataOrigin [3]

int	FileNameSliceOffset

int	FileNameSliceSpacing

Protected Attributes inherited from vtkAlgorithm
vtkInformation *	Information

double	Progress

char *	ProgressText

vtkProgressObserver *	ProgressObserver

unsigned long	ErrorCode

Protected Attributes inherited from vtkObject
bool	Debug

vtkTimeStamp	MTime

vtkSubjectHelper *	SubjectHelper

Protected Attributes inherited from vtkObjectBase
vtkAtomicInt32	ReferenceCount

vtkWeakPointerBase **	WeakPointers

typedef vtkImageReader2	Superclass

static vtkNIFTIImageReader *	New ()

static int	IsTypeOf (const char *type)

static vtkNIFTIImageReader *	SafeDownCast (vtkObjectBase *o)

virtual int	IsA (const char *type)

vtkNIFTIImageReader *	NewInstance () const

virtual vtkObjectBase *	NewInstanceInternal () const

Additional Inherited Members
Public Types inherited from vtkImageReader2
typedef vtkImageAlgorithm	Superclass

Public Types inherited from vtkImageAlgorithm
typedef vtkAlgorithm	Superclass

Public Types inherited from vtkAlgorithm
typedef vtkObject	Superclass

enum	DesiredOutputPrecision { SINGLE_PRECISION, DOUBLE_PRECISION, DEFAULT_PRECISION }

Public Types inherited from vtkObject
typedef vtkObjectBase	Superclass

Static Public Member Functions inherited from vtkImageReader2
static vtkImageReader2 *	New ()

static int	IsTypeOf (const char *type)

static vtkImageReader2 *	SafeDownCast (vtkObjectBase *o)

Static Public Member Functions inherited from vtkImageAlgorithm
static int	IsTypeOf (const char *type)

static vtkImageAlgorithm *	SafeDownCast (vtkObjectBase *o)

Static Public Member Functions inherited from vtkAlgorithm
static vtkAlgorithm *	New ()

static int	IsTypeOf (const char *type)

static vtkAlgorithm *	SafeDownCast (vtkObjectBase *o)

static vtkInformationIntegerKey *	INPUT_IS_OPTIONAL ()

static vtkInformationIntegerKey *	INPUT_IS_REPEATABLE ()

static vtkInformationInformationVectorKey *	INPUT_REQUIRED_FIELDS ()

static vtkInformationStringVectorKey *	INPUT_REQUIRED_DATA_TYPE ()

static vtkInformationInformationVectorKey *	INPUT_ARRAYS_TO_PROCESS ()

static vtkInformationIntegerKey *	INPUT_PORT ()

static vtkInformationIntegerKey *	INPUT_CONNECTION ()

static vtkInformationIntegerKey *	CAN_PRODUCE_SUB_EXTENT ()

static vtkInformationIntegerKey *	CAN_HANDLE_PIECE_REQUEST ()

static void	SetDefaultExecutivePrototype (vtkExecutive *proto)

Static Public Member Functions inherited from vtkObject
static int	IsTypeOf (const char *type)

static vtkObject *	SafeDownCast (vtkObjectBase *o)

static vtkObject *	New ()

static void	BreakOnError ()

static void	SetGlobalWarningDisplay (int val)

static void	GlobalWarningDisplayOn ()

static void	GlobalWarningDisplayOff ()

static int	GetGlobalWarningDisplay ()

Static Public Member Functions inherited from vtkObjectBase
static int	IsTypeOf (const char *name)

static vtkObjectBase *	New ()

Public Attributes inherited from vtkAlgorithm
int	AbortExecute

Static Protected Attributes inherited from vtkAlgorithm
static vtkExecutive *	DefaultExecutivePrototype

Detailed Description

Read NIfTI-1 and NIfTI-2 medical image files.

This class reads NIFTI files, either in .nii format or as separate .img and .hdr files. If two files are used, then they can be passed by using SetFileNames() instead of SetFileName(). Files ending in .gz are decompressed on-the-fly while they are being read. Files with complex numbers or vector dimensions will be read as multi-component images. If a NIFTI file has a time dimension, then by default only the first image in the time series will be read, but the TimeAsVector flag can be set to read the time steps as vector components. Files in Analyze 7.5 format are also supported by this reader.

