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vtkNIFTIImageReader Class Reference

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

#include <vtkNIFTIImageReader.h>

Inheritance diagram for vtkNIFTIImageReader:
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Collaboration diagram for vtkNIFTIImageReader:
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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 }
 Values used for setting the desired output precision for various algorithms. More...
 
typedef vtkObject Superclass
 

Public Member Functions

virtual vtkTypeBool IsA (const char *type)
 Return 1 if this class is the same type of (or a subclass of) the named class. More...
 
vtkNIFTIImageReaderNewInstance () const
 
void PrintSelf (ostream &os, vtkIndent indent) override
 Print information about this object. More...
 
const char * GetFileExtensions () override
 Valid extensions for this file type. More...
 
const char * GetDescriptiveName () override
 Return a descriptive name that might be useful in a GUI. More...
 
int CanReadFile (const char *filename) override
 Return true if this reader can read the given file. More...
 
virtual bool GetTimeAsVector ()
 Read the time dimension as scalar components (default: Off). More...
 
virtual void SetTimeAsVector (bool)
 
virtual void TimeAsVectorOn ()
 
virtual void TimeAsVectorOff ()
 
int GetTimeDimension ()
 Get the time dimension that was stored in the NIFTI header. More...
 
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...
 
vtkMatrix4x4GetQFormMatrix ()
 Get a matrix that gives the "qform" orientation and offset for the data. More...
 
vtkMatrix4x4GetSFormMatrix ()
 Get a matrix that gives the "sform" orientation and offset for the data. More...
 
vtkNIFTIImageHeaderGetNIFTIHeader ()
 Get the raw header information from the NIfTI file. More...
 
- Public Member Functions inherited from vtkImageReader2
vtkImageReader2NewInstance () const
 
virtual void SetFileName (const char *)
 Specify file name for the image file. More...
 
virtual char * GetFileName ()
 
virtual void SetFileNames (vtkStringArray *)
 Specify a list of file names. More...
 
virtual vtkStringArrayGetFileNames ()
 
virtual void SetFilePrefix (const char *)
 Specify file prefix for the image file or files. More...
 
virtual char * GetFilePrefix ()
 
virtual void SetFilePattern (const char *)
 The snprintf-style format string used to build filename from FilePrefix and slice number. More...
 
virtual char * GetFilePattern ()
 
virtual void SetMemoryBuffer (const void *)
 Specify the in memory image buffer. More...
 
virtual const void * GetMemoryBuffer ()
 
virtual void SetMemoryBufferLength (vtkIdType buflen)
 Specify the in memory image buffer length. More...
 
vtkIdType GetMemoryBufferLength ()
 
virtual void SetDataScalarType (int type)
 Set the data type of pixels in the file. More...
 
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 ()
 Get the file format. More...
 
virtual void SetNumberOfScalarComponents (int)
 Set/Get the number of scalar components. More...
 
virtual int GetNumberOfScalarComponents ()
 
virtual void SetDataExtent (int, int, int, int, int, int)
 Get/Set the extent of the data on disk. More...
 
virtual void SetDataExtent (int[6])
 
virtual intGetDataExtent ()
 
virtual void GetDataExtent (int &, int &, int &, int &, int &, int &)
 
virtual void GetDataExtent (int[6])
 
virtual void SetFileDimensionality (int)
 The number of dimensions stored in a file. More...
 
int GetFileDimensionality ()
 
virtual void SetDataSpacing (double, double, double)
 Set/Get the spacing of the data in the file. More...
 
virtual void SetDataSpacing (double[3])
 
virtual doubleGetDataSpacing ()
 
virtual void GetDataSpacing (double &, double &, double &)
 
virtual void GetDataSpacing (double[3])
 
virtual void SetDataOrigin (double, double, double)
 Set/Get the origin of the data (location of first pixel in the file). More...
 
virtual void SetDataOrigin (double[3])
 
virtual doubleGetDataOrigin ()
 
virtual void GetDataOrigin (double &, double &, double &)
 
virtual void GetDataOrigin (double[3])
 
virtual void SetDataDirection (double data[])
 Set/Get the direction of the data (9 elements: 3x3 matrix). More...
 
