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

#include <vtkNIFTIImageReader.h>

Inheritance diagram for vtkNIFTIImageReader:

Collaboration diagram for vtkNIFTIImageReader:

Public Member Functions
void	PrintSelf (ostream &os, vtkIndent indent) override
	Print information about this object.

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

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

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

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.

double	GetRescaleIntercept ()

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

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

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

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


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

virtual void	SetTimeAsVector (bool)
	Read the time dimension as scalar components (default: Off).

virtual void	TimeAsVectorOn ()
	Read the time dimension as scalar components (default: Off).

virtual void	TimeAsVectorOff ()
	Read the time dimension as scalar components (default: Off).


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

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

virtual void	PlanarRGBOn ()
	Read planar RGB (separate R, G, and B planes), rather than packed RGB.

virtual void	PlanarRGBOff ()
	Read planar RGB (separate R, G, and B planes), rather than packed RGB.

Public Member Functions inherited from vtkImageReader2
virtual vtkTypeBool	IsA (const char *type)
	Return 1 if this class is the same type of (or a subclass of) the named class.

vtkImageReader2 *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

virtual void	SetMemoryBuffer (const void *)
	Specify the in memory image buffer.

virtual const void *	GetMemoryBuffer ()

virtual void	SetMemoryBufferLength (vtkIdType buflen)
	Specify the in memory image buffer length.

vtkIdType	GetMemoryBufferLength ()

virtual void	SetDataScalarType (int type)
	Set the data type of pixels in the file.

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 void	SetHeaderSize (unsigned long size)
	If there is a tail on the file, you want to explicitly set the header size.

istream *	GetFile ()

virtual unsigned long *	GetDataIncrements ()

virtual void	GetDataIncrements (unsigned long data[4])

virtual int	OpenFile ()

void	CloseFile ()

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

virtual int	CanReadFile (VTK_FILEPATH const char *vtkNotUsed(fname))
	Return non zero if the reader can read the given file name.

virtual const char *	GetFileExtensions ()
	Get the file extensions for this format.

virtual void	SetFileName (VTK_FILEPATH const char *)
	Specify file name for the image file.

	vtkGetFilePathMacro (FileName)
	Specify file name for the image file.

virtual void	SetFileNames (vtkStringArray *)
	Specify a list of file names.

virtual vtkStringArray *	GetFileNames ()
	Specify a list of file names.

virtual void	SetFilePrefix (VTK_FILEPATH const char *)
	Specify file prefix for the image file or files.

	vtkGetFilePathMacro (FilePrefix)
	Specify file prefix for the image file or files.

virtual void	SetFilePattern (VTK_FILEPATH const char *)
	The snprintf-style format string used to build filename from FilePrefix and slice number.

	vtkGetFilePathMacro (FilePattern)
	The snprintf-style format string used to build filename from FilePrefix and slice number.

virtual int	GetDataScalarType ()
	Get the file format.

virtual void	SetNumberOfScalarComponents (int)
	Set/Get the number of scalar components.

virtual int	GetNumberOfScalarComponents ()
	Set/Get the number of scalar components.

virtual void	SetDataExtent (int, int, int, int, int, int)
	Get/Set the extent of the data on disk.

virtual void	SetDataExtent (int[6])
	Get/Set the extent of the data on disk.

virtual int *	GetDataExtent ()
	Get/Set the extent of the data on disk.

virtual void	GetDataExtent (int &, int &, int &, int &, int &, int &)
	Get/Set the extent of the data on disk.

virtual void	GetDataExtent (int[6])
	Get/Set the extent of the data on disk.

virtual void	SetFileDimensionality (int)
	The number of dimensions stored in a file.

int	GetFileDimensionality ()
	The number of dimensions stored in a file.

virtual void	SetDataSpacing (double, double, double)
	Set/Get the spacing of the data in the file.

virtual void	SetDataSpacing (double[3])
	Set/Get the spacing of the data in the file.

virtual double *	GetDataSpacing ()
	Set/Get the spacing of the data in the file.

virtual void	GetDataSpacing (double &, double &, double &)
	Set/Get the spacing of the data in the file.

virtual void	GetDataSpacing (double[3])
	Set/Get the spacing of the data in the file.

virtual void	SetDataOrigin (double, double, double)
	Set/Get the origin of the data (location of first pixel in the file).

virtual void	SetDataOrigin (double[3])
	Set/Get the origin of the data (location of first pixel in the file).

virtual double *	GetDataOrigin ()
	Set/Get the origin of the data (location of first pixel in the file).

virtual void	GetDataOrigin (double &, double &, double &)
	Set/Get the origin of the data (location of first pixel in the file).

virtual void	GetDataOrigin (double[3])
	Set/Get the origin of the data (location of first pixel in the file).

virtual void	SetDataDirection (double data[])
	Set/Get the direction of the data (9 elements: 3x3 matrix).

virtual double *	GetDataDirection ()
	Set/Get the direction of the data (9 elements: 3x3 matrix).

virtual void	GetDataDirection (double data[9])
	Set/Get the direction of the data (9 elements: 3x3 matrix).

unsigned long	GetHeaderSize ()
	Get the size of the header computed by this object.

unsigned long	GetHeaderSize (unsigned long slice)
	Get the size of the header computed by this object.

virtual void	SetDataByteOrderToBigEndian ()
	These methods should be used instead of the SwapBytes methods.

virtual void	SetDataByteOrderToLittleEndian ()
	These methods should be used instead of the SwapBytes methods.

virtual int	GetDataByteOrder ()
	These methods should be used instead of the SwapBytes methods.