Thanks:: This class was contributed to VTK by the Calgary Image Processing and Analysis Centre (CIPAC).

See also: vtkNIFTIImageWriter, vtkNIFTIImageHeader

Tests:: vtkNIFTIImageReader (Tests)

Definition at line 49 of file vtkNIFTIImageReader.h.

Member Typedef Documentation

typedef vtkImageReader2 vtkNIFTIImageReader::Superclass

Static method for construction.

Definition at line 55 of file vtkNIFTIImageReader.h.

Constructor & Destructor Documentation

vtkNIFTIImageReader::vtkNIFTIImageReader ( )

protected

vtkNIFTIImageReader::~vtkNIFTIImageReader ( )

protected

Member Function Documentation

static vtkNIFTIImageReader* vtkNIFTIImageReader::New ( )

static

Static method for construction.

static int vtkNIFTIImageReader::IsTypeOf ( const char * type )

static

Static method for construction.

virtual int vtkNIFTIImageReader::IsA ( const char * type )

virtual

Static method for construction.

Reimplemented from vtkImageReader2.

static vtkNIFTIImageReader* vtkNIFTIImageReader::SafeDownCast ( vtkObjectBase * o )

static

Static method for construction.

virtual vtkObjectBase* vtkNIFTIImageReader::NewInstanceInternal ( ) const

protectedvirtual

Static method for construction.

Reimplemented from vtkImageReader2.

vtkNIFTIImageReader* vtkNIFTIImageReader::NewInstance ( ) const

Static method for construction.

virtual void vtkNIFTIImageReader::PrintSelf	(	ostream &	os,
		vtkIndent	indent
	)

virtual

Print information about this object.

Reimplemented from vtkImageReader2.

virtual const char* vtkNIFTIImageReader::GetFileExtensions ( )

inlinevirtual

Valid extensions for this file type.

Reimplemented from vtkImageReader2.

Definition at line 63 of file vtkNIFTIImageReader.h.

virtual const char* vtkNIFTIImageReader::GetDescriptiveName ( )

inlinevirtual

Return a descriptive name that might be useful in a GUI.

Reimplemented from vtkImageReader2.

Definition at line 69 of file vtkNIFTIImageReader.h.

int vtkNIFTIImageReader::CanReadFile ( const char * filename )

Return true if this reader can read the given file.

virtual bool vtkNIFTIImageReader::GetTimeAsVector ( )

virtual

Read the time dimension as scalar components (default: Off). If this is on, then each time point will be stored as a component in the image data. If the file has both a time dimension and a vector dimension, then the number of components will be the product of these two dimensions, i.e. the components will store a sequence of vectors.

virtual void vtkNIFTIImageReader::SetTimeAsVector ( bool )

virtual

Read the time dimension as scalar components (default: Off). If this is on, then each time point will be stored as a component in the image data. If the file has both a time dimension and a vector dimension, then the number of components will be the product of these two dimensions, i.e. the components will store a sequence of vectors.

virtual void vtkNIFTIImageReader::TimeAsVectorOn ( )

virtual

Read the time dimension as scalar components (default: Off). If this is on, then each time point will be stored as a component in the image data. If the file has both a time dimension and a vector dimension, then the number of components will be the product of these two dimensions, i.e. the components will store a sequence of vectors.

virtual void vtkNIFTIImageReader::TimeAsVectorOff ( )

virtual

Read the time dimension as scalar components (default: Off). If this is on, then each time point will be stored as a component in the image data. If the file has both a time dimension and a vector dimension, then the number of components will be the product of these two dimensions, i.e. the components will store a sequence of vectors.

int vtkNIFTIImageReader::GetTimeDimension ( )

inline

Get the time dimension that was stored in the NIFTI header.

Definition at line 89 of file vtkNIFTIImageReader.h.

double vtkNIFTIImageReader::GetTimeSpacing ( )

inline

Get the time dimension that was stored in the NIFTI header.