virtual doubleGetDataDirection ()
 
virtual void GetDataDirection (double data[9])
 
unsigned long GetHeaderSize ()
 Get the size of the header computed by this object. More...
 
unsigned long GetHeaderSize (unsigned long slice)
 
virtual void SetHeaderSize (unsigned long size)
 If there is a tail on the file, you want to explicitly set the header size. More...
 
virtual void SetDataByteOrderToBigEndian ()
 These methods should be used instead of the SwapBytes methods. More...
 
virtual void SetDataByteOrderToLittleEndian ()
 
virtual int GetDataByteOrder ()
 
virtual void SetDataByteOrder (int)
 
virtual const char * GetDataByteOrderAsString ()
 
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) More...
 
virtual int GetFileNameSliceOffset ()
 
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) More...
 
virtual int GetFileNameSliceSpacing ()
 
virtual void SetSwapBytes (vtkTypeBool)
 Set/Get the byte swapping to explicitly swap the bytes of a file. More...
 
virtual vtkTypeBool 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 ()
 Set/Get whether the data comes from the file starting in the lower left corner or upper left corner. More...
 
virtual void FileLowerLeftOff ()
 
virtual vtkTypeBool GetFileLowerLeft ()
 
virtual void SetFileLowerLeft (vtkTypeBool)
 
virtual void ComputeInternalFileName (int slice)
 Set/Get the internal file name. More...
 
virtual char * GetInternalFileName ()
 
virtual int CanReadFile (const char *vtkNotUsed(fname))
 Return non zero if the reader can read the given file name. More...
 
- Public Member Functions inherited from vtkImageAlgorithm
vtkImageAlgorithmNewInstance () const
 
vtkImageDataGetOutput ()
 Get the output data object for a port on this algorithm. More...
 
vtkImageDataGetOutput (int)
 
virtual void SetOutput (vtkDataObject *d)
 
vtkTypeBool ProcessRequest (vtkInformation *, vtkInformationVector **, vtkInformationVector *) override
 Process a request from the executive. More...
 
void SetInputData (vtkDataObject *)
 Assign a data object as input. More...
 
void SetInputData (int, vtkDataObject *)
 
vtkDataObjectGetInput (int port)
 Get a data object for one of the input port connections. More...
 
vtkDataObjectGetInput ()
 
vtkImageDataGetImageDataInput (int port)
 
virtual void AddInputData (vtkDataObject *)
 Assign a data object as input. More...
 
virtual void AddInputData (int, vtkDataObject *)
 
- Public Member Functions inherited from vtkAlgorithm
vtkAlgorithmNewInstance () const
 
int HasExecutive ()
 Check whether this algorithm has an assigned executive. More...
 
vtkExecutiveGetExecutive ()
 Get this algorithm's executive. More...
 
virtual void SetExecutive (vtkExecutive *executive)
 Set this algorithm's executive. More...
 
vtkTypeBool ProcessRequest (vtkInformation *request, vtkCollection *inInfo, vtkInformationVector *outInfo)
 Version of ProcessRequest() that is wrapped. More...
 
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. More...
 
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. More...
 
vtkInformationGetInputPortInformation (int port)
 Get the information object associated with an input port. More...
 
vtkInformationGetOutputPortInformation (int port)
 Get the information object associated with an output port. More...
 
virtual vtkInformationGetInformation ()
 Set/Get the information object associated with this algorithm. More...
 
virtual void SetInformation (vtkInformation *)
 
int GetNumberOfInputPorts ()
 Get the number of input ports used by the algorithm. More...
 
int GetNumberOfOutputPorts ()
 Get the number of output ports provided by the algorithm. More...
 
void Register (vtkObjectBase *o) override
 Participate in garbage collection. More...
 
void UnRegister (vtkObjectBase *o) override
 Decrease the reference count (release by another object). More...
 
virtual void SetAbortExecute (vtkTypeBool)
 Set/Get the AbortExecute flag for the process object. More...
 
virtual vtkTypeBool GetAbortExecute ()
 
virtual void AbortExecuteOn ()
 
virtual void AbortExecuteOff ()
 
virtual double GetProgress ()
 Get the execution progress of a process object. More...
 
void SetProgress (double)
 SetProgress is deprecated. More...
 