virtual void	SetDataByteOrder (int)
	These methods should be used instead of the SwapBytes methods.

virtual const char *	GetDataByteOrderAsString ()
	These methods should be used instead of the SwapBytes methods.

virtual void	SetFileNameSliceOffset (int)
	When reading files which start at an unusual index, this can be added to the slice number when generating the file name (default = 0)

virtual int	GetFileNameSliceOffset ()
	When reading files which start at an unusual index, this can be added to the slice number when generating the file name (default = 0)

virtual void	SetFileNameSliceSpacing (int)
	When reading files which have regular, but non contiguous slices (eg filename.1,filename.3,filename.5) a spacing can be specified to skip missing files (default = 1)

virtual int	GetFileNameSliceSpacing ()
	When reading files which have regular, but non contiguous slices (eg filename.1,filename.3,filename.5) a spacing can be specified to skip missing files (default = 1)

virtual void	SetSwapBytes (vtkTypeBool)
	Set/Get the byte swapping to explicitly swap the bytes of a file.

virtual vtkTypeBool	GetSwapBytes ()
	Set/Get the byte swapping to explicitly swap the bytes of a file.

virtual void	SwapBytesOn ()
	Set/Get the byte swapping to explicitly swap the bytes of a file.

virtual void	SwapBytesOff ()
	Set/Get the byte swapping to explicitly swap the bytes of a file.

virtual void	FileLowerLeftOn ()
	Set/Get whether the data comes from the file starting in the lower left corner or upper left corner.

virtual void	FileLowerLeftOff ()
	Set/Get whether the data comes from the file starting in the lower left corner or upper left corner.

virtual vtkTypeBool	GetFileLowerLeft ()
	Set/Get whether the data comes from the file starting in the lower left corner or upper left corner.

virtual void	SetFileLowerLeft (vtkTypeBool)
	Set/Get whether the data comes from the file starting in the lower left corner or upper left corner.

virtual void	ComputeInternalFileName (int slice)
	Set/Get the internal file name.

	vtkGetFilePathMacro (InternalFileName)
	Set/Get the internal file name.

Public Member Functions inherited from vtkImageAlgorithm
virtual vtkTypeBool	IsA (const char *type)
	Return 1 if this class is the same type of (or a subclass of) the named class.

vtkImageAlgorithm *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

vtkTypeBool	ProcessRequest (vtkInformation , vtkInformationVector , vtkInformationVector ) override
	Process a request from the executive.

vtkImageData *	GetOutput ()
	Get the output data object for a port on this algorithm.

vtkImageData *	GetOutput (int)
	Get the output data object for a port on this algorithm.

virtual void	SetOutput (vtkDataObject *d)
	Get the output data object for a port on this algorithm.

void	SetInputData (vtkDataObject *)
	Assign a data object as input.

void	SetInputData (int, vtkDataObject *)
	Assign a data object as input.

vtkDataObject *	GetInput (int port)
	Get a data object for one of the input port connections.

vtkDataObject *	GetInput ()
	Get a data object for one of the input port connections.

vtkImageData *	GetImageDataInput (int port)
	Get a data object for one of the input port connections.

virtual void	AddInputData (vtkDataObject *)
	Assign a data object as input.

virtual void	AddInputData (int, vtkDataObject *)
	Assign a data object as input.

Public Member Functions inherited from vtkAlgorithm
virtual vtkTypeBool	IsA (const char *type)
	Return 1 if this class is the same type of (or a subclass of) the named class.

vtkAlgorithm *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

vtkTypeBool	HasExecutive ()
	Check whether this algorithm has an assigned executive.

vtkExecutive *	GetExecutive ()
	Get this algorithm's executive.

virtual void	SetExecutive (vtkExecutive *executive)
	Set this algorithm's executive.

virtual vtkTypeBool	ProcessRequest (vtkInformation request, vtkInformationVector inInfo, vtkInformationVector outInfo)
	Upstream/Downstream requests form the generalized interface through which executives invoke a algorithm's functionality.

vtkTypeBool	ProcessRequest (vtkInformation request, vtkCollection inInfo, vtkInformationVector *outInfo)
	Version of ProcessRequest() that is wrapped.

virtual int	ComputePipelineMTime (vtkInformation request, vtkInformationVector inInfoVec, vtkInformationVector outInfoVec, int requestFromOutputPort, vtkMTimeType *mtime)
	A special version of ProcessRequest meant specifically for the pipeline modified time request.

virtual int	ModifyRequest (vtkInformation *request, int when)
	This method gives the algorithm a chance to modify the contents of a request before or after (specified in the when argument) it is forwarded.

vtkInformation *	GetInputPortInformation (int port)
	Get the information object associated with an input port.

vtkInformation *	GetOutputPortInformation (int port)
	Get the information object associated with an output port.

int	GetNumberOfInputPorts ()
	Get the number of input ports used by the algorithm.

int	GetNumberOfOutputPorts ()
	Get the number of output ports provided by the algorithm.

void	SetAbortExecuteAndUpdateTime ()
	Set AbortExecute Flag and update LastAbortTime.

void	UpdateProgress (double amount)
	Update the progress of the process object.

bool	CheckAbort ()
	Checks to see if this filter should abort.

vtkInformation *	GetInputArrayInformation (int idx)
	Get the info object for the specified input array to this algorithm.

void	RemoveAllInputs ()
	Remove all the input data.

vtkDataObject *	GetOutputDataObject (int port)
	Get the data object that will contain the algorithm output for the given port.

