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vtkMINCImageReader Class Reference

A reader for MINC files. More...

#include <vtkMINCImageReader.h>

Inheritance diagram for vtkMINCImageReader:
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Collaboration diagram for vtkMINCImageReader:
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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
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 void SetFileName (const char *name)
virtual int CanReadFile (const char *name)
virtual vtkMatrix4x4GetDirectionCosines ()
virtual int GetNumberOfTimeSteps ()
virtual vtkMINCImageAttributesGetImageAttributes ()
virtual const char * GetFileExtensions ()
virtual const char * GetDescriptiveName ()
virtual double GetRescaleSlope ()
virtual double GetRescaleIntercept ()
virtual void SetRescaleRealValues (int)
virtual void RescaleRealValuesOn ()
virtual void RescaleRealValuesOff ()
virtual int GetRescaleRealValues ()
virtual double * GetDataRange ()
virtual void GetDataRange (double range[2])
virtual void SetTimeStep (int)
virtual int GetTimeStep ()
- 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 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))
- 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 vtkMINCImageReaderSafeDownCast (vtkObject *o)
static vtkMINCImageReaderNew ()

Protected Member Functions

 vtkMINCImageReader ()
 ~vtkMINCImageReader ()
virtual int OpenNetCDFFile (const char *filename, int &ncid)
virtual int CloseNetCDFFile (int ncid)
virtual int IndexFromDimensionName (const char *dimName)
virtual int ReadMINCFileAttributes ()
virtual void FindRangeAndRescaleValues ()
virtual void ExecuteInformation ()
virtual void ExecuteData (vtkDataObject *out)
- Protected Member Functions inherited from vtkImageReader2
virtual int RequestInformation (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector)
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 int RequestData (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector)
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 &)

Static Protected Member Functions

static int ConvertMINCTypeToVTKType (int minctype, int mincsigned)

Protected Attributes

int MINCImageType
int MINCImageTypeSigned
double ValidRange [2]
double ImageRange [2]
double DataRange [2]
int NumberOfTimeSteps
int TimeStep
vtkMatrix4x4DirectionCosines
double RescaleSlope
double RescaleIntercept
int RescaleRealValues
vtkMINCImageAttributesImageAttributes
int FileNameHasChanged
- 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

Additional Inherited Members

- Public Attributes inherited from vtkAlgorithm
int AbortExecute
- Static Protected Attributes inherited from vtkAlgorithm
static vtkExecutiveDefaultExecutivePrototype
- Friends inherited from vtkObject

Detailed Description

A reader for MINC files.

MINC is a NetCDF-based medical image file format that was developed at the Montreal Neurological Institute in 1992. This class will read a MINC file into VTK, rearranging the data to match the VTK x, y, and z dimensions, and optionally rescaling real-valued data to VTK_FLOAT if RescaleRealValuesOn() is set. If RescaleRealValues is off, then the data will be stored in its original data type and the GetRescaleSlope(), GetRescaleIntercept() method can be used to retrieve global rescaling parameters. If the original file had a time dimension, the SetTimeStep() method can be used to specify a time step to read. All of the original header information can be accessed though the GetImageAttributes() method.

See Also
vtkMINCImageWriter vtkMINCImageAttributes
Thanks:
Thanks to David Gobbi for writing this class and Atamai Inc. for contributing it to VTK.
Tests:
vtkMINCImageReader (Tests)

Definition at line 86 of file vtkMINCImageReader.h.

Member Typedef Documentation

Definition at line 89 of file vtkMINCImageReader.h.

Constructor & Destructor Documentation

vtkMINCImageReader::vtkMINCImageReader ( )
protected
vtkMINCImageReader::~vtkMINCImageReader ( )
protected

Member Function Documentation

virtual const char* vtkMINCImageReader::GetClassName ( )
virtual

Reimplemented from vtkImageReader2.

static int vtkMINCImageReader::IsTypeOf ( const char *  name)
static

Return 1 if this class type 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.

virtual int vtkMINCImageReader::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.

static vtkMINCImageReader* vtkMINCImageReader::SafeDownCast ( vtkObject o)
static

Reimplemented from vtkImageReader2.

static vtkMINCImageReader* vtkMINCImageReader::New ( )
static

Create an object with Debug turned off, modified time initialized to zero, and reference counting on.

Reimplemented from vtkImageReader2.

virtual void vtkMINCImageReader::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 vtkImageReader2.

virtual void vtkMINCImageReader::SetFileName ( const char *  name)
virtual

Set the file name.