void UpdateProgress (double amount)
 Update the progress of the process object. More...
 
void SetProgressShiftScale (double shift, double scale)
 Specify the shift and scale values to use to apply to the progress amount when UpdateProgress is called. More...
 
virtual double GetProgressShift ()
 
virtual double GetProgressScale ()
 
void SetProgressText (const char *ptext)
 Set the current text message associated with the progress state. More...
 
virtual char * GetProgressText ()
 
virtual unsigned long GetErrorCode ()
 The error code contains a possible error that occurred while reading or writing the file. More...
 
virtual void SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, const char *name)
 Set the input data arrays that this algorithm will process. More...
 
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)
 String based versions of SetInputArrayToProcess(). More...
 
vtkInformationGetInputArrayInformation (int idx)
 Get the info object for the specified input array to this algorithm. More...
 
void RemoveAllInputs ()
 Remove all the input data. More...
 
vtkDataObjectGetOutputDataObject (int port)
 Get the data object that will contain the algorithm output for the given port. More...
 
vtkDataObjectGetInputDataObject (int port, int connection)
 Get the data object that will contain the algorithm input for the given port and given connection. More...
 
virtual void SetInputConnection (int port, vtkAlgorithmOutput *input)
 Set the connection for the given input port index. More...
 
virtual void SetInputConnection (vtkAlgorithmOutput *input)
 
virtual void AddInputConnection (int port, vtkAlgorithmOutput *input)
 Add a connection to the given input port index. More...
 
virtual void AddInputConnection (vtkAlgorithmOutput *input)
 
virtual void RemoveInputConnection (int port, vtkAlgorithmOutput *input)
 Remove a connection from the given input port index. More...
 
virtual void RemoveInputConnection (int port, int idx)
 Remove a connection given by index idx. More...
 
virtual void RemoveAllInputConnections (int port)
 Removes all input connections. More...
 
virtual void SetInputDataObject (int port, vtkDataObject *data)
 Sets the data-object as an input on the given port index. More...
 
virtual void SetInputDataObject (vtkDataObject *data)
 
virtual void AddInputDataObject (int port, vtkDataObject *data)
 Add the data-object as an input to this given port. More...
 
virtual void AddInputDataObject (vtkDataObject *data)
 
vtkAlgorithmOutputGetOutputPort (int index)
 Get a proxy object corresponding to the given output port of this algorithm. More...
 
vtkAlgorithmOutputGetOutputPort ()
 
int GetNumberOfInputConnections (int port)
 Get the number of inputs currently connected to a port. More...
 
int GetTotalNumberOfInputConnections ()
 Get the total number of inputs for this algorithm. More...
 
vtkAlgorithmOutputGetInputConnection (int port, int index)
 Get the algorithm output port connected to an input port. More...
 
vtkAlgorithmGetInputAlgorithm (int port, int index, int &algPort)
 Returns the algorithm and the output port index of that algorithm connected to a port-index pair. More...
 
vtkAlgorithmGetInputAlgorithm (int port, int index)
 Returns the algorithm connected to a port-index pair. More...
 
vtkAlgorithmGetInputAlgorithm ()
 Equivalent to GetInputAlgorithm(0, 0). More...
 
vtkExecutiveGetInputExecutive (int port, int index)
 Returns the executive associated with a particular input connection. More...
 
vtkExecutiveGetInputExecutive ()
 Equivalent to GetInputExecutive(0, 0) More...
 
vtkInformationGetInputInformation (int port, int index)
 Return the information object that is associated with a particular input connection. More...
 
vtkInformationGetInputInformation ()
 Equivalent to GetInputInformation(0, 0) More...
 
vtkInformationGetOutputInformation (int port)
 Return the information object that is associated with a particular output port. More...
 
virtual void Update (int port)
 Bring this algorithm's outputs up-to-date. More...
 
virtual void Update ()
 
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). More...
 
virtual vtkTypeBool Update (vtkInformation *requests)
 Convenience method to update an algorithm after passing requests to its first output port. More...
 