vtkDataObject *	GetInputDataObject (int port, int connection)
	Get the data object that will contain the algorithm input for the given port and given connection.

virtual void	RemoveInputConnection (int port, vtkAlgorithmOutput *input)
	Remove a connection from the given input port index.

virtual void	RemoveInputConnection (int port, int idx)
	Remove a connection given by index idx.

virtual void	RemoveAllInputConnections (int port)
	Removes all input connections.

virtual void	SetInputDataObject (int port, vtkDataObject *data)
	Sets the data-object as an input on the given port index.

virtual void	SetInputDataObject (vtkDataObject *data)

virtual void	AddInputDataObject (int port, vtkDataObject *data)
	Add the data-object as an input to this given port.

virtual void	AddInputDataObject (vtkDataObject *data)

vtkAlgorithmOutput *	GetOutputPort (int index)
	Get a proxy object corresponding to the given output port of this algorithm.

vtkAlgorithmOutput *	GetOutputPort ()

int	GetNumberOfInputConnections (int port)
	Get the number of inputs currently connected to a port.

int	GetTotalNumberOfInputConnections ()
	Get the total number of inputs for this algorithm.

vtkAlgorithmOutput *	GetInputConnection (int port, int index)
	Get the algorithm output port connected to an input port.

vtkAlgorithm *	GetInputAlgorithm (int port, int index, int &algPort)
	Returns the algorithm and the output port index of that algorithm connected to a port-index pair.

vtkAlgorithm *	GetInputAlgorithm (int port, int index)
	Returns the algorithm connected to a port-index pair.

vtkAlgorithm *	GetInputAlgorithm ()
	Equivalent to GetInputAlgorithm(0, 0).

vtkExecutive *	GetInputExecutive (int port, int index)
	Returns the executive associated with a particular input connection.

vtkExecutive *	GetInputExecutive ()
	Equivalent to GetInputExecutive(0, 0)

vtkInformation *	GetInputInformation (int port, int index)
	Return the information object that is associated with a particular input connection.

vtkInformation *	GetInputInformation ()
	Equivalent to GetInputInformation(0, 0)

vtkInformation *	GetOutputInformation (int port)
	Return the information object that is associated with a particular output port.

virtual vtkTypeBool	Update (int port, vtkInformationVector *requests)
	This method enables the passing of data requests to the algorithm to be used during execution (in addition to bringing a particular port up-to-date).

virtual vtkTypeBool	Update (vtkInformation *requests)
	Convenience method to update an algorithm after passing requests to its first output port.

virtual int	UpdatePiece (int piece, int numPieces, int ghostLevels, const int extents[6]=nullptr)
	Convenience method to update an algorithm after passing requests to its first output port.

virtual VTK_UNBLOCKTHREADS int	UpdateExtent (const int extents[6])
	Convenience method to update an algorithm after passing requests to its first output port.

virtual VTK_UNBLOCKTHREADS int	UpdateTimeStep (double time, int piece=-1, int numPieces=1, int ghostLevels=0, const int extents[6]=nullptr)
	Convenience method to update an algorithm after passing requests to its first output port.

virtual VTK_UNBLOCKTHREADS void	UpdateInformation ()
	Bring the algorithm's information up-to-date.

virtual void	UpdateDataObject ()
	Create output object(s).

virtual void	PropagateUpdateExtent ()
	Propagate meta-data upstream.

virtual VTK_UNBLOCKTHREADS void	UpdateWholeExtent ()
	Bring this algorithm's outputs up-to-date.

void	ConvertTotalInputToPortConnection (int ind, int &port, int &conn)
	Convenience routine to convert from a linear ordering of input connections to a port/connection pair.

void	RemoveNoPriorTemporalAccessInformationKey ()
	Removes any information key `vtkStreamingDemandDrivenPipeline::NO_PRIOR_TEMPORAL_ACCESS()` to all output ports of this `vtkAlgorithm`.

virtual vtkInformation *	GetInformation ()
	Set/Get the information object associated with this algorithm.

virtual void	SetInformation (vtkInformation *)
	Set/Get the information object associated with this algorithm.

bool	UsesGarbageCollector () const override
	Participate in garbage collection.

virtual void	SetAbortExecute (vtkTypeBool)
	Set/Get the AbortExecute flag for the process object.

virtual vtkTypeBool	GetAbortExecute ()
	Set/Get the AbortExecute flag for the process object.

virtual void	AbortExecuteOn ()
	Set/Get the AbortExecute flag for the process object.

virtual void	AbortExecuteOff ()
	Set/Get the AbortExecute flag for the process object.

virtual double	GetProgress ()
	Get the execution progress of a process object.

void	SetContainerAlgorithm (vtkAlgorithm *containerAlg)
	Set/get a Container algorithm for this algorithm.

vtkAlgorithm *	GetContainerAlgorithm ()
	Set/get a Container algorithm for this algorithm.

virtual void	SetAbortOutput (bool)
	Set/Get an internal variable used to communicate between the algorithm and executive.

virtual bool	GetAbortOutput ()
	Set/Get an internal variable used to communicate between the algorithm and executive.

void	SetProgressShiftScale (double shift, double scale)
	Specify the shift and scale values to use to apply to the progress amount when `UpdateProgress` is called.

virtual double	GetProgressShift ()
	Specify the shift and scale values to use to apply to the progress amount when `UpdateProgress` is called.

virtual double	GetProgressScale ()
	Specify the shift and scale values to use to apply to the progress amount when `UpdateProgress` is called.

void	SetProgressText (const char *ptext)
	Set the current text message associated with the progress state.

