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

#include <vtkNIFTIReader.h>

Inheritance diagram for vtkNIFTIReader:

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Collaboration diagram for vtkNIFTIReader:

[legend]

Public Types
typedef vtkImageReader2	Superclass

Public Types inherited from vtkImageReader2
typedef vtkImageAlgorithm	Superclass

Public Types inherited from vtkImageAlgorithm
typedef vtkAlgorithm	Superclass

Public Types inherited from vtkAlgorithm
enum	DesiredOutputPrecision { SINGLE_PRECISION , DOUBLE_PRECISION , DEFAULT_PRECISION }

typedef vtkObject	Superclass

Public Member Functions
virtual vtkTypeBool	IsA (const char *type)

vtkNIFTIReader *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent) VTK_DICOM_OVERRIDE
	Print information about this object.

const char *	GetFileExtensions () VTK_DICOM_OVERRIDE
	Valid extensions for this file type.

const char *	GetDescriptiveName () VTK_DICOM_OVERRIDE
	Return a descriptive name that might be useful in a GUI.

int	CanReadFile (const char *filename) VTK_DICOM_OVERRIDE
	Return true if this reader can read the given file.

virtual int	GetTimeAsVector ()
	Read the time dimension as scalar components (default: Off). More...

virtual void	SetTimeAsVector (int)

virtual void	TimeAsVectorOn ()

virtual void	TimeAsVectorOff ()

int	GetTimeDimension ()
	Get the time dimension that was stored in the NIFTI header.

double	GetTimeSpacing ()

double	GetRescaleSlope ()
	Get the slope and intercept for rescaling the scalar values. More...

double	GetRescaleIntercept ()

virtual bool	GetPlanarRGB ()
	Read planar RGB (separate R, G, and B planes), rather than packed RGB. More...

virtual void	SetPlanarRGB (bool)

virtual void	PlanarRGBOn ()

virtual void	PlanarRGBOff ()

double	GetQFac ()
	QFac gives the slice order in the NIFTI file versus the VTK image. More...

vtkMatrix4x4 *	GetQFormMatrix ()
	Get a matrix that gives the "qform" orientation and offset for the data. More...

vtkMatrix4x4 *	GetSFormMatrix ()
	Get a matrix that gives the "sform" orientation and offset for the data. More...

vtkNIFTIHeader *	GetNIFTIHeader ()
	Get the raw header information from the NIfTI file.

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

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	SetHeaderSize (unsigned long size)

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 ()

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	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)

int	ProcessRequest (vtkInformation , vtkInformationVector , vtkInformationVector ) VTK_OVERRIDE

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)

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

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

virtual int	ModifyRequest (vtkInformation *request, int when)

vtkInformation *	GetInputPortInformation (int port)

vtkInformation *	GetOutputPortInformation (int port)

virtual vtkInformation *	GetInformation ()

virtual void	SetInformation (vtkInformation *)

int	GetNumberOfInputPorts ()

int	GetNumberOfOutputPorts ()

void	Register (vtkObjectBase *o) VTK_OVERRIDE

void	UnRegister (vtkObjectBase *o) VTK_OVERRIDE

virtual void	SetAbortExecute (int)

virtual int	GetAbortExecute ()

virtual void	AbortExecuteOn ()

virtual void	AbortExecuteOff ()

virtual void	SetProgress (double)

virtual double	GetProgress ()

void	UpdateProgress (double amount)

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)

vtkInformation *	GetInputArrayInformation (int idx)

void	RemoveAllInputs ()

vtkDataObject *	GetOutputDataObject (int port)

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	RemoveInputConnection (int port, vtkAlgorithmOutput *input)

virtual void	RemoveInputConnection (int port, int idx)

virtual void	RemoveAllInputConnections (int port)

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 ()

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)

vtkAlgorithm *	GetInputAlgorithm ()

vtkExecutive *	GetInputExecutive (int port, int index)

vtkExecutive *	GetInputExecutive ()

vtkInformation *	GetInputInformation (int port, int index)

vtkInformation *	GetInputInformation ()

vtkInformation *	GetOutputInformation (int port)

virtual void	Update (int port)

virtual void	Update ()

virtual int	Update (int port, vtkInformationVector *requests)

virtual int	Update (vtkInformation *requests)

virtual int	UpdatePiece (int piece, int numPieces, int ghostLevels, const int extents[6]=0)

virtual int	UpdateExtent (const int extents[6])

virtual int	UpdateTimeStep (double time, int piece=-1, int numPieces=1, int ghostLevels=0, const int extents[6]=0)

virtual void	UpdateInformation ()

virtual void	UpdateDataObject ()

virtual void	PropagateUpdateExtent ()

virtual void	UpdateWholeExtent ()

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

virtual void	SetReleaseDataFlag (int)

virtual int	GetReleaseDataFlag ()

void	ReleaseDataFlagOn ()

void	ReleaseDataFlagOff ()

int	UpdateExtentIsEmpty (vtkInformation pinfo, vtkDataObject output)

int	UpdateExtentIsEmpty (vtkInformation *pinfo, int extentType)

int	SetUpdateExtentToWholeExtent (int port)

int	SetUpdateExtentToWholeExtent ()

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

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

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

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
	vtkBaseTypeMacro (vtkObject, vtkObjectBase)

virtual void	DebugOn ()

virtual void	DebugOff ()

bool	GetDebug ()

void	SetDebug (bool debugFlag)

virtual void	Modified ()

virtual vtkMTimeType	GetMTime ()

void	PrintSelf (ostream &os, vtkIndent indent) VTK_OVERRIDE

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	InitializeObjectBase ()

void	Print (ostream &os)

virtual void	PrintHeader (ostream &os, vtkIndent indent)

virtual void	PrintTrailer (ostream &os, vtkIndent indent)

int	GetReferenceCount ()

void	SetReferenceCount (int)

void	PrintRevisions (ostream &)