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. More...
 
virtual int UpdateExtent (const int extents[6])
 Convenience method to update an algorithm after passing requests to its first output port. More...
 
virtual 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. More...
 
virtual void UpdateInformation ()
 Bring the algorithm's information up-to-date. More...
 
virtual void UpdateDataObject ()
 Create output object(s). More...
 
virtual void PropagateUpdateExtent ()
 Propagate meta-data upstream. More...
 
virtual void UpdateWholeExtent ()
 Bring this algorithm's outputs up-to-date. More...
 
void ConvertTotalInputToPortConnection (int ind, int &port, int &conn)
 Convenience routine to convert from a linear ordering of input connections to a port/connection pair. More...
 
virtual void SetReleaseDataFlag (int)
 Turn release data flag on or off for all output ports. More...
 
virtual int GetReleaseDataFlag ()
 
void ReleaseDataFlagOn ()
 
void ReleaseDataFlagOff ()
 
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. More...
 
int UpdateExtentIsEmpty (vtkInformation *pinfo, int extentType)
 
intGetUpdateExtent ()
 These functions return the update extent for output ports that use 3D extents. More...
 
intGetUpdateExtent (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 ()
 These functions return the update extent for output ports that use piece extents. More...
 
int GetUpdatePiece (int port)
 
int GetUpdateNumberOfPieces ()
 
int GetUpdateNumberOfPieces (int port)
 
int GetUpdateGhostLevel ()
 
int GetUpdateGhostLevel (int port)
 
void SetProgressObserver (vtkProgressObserver *)
 If an ProgressObserver is set, the algorithm will report progress through it rather than directly. More...
 
virtual vtkProgressObserverGetProgressObserver ()
 
- Public Member Functions inherited from vtkObject
 vtkBaseTypeMacro (vtkObject, vtkObjectBase)
 
virtual void DebugOn ()
 Turn debugging output on. More...
 
virtual void DebugOff ()
 Turn debugging output off. More...
 
bool GetDebug ()
 Get the value of the debug flag. More...
 
void SetDebug (bool debugFlag)
 Set the value of the debug flag. More...
 
virtual void Modified ()
 Update the modification time for this object. More...
 
virtual vtkMTimeType GetMTime ()
 Return this object's modified time. More...
 
unsigned long AddObserver (unsigned long event, vtkCommand *, float priority=0.0f)
 Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...
 
unsigned long AddObserver (const char *event, vtkCommand *, float priority=0.0f)
 
vtkCommandGetCommand (unsigned long tag)
 
void RemoveObserver (vtkCommand *)
 
void RemoveObservers (unsigned long event, vtkCommand *)
 
void RemoveObservers (const char *event, vtkCommand *)
 
vtkTypeBool HasObserver (unsigned long event, vtkCommand *)
 
vtkTypeBool HasObserver (const char *event, vtkCommand *)
 
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)
 
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. More...
 
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)
 Allow user to set the AbortFlagOn() with the return value of the callback method. More...
 
int InvokeEvent (unsigned long event, void *callData)
 This method invokes an event and return whether the event was aborted or not. More...
 
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
 Return the class name as a string. More...
 
virtual void Delete ()
 Delete a VTK object. More...
 
virtual void FastDelete ()
 Delete a reference to this object. More...
 
void InitializeObjectBase ()
 
void Print (ostream &os)
 Print an object to an ostream. More...
 
virtual void PrintHeader (ostream &os, vtkIndent indent)
 
virtual void PrintTrailer (ostream &os, vtkIndent indent)
 
int GetReferenceCount ()
 Return the current reference count of this object. More...
 
void SetReferenceCount (int)
 Sets the reference count. More...
 
void PrintRevisions (ostream &)
 Legacy. More...
 

Static Public Member Functions

static vtkNIFTIImageReaderNew ()
 Static method for construction. More...
 
static vtkTypeBool IsTypeOf (const char *type)
 
static vtkNIFTIImageReaderSafeDownCast (vtkObjectBase *o)
 
- Static Public Member Functions inherited from vtkImageReader2
static vtkImageReader2New ()
 
static vtkTypeBool IsTypeOf (const char *type)
 
static vtkImageReader2SafeDownCast (vtkObjectBase *o)
 
- Static Public Member Functions inherited from vtkImageAlgorithm
static vtkTypeBool IsTypeOf (const char *type)
 
static vtkImageAlgorithmSafeDownCast (vtkObjectBase *o)
 
