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vtkPNrrdReader Class Reference

Read nrrd files efficiently from parallel file systems (and reasonably well elsewhere). More...

#include <vtkPNrrdReader.h>

Inheritance diagram for vtkPNrrdReader:
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Collaboration diagram for vtkPNrrdReader:
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Public Types

typedef vtkMPIImageReader Superclass
 
- Public Types inherited from vtkMPIImageReader
typedef vtkImageReader Superclass
 
- Public Types inherited from vtkImageReader
typedef vtkImageReader2 Superclass
 
- Public Types inherited from vtkImageReader2
typedef vtkImageAlgorithm Superclass
 
- Public Types inherited from vtkImageAlgorithm
typedef vtkAlgorithm Superclass
 
- Public Types inherited from vtkAlgorithm
typedef vtkObject Superclass
 
- Public Types inherited from vtkObject
typedef vtkObjectBase Superclass
 

Public Member Functions

virtual const char * GetClassName ()
 
virtual int IsA (const char *type)
 
virtual void PrintSelf (ostream &os, vtkIndent indent)
 
virtual int CanReadFile (const char *filename)
 
- Public Member Functions inherited from vtkMPIImageReader
virtual vtkMultiProcessControllerGetController ()
 
virtual void SetController (vtkMultiProcessController *)
 
- Public Member Functions inherited from vtkImageReader
void ComputeInverseTransformedExtent (int inExtent[6], int outExtent[6])
 
void ComputeInverseTransformedIncrements (vtkIdType inIncr[3], vtkIdType outIncr[3])
 
int OpenAndSeekFile (int extent[6], int slice)
 
virtual void SetDataVOI (int, int, int, int, int, int)
 
virtual void SetDataVOI (int[6])
 
virtual int * GetDataVOI ()
 
virtual void GetDataVOI (int &, int &, int &, int &, int &, int &)
 
virtual void GetDataVOI (int[6])
 
virtual vtkTypeUInt64 GetDataMask ()
 
virtual void SetDataMask (vtkTypeUInt64)
 
virtual void SetTransform (vtkTransform *)
 
virtual vtkTransformGetTransform ()
 
virtual void SetScalarArrayName (const char *)
 
virtual char * GetScalarArrayName ()
 
- Public Member Functions inherited from vtkImageReader2
virtual void SetHeaderSize (unsigned long size)
 
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 SetFileName (const char *)
 
virtual char * GetFileName ()
 
virtual void SetFileNames (vtkStringArray *)
 
virtual vtkStringArrayGetFileNames ()
 
virtual void SetFilePrefix (const char *)
 
virtual char * GetFilePrefix ()
 
virtual void SetFilePattern (const char *)
 
virtual char * GetFilePattern ()
 
virtual void SetDataScalarType (int type)
 
virtual void SetDataScalarTypeToFloat ()
 
virtual void SetDataScalarTypeToDouble ()
 
virtual void SetDataScalarTypeToInt ()
 
virtual void SetDataScalarTypeToUnsignedInt ()
 
virtual void SetDataScalarTypeToShort ()
 
virtual void SetDataScalarTypeToUnsignedShort ()
 
virtual void SetDataScalarTypeToChar ()
 
virtual void SetDataScalarTypeToSignedChar ()
 
virtual void SetDataScalarTypeToUnsignedChar ()
 
virtual int GetDataScalarType ()
 
virtual void SetNumberOfScalarComponents (int)
 
virtual int GetNumberOfScalarComponents ()
 
virtual void SetDataExtent (int, int, int, int, int, int)
 
virtual void SetDataExtent (int[6])
 
virtual int * GetDataExtent ()
 
virtual void GetDataExtent (int &, int &, int &, int &, int &, int &)
 
virtual void GetDataExtent (int[6])
 
virtual void SetFileDimensionality (int)
 
int GetFileDimensionality ()
 
virtual void SetDataSpacing (double, double, double)
 
virtual void SetDataSpacing (double[3])
 
virtual double * GetDataSpacing ()
 
virtual void GetDataSpacing (double &, double &, double &)
 
virtual void GetDataSpacing (double[3])
 
virtual void SetDataOrigin (double, double, double)
 
virtual void SetDataOrigin (double[3])
 
virtual double * GetDataOrigin ()
 
virtual void GetDataOrigin (double &, double &, double &)
 
virtual void GetDataOrigin (double[3])
 
unsigned long GetHeaderSize ()
 
unsigned long GetHeaderSize (unsigned long slice)
 
virtual void SetDataByteOrderToBigEndian ()
 
virtual void SetDataByteOrderToLittleEndian ()
 
