Store NIfTI header information. More...

#include <vtkNIFTIImageHeader.h>

Inheritance diagram for vtkNIFTIImageHeader:

Collaboration diagram for vtkNIFTIImageHeader:

Public Types

enum	IntentCodeEnum { IntentNone = 0, IntentCorrel = 2, IntentTTest = 3, IntentFTest = 4, IntentZScore = 5, IntentChiSQ = 6, IntentBeta = 7, IntentBinom = 8, IntentGamma = 9, IntentPoisson = 10, IntentNormal = 11, IntentFTestNonc = 12, IntentChiSQNonc = 13, IntentLogistic = 14, IntentLaplace = 15, IntentUniform = 16, IntentTTestNonc = 17, IntentWeibull = 18, IntentChi = 19, IntentInvGauss = 20, IntentExtVal = 21, IntentPVal = 22, IntentLogPVal = 23, IntentLog10PVal = 24, IntentEstimate = 1001, IntentLabel = 1002, IntentNeuroName = 1003, IntentGenMatrix = 1004, IntentSymMatrix = 1005, IntentDispVect = 1006, IntentVector = 1007, IntentPointSet = 1008, IntentTriangle = 1009, IntentQuaternion = 1010, IntentDimless = 1011, IntentTimeSeries = 2001, IntentNodeIndex = 2002, IntentRGBVector = 2003, IntentRGBAVector = 2004, IntentShape = 2005 }

enum	XFormCodeEnum { XFormUnkown = 0, XFormScannerAnat = 1, XFormAlignedAnat = 2, XFormTalairach = 3, XFormMNI152 = 4 }

enum	SliceCodeEnum { SliceUnknown = 0, SliceSeqInc = 1, SliceSeqDec = 2, SliceAltInc = 3, SliceAltDec = 4, SliceAltInc2 = 5, SliceAltDec2 = 6 }

enum	UnitsXYZTEnum { UnitsUnknown = 0, UnitsMeter = 1, UnitsMM = 2, UnitsMicron = 3, UnitsSpace = 7, UnitsSec = 8, UnitsMSec = 16, UnitsUSec = 24, UnitsHz = 32, UnitsPPM = 40, UnitsRads = 48, UnitsTime = 56 }

enum	DataTypeEnum { TypeUInt8 = 2, TypeInt16 = 4, TypeInt32 = 8, TypeFloat32 = 16, TypeComplex64 = 32, TypeFloat64 = 64, TypeRGB24 = 128, TypeInt8 = 256, TypeUInt16 = 512, TypeUInt32 = 768, TypeInt64 = 1024, TypeUInt64 = 1280, TypeFloat128 = 1536, TypeComplex128 = 1792, TypeComplex256 = 2048, TypeRGBA32 = 2304 }

enum	HeaderSizeEnum { NIFTI1HeaderSize = 348, NIFTI2HeaderSize = 540 }
Public Member Functions
virtual void	PrintSelf (ostream &os, vtkIndent indent)
const char *	GetMagic ()
vtkTypeInt64	GetVoxOffset ()
int	GetDataType ()
int	GetBitPix ()
void	Initialize ()
void	DeepCopy (vtkNIFTIImageHeader *o)

vtkTypeInt64	GetDim (int i)

double	GetPixDim (int i)

virtual void	SetIntentCode (int)
int	GetIntentCode ()

void	SetIntentName (const char *name)
const char *	GetIntentName ()

virtual void	SetIntentP1 (double)
double	GetIntentP1 ()
virtual void	SetIntentP2 (double)
double	GetIntentP2 ()
virtual void	SetIntentP3 (double)
double	GetIntentP3 ()

virtual void	SetSclSlope (double)
double	GetSclSlope ()
virtual void	SetSclInter (double)
double	GetSclInter ()

virtual void	SetCalMin (double)
double	GetCalMin ()
virtual void	SetCalMax (double)
double	GetCalMax ()

virtual void	SetSliceDuration (double)
double	GetSliceDuration ()
virtual void	SetTOffset (double)
double	GetTOffset ()

virtual void	SetSliceStart (vtkTypeInt64)
vtkTypeInt64	GetSliceStart ()
virtual void	SetSliceEnd (vtkTypeInt64)
vtkTypeInt64	GetSliceEnd ()