Static Public Member Functions
static vtkNIFTIReader *	New ()
	Static method for construction.

static vtkTypeBool	IsTypeOf (const char *type)

static vtkNIFTIReader *	SafeDownCast (vtkObjectBase *o)

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

static vtkTypeBool	IsTypeOf (const char *type)

static vtkImageReader2 *	SafeDownCast (vtkObjectBase *o)

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

static vtkImageAlgorithm *	SafeDownCast (vtkObjectBase *o)

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

static vtkTypeBool	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 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 vtkTypeBool	IsTypeOf (const char *name)

static vtkObjectBase *	New ()

Protected Member Functions
virtual vtkObjectBase *	NewInstanceInternal () const

int	RequestInformation (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector) VTK_DICOM_OVERRIDE
	Read the header information.

int	RequestData (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector) VTK_DICOM_OVERRIDE
	Read the voxel data.

Protected Member Functions inherited from vtkImageReader2
virtual void	ExecuteInformation ()

virtual void	ExecuteDataWithInformation (vtkDataObject data, vtkInformation outInfo)

virtual void	ComputeDataIncrements ()

Protected Member Functions inherited from 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)

int	FillOutputPortInformation (int port, vtkInformation *info) VTK_OVERRIDE

int	FillInputPortInformation (int port, vtkInformation *info) VTK_OVERRIDE

Protected Member Functions inherited from 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)

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 vtkExecutive *	CreateDefaultExecutive ()

virtual void	SetErrorCode (unsigned long)

void	ReportReferences (vtkGarbageCollector *) VTK_OVERRIDE

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

virtual void	SetNumberOfInputConnections (int port, int n)

void	SetInputDataInternal (int port, vtkDataObject *input)

void	AddInputDataInternal (int port, vtkDataObject *input)

Protected Member Functions inherited from vtkObject
void	RegisterInternal (vtkObjectBase *, vtkTypeBool check) VTK_OVERRIDE

void	UnRegisterInternal (vtkObjectBase *, vtkTypeBool check) VTK_OVERRIDE

void	InternalGrabFocus (vtkCommand mouseEvents, vtkCommand keypressEvents=NULL)

void	InternalReleaseFocus ()

Protected Member Functions inherited from 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)
	Doe a case-insensitive check for the given extension. More...

static char *	ReplaceExtension (const char fname, const char ext1, const char *ext2)
	Make a new filename by replacing extension "ext1" with "ext2". More...

static int	CheckNIFTIVersion (const nifti_1_header *hdr)
	Check the version of the header.

static bool	CheckAnalyzeHeader (const nifti_1_header *hdr)
	Check for Analyze 7.5 header.

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

Protected Attributes
int	TimeAsVector
	Read the time dimension as if it was a vector dimension.

double	RescaleIntercept
	Information for rescaling data to quantitative units.

double	RescaleSlope

double	QFac
	Set to -1 when VTK slice order is opposite to NIFTI slice order.

vtkMatrix4x4 *	QFormMatrix
	The orientation matrices for the NIFTI file.

vtkMatrix4x4 *	SFormMatrix

int	Dim [8]
	The dimensions of the NIFTI file.

double	PixDim [8]
	The spacings in the NIFTI file.

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

bool	PlanarRGB
	Use planar RGB instead of the default (packed).

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

unsigned long	ErrorCode

double	Progress

char *	ProgressText

vtkProgressObserver *	ProgressObserver

Protected Attributes inherited from vtkObject
bool	Debug

vtkTimeStamp	MTime

vtkSubjectHelper *	SubjectHelper

Protected Attributes inherited from vtkObjectBase
vtkAtomicInt32	ReferenceCount

vtkWeakPointerBase **	WeakPointers

Additional Inherited Members
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.

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

See also: vtkNIFTIWriter, vtkNIFTIHeader

Member Function Documentation

◆ CheckExtension()

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

staticprotected

Doe 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".

◆ GetPlanarRGB()

virtual bool vtkNIFTIReader::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.

◆ GetQFac()

double vtkNIFTIReader::GetQFac ( )

inline

QFac gives the slice order in the NIFTI file versus the VTK image.

If QFac is -1, then the VTK slice index K is related to the NIFTI slice index k by the equation K = (num_slices - k - 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.

◆ GetQFormMatrix()

vtkMatrix4x4* vtkNIFTIReader::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.

◆ GetRescaleSlope()

double vtkNIFTIReader::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.

◆ GetSFormMatrix()

vtkMatrix4x4* vtkNIFTIReader::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.

◆ GetTimeAsVector()

virtual int vtkNIFTIReader::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.

◆ IsA()

virtual vtkTypeBool vtkNIFTIReader::IsA ( const char * name )

virtual

Return 1 if this class is the same type of (or a subclass of) the named class. Returns 0 otherwise. This method works in combination with vtkTypeMacro found in vtkSetGet.h.

Reimplemented from vtkImageReader2.

◆ ReplaceExtension()

static char* vtkNIFTIReader::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.

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

vtkNIFTIReader.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ CheckExtension()

◆ GetPlanarRGB()

◆ GetQFac()

◆ GetQFormMatrix()

◆ GetRescaleSlope()

◆ GetSFormMatrix()

◆ GetTimeAsVector()

◆ IsA()

◆ ReplaceExtension()