virtual int GetDataByteOrder ()
 
virtual void SetDataByteOrder (int)
 
virtual const char * GetDataByteOrderAsString ()
 
virtual void SetFileNameSliceOffset (int)
 
virtual int GetFileNameSliceOffset ()
 
virtual void SetFileNameSliceSpacing (int)
 
virtual int GetFileNameSliceSpacing ()
 
virtual void SetSwapBytes (int)
 
virtual int GetSwapBytes ()
 
virtual void SwapBytesOn ()
 
virtual void SwapBytesOff ()
 
virtual void FileLowerLeftOn ()
 
virtual void FileLowerLeftOff ()
 
virtual int GetFileLowerLeft ()
 
virtual void SetFileLowerLeft (int)
 
virtual void ComputeInternalFileName (int slice)
 
virtual char * GetInternalFileName ()
 
virtual int CanReadFile (const char *vtkNotUsed(fname))
 
virtual const char * GetFileExtensions ()
 
virtual const char * GetDescriptiveName ()
 
- Public Member Functions inherited from vtkImageAlgorithm
vtkDataObjectGetInput (int port)
 
vtkDataObjectGetInput ()
 
vtkImageDataGetImageDataInput (int port)
 
vtkImageDataGetOutput ()
 
vtkImageDataGetOutput (int)
 
virtual void SetOutput (vtkDataObject *d)
 
virtual int ProcessRequest (vtkInformation *, vtkInformationVector **, vtkInformationVector *)
 
void SetInput (vtkDataObject *)
 
void SetInput (int, vtkDataObject *)
 
virtual void AddInput (vtkDataObject *)
 
virtual void AddInput (int, vtkDataObject *)
 
- Public Member Functions inherited from vtkAlgorithm
int HasExecutive ()
 
vtkExecutiveGetExecutive ()
 
virtual void SetExecutive (vtkExecutive *executive)
 
virtual int ModifyRequest (vtkInformation *request, int when)
 
vtkInformationGetInputPortInformation (int port)
 
vtkInformationGetOutputPortInformation (int port)
 
int GetNumberOfInputPorts ()
 
int GetNumberOfOutputPorts ()
 
void UpdateProgress (double amount)
 
vtkInformationGetInputArrayInformation (int idx)
 
void RemoveAllInputs ()
 
vtkDataObjectGetOutputDataObject (int port)
 
virtual void RemoveInputConnection (int port, vtkAlgorithmOutput *input)
 
int GetNumberOfInputConnections (int port)
 
int GetTotalNumberOfInputConnections ()
 
vtkAlgorithmOutputGetInputConnection (int port, int index)
 
virtual void Update ()
 
virtual void UpdateInformation ()
 
virtual void UpdateWholeExtent ()
 
void ConvertTotalInputToPortConnection (int ind, int &port, int &conn)
 
virtual double ComputePriority ()
 
int ProcessRequest (vtkInformation *request, vtkCollection *inInfo, vtkInformationVector *outInfo)
 
virtual int ComputePipelineMTime (vtkInformation *request, vtkInformationVector **inInfoVec, vtkInformationVector *outInfoVec, int requestFromOutputPort, unsigned long *mtime)
 
virtual vtkInformationGetInformation ()
 
virtual void SetInformation (vtkInformation *)
 
virtual void Register (vtkObjectBase *o)
 
virtual void UnRegister (vtkObjectBase *o)
 
virtual void SetAbortExecute (int)
 
virtual int GetAbortExecute ()
 
virtual void AbortExecuteOn ()
 
virtual void AbortExecuteOff ()
 
virtual void SetProgress (double)
 
virtual double GetProgress ()
 
void SetProgressText (const char *ptext)
 
virtual char * GetProgressText ()
 
virtual unsigned long GetErrorCode ()
 
virtual void SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, const char *name)
 
virtual void SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, int fieldAttributeType)
 
virtual void SetInputArrayToProcess (int idx, vtkInformation *info)
 
virtual void SetInputArrayToProcess (int idx, int port, int connection, const char *fieldAssociation, const char *attributeTypeorName)
 
vtkDataObjectGetInputDataObject (int port, int connection)
 
virtual void SetInputConnection (int port, vtkAlgorithmOutput *input)
 
virtual void SetInputConnection (vtkAlgorithmOutput *input)
 
virtual void AddInputConnection (int port, vtkAlgorithmOutput *input)
 
virtual void AddInputConnection (vtkAlgorithmOutput *input)
 
vtkAlgorithmOutputGetOutputPort (int index)
 
vtkAlgorithmOutputGetOutputPort ()
 
virtual void SetReleaseDataFlag (int)
 
virtual int GetReleaseDataFlag ()
 
void ReleaseDataFlagOn ()
 
void ReleaseDataFlagOff ()
 
int UpdateExtentIsEmpty (vtkDataObject *output)
 
int UpdateExtentIsEmpty (vtkInformation *pinfo, int extentType)
 