virtual char *	GetProgressText ()
	Set the current text message associated with the progress state.

virtual unsigned long	GetErrorCode ()
	The error code contains a possible error that occurred while reading or writing the file.

void	SetInputArrayToProcess (const char *name, int fieldAssociation)
	Set the input data arrays that this algorithm will process.

virtual void	SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, const char *name)
	Set the input data arrays that this algorithm will process.

virtual void	SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, int fieldAttributeType)
	Set the input data arrays that this algorithm will process.

virtual void	SetInputArrayToProcess (int idx, vtkInformation *info)
	Set the input data arrays that this algorithm will process.

virtual void	SetInputArrayToProcess (int idx, int port, int connection, const char fieldAssociation, const char attributeTypeorName)
	Set the input data arrays that this algorithm will process.

virtual void	SetInputConnection (int port, vtkAlgorithmOutput *input)
	Set the connection for the given input port index.

virtual void	SetInputConnection (vtkAlgorithmOutput *input)
	Set the connection for the given input port index.

virtual void	AddInputConnection (int port, vtkAlgorithmOutput *input)
	Add a connection to the given input port index.

virtual void	AddInputConnection (vtkAlgorithmOutput *input)
	Add a connection to the given input port index.

virtual VTK_UNBLOCKTHREADS void	Update (int port)
	Bring this algorithm's outputs up-to-date.

virtual VTK_UNBLOCKTHREADS void	Update ()
	Bring this algorithm's outputs up-to-date.

virtual void	SetReleaseDataFlag (vtkTypeBool)
	Turn release data flag on or off for all output ports.

virtual vtkTypeBool	GetReleaseDataFlag ()
	Turn release data flag on or off for all output ports.

void	ReleaseDataFlagOn ()
	Turn release data flag on or off for all output ports.

void	ReleaseDataFlagOff ()
	Turn release data flag on or off for all output ports.

int	UpdateExtentIsEmpty (vtkInformation pinfo, vtkDataObject output)
	This detects when the UpdateExtent will generate no data This condition is satisfied when the UpdateExtent has zero volume (0,-1,...) or the UpdateNumberOfPieces is 0.

int	UpdateExtentIsEmpty (vtkInformation *pinfo, int extentType)
	This detects when the UpdateExtent will generate no data This condition is satisfied when the UpdateExtent has zero volume (0,-1,...) or the UpdateNumberOfPieces is 0.

int *	GetUpdateExtent ()
	These functions return the update extent for output ports that use 3D extents.

int *	GetUpdateExtent (int port)
	These functions return the update extent for output ports that use 3D extents.

void	GetUpdateExtent (int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)
	These functions return the update extent for output ports that use 3D extents.

void	GetUpdateExtent (int port, int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)
	These functions return the update extent for output ports that use 3D extents.

void	GetUpdateExtent (int extent[6])
	These functions return the update extent for output ports that use 3D extents.

void	GetUpdateExtent (int port, int extent[6])
	These functions return the update extent for output ports that use 3D extents.

int	GetUpdatePiece ()
	These functions return the update extent for output ports that use piece extents.

int	GetUpdatePiece (int port)
	These functions return the update extent for output ports that use piece extents.

int	GetUpdateNumberOfPieces ()
	These functions return the update extent for output ports that use piece extents.

int	GetUpdateNumberOfPieces (int port)
	These functions return the update extent for output ports that use piece extents.

int	GetUpdateGhostLevel ()
	These functions return the update extent for output ports that use piece extents.

int	GetUpdateGhostLevel (int port)
	These functions return the update extent for output ports that use piece extents.

void	SetProgressObserver (vtkProgressObserver *)
	If an ProgressObserver is set, the algorithm will report progress through it rather than directly.

virtual vtkProgressObserver *	GetProgressObserver ()
	If an ProgressObserver is set, the algorithm will report progress through it rather than directly.

void	SetNoPriorTemporalAccessInformationKey (int key)
	Set to all output ports of this algorithm the information key `vtkStreamingDemandDrivenPipeline::NO_PRIOR_TEMPORAL_ACCESS()`.

void	SetNoPriorTemporalAccessInformationKey ()
	Set to all output ports of this algorithm the information key `vtkStreamingDemandDrivenPipeline::NO_PRIOR_TEMPORAL_ACCESS()`.

Public Member Functions inherited from vtkObject
	vtkBaseTypeMacro (vtkObject, vtkObjectBase)

virtual void	DebugOn ()
	Turn debugging output on.

virtual void	DebugOff ()
	Turn debugging output off.

bool	GetDebug ()
	Get the value of the debug flag.

void	SetDebug (bool debugFlag)
	Set the value of the debug flag.

virtual void	Modified ()
	Update the modification time for this object.

virtual vtkMTimeType	GetMTime ()
	Return this object's modified time.

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

void	RemoveObserver (unsigned long tag)

void	RemoveObservers (unsigned long event)

void	RemoveObservers (const char *event)

void	RemoveAllObservers ()

vtkTypeBool	HasObserver (unsigned long event)

vtkTypeBool	HasObserver (const char *event)

vtkTypeBool	InvokeEvent (unsigned long event)

vtkTypeBool	InvokeEvent (const char *event)

std::string	GetObjectDescription () const override
	The object description printed in messages and PrintSelf output.

unsigned long	AddObserver (unsigned long event, vtkCommand *, float priority=0.0f)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

unsigned long	AddObserver (const char event, vtkCommand , float priority=0.0f)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

vtkCommand *	GetCommand (unsigned long tag)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

void	RemoveObserver (vtkCommand *)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

void	RemoveObservers (unsigned long event, vtkCommand *)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

void	RemoveObservers (const char event, vtkCommand )
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

vtkTypeBool	HasObserver (unsigned long event, vtkCommand *)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

vtkTypeBool	HasObserver (const char event, vtkCommand )
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, void(T::*callback)(), float priority=0.0f)
	Overloads to AddObserver that allow developers to add class member functions as callbacks for events.