Definition at line 90 of file vtkNIFTIImageReader.h.

double vtkNIFTIImageReader::GetRescaleSlope ( )

inline

Get the slope and intercept for rescaling the scalar values. These values allow calibration of the data to real values. Use the equation v = u*RescaleSlope + RescaleIntercept. This directly returns the values stored in the scl_slope and scl_inter fields in the NIFTI header.

Definition at line 99 of file vtkNIFTIImageReader.h.

double vtkNIFTIImageReader::GetRescaleIntercept ( )

inline

Get the slope and intercept for rescaling the scalar values. These values allow calibration of the data to real values. Use the equation v = u*RescaleSlope + RescaleIntercept. This directly returns the values stored in the scl_slope and scl_inter fields in the NIFTI header.

Definition at line 100 of file vtkNIFTIImageReader.h.

virtual bool vtkNIFTIImageReader::GetPlanarRGB ( )

virtual

Read planar RGB (separate R, G, and B planes), rather than packed RGB. The NIFTI format should always use packed RGB. The Analyze format, however, was used to store both planar RGB and packed RGB depending on the software, without any indication in the header about which convention was being used. Use this if you have a planar RGB file.

virtual void vtkNIFTIImageReader::SetPlanarRGB ( bool )

virtual

Read planar RGB (separate R, G, and B planes), rather than packed RGB. The NIFTI format should always use packed RGB. The Analyze format, however, was used to store both planar RGB and packed RGB depending on the software, without any indication in the header about which convention was being used. Use this if you have a planar RGB file.

virtual void vtkNIFTIImageReader::PlanarRGBOn ( )

virtual

Read planar RGB (separate R, G, and B planes), rather than packed RGB. The NIFTI format should always use packed RGB. The Analyze format, however, was used to store both planar RGB and packed RGB depending on the software, without any indication in the header about which convention was being used. Use this if you have a planar RGB file.

virtual void vtkNIFTIImageReader::PlanarRGBOff ( )

virtual

Read planar RGB (separate R, G, and B planes), rather than packed RGB. The NIFTI format should always use packed RGB. The Analyze format, however, was used to store both planar RGB and packed RGB depending on the software, without any indication in the header about which convention was being used. Use this if you have a planar RGB file.

double vtkNIFTIImageReader::GetQFac ( )

inline

QFac gives the slice order in the NIFTI file versus the VTK image. If QFac is -1, then the VTK slice index J is related to the NIFTI slice index j by the equation J = (num_slices - j - 1). VTK requires the slices to be ordered so that the voxel indices (I,J,K) provide a right-handed coordinate system, whereas NIFTI does not. Instead, NIFTI stores a factor called "qfac" in the header to signal when the (i,j,k) indices form a left-handed coordinate system. QFac will only ever have values of +1 or -1.

Definition at line 123 of file vtkNIFTIImageReader.h.

vtkMatrix4x4* vtkNIFTIImageReader::GetQFormMatrix ( )

inline

Get a matrix that gives the "qform" orientation and offset for the data. If no qform matrix was stored in the file, the return value is NULL. This matrix will transform VTK data coordinates into the NIFTI oriented data coordinates, where +X points right, +Y points anterior (toward the front), and +Z points superior (toward the head). The qform matrix will always have a positive determinant. The offset that is stored in the matrix gives the position of the first pixel in the first slice of the VTK image data. Note that if QFac is -1, then the first slice in the VTK image data is the last slice in the NIFTI file, and the Z offset will automatically be adjusted to compensate for this.

Definition at line 136 of file vtkNIFTIImageReader.h.

vtkMatrix4x4* vtkNIFTIImageReader::GetSFormMatrix ( )

inline

Get a matrix that gives the "sform" orientation and offset for the data. If no sform matrix was stored in the file, the return value is NULL. Like the qform matrix, this matrix will transform VTK data coordinates into a NIFTI coordinate system. Unlike the qform matrix, the sform matrix can contain scaling information and can even (rarely) have a negative determinant, i.e. a flip. This matrix is modified slightly as compared to the sform matrix stored in the NIFTI header: the pixdim pixel spacing is factored out. Also, if QFac is -1, then the VTK slices are in reverse order as compared to the NIFTI slices, hence as compared to the sform matrix stored in the header, the third column of this matrix is multiplied by -1 and the Z offset is shifted to compensate for the fact that the last slice has become the first.