- Public Member Functions inherited from vtkObject
virtual void DebugOn ()
 
virtual void DebugOff ()
 
unsigned char GetDebug ()
 
void SetDebug (unsigned char debugFlag)
 
virtual void Modified ()
 
virtual unsigned long GetMTime ()
 
unsigned long AddObserver (unsigned long event, vtkCommand *, float priority=0.0f)
 
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 *)
 
int HasObserver (unsigned long event, vtkCommand *)
 
int HasObserver (const char *event, vtkCommand *)
 
void RemoveObserver (unsigned long tag)
 
void RemoveObservers (unsigned long event)
 
void RemoveObservers (const char *event)
 
void RemoveAllObservers ()
 
int HasObserver (unsigned long event)
 
int HasObserver (const char *event)
 
template<class U , class T >
unsigned long AddObserver (unsigned long event, U observer, void(T::*callback)(), float priority=0.0f)
 
template<class U , class T >
unsigned long AddObserver (unsigned long event, U observer, void(T::*callback)(vtkObject *, unsigned long, void *), float priority=0.0f)
 
int InvokeEvent (unsigned long event, void *callData)
 
int InvokeEvent (const char *event, void *callData)
 
int InvokeEvent (unsigned long event)
 
int InvokeEvent (const char *event)
 
- Public Member Functions inherited from vtkObjectBase
const char * GetClassName () const
 
virtual void Delete ()
 
virtual void FastDelete ()
 
void Print (ostream &os)
 
void SetReferenceCount (int)
 
void PrintRevisions (ostream &os)
 
virtual void PrintHeader (ostream &os, vtkIndent indent)
 
virtual void PrintTrailer (ostream &os, vtkIndent indent)
 
int GetReferenceCount ()
 

Static Public Member Functions

static int IsTypeOf (const char *type)
 
static vtkPNrrdReaderSafeDownCast (vtkObject *o)
 
static vtkPNrrdReaderNew ()
 
- Static Public Member Functions inherited from vtkMPIImageReader
static int IsTypeOf (const char *type)
 
static vtkMPIImageReaderSafeDownCast (vtkObject *o)
 
static vtkMPIImageReaderNew ()
 
- Static Public Member Functions inherited from vtkImageReader
static vtkImageReaderNew ()
 
static int IsTypeOf (const char *type)
 
static vtkImageReaderSafeDownCast (vtkObject *o)
 
- Static Public Member Functions inherited from vtkImageReader2
static vtkImageReader2New ()
 
static int IsTypeOf (const char *type)
 
static vtkImageReader2SafeDownCast (vtkObject *o)
 
- Static Public Member Functions inherited from vtkImageAlgorithm
static int IsTypeOf (const char *type)
 
static vtkImageAlgorithmSafeDownCast (vtkObject *o)
 
- Static Public Member Functions inherited from vtkAlgorithm
static vtkAlgorithmNew ()
 
static int IsTypeOf (const char *type)
 
static vtkAlgorithmSafeDownCast (vtkObject *o)
 
static void SetDefaultExecutivePrototype (vtkExecutive *proto)
 
static vtkInformationIntegerKeyINPUT_IS_OPTIONAL ()
 
static vtkInformationIntegerKeyINPUT_IS_REPEATABLE ()
 
static
vtkInformationInformationVectorKey
INPUT_REQUIRED_FIELDS ()
 
static
vtkInformationStringVectorKey
INPUT_REQUIRED_DATA_TYPE ()
 
static
vtkInformationInformationVectorKey
INPUT_ARRAYS_TO_PROCESS ()
 
static vtkInformationIntegerKeyINPUT_PORT ()
 
static vtkInformationIntegerKeyINPUT_CONNECTION ()
 
static vtkInformationIntegerKeyPRESERVES_DATASET ()
 
static vtkInformationIntegerKeyPRESERVES_GEOMETRY ()
 
static vtkInformationIntegerKeyPRESERVES_BOUNDS ()
 
static vtkInformationIntegerKeyPRESERVES_TOPOLOGY ()
 
static vtkInformationIntegerKeyPRESERVES_ATTRIBUTES ()
 
static vtkInformationIntegerKeyPRESERVES_RANGES ()
 