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, void(T::callback)(vtkObject , unsigned long, void *), float priority=0.0f)
	Overloads to AddObserver that allow developers to add class member functions as callbacks for events.

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, bool(T::callback)(vtkObject , unsigned long, void *), float priority=0.0f)
	Allow user to set the AbortFlagOn() with the return value of the callback method.

vtkTypeBool	InvokeEvent (unsigned long event, void *callData)
	This method invokes an event and return whether the event was aborted or not.

vtkTypeBool	InvokeEvent (const char event, void callData)
	This method invokes an event and return whether the event was aborted or not.

virtual void	SetObjectName (const std::string &objectName)
	Set/get the name of this object for reporting purposes.

virtual std::string	GetObjectName () const
	Set/get the name of this object for reporting purposes.

Public Member Functions inherited from vtkObjectBase
const char *	GetClassName () const
	Return the class name as a string.

virtual std::string	GetObjectDescription () const
	The object description printed in messages and PrintSelf output.

virtual vtkTypeBool	IsA (const char *name)
	Return 1 if this class is the same type of (or a subclass of) the named class.

virtual vtkIdType	GetNumberOfGenerationsFromBase (const char *name)
	Given the name of a base class of this class type, return the distance of inheritance between this class type and the named class (how many generations of inheritance are there between this class and the named class).

virtual void	Delete ()
	Delete a VTK object.

virtual void	FastDelete ()
	Delete a reference to this object.

void	InitializeObjectBase ()

void	Print (ostream &os)
	Print an object to an ostream.

void	Register (vtkObjectBase *o)
	Increase the reference count (mark as used by another object).

virtual void	UnRegister (vtkObjectBase *o)
	Decrease the reference count (release by another object).

int	GetReferenceCount ()
	Return the current reference count of this object.

void	SetReferenceCount (int)
	Sets the reference count.

bool	GetIsInMemkind () const
	A local state flag that remembers whether this object lives in the normal or extended memory space.

virtual void	PrintHeader (ostream &os, vtkIndent indent)
	Methods invoked by print to print information about the object including superclasses.

virtual void	PrintTrailer (ostream &os, vtkIndent indent)
	Methods invoked by print to print information about the object including superclasses.

Protected Member Functions
	vtkNIFTIImageReader ()

	~vtkNIFTIImageReader () override

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

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

Protected Member Functions inherited from vtkImageReader2
virtual vtkObjectBase *	NewInstanceInternal () const

int	RequestInformation (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector) override
	Subclasses can reimplement this method to collect information from their inputs and set information for their outputs.

virtual void	ExecuteInformation ()

void	ExecuteDataWithInformation (vtkDataObject data, vtkInformation outInfo) override
	This is a convenience method that is implemented in many subclasses instead of RequestData.

virtual void	ComputeDataIncrements ()

Protected Member Functions inherited from vtkImageAlgorithm
virtual vtkObjectBase *	NewInstanceInternal () const

	vtkImageAlgorithm ()

	~vtkImageAlgorithm () override

virtual int	RequestInformation (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)
	Subclasses can reimplement this method to collect information from their inputs and set information for their outputs.

virtual int	RequestUpdateExtent (vtkInformation , vtkInformationVector , vtkInformationVector )
	Subclasses can reimplement this method to translate the update extent requests from each output port into update extent requests for the input connections.

virtual int	RequestUpdateTime (vtkInformation , vtkInformationVector , vtkInformationVector )

virtual void	CopyInputArrayAttributesToOutput (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)
	Convenience method to copy the scalar type and number of components from the input data to the output data.

virtual int	RequestData (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)
	This is called in response to a REQUEST_DATA request from the executive.

virtual void	ExecuteDataWithInformation (vtkDataObject output, vtkInformation outInfo)
	This is a convenience method that is implemented in many subclasses instead of RequestData.

virtual void	CopyAttributeData (vtkImageData in, vtkImageData out, vtkInformationVector **inputVector)
	Copy the other point and cell data.

virtual void	ExecuteData (vtkDataObject *output)
	This method is the old style execute method, provided for the sake of backwards compatibility with older filters and readers.

virtual void	Execute ()
	This method is the old style execute method, provided for the sake of backwards compatibility with older filters and readers.

virtual void	AllocateOutputData (vtkImageData out, vtkInformation outInfo, int *uExtent)
	Allocate the output data.

virtual vtkImageData *	AllocateOutputData (vtkDataObject out, vtkInformation outInfo)
	Allocate the output data.

int	FillOutputPortInformation (int port, vtkInformation *info) override
	These method should be reimplemented by subclasses that have more than a single input or single output.

int	FillInputPortInformation (int port, vtkInformation *info) override
	These method should be reimplemented by subclasses that have more than a single input or single output.