virtual void	SetSliceCode (int)
int	GetSliceCode ()

virtual void	SetXYZTUnits (int)
int	GetXYZTUnits ()

virtual void	SetDimInfo (int)
int	GetDimInfo ()

void	SetDescrip (const char *descrip)
const char *	GetDescrip ()

void	SetAuxFile (const char *auxfile)
const char *	GetAuxFile ()

virtual void	SetQFormCode (int)
int	GetQFormCode ()
virtual void	SetSFormCode (int)
int	GetSFormCode ()

virtual void	SetQuaternB (double)
double	GetQuaternB ()
virtual void	SetQuaternC (double)
double	GetQuaternC ()
virtual void	SetQuaternD (double)
double	GetQuaternD ()
virtual void	SetQOffsetX (double)
double	GetQOffsetX ()
virtual void	SetQOffsetY (double)
double	GetQOffsetY ()
virtual void	SetQOffsetZ (double)
double	GetQOffsetZ ()

virtual void	SetSRowX (double, double, double, double)
virtual void	SetSRowX (double[4])
virtual double *	GetSRowX ()
virtual void	GetSRowX (double &, double &, double &, double &)
virtual void	GetSRowX (double[4])
virtual void	SetSRowY (double, double, double, double)
virtual void	SetSRowY (double[4])
virtual double *	GetSRowY ()
virtual void	GetSRowY (double &, double &, double &, double &)
virtual void	GetSRowY (double[4])
virtual void	SetSRowZ (double, double, double, double)
virtual void	SetSRowZ (double[4])
virtual double *	GetSRowZ ()
virtual void	GetSRowZ (double &, double &, double &, double &)
virtual void	GetSRowZ (double[4])

void	SetHeader (const nifti_1_header *hdr)
void	GetHeader (nifti_1_header *hdr)
void	SetHeader (const nifti_2_header *hdr)
void	GetHeader (nifti_2_header *hdr)
Protected Member Functions
	vtkNIFTIImageHeader ()
	~vtkNIFTIImageHeader ()
void	SetStringValue (char x, const char y, size_t n)
Protected Attributes
char	Magic [12]
vtkTypeInt64	VoxOffset
int	DataType
int	BitPix
vtkTypeInt64	Dim [8]
double	PixDim [8]
int	IntentCode
char	IntentName [18]
double	IntentP1
double	IntentP2
double	IntentP3
double	SclSlope
double	SclInter
double	CalMin
double	CalMax
double	SliceDuration
double	TOffset
vtkTypeInt64	SliceStart
vtkTypeInt64	SliceEnd
int	SliceCode
int	XYZTUnits
int	DimInfo
char	Descrip [82]
char	AuxFile [26]
int	QFormCode
int	SFormCode
double	QuaternB
double	QuaternC
double	QuaternD
double	QOffsetX
double	QOffsetY
double	QOffsetZ
double	SRowX [4]
double	SRowY [4]
double	SRowZ [4]
typedef vtkObject	Superclass
static vtkNIFTIImageHeader *	New ()
static int	IsTypeOf (const char *type)
static vtkNIFTIImageHeader *	SafeDownCast (vtkObjectBase *o)
virtual int	IsA (const char *type)
vtkNIFTIImageHeader *	NewInstance () const
virtual vtkObjectBase *	NewInstanceInternal () const

Detailed Description

Store NIfTI header information.

This class stores the header of a NIfTI file in a VTK-friendly format. By using this class, it is possible to specify the header information that will be stored in a file written by the vtkNIFTIImageWriter. Note that the SForm and QForm orientation information in this class will be ignored by the writer if an SForm and QForm have been explicitly set via the writer's SetSForm and SetQForm methods. Also note that all info like Dim, PixDim, DataType, etc. will be ignored by the writer because this information must instead be taken from the vtkImageData information. Finally, note that the vtkNIFTIImageWriter will ignore the Descrip field, since it has its own SetDescription method.

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

See also:: vtkNIFTIImageReader, vtkNIFTIImageWriter

Tests:: vtkNIFTIImageHeader (Tests)

Definition at line 48 of file vtkNIFTIImageHeader.h.