- Static Public Member Functions inherited from vtkObject
static int IsTypeOf (const char *type)
 
static vtkObjectSafeDownCast (vtkObject *o)
 
static vtkObjectNew ()
 
static void BreakOnError ()
 
static void SetGlobalWarningDisplay (int val)
 
static void GlobalWarningDisplayOn ()
 
static void GlobalWarningDisplayOff ()
 
static int GetGlobalWarningDisplay ()
 
- Static Public Member Functions inherited from vtkObjectBase
static int IsTypeOf (const char *name)
 
static vtkObjectBaseNew ()
 

Protected Member Functions

 vtkPNrrdReader ()
 
 ~vtkPNrrdReader ()
 
virtual int RequestInformation (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector)
 
virtual int RequestData (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector)
 
virtual int ReadHeader ()
 
virtual int ReadHeader (vtkCharArray *headerBuffer)
 
- Protected Member Functions inherited from vtkMPIImageReader
 vtkMPIImageReader ()
 
 ~vtkMPIImageReader ()
 
int GetDataScalarTypeSize ()
 
virtual void PartitionController (const int extent[6])
 
virtual unsigned long GetHeaderSize (vtkMPIOpaqueFileHandle &file)
 
virtual void SetupFileView (vtkMPIOpaqueFileHandle &file, const int extent[6])
 
virtual void ReadSlice (int slice, const int extent[6], void *buffer)
 
virtual void TransformData (vtkImageData *data)
 
virtual void ExecuteData (vtkDataObject *data)
 
void SetGroupedController (vtkMultiProcessController *)
 
- Protected Member Functions inherited from vtkImageReader
 vtkImageReader ()
 
 ~vtkImageReader ()
 
void ComputeTransformedSpacing (double Spacing[3])
 
void ComputeTransformedOrigin (double origin[3])
 
void ComputeTransformedExtent (int inExtent[6], int outExtent[6])
 
void ComputeTransformedIncrements (vtkIdType inIncr[3], vtkIdType outIncr[3])
 
- Protected Member Functions inherited from vtkImageReader2
virtual void ExecuteInformation ()
 
virtual void ComputeDataIncrements ()
 
 vtkImageReader2 ()
 
 ~vtkImageReader2 ()
 
- Protected Member Functions inherited from vtkImageAlgorithm
 vtkImageAlgorithm ()
 
 ~vtkImageAlgorithm ()
 
virtual int RequestUpdateExtent (vtkInformation *, vtkInformationVector **, vtkInformationVector *)
 
virtual void CopyInputArrayAttributesToOutput (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector)
 
virtual void AllocateOutputData (vtkImageData *out, int *uExtent)
 
virtual vtkImageDataAllocateOutputData (vtkDataObject *out)
 
virtual void CopyAttributeData (vtkImageData *in, vtkImageData *out, vtkInformationVector **inputVector)
 
virtual int FillOutputPortInformation (int port, vtkInformation *info)
 
virtual int FillInputPortInformation (int port, vtkInformation *info)
 
virtual void Execute ()
 
- Protected Member Functions inherited from vtkAlgorithm
 vtkAlgorithm ()
 
 ~vtkAlgorithm ()
 
virtual void SetNumberOfInputPorts (int n)
 
virtual void SetNumberOfOutputPorts (int n)
 
int InputPortIndexInRange (int index, const char *action)
 
int OutputPortIndexInRange (int index, const char *action)
 
int GetInputArrayAssociation (int idx, vtkInformationVector **inputVector)
 
virtual vtkExecutiveCreateDefaultExecutive ()
 
virtual void ReportReferences (vtkGarbageCollector *)
 
virtual void SetNumberOfInputConnections (int port, int n)
 
int GetInputArrayAssociation (int idx, int connection, vtkInformationVector **inputVector)
 
int GetInputArrayAssociation (int idx, vtkDataObject *input)
 
vtkDataArrayGetInputArrayToProcess (int idx, vtkInformationVector **inputVector)
 
vtkDataArrayGetInputArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
 
vtkDataArrayGetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
 
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)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
 
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)
 
virtual void SetNthInputConnection (int port, int index, vtkAlgorithmOutput *input)
 
virtual void SetErrorCode (unsigned long)
 
- Protected Member Functions inherited from vtkObject
 vtkObject ()
 
virtual ~vtkObject ()
 
virtual void RegisterInternal (vtkObjectBase *, int check)
 
virtual void UnRegisterInternal (vtkObjectBase *, int check)
 
void InternalGrabFocus (vtkCommand *mouseEvents, vtkCommand *keypressEvents=NULL)
 
void InternalReleaseFocus ()
 