Protected Member Functions inherited from vtkAlgorithm
virtual vtkObjectBase *	NewInstanceInternal () const

	vtkAlgorithm ()

	~vtkAlgorithm () override

bool	CheckUpstreamAbort ()
	Checks to see if an upstream filter has been aborted.

virtual int	FillInputPortInformation (int port, vtkInformation *info)
	Fill the input port information objects for this algorithm.

virtual int	FillOutputPortInformation (int port, vtkInformation *info)
	Fill the output port information objects for this algorithm.

virtual void	SetNumberOfInputPorts (int n)
	Set the number of input ports used by the algorithm.

virtual void	SetNumberOfOutputPorts (int n)
	Set the number of output ports provided by the algorithm.

int	InputPortIndexInRange (int index, const char *action)

int	OutputPortIndexInRange (int index, const char *action)

int	GetInputArrayAssociation (int idx, vtkInformationVector **inputVector)
	Get the association of the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass.

vtkInformation *	GetInputArrayFieldInformation (int idx, vtkInformationVector **inputVector)
	This method takes in an index (as specified in SetInputArrayToProcess) and a pipeline information vector.

virtual vtkExecutive *	CreateDefaultExecutive ()
	Create a default executive.

void	ReportReferences (vtkGarbageCollector *) override

virtual void	SetNthInputConnection (int port, int index, vtkAlgorithmOutput *input)
	Replace the Nth connection on the given input port.

virtual void	SetNumberOfInputConnections (int port, int n)
	Set the number of input connections on the given input port.

void	SetInputDataInternal (int port, vtkDataObject *input)
	These methods are used by subclasses to implement methods to set data objects directly as input.

void	AddInputDataInternal (int port, vtkDataObject *input)

int	GetInputArrayAssociation (int idx, int connection, vtkInformationVector **inputVector)
	Filters that have multiple connections on one port can use this signature.

int	GetInputArrayAssociation (int idx, vtkDataObject *input)
	Filters that have multiple connections on one port can use this signature.

vtkDataArray *	GetInputArrayToProcess (int idx, vtkInformationVector **inputVector)
	Get the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass.

vtkDataArray *	GetInputArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
	Get the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass.

vtkDataArray *	GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
	Filters that have multiple connections on one port can use this signature.

vtkDataArray *	GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
	Filters that have multiple connections on one port can use this signature.

vtkDataArray *	GetInputArrayToProcess (int idx, vtkDataObject *input)
	Filters that have multiple connections on one port can use this signature.

vtkDataArray *	GetInputArrayToProcess (int idx, vtkDataObject *input, int &association)
	Filters that have multiple connections on one port can use this signature.

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector)
	Get the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass.

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
	Get the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass.

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
	Filters that have multiple connections on one port can use this signature.

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
	Filters that have multiple connections on one port can use this signature.

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkDataObject *input)
	Filters that have multiple connections on one port can use this signature.

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkDataObject *input, int &association)
	Filters that have multiple connections on one port can use this signature.

virtual void	SetErrorCode (unsigned long)
	The error code contains a possible error that occurred while reading or writing the file.

Protected Member Functions inherited from vtkObject
	vtkObject ()

	~vtkObject () override

void	RegisterInternal (vtkObjectBase *, vtkTypeBool check) override

void	UnRegisterInternal (vtkObjectBase *, vtkTypeBool check) override

void	InternalGrabFocus (vtkCommand mouseEvents, vtkCommand keypressEvents=nullptr)
	These methods allow a command to exclusively grab all events.

void	InternalReleaseFocus ()
	These methods allow a command to exclusively grab all events.

Protected Member Functions inherited from vtkObjectBase
	vtkObjectBase ()

virtual	~vtkObjectBase ()

virtual void	RegisterInternal (vtkObjectBase *, vtkTypeBool check)

virtual void	UnRegisterInternal (vtkObjectBase *, vtkTypeBool check)

virtual void	ReportReferences (vtkGarbageCollector *)

virtual void	ObjectFinalize ()

	vtkObjectBase (const vtkObjectBase &)

void	operator= (const vtkObjectBase &)

Static Protected Member Functions
static bool	CheckExtension (const char filename, const char ext)
	Do a case-insensitive check for the given extension.

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

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

static bool	CheckAnalyzeHeader (const nifti_1_header *hdr)
	Return true if an Analyze 7.5 header was found.

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

Static Protected Member Functions inherited from vtkObjectBase
static vtkMallocingFunction	GetCurrentMallocFunction ()

static vtkReallocingFunction	GetCurrentReallocFunction ()

static vtkFreeingFunction	GetCurrentFreeFunction ()

static vtkFreeingFunction	GetAlternateFreeFunction ()

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

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

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

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

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

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


double	RescaleIntercept
	Information for rescaling data to quantitative units.

double	RescaleSlope
	Information for rescaling data to quantitative units.


vtkMatrix4x4 *	QFormMatrix
	The orientation matrices for the NIFTI file.

vtkMatrix4x4 *	SFormMatrix
	The orientation matrices for the NIFTI file.

Protected Attributes inherited from vtkImageReader2
vtkStringArray *	FileNames

char *	InternalFileName

char *	FileName

char *	FilePrefix

char *	FilePattern

int	NumberOfScalarComponents

vtkTypeBool	FileLowerLeft

const void *	MemoryBuffer

vtkIdType	MemoryBufferLength

istream *	File

unsigned long	DataIncrements [4]

int	DataExtent [6]

vtkTypeBool	SwapBytes

int	FileDimensionality

unsigned long	HeaderSize

int	DataScalarType

unsigned long	ManualHeaderSize

double	DataSpacing [3]

double	DataOrigin [3]

double	DataDirection [9]

int	FileNameSliceOffset

int	FileNameSliceSpacing

Protected Attributes inherited from vtkAlgorithm
vtkTimeStamp	LastAbortCheckTime

vtkInformation *	Information

double	Progress

char *	ProgressText

vtkProgressObserver *	ProgressObserver

unsigned long	ErrorCode
	The error code contains a possible error that occurred while reading or writing the file.