Member Typedef Documentation

typedef vtkObject vtkNIFTIImageHeader::Superclass

Static method for construction.

Reimplemented from vtkObject.

Definition at line 176 of file vtkNIFTIImageHeader.h.

Member Enumeration Documentation

enum vtkNIFTIImageHeader::IntentCodeEnum

NIFTI intent codes.

Enumerator:

IntentNone
IntentCorrel
IntentTTest
IntentFTest
IntentZScore
IntentChiSQ
IntentBeta
IntentBinom
IntentGamma
IntentPoisson
IntentNormal
IntentFTestNonc
IntentChiSQNonc
IntentLogistic
IntentLaplace
IntentUniform
IntentTTestNonc
IntentWeibull
IntentChi
IntentInvGauss
IntentExtVal
IntentPVal
IntentLogPVal
IntentLog10PVal
IntentEstimate
IntentLabel
IntentNeuroName
IntentGenMatrix
IntentSymMatrix
IntentDispVect
IntentVector
IntentPointSet
IntentTriangle
IntentQuaternion
IntentDimless
IntentTimeSeries
IntentNodeIndex
IntentRGBVector
IntentRGBAVector
IntentShape

Definition at line 54 of file vtkNIFTIImageHeader.h.

enum vtkNIFTIImageHeader::XFormCodeEnum

NIFTI transform codes.

Enumerator:

XFormUnkown
XFormScannerAnat
XFormAlignedAnat
XFormTalairach
XFormMNI152

Definition at line 100 of file vtkNIFTIImageHeader.h.

enum vtkNIFTIImageHeader::SliceCodeEnum

NIFTI slice codes.

Enumerator:

SliceUnknown
SliceSeqInc
SliceSeqDec
SliceAltInc
SliceAltDec
SliceAltInc2
SliceAltDec2

Definition at line 111 of file vtkNIFTIImageHeader.h.

enum vtkNIFTIImageHeader::UnitsXYZTEnum

NIFTI unit codes.

Enumerator:

UnitsUnknown
UnitsMeter
UnitsMM
UnitsMicron
UnitsSpace
UnitsSec
UnitsMSec
UnitsUSec
UnitsHz
UnitsPPM
UnitsRads
UnitsTime

Definition at line 124 of file vtkNIFTIImageHeader.h.

enum vtkNIFTIImageHeader::DataTypeEnum

NIFTI data types. Types RGB24 and RGB32 are represented in VTK as a multi-component unsigned char image. Complex values are represented as two-component images. The NIFTI types Float128 and Complex256 are not supported.

Enumerator:

TypeUInt8
TypeInt16
TypeInt32
TypeFloat32
TypeComplex64
TypeFloat64
TypeRGB24
TypeInt8
TypeUInt16
TypeUInt32
TypeInt64
TypeUInt64
TypeFloat128
TypeComplex128
TypeComplex256
TypeRGBA32

Definition at line 145 of file vtkNIFTIImageHeader.h.

enum vtkNIFTIImageHeader::HeaderSizeEnum

NIFTI header sizes.

Enumerator:

NIFTI1HeaderSize
NIFTI2HeaderSize

Definition at line 167 of file vtkNIFTIImageHeader.h.

Constructor & Destructor Documentation

vtkNIFTIImageHeader::vtkNIFTIImageHeader ( ) [protected]

vtkNIFTIImageHeader::~vtkNIFTIImageHeader ( ) [protected]

Member Function Documentation

static vtkNIFTIImageHeader* vtkNIFTIImageHeader::New ( ) [static]

Static method for construction.

Reimplemented from vtkObject.

static int vtkNIFTIImageHeader::IsTypeOf ( const char * type ) [static]

Static method for construction.

Reimplemented from vtkObject.

virtual int vtkNIFTIImageHeader::IsA ( const char * type ) [virtual]

Static method for construction.

Reimplemented from vtkObject.

static vtkNIFTIImageHeader* vtkNIFTIImageHeader::SafeDownCast ( vtkObjectBase * o ) [static]

Static method for construction.