- Protected Member Functions inherited from vtkObjectBase
 vtkObjectBase ()
 
virtual ~vtkObjectBase ()
 
virtual void CollectRevisions (ostream &os)
 
 vtkObjectBase (const vtkObjectBase &)
 
void operator= (const vtkObjectBase &)
 

Protected Attributes

vtkStringArrayDataFiles
 
- Protected Attributes inherited from vtkMPIImageReader
vtkMultiProcessControllerController
 
vtkMultiProcessControllerGroupedController
 
- Protected Attributes inherited from vtkImageReader
vtkTypeUInt64 DataMask
 
vtkTransformTransform
 
int DataVOI [6]
 
char * ScalarArrayName
 
- Protected Attributes inherited from vtkImageReader2
vtkStringArrayFileNames
 
char * InternalFileName
 
char * FileName
 
char * FilePrefix
 
char * FilePattern
 
int NumberOfScalarComponents
 
int FileLowerLeft
 
ifstream * File
 
unsigned long DataIncrements [4]
 
int DataExtent [6]
 
int SwapBytes
 
int FileDimensionality
 
unsigned long HeaderSize
 
int DataScalarType
 
unsigned long ManualHeaderSize
 
double DataSpacing [3]
 
double DataOrigin [3]
 
int FileNameSliceOffset
 
int FileNameSliceSpacing
 
- Protected Attributes inherited from vtkAlgorithm
vtkInformationInformation
 
double Progress
 
char * ProgressText
 
unsigned long ErrorCode
 
- Protected Attributes inherited from vtkObject
unsigned char Debug
 
vtkTimeStamp MTime
 
vtkSubjectHelper * SubjectHelper
 
- Protected Attributes inherited from vtkObjectBase
int ReferenceCount
 
vtkWeakPointerBase ** WeakPointers
 

Additional Inherited Members

- Public Attributes inherited from vtkAlgorithm
int AbortExecute
 
- Static Protected Member Functions inherited from vtkAlgorithm
static vtkInformationIntegerKeyPORT_REQUIREMENTS_FILLED ()
 
- Static Protected Attributes inherited from vtkAlgorithm
static vtkExecutiveDefaultExecutivePrototype
 

Detailed Description

Read nrrd files efficiently from parallel file systems (and reasonably well elsewhere).

vtkPNrrdReader is a subclass of vtkMPIImageReader that will read Nrrd format header information of the image before reading the data. This means that the reader will automatically set information like file dimensions.

Bug:
There are several limitations on what type of nrrd files we can read. This reader only supports nrrd files in raw format. Other encodings like ascii and hex will result in errors. When reading in detached headers, this only supports reading one file that is detached.
Tests:
vtkPNrrdReader (Tests)

Definition at line 49 of file vtkPNrrdReader.h.

Member Typedef Documentation

Definition at line 52 of file vtkPNrrdReader.h.

Constructor & Destructor Documentation

vtkPNrrdReader::vtkPNrrdReader ( )
protected
vtkPNrrdReader::~vtkPNrrdReader ( )
protected

Member Function Documentation

virtual const char* vtkPNrrdReader::GetClassName ( )
virtual

Reimplemented from vtkMPIImageReader.

static int vtkPNrrdReader::IsTypeOf ( const char *  type)
static
virtual int vtkPNrrdReader::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 vtkMPIImageReader.

static vtkPNrrdReader* vtkPNrrdReader::SafeDownCast ( vtkObject o)
static
static vtkPNrrdReader* vtkPNrrdReader::New ( )
static
virtual void vtkPNrrdReader::PrintSelf ( ostream &  os,
vtkIndent  indent 
)
virtual

Methods invoked by print to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from vtkMPIImageReader.

virtual int vtkPNrrdReader::CanReadFile ( const char *  filename)
virtual
virtual int vtkPNrrdReader::RequestInformation ( vtkInformation request,
vtkInformationVector **  inputVector,
vtkInformationVector outputVector 
)
protectedvirtual

Reimplemented from vtkImageReader.

virtual int vtkPNrrdReader::RequestData ( vtkInformation request,
vtkInformationVector **  inputVector,
vtkInformationVector outputVector 
)
protectedvirtual

This is called by the superclass. This is the method you should override.

Reimplemented from vtkImageAlgorithm.

virtual int vtkPNrrdReader::ReadHeader ( )
protectedvirtual
virtual int vtkPNrrdReader::ReadHeader ( vtkCharArray headerBuffer)
protectedvirtual

Member Data Documentation

vtkStringArray* vtkPNrrdReader::DataFiles
protected

Definition at line 73 of file vtkPNrrdReader.h.


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