Protected Attributes inherited from vtkObject
bool	Debug

vtkTimeStamp	MTime

vtkSubjectHelper *	SubjectHelper

std::string	ObjectName

Protected Attributes inherited from vtkObjectBase
std::atomic< int32_t >	ReferenceCount

vtkWeakPointerBase **	WeakPointers

typedef vtkImageReader2	Superclass
	Static method for construction.

static vtkNIFTIImageReader *	New ()
	Static method for construction.

static vtkTypeBool	IsTypeOf (const char *type)
	Static method for construction.

static vtkNIFTIImageReader *	SafeDownCast (vtkObjectBase *o)
	Static method for construction.

virtual vtkTypeBool	IsA (const char *type)
	Static method for construction.

vtkNIFTIImageReader *	NewInstance () const
	Static method for construction.

virtual vtkObjectBase *	NewInstanceInternal () const
	Static method for construction.

Additional Inherited Members
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 }
	Values used for setting the desired output precision for various algorithms. More...

typedef vtkObject	Superclass

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 ()
	Keys used to specify input port requirements.

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 ()
	This key tells the executive that a particular output port is capable of producing an arbitrary subextent of the whole extent.

static vtkInformationIntegerKey *	CAN_HANDLE_PIECE_REQUEST ()
	Key that tells the pipeline that a particular algorithm can or cannot handle piece request.

static vtkInformationIntegerKey *	ABORTED ()

static void	SetDefaultExecutivePrototype (vtkExecutive *proto)
	If the DefaultExecutivePrototype is set, a copy of it is created in CreateDefaultExecutive() using NewInstance().

Static Public Member Functions inherited from vtkObject
static vtkObject *	New ()
	Create an object with Debug turned off, modified time initialized to zero, and reference counting on.

static void	BreakOnError ()
	This method is called when vtkErrorMacro executes.

static void	SetGlobalWarningDisplay (vtkTypeBool val)
	This is a global flag that controls whether any debug, warning or error messages are displayed.

static void	GlobalWarningDisplayOn ()
	This is a global flag that controls whether any debug, warning or error messages are displayed.

static void	GlobalWarningDisplayOff ()
	This is a global flag that controls whether any debug, warning or error messages are displayed.

static vtkTypeBool	GetGlobalWarningDisplay ()
	This is a global flag that controls whether any debug, warning or error messages are displayed.

Static Public Member Functions inherited from vtkObjectBase
static vtkTypeBool	IsTypeOf (const char *name)
	Return 1 if this class type is the same type of (or a subclass of) the named class.

static vtkIdType	GetNumberOfGenerationsFromBaseType (const char *name)
	Given a the name of a base class of this class type, return the distance of inheritance between this class type and the named class (how many generations of inheritance are there between this class and the named class).

static vtkObjectBase *	New ()
	Create an object with Debug turned off, modified time initialized to zero, and reference counting on.

static void	SetMemkindDirectory (const char *directoryname)
	The name of a directory, ideally mounted -o dax, to memory map an extended memory space within.

static bool	GetUsingMemkind ()
	A global state flag that controls whether vtkObjects are constructed in the usual way (the default) or within the extended memory space.

Public Attributes inherited from vtkAlgorithm
std::atomic< vtkTypeBool >	AbortExecute

Static Protected Attributes inherited from vtkAlgorithm
static vtkTimeStamp	LastAbortTime

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 42 of file vtkNIFTIImageReader.h.

Member Typedef Documentation

◆ Superclass

typedef vtkImageReader2 vtkNIFTIImageReader::Superclass

Static method for construction.

Definition at line 50 of file vtkNIFTIImageReader.h.

Constructor & Destructor Documentation

◆ vtkNIFTIImageReader()

vtkNIFTIImageReader::vtkNIFTIImageReader ( )

protected

◆ ~vtkNIFTIImageReader()

vtkNIFTIImageReader::~vtkNIFTIImageReader ( )

overrideprotected

Member Function Documentation

◆ New()

static vtkNIFTIImageReader * vtkNIFTIImageReader::New ( )

static

Static method for construction.

◆ IsTypeOf()

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

static

Static method for construction.

◆ IsA()

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

virtual

Static method for construction.

Reimplemented from vtkImageReader2.

◆ SafeDownCast()

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

static

Static method for construction.

◆ NewInstanceInternal()

virtual vtkObjectBase * vtkNIFTIImageReader::NewInstanceInternal ( ) const

protectedvirtual

Static method for construction.

Reimplemented from vtkImageReader2.

◆ NewInstance()

vtkNIFTIImageReader * vtkNIFTIImageReader::NewInstance ( ) const

Static method for construction.

◆ PrintSelf()

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

overridevirtual

Print information about this object.

Reimplemented from vtkImageReader2.

◆ GetFileExtensions()

const char * vtkNIFTIImageReader::GetFileExtensions ( )

inlineoverridevirtual

Valid extensions for this file type.

Reimplemented from vtkImageReader2.

Definition at line 61 of file vtkNIFTIImageReader.h.

◆ GetDescriptiveName()

const char * vtkNIFTIImageReader::GetDescriptiveName ( )

inlineoverridevirtual

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

Reimplemented from vtkImageReader2.

Definition at line 66 of file vtkNIFTIImageReader.h.

◆ CanReadFile()

int vtkNIFTIImageReader::CanReadFile ( VTK_FILEPATH const char * filename )

override

Return true if this reader can read the given file.

◆ GetTimeAsVector()

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.