- Static Public Member Functions inherited from vtkAlgorithm
static vtkAlgorithmNew ()
 
static vtkTypeBool IsTypeOf (const char *type)
 
static vtkAlgorithmSafeDownCast (vtkObjectBase *o)
 
static vtkInformationIntegerKeyINPUT_IS_OPTIONAL ()
 Keys used to specify input port requirements. More...
 
static vtkInformationIntegerKeyINPUT_IS_REPEATABLE ()
 
static vtkInformationInformationVectorKeyINPUT_REQUIRED_FIELDS ()
 
static vtkInformationStringVectorKeyINPUT_REQUIRED_DATA_TYPE ()
 
static vtkInformationInformationVectorKeyINPUT_ARRAYS_TO_PROCESS ()
 
static vtkInformationIntegerKeyINPUT_PORT ()
 
static vtkInformationIntegerKeyINPUT_CONNECTION ()
 
static vtkInformationIntegerKeyCAN_PRODUCE_SUB_EXTENT ()
 This key tells the executive that a particular output port is capable of producing an arbitrary subextent of the whole extent. More...
 
static vtkInformationIntegerKeyCAN_HANDLE_PIECE_REQUEST ()
 Key that tells the pipeline that a particular algorithm can or cannot handle piece request. More...
 
static void SetDefaultExecutivePrototype (vtkExecutive *proto)
 If the DefaultExecutivePrototype is set, a copy of it is created in CreateDefaultExecutive() using NewInstance(). More...
 
- Static Public Member Functions inherited from vtkObject
static vtkObjectNew ()
 Create an object with Debug turned off, modified time initialized to zero, and reference counting on. More...
 
static void BreakOnError ()
 This method is called when vtkErrorMacro executes. More...
 
static void SetGlobalWarningDisplay (int val)
 This is a global flag that controls whether any debug, warning or error messages are displayed. More...
 
static void GlobalWarningDisplayOn ()
 
static void GlobalWarningDisplayOff ()
 
static int GetGlobalWarningDisplay ()
 
- 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. More...
 
static vtkObjectBaseNew ()
 Create an object with Debug turned off, modified time initialized to zero, and reference counting on. More...
 

Protected Member Functions

virtual vtkObjectBaseNewInstanceInternal () const
 
 vtkNIFTIImageReader ()
 
 ~vtkNIFTIImageReader () override
 
int RequestInformation (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector) override
 Read the header information. More...
 
int RequestData (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector) override
 Read the voxel data. More...
 
- Protected Member Functions inherited from vtkImageReader2
 vtkImageReader2 ()
 
 ~vtkImageReader2 () override
 
virtual void ExecuteInformation ()
 
void ExecuteDataWithInformation (vtkDataObject *data, vtkInformation *outInfo) override
 This is a convenience method that is implemented in many subclasses instead of RequestData. More...
 
virtual void ComputeDataIncrements ()
 
- Protected Member Functions inherited from vtkImageAlgorithm
 vtkImageAlgorithm ()
 
 ~vtkImageAlgorithm () override
 
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. More...
 
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. More...
 
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. More...
 
virtual void Execute ()
 
virtual void AllocateOutputData (vtkImageData *out, vtkInformation *outInfo, int *uExtent)
 Allocate the output data. More...
 
virtual vtkImageDataAllocateOutputData (vtkDataObject *out, vtkInformation *outInfo)
 
virtual void CopyAttributeData (vtkImageData *in, vtkImageData *out, vtkInformationVector **inputVector)
 Copy the other point and cell data. More...
 
int FillOutputPortInformation (int port, vtkInformation *info) override
 These method should be reimplemented by subclasses that have more than a single input or single output. More...
 
int FillInputPortInformation (int port, vtkInformation *info) override
 Fill the input port information objects for this algorithm. More...
 
