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

#include <vtkNIFTIImageWriter.h>

Inheritance diagram for vtkNIFTIImageWriter:

Collaboration diagram for vtkNIFTIImageWriter:

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

virtual void	SetNIFTIVersion (int)
virtual int	GetNIFTIVersion ()

virtual void	SetDescription (const char *)
virtual char *	GetDescription ()

virtual int	GetTimeDimension ()
virtual void	SetTimeDimension (int)
virtual double	GetTimeSpacing ()
virtual void	SetTimeSpacing (double)

virtual void	SetRescaleSlope (double)
virtual double	GetRescaleSlope ()
virtual void	SetRescaleIntercept (double)
virtual double	GetRescaleIntercept ()

virtual void	SetQFac (double)
virtual double	GetQFac ()

void	SetQFormMatrix (vtkMatrix4x4 *)
vtkMatrix4x4 *	GetQFormMatrix ()

void	SetSFormMatrix (vtkMatrix4x4 *)
vtkMatrix4x4 *	GetSFormMatrix ()

void	SetNIFTIHeader (vtkNIFTIImageHeader *hdr)
vtkNIFTIImageHeader *	GetNIFTIHeader ()
Protected Member Functions
	vtkNIFTIImageWriter ()
	~vtkNIFTIImageWriter ()
int	GenerateHeader (vtkInformation *info, bool singleFile)

virtual int	RequestData (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)
Static Protected Member Functions

static char *	ReplaceExtension (const char fname, const char ext1, const char *ext2)
Protected Attributes
double	QFac
char *	Description

int	TimeDimension
double	TimeSpacing

double	RescaleIntercept
double	RescaleSlope

vtkMatrix4x4 *	QFormMatrix
vtkMatrix4x4 *	SFormMatrix

vtkNIFTIImageHeader *	NIFTIHeader
vtkNIFTIImageHeader *	OwnHeader
int	NIFTIVersion
typedef vtkImageWriter	Superclass
static vtkNIFTIImageWriter *	New ()
static int	IsTypeOf (const char *type)
static vtkNIFTIImageWriter *	SafeDownCast (vtkObjectBase *o)
virtual int	IsA (const char *type)
vtkNIFTIImageWriter *	NewInstance () const
virtual vtkObjectBase *	NewInstanceInternal () const

Detailed Description

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

This class writes NIFTI files, either in .nii format or as separate .img and .hdr files. If told to write a file that ends in ".gz", then the writer will automatically compress the file with zlib. Images of type unsigned char that have 3 or 4 scalar components will automatically be written as RGB or RGBA respectively. Images of type float or double that have 2 components will automatically be written as complex values.

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

See also:: vtkNIFTIImageReader

Tests:: vtkNIFTIImageWriter (Tests)

Definition at line 44 of file vtkNIFTIImageWriter.h.

Member Typedef Documentation

typedef vtkImageWriter vtkNIFTIImageWriter::Superclass

Static method for construction.

Reimplemented from vtkImageWriter.

Definition at line 50 of file vtkNIFTIImageWriter.h.

Constructor & Destructor Documentation

vtkNIFTIImageWriter::vtkNIFTIImageWriter ( ) [protected]

vtkNIFTIImageWriter::~vtkNIFTIImageWriter ( ) [protected]

Member Function Documentation

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

Static method for construction.

Reimplemented from vtkImageWriter.

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

Static method for construction.

Reimplemented from vtkImageWriter.

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

Static method for construction.

Reimplemented from vtkImageWriter.

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

Static method for construction.

Reimplemented from vtkImageWriter.

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

Static method for construction.

Reimplemented from vtkImageWriter.

vtkNIFTIImageWriter* vtkNIFTIImageWriter::NewInstance ( ) const

Static method for construction.

Reimplemented from vtkImageWriter.

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

Print information about this object.

Reimplemented from vtkImageWriter.

virtual void vtkNIFTIImageWriter::SetNIFTIVersion ( int ) [virtual]

Set the version number for the NIfTI file format to use. This can be 1, 2, or 0 (the default). If set to zero, then it will save as NIfTI version 1 unless SetNIFTIHeader() provided header information from a NIfTI version 2 file.

virtual int vtkNIFTIImageWriter::GetNIFTIVersion ( ) [virtual]

Set the version number for the NIfTI file format to use. This can be 1, 2, or 0 (the default). If set to zero, then it will save as NIfTI version 1 unless SetNIFTIHeader() provided header information from a NIfTI version 2 file.

virtual void vtkNIFTIImageWriter::SetDescription ( const char * ) [virtual]

Set a short description (max 80 chars) of how the file was produced. The default description is "VTKX.Y" where X.Y is the VTK version.

virtual char* vtkNIFTIImageWriter::GetDescription ( ) [virtual]

Set a short description (max 80 chars) of how the file was produced. The default description is "VTKX.Y" where X.Y is the VTK version.

virtual int vtkNIFTIImageWriter::GetTimeDimension ( ) [virtual]

Set the time dimension to use in the NIFTI file (or zero if none). The number of components of the input data must be divisible by the time dimension if the time dimension is not set to zero. The vector dimension will be set to the number of components divided by the time dimension.

virtual void vtkNIFTIImageWriter::SetTimeDimension ( int ) [virtual]

Set the time dimension to use in the NIFTI file (or zero if none). The number of components of the input data must be divisible by the time dimension if the time dimension is not set to zero. The vector dimension will be set to the number of components divided by the time dimension.

virtual double vtkNIFTIImageWriter::GetTimeSpacing ( ) [virtual]