Definition at line 151 of file vtkNIFTIImageReader.h.

vtkNIFTIImageHeader* vtkNIFTIImageReader::GetNIFTIHeader ( )

Get the raw header information from the NIfTI file.

virtual int vtkNIFTIImageReader::RequestInformation	(	vtkInformation *	request,
		vtkInformationVector **	inputVector,
		vtkInformationVector *	outputVector
	)

protectedvirtual

Read the header information.

Reimplemented from vtkImageReader2.

virtual int vtkNIFTIImageReader::RequestData	(	vtkInformation *	request,
		vtkInformationVector **	inputVector,
		vtkInformationVector *	outputVector
	)

protectedvirtual

Read the voxel data.

Reimplemented from vtkImageAlgorithm.

static bool vtkNIFTIImageReader::CheckExtension	(	const char *	fname,
		const char *	ext
	)

staticprotected

Do a case-insensitive check for the given extension. The check will succeed if the filename ends in ".gz", and if the extension matches after removing the ".gz".

static char* vtkNIFTIImageReader::ReplaceExtension	(	const char *	fname,
		const char *	ext1,
		const char *	ext2
	)

staticprotected

Make a new filename by replacing extension "ext1" with "ext2". The extensions must include a period, must be three characters long, and must be lower case. This method also verifies that the file exists, and adds or subtracts a ".gz" as necessary If the file exists, a new string is returned that must be deleted by the caller. Otherwise, the return value is NULL.

static int vtkNIFTIImageReader::CheckNIFTIVersion ( const nifti_1_header * hdr )

staticprotected

Check the version of the header.

static bool vtkNIFTIImageReader::CheckAnalyzeHeader ( const nifti_1_header * hdr )

staticprotected

Return true if an Analyze 7.5 header was found.

Member Data Documentation

bool vtkNIFTIImageReader::TimeAsVector

protected

Read the time dimension as if it was a vector dimension.

Definition at line 197 of file vtkNIFTIImageReader.h.

double vtkNIFTIImageReader::RescaleIntercept

protected

Information for rescaling data to quantitative units.

Definition at line 201 of file vtkNIFTIImageReader.h.

double vtkNIFTIImageReader::RescaleSlope

protected

Information for rescaling data to quantitative units.

Definition at line 202 of file vtkNIFTIImageReader.h.

double vtkNIFTIImageReader::QFac

protected

Is -1 if VTK slice order is opposite to NIFTI slice order, +1 otherwise.

Definition at line 207 of file vtkNIFTIImageReader.h.

vtkMatrix4x4* vtkNIFTIImageReader::QFormMatrix

protected

The orientation matrices for the NIFTI file.

Definition at line 211 of file vtkNIFTIImageReader.h.

vtkMatrix4x4* vtkNIFTIImageReader::SFormMatrix

protected

The orientation matrices for the NIFTI file.

Definition at line 212 of file vtkNIFTIImageReader.h.

int vtkNIFTIImageReader::Dim[8]

protected

The dimensions of the NIFTI file.

Definition at line 216 of file vtkNIFTIImageReader.h.

double vtkNIFTIImageReader::PixDim[8]

protected

The spacings in the NIFTI file.

Definition at line 219 of file vtkNIFTIImageReader.h.

vtkNIFTIImageHeader* vtkNIFTIImageReader::NIFTIHeader

protected

A copy of the header from the file that was most recently read.

Definition at line 222 of file vtkNIFTIImageReader.h.

bool vtkNIFTIImageReader::PlanarRGB

protected

Use planar RGB instead of the default (packed).

Definition at line 225 of file vtkNIFTIImageReader.h.

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

/home/boeckb/code/depot/group-kitware/vtk/build-release/Utilities/Doxygen/dox/IO/Image/vtkNIFTIImageReader.h

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