- Protected Member Functions inherited from vtkAlgorithm
 vtkAlgorithm ()
 
 ~vtkAlgorithm () override
 
virtual void SetNumberOfInputPorts (int n)
 Set the number of input ports used by the algorithm. More...
 
virtual void SetNumberOfOutputPorts (int n)
 Set the number of output ports provided by the algorithm. More...
 
int InputPortIndexInRange (int index, const char *action)
 
int OutputPortIndexInRange (int index, const char *action)
 
int GetInputArrayAssociation (int idx, vtkInformationVector **inputVector)
 Get the assocition of the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass. More...
 
int GetInputArrayAssociation (int idx, int connection, vtkInformationVector **inputVector)
 Filters that have multiple connections on one port can use this signature. More...
 
int GetInputArrayAssociation (int idx, vtkDataObject *input)
 
vtkDataArrayGetInputArrayToProcess (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. More...
 
vtkDataArrayGetInputArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
 
vtkDataArrayGetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
 Filters that have multiple connections on one port can use this signature. More...
 
vtkDataArrayGetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
 
vtkDataArrayGetInputArrayToProcess (int idx, vtkDataObject *input)
 
vtkDataArrayGetInputArrayToProcess (int idx, vtkDataObject *input, int &association)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (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. More...
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
 Filters that have multiple connections on one port can use this signature. More...
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, vtkDataObject *input)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, vtkDataObject *input, int &association)
 
vtkInformationGetInputArrayFieldInformation (int idx, vtkInformationVector **inputVector)
 This method takes in an index (as specified in SetInputArrayToProcess) and a pipeline information vector. More...
 
virtual vtkExecutiveCreateDefaultExecutive ()
 Create a default executive. More...
 
virtual void SetErrorCode (unsigned long)
 The error code contains a possible error that occurred while reading or writing the file. More...
 
void ReportReferences (vtkGarbageCollector *) override
 
virtual void SetNthInputConnection (int port, int index, vtkAlgorithmOutput *input)
 Replace the Nth connection on the given input port. More...
 
virtual void SetNumberOfInputConnections (int port, int n)
 Set the number of input connections on the given input port. More...
 
void SetInputDataInternal (int port, vtkDataObject *input)
 These methods are used by subclasses to implement methods to set data objects directly as input. More...
 
void AddInputDataInternal (int port, vtkDataObject *input)
 
- 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. More...
 
void InternalReleaseFocus ()
 
- Protected Member Functions inherited from vtkObjectBase
 vtkObjectBase ()
 
virtual ~vtkObjectBase ()
 
virtual void CollectRevisions (ostream &)
 
 vtkObjectBase (const vtkObjectBase &)
 
void operator= (const vtkObjectBase &)
 

Static Protected Member Functions

static bool CheckExtension (const char *fname, const char *ext)
 Do 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. More...
 
static bool CheckAnalyzeHeader (const nifti_1_header *hdr)
 Return true if an Analyze 7.5 header was found. More...
 
- Static Protected Member Functions inherited from vtkAlgorithm
static vtkInformationIntegerKeyPORT_REQUIREMENTS_FILLED ()
 

Protected Attributes

bool TimeAsVector
 Read the time dimension as if it was a vector dimension. More...
 
double RescaleIntercept
 Information for rescaling data to quantitative units. More...
 
double RescaleSlope
 
double QFac
 Is -1 if VTK slice order is opposite to NIFTI slice order, +1 otherwise. More...
 
vtkMatrix4x4QFormMatrix
 The orientation matrices for the NIFTI file. More...
 
vtkMatrix4x4SFormMatrix
 
int Dim [8]
 The dimensions of the NIFTI file. More...
 
double PixDim [8]
 The spacings in the NIFTI file. More...
 
vtkNIFTIImageHeaderNIFTIHeader
 A copy of the header from the file that was most recently read. More...
 
bool PlanarRGB
 Use planar RGB instead of the default (packed). More...
 
- Protected Attributes inherited from vtkImageReader2
vtkStringArrayFileNames
 
char * InternalFileName
 
char * FileName
 
char * FilePrefix
 
char * FilePattern
 
int NumberOfScalarComponents
 
vtkTypeBool FileLowerLeft
 
const void * MemoryBuffer
 
vtkIdType MemoryBufferLength
 
ifstream * 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
vtkInformationInformation
 
unsigned long ErrorCode
 
double Progress
 
char * ProgressText
 
vtkProgressObserverProgressObserver
 
- Protected Attributes inherited from vtkObject
bool Debug
 
vtkTimeStamp MTime
 
vtkSubjectHelper * SubjectHelper
 
- Protected Attributes inherited from vtkObjectBase
std::atomic< int32_t > ReferenceCount
 
vtkWeakPointerBase ** WeakPointers
 

Additional Inherited Members

- Public Attributes inherited from vtkAlgorithm
vtkTypeBool AbortExecute
 
- Static Protected Attributes inherited from vtkAlgorithm
static vtkExecutiveDefaultExecutivePrototype
 

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 50 of file vtkNIFTIImageReader.h.