Set the time dimension to use in the NIFTI file (or zero if none). The number of components of the input data must be divisible by the time dimension if the time dimension is not set to zero. The vector dimension will be set to the number of components divided by the time dimension.

virtual void vtkNIFTIImageWriter::SetTimeSpacing ( double ) [virtual]

Set the time dimension to use in the NIFTI file (or zero if none). The number of components of the input data must be divisible by the time dimension if the time dimension is not set to zero. The vector dimension will be set to the number of components divided by the time dimension.

virtual void vtkNIFTIImageWriter::SetRescaleSlope ( double ) [virtual]

Set the slope and intercept for calibrating the scalar values. Other programs that read the NIFTI file can use the equation v = u*RescaleSlope + RescaleIntercept to rescale the data to real values. If both the slope and the intercept are zero, then the SclSlope and SclIntercept in the header info provided via SetNIFTIHeader() are used instead.

virtual double vtkNIFTIImageWriter::GetRescaleSlope ( ) [virtual]

Set the slope and intercept for calibrating the scalar values. Other programs that read the NIFTI file can use the equation v = u*RescaleSlope + RescaleIntercept to rescale the data to real values. If both the slope and the intercept are zero, then the SclSlope and SclIntercept in the header info provided via SetNIFTIHeader() are used instead.

virtual void vtkNIFTIImageWriter::SetRescaleIntercept ( double ) [virtual]

Set the slope and intercept for calibrating the scalar values. Other programs that read the NIFTI file can use the equation v = u*RescaleSlope + RescaleIntercept to rescale the data to real values. If both the slope and the intercept are zero, then the SclSlope and SclIntercept in the header info provided via SetNIFTIHeader() are used instead.

virtual double vtkNIFTIImageWriter::GetRescaleIntercept ( ) [virtual]

Set the slope and intercept for calibrating the scalar values. Other programs that read the NIFTI file can use the equation v = u*RescaleSlope + RescaleIntercept to rescale the data to real values. If both the slope and the intercept are zero, then the SclSlope and SclIntercept in the header info provided via SetNIFTIHeader() are used instead.

virtual void vtkNIFTIImageWriter::SetQFac ( double ) [virtual]

The QFac sets the ordering of the slices in the NIFTI file. If QFac is -1, then the slice ordering in the file will be reversed as compared to VTK. Use with caution.

virtual double vtkNIFTIImageWriter::GetQFac ( ) [virtual]

The QFac sets the ordering of the slices in the NIFTI file. If QFac is -1, then the slice ordering in the file will be reversed as compared to VTK. Use with caution.

void vtkNIFTIImageWriter::SetQFormMatrix ( vtkMatrix4x4 * )

Set the "qform" orientation and offset for the image data. The 3x3 portion of the matrix must be orthonormal and have a positive determinant, it will be used to compute the quaternion. The last column of the matrix will be used for the offset. In the NIFTI header, the qform_code will be set to 1.

vtkMatrix4x4* vtkNIFTIImageWriter::GetQFormMatrix ( ) [inline]

Set the "qform" orientation and offset for the image data. The 3x3 portion of the matrix must be orthonormal and have a positive determinant, it will be used to compute the quaternion. The last column of the matrix will be used for the offset. In the NIFTI header, the qform_code will be set to 1.

Definition at line 112 of file vtkNIFTIImageWriter.h.

void vtkNIFTIImageWriter::SetSFormMatrix ( vtkMatrix4x4 * )

Set a matrix for the "sform" transformation stored in the file. Unlike the qform matrix, the sform matrix can contain scaling information. Before being stored in the NIFTI header, the first three columns of the matrix will be multipled by the voxel spacing. In the NIFTI header, the sform_code will be set to 2.

vtkMatrix4x4* vtkNIFTIImageWriter::GetSFormMatrix ( ) [inline]

Set a matrix for the "sform" transformation stored in the file. Unlike the qform matrix, the sform matrix can contain scaling information. Before being stored in the NIFTI header, the first three columns of the matrix will be multipled by the voxel spacing. In the NIFTI header, the sform_code will be set to 2.

Definition at line 122 of file vtkNIFTIImageWriter.h.

void vtkNIFTIImageWriter::SetNIFTIHeader ( vtkNIFTIImageHeader * hdr )

Set the NIFTI header information to use when writing the file. The data dimensions and pixdim from the supplied header will be ignored. Likewise, the QForm and SForm information in the supplied header will be ignored if you have called SetQFormMatrix() or SetSFormMatrix() to provide the orientation information for the file.

vtkNIFTIImageHeader* vtkNIFTIImageWriter::GetNIFTIHeader ( )

Set the NIFTI header information to use when writing the file. The data dimensions and pixdim from the supplied header will be ignored. Likewise, the QForm and SForm information in the supplied header will be ignored if you have called SetQFormMatrix() or SetSFormMatrix() to provide the orientation information for the file.

int vtkNIFTIImageWriter::GenerateHeader	(	vtkInformation *	info,
		bool	singleFile
	)		`[protected]`

Generate the header information for the file.

virtual int vtkNIFTIImageWriter::RequestData	(	vtkInformation *	request,
		vtkInformationVector **	inputVector,
		vtkInformationVector *	outputVector
	)		`[protected, virtual]`

The main execution method, which writes the file.

Reimplemented from vtkImageWriter.

static char* vtkNIFTIImageWriter::ReplaceExtension	(	const char *	fname,
		const char *	ext1,
		const char *	ext2
	)		`[static, protected]`

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. A new string is returned that must be deleted by the caller.