Reimplemented from vtkObject.

virtual vtkObjectBase* vtkNIFTIImageHeader::NewInstanceInternal ( ) const [protected, virtual]

Static method for construction.

Reimplemented from vtkObject.

vtkNIFTIImageHeader* vtkNIFTIImageHeader::NewInstance ( ) const

Static method for construction.

Reimplemented from vtkObject.

virtual void vtkNIFTIImageHeader::PrintSelf	(	ostream &	os,
		vtkIndent	indent
	)		`[virtual]`

Print information about this object.

Reimplemented from vtkObject.

const char* vtkNIFTIImageHeader::GetMagic ( ) [inline]

Get the magic number for the NIFTI file as a null-terminated string.

Definition at line 183 of file vtkNIFTIImageHeader.h.

vtkTypeInt64 vtkNIFTIImageHeader::GetVoxOffset ( ) [inline]

Get the offset to the pixel data within the file.

Definition at line 186 of file vtkNIFTIImageHeader.h.

int vtkNIFTIImageHeader::GetDataType ( ) [inline]

Get the data type.

Definition at line 189 of file vtkNIFTIImageHeader.h.

int vtkNIFTIImageHeader::GetBitPix ( ) [inline]

Get the number of bits per pixel.

Definition at line 192 of file vtkNIFTIImageHeader.h.

vtkTypeInt64 vtkNIFTIImageHeader::GetDim ( int i ) [inline]

Get the nth dimension of the data, where GetDim(0) returns the number of dimensions that are defined for the file.

Definition at line 197 of file vtkNIFTIImageHeader.h.

double vtkNIFTIImageHeader::GetPixDim ( int i ) [inline]

Get the sample spacing in the nth dimension. If GetPixDim(0) is negative, then the quaternion for the qform describes the correct orientation only after the slice ordering has been reversed.

Definition at line 205 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetIntentCode ( int ) [virtual]

Get the NIFTI intent code. This is an enumerated value in the NIFTI header that states what the data is intended to be used for.

int vtkNIFTIImageHeader::GetIntentCode ( ) [inline]

Get the NIFTI intent code. This is an enumerated value in the NIFTI header that states what the data is intended to be used for.

Definition at line 213 of file vtkNIFTIImageHeader.h.

void vtkNIFTIImageHeader::SetIntentName ( const char * name )

Get the intent name. This should match the intent code.

const char* vtkNIFTIImageHeader::GetIntentName ( ) [inline]

Get the intent name. This should match the intent code.

Definition at line 219 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetIntentP1 ( double ) [virtual]

Get one of the NIFTI intent parameters. The definition of these parameters varies according to the IntentCode.

double vtkNIFTIImageHeader::GetIntentP1 ( ) [inline]

Get one of the NIFTI intent parameters. The definition of these parameters varies according to the IntentCode.

Definition at line 226 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetIntentP2 ( double ) [virtual]

Get one of the NIFTI intent parameters. The definition of these parameters varies according to the IntentCode.

double vtkNIFTIImageHeader::GetIntentP2 ( ) [inline]

Get one of the NIFTI intent parameters. The definition of these parameters varies according to the IntentCode.

Definition at line 228 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetIntentP3 ( double ) [virtual]

Get one of the NIFTI intent parameters. The definition of these parameters varies according to the IntentCode.

double vtkNIFTIImageHeader::GetIntentP3 ( ) [inline]

Get one of the NIFTI intent parameters. The definition of these parameters varies according to the IntentCode.

Definition at line 230 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetSclSlope ( double ) [virtual]

Get the scale and slope to apply to the data in order to get the real-valued data values.

double vtkNIFTIImageHeader::GetSclSlope ( ) [inline]

Get the scale and slope to apply to the data in order to get the real-valued data values.

Definition at line 237 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetSclInter ( double ) [virtual]

Get the scale and slope to apply to the data in order to get the real-valued data values.

double vtkNIFTIImageHeader::GetSclInter ( ) [inline]

Get the scale and slope to apply to the data in order to get the real-valued data values.

Definition at line 239 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetCalMin ( double ) [virtual]

Get the calibrated range of the data, i.e. the values stored in the cal_min and cal_max fields in the header.

double vtkNIFTIImageHeader::GetCalMin ( ) [inline]

Get the calibrated range of the data, i.e. the values stored in the cal_min and cal_max fields in the header.