Member Typedef Documentation

◆ Superclass

Definition at line 58 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

◆ IsA()

virtual vtkTypeBool vtkNIFTIImageReader::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.

◆ SafeDownCast()

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

◆ NewInstanceInternal()

virtual vtkObjectBase* vtkNIFTIImageReader::NewInstanceInternal ( ) const
protectedvirtual

Reimplemented from vtkImageReader2.

◆ NewInstance()

vtkNIFTIImageReader* vtkNIFTIImageReader::NewInstance ( ) const

◆ 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 69 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 75 of file vtkNIFTIImageReader.h.

◆ CanReadFile()

int vtkNIFTIImageReader::CanReadFile ( 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

◆ TimeAsVectorOn()

virtual void vtkNIFTIImageReader::TimeAsVectorOn ( )
virtual

◆ TimeAsVectorOff()

virtual void vtkNIFTIImageReader::TimeAsVectorOff ( )
virtual

◆ GetTimeDimension()

int vtkNIFTIImageReader::GetTimeDimension ( )
inline

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

Definition at line 99 of file vtkNIFTIImageReader.h.

◆ GetTimeSpacing()

double vtkNIFTIImageReader::GetTimeSpacing ( )
inline

Definition at line 100 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 109 of file vtkNIFTIImageReader.h.

◆ GetRescaleIntercept()

double vtkNIFTIImageReader::GetRescaleIntercept ( )
inline

Definition at line 110 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

◆ PlanarRGBOn()

virtual void vtkNIFTIImageReader::PlanarRGBOn ( )
virtual

◆ PlanarRGBOff()

virtual void vtkNIFTIImageReader::PlanarRGBOff ( )
virtual

◆ 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 135 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 149 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 165 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 *  fname,
const char *  ext 
)
staticprotected

Do a case-insensitive check for the given extension.

The check will succeed if the filename ends in ".gz", and if the extension matches after removing the ".gz".

◆ ReplaceExtension()

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

Make a new filename by replacing extension "ext1" with "ext2".

The extensions must include a period, must be three characters long, and must be lower case. This method also verifies that the file exists, and adds or subtracts a ".gz" as necessary If the file exists, a new string is returned that must be deleted by the caller. Otherwise, the return value is 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 221 of file vtkNIFTIImageReader.h.

◆ RescaleIntercept

double vtkNIFTIImageReader::RescaleIntercept
protected

Information for rescaling data to quantitative units.

Definition at line 227 of file vtkNIFTIImageReader.h.

◆ RescaleSlope

double vtkNIFTIImageReader::RescaleSlope
protected

Definition at line 228 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 234 of file vtkNIFTIImageReader.h.

◆ QFormMatrix

vtkMatrix4x4* vtkNIFTIImageReader::QFormMatrix
protected

The orientation matrices for the NIFTI file.

Definition at line 240 of file vtkNIFTIImageReader.h.

◆ SFormMatrix

vtkMatrix4x4* vtkNIFTIImageReader::SFormMatrix
protected

Definition at line 241 of file vtkNIFTIImageReader.h.

◆ Dim

int vtkNIFTIImageReader::Dim[8]
protected

The dimensions of the NIFTI file.

Definition at line 247 of file vtkNIFTIImageReader.h.

◆ PixDim

double vtkNIFTIImageReader::PixDim[8]
protected

The spacings in the NIFTI file.

Definition at line 252 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 257 of file vtkNIFTIImageReader.h.

◆ PlanarRGB

bool vtkNIFTIImageReader::PlanarRGB
protected

Use planar RGB instead of the default (packed).

Definition at line 262 of file vtkNIFTIImageReader.h.


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