◆ SetTimeAsVector()

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.

◆ TimeAsVectorOn()

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.

◆ TimeAsVectorOff()

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.

◆ GetTimeDimension()

int vtkNIFTIImageReader::GetTimeDimension ( )

inline

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

Definition at line 89 of file vtkNIFTIImageReader.h.

◆ GetTimeSpacing()

double vtkNIFTIImageReader::GetTimeSpacing ( )

inline

Definition at line 90 of file vtkNIFTIImageReader.h.

◆ GetRescaleSlope()

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.

◆ GetRescaleIntercept()

double vtkNIFTIImageReader::GetRescaleIntercept ( )

inline

Definition at line 100 of file vtkNIFTIImageReader.h.

◆ GetPlanarRGB()

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.

◆ SetPlanarRGB()

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.

◆ PlanarRGBOn()

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.

◆ PlanarRGBOff()

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.

◆ GetQFac()

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 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.

Definition at line 125 of file vtkNIFTIImageReader.h.

◆ GetQFormMatrix()

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 nullptr. 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 139 of file vtkNIFTIImageReader.h.

◆ GetSFormMatrix()

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 nullptr. 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 155 of file vtkNIFTIImageReader.h.

◆ GetNIFTIHeader()

vtkNIFTIImageHeader * vtkNIFTIImageReader::GetNIFTIHeader ( )

Get the raw header information from the NIfTI file.

◆ RequestInformation()

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

overrideprotectedvirtual

Read the header information.

Reimplemented from vtkImageReader2.

◆ RequestData()

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

overrideprotectedvirtual

Read the voxel data.

Reimplemented from vtkImageAlgorithm.

◆ CheckExtension()

static bool vtkNIFTIImageReader::CheckExtension	(	const char *	filename,
		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".

◆ ReplaceExtension()

static char * vtkNIFTIImageReader::ReplaceExtension	(	const char *	filename,
		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 nullptr.

◆ CheckNIFTIVersion()

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

staticprotected

Check the version of the header.

◆ CheckAnalyzeHeader()

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

staticprotected

Return true if an Analyze 7.5 header was found.

Member Data Documentation

◆ TimeAsVector

bool vtkNIFTIImageReader::TimeAsVector

protected

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

Definition at line 208 of file vtkNIFTIImageReader.h.

◆ RescaleIntercept

double vtkNIFTIImageReader::RescaleIntercept

protected

Information for rescaling data to quantitative units.

Definition at line 214 of file vtkNIFTIImageReader.h.

◆ RescaleSlope

double vtkNIFTIImageReader::RescaleSlope

protected

Information for rescaling data to quantitative units.

Definition at line 215 of file vtkNIFTIImageReader.h.

◆ QFac

double vtkNIFTIImageReader::QFac

protected

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

Definition at line 221 of file vtkNIFTIImageReader.h.

◆ QFormMatrix

vtkMatrix4x4* vtkNIFTIImageReader::QFormMatrix

protected

The orientation matrices for the NIFTI file.

Definition at line 227 of file vtkNIFTIImageReader.h.

◆ SFormMatrix

vtkMatrix4x4* vtkNIFTIImageReader::SFormMatrix

protected

The orientation matrices for the NIFTI file.

Definition at line 228 of file vtkNIFTIImageReader.h.

◆ Dim

int vtkNIFTIImageReader::Dim[8]

protected

The dimensions of the NIFTI file.

Definition at line 234 of file vtkNIFTIImageReader.h.

◆ PixDim

double vtkNIFTIImageReader::PixDim[8]

protected

The spacings in the NIFTI file.

Definition at line 239 of file vtkNIFTIImageReader.h.

◆ NIFTIHeader

vtkNIFTIImageHeader* vtkNIFTIImageReader::NIFTIHeader

protected

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

Definition at line 244 of file vtkNIFTIImageReader.h.

◆ PlanarRGB

bool vtkNIFTIImageReader::PlanarRGB

protected

Use planar RGB instead of the default (packed).

Definition at line 249 of file vtkNIFTIImageReader.h.

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

IO/Image/vtkNIFTIImageReader.h

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Superclass

Constructor & Destructor Documentation

◆ vtkNIFTIImageReader()

◆ ~vtkNIFTIImageReader()

Member Function Documentation

◆ New()

◆ IsTypeOf()

◆ IsA()

◆ SafeDownCast()

◆ NewInstanceInternal()

◆ NewInstance()

◆ PrintSelf()

◆ GetFileExtensions()

◆ GetDescriptiveName()

◆ CanReadFile()

◆ GetTimeAsVector()

◆ SetTimeAsVector()

◆ TimeAsVectorOn()

◆ TimeAsVectorOff()

◆ GetTimeDimension()

◆ GetTimeSpacing()

◆ GetRescaleSlope()

◆ GetRescaleIntercept()

◆ GetPlanarRGB()

◆ SetPlanarRGB()

◆ PlanarRGBOn()

◆ PlanarRGBOff()

◆ GetQFac()

◆ GetQFormMatrix()

◆ GetSFormMatrix()

◆ GetNIFTIHeader()

◆ RequestInformation()

◆ RequestData()

◆ CheckExtension()

◆ ReplaceExtension()

◆ CheckNIFTIVersion()

◆ CheckAnalyzeHeader()

Member Data Documentation

◆ TimeAsVector

◆ RescaleIntercept

◆ RescaleSlope

◆ QFac

◆ QFormMatrix

◆ SFormMatrix

◆ Dim

◆ PixDim

◆ NIFTIHeader

◆ PlanarRGB