Definition at line 246 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetCalMax ( double ) [virtual]

Get the calibrated range of the data, i.e. the values stored in the cal_min and cal_max fields in the header.

double vtkNIFTIImageHeader::GetCalMax ( ) [inline]

Get the calibrated range of the data, i.e. the values stored in the cal_min and cal_max fields in the header.

Definition at line 248 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetSliceDuration ( double ) [virtual]

Get the slice_duration and toffset from the header.

double vtkNIFTIImageHeader::GetSliceDuration ( ) [inline]

Get the slice_duration and toffset from the header.

Definition at line 254 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetTOffset ( double ) [virtual]

Get the slice_duration and toffset from the header.

double vtkNIFTIImageHeader::GetTOffset ( ) [inline]

Get the slice_duration and toffset from the header.

Definition at line 256 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetSliceStart ( vtkTypeInt64 ) [virtual]

Get the slice range for the data.

vtkTypeInt64 vtkNIFTIImageHeader::GetSliceStart ( ) [inline]

Get the slice range for the data.

Definition at line 262 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetSliceEnd ( vtkTypeInt64 ) [virtual]

Get the slice range for the data.

vtkTypeInt64 vtkNIFTIImageHeader::GetSliceEnd ( ) [inline]

Get the slice range for the data.

Definition at line 264 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetSliceCode ( int ) [virtual]

Get the slice code for the data.

int vtkNIFTIImageHeader::GetSliceCode ( ) [inline]

Get the slice code for the data.

Definition at line 270 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetXYZTUnits ( int ) [virtual]

Get a bitfield that describes the units for the first 4 dims.

int vtkNIFTIImageHeader::GetXYZTUnits ( ) [inline]

Get a bitfield that describes the units for the first 4 dims.

Definition at line 276 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetDimInfo ( int ) [virtual]

Get a bitfield with extra information about the dimensions, it states which dimensions are the phase encode, frequency encode, and slice encode dimensions for MRI acquisitions.

int vtkNIFTIImageHeader::GetDimInfo ( ) [inline]

Get a bitfield with extra information about the dimensions, it states which dimensions are the phase encode, frequency encode, and slice encode dimensions for MRI acquisitions.

Definition at line 284 of file vtkNIFTIImageHeader.h.

void vtkNIFTIImageHeader::SetDescrip ( const char * descrip )

Get a null-terminated file descriptor, this usually gives the name of the software that wrote the file. It will have a maximum length of 80 characters. Use ASCII to ensure compatibility with all NIFTI software, the NIFTI standard itself does not specify what encodings are permitted.

const char* vtkNIFTIImageHeader::GetDescrip ( ) [inline]

Get a null-terminated file descriptor, this usually gives the name of the software that wrote the file. It will have a maximum length of 80 characters. Use ASCII to ensure compatibility with all NIFTI software, the NIFTI standard itself does not specify what encodings are permitted.

Definition at line 294 of file vtkNIFTIImageHeader.h.

void vtkNIFTIImageHeader::SetAuxFile ( const char * auxfile )

Get an auxilliary file, e.g. a color table, that is associated with this data. The length of the filename must be a maximum of 24 characters, and it will be assumed to be in the same directory as the NIFTI file.

const char* vtkNIFTIImageHeader::GetAuxFile ( ) [inline]

Get an auxilliary file, e.g. a color table, that is associated with this data. The length of the filename must be a maximum of 24 characters, and it will be assumed to be in the same directory as the NIFTI file.

Definition at line 303 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetQFormCode ( int ) [virtual]

Get the QForm or SForm code.

int vtkNIFTIImageHeader::GetQFormCode ( ) [inline]

Get the QForm or SForm code.

Definition at line 309 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetSFormCode ( int ) [virtual]

Get the QForm or SForm code.

int vtkNIFTIImageHeader::GetSFormCode ( ) [inline]

Get the QForm or SForm code.

Definition at line 311 of file vtkNIFTIImageHeader.h.

virtual void vtkNIFTIImageHeader::SetQuaternB ( double ) [virtual]