Reimplemented from vtkImageReader2.

virtual const char* vtkMINCImageReader::GetFileExtensions ( )
inlinevirtual

Get the entension for this file format.

Reimplemented from vtkImageReader2.

Definition at line 99 of file vtkMINCImageReader.h.

virtual const char* vtkMINCImageReader::GetDescriptiveName ( )
inlinevirtual

Get the name of this file format.

Reimplemented from vtkImageReader2.

Definition at line 105 of file vtkMINCImageReader.h.

virtual int vtkMINCImageReader::CanReadFile ( const char *  name)
virtual

Test whether the specified file can be read.

virtual vtkMatrix4x4* vtkMINCImageReader::GetDirectionCosines ( )
virtual

Get a matrix that describes the orientation of the data. The three columns of the matrix are the direction cosines for the x, y and z dimensions respectively.

virtual double vtkMINCImageReader::GetRescaleSlope ( )
virtual

Get the slope and intercept for rescaling the scalar values to real data values. To convert scalar values to real values, use the equation y = x*RescaleSlope + RescaleIntercept.

virtual double vtkMINCImageReader::GetRescaleIntercept ( )
virtual

Get the slope and intercept for rescaling the scalar values to real data values. To convert scalar values to real values, use the equation y = x*RescaleSlope + RescaleIntercept.

virtual void vtkMINCImageReader::SetRescaleRealValues ( int  )
virtual

Rescale real data values to float. If this is done, the RescaleSlope and RescaleIntercept will be set to 1 and 0 respectively. This is off by default.

virtual void vtkMINCImageReader::RescaleRealValuesOn ( )
virtual

Rescale real data values to float. If this is done, the RescaleSlope and RescaleIntercept will be set to 1 and 0 respectively. This is off by default.

virtual void vtkMINCImageReader::RescaleRealValuesOff ( )
virtual

Rescale real data values to float. If this is done, the RescaleSlope and RescaleIntercept will be set to 1 and 0 respectively. This is off by default.

virtual int vtkMINCImageReader::GetRescaleRealValues ( )
virtual

Rescale real data values to float. If this is done, the RescaleSlope and RescaleIntercept will be set to 1 and 0 respectively. This is off by default.

virtual double* vtkMINCImageReader::GetDataRange ( )
virtual

Get the scalar range of the output from the information in the file header. This is more efficient that computing the scalar range, but in some cases the MINC file stores an incorrect valid_range and the DataRange will be incorrect.

virtual void vtkMINCImageReader::GetDataRange ( double  range[2])
inlinevirtual

Get the scalar range of the output from the information in the file header. This is more efficient that computing the scalar range, but in some cases the MINC file stores an incorrect valid_range and the DataRange will be incorrect.

Definition at line 140 of file vtkMINCImageReader.h.

virtual int vtkMINCImageReader::GetNumberOfTimeSteps ( )
virtual

Get the number of time steps in the file.

virtual void vtkMINCImageReader::SetTimeStep ( int  )
virtual

Set the time step to read.

virtual int vtkMINCImageReader::GetTimeStep ( )
virtual

Set the time step to read.

virtual vtkMINCImageAttributes* vtkMINCImageReader::GetImageAttributes ( )
virtual

Get the image attributes, which contain patient information and other useful metadata.

virtual int vtkMINCImageReader::OpenNetCDFFile ( const char *  filename,
int &  ncid 
)
protectedvirtual
virtual int vtkMINCImageReader::CloseNetCDFFile ( int  ncid)
protectedvirtual
virtual int vtkMINCImageReader::IndexFromDimensionName ( const char *  dimName)
protectedvirtual
virtual int vtkMINCImageReader::ReadMINCFileAttributes ( )
protectedvirtual
virtual void vtkMINCImageReader::FindRangeAndRescaleValues ( )
protectedvirtual
static int vtkMINCImageReader::ConvertMINCTypeToVTKType ( int  minctype,
int  mincsigned 
)
staticprotected
virtual void vtkMINCImageReader::ExecuteInformation ( )
protectedvirtual

Reimplemented from vtkImageReader2.

virtual void vtkMINCImageReader::ExecuteData ( vtkDataObject output)
protectedvirtual

This method is the old style execute method

Reimplemented from vtkImageReader2.

Member Data Documentation

int vtkMINCImageReader::MINCImageType
protected

Definition at line 162 of file vtkMINCImageReader.h.

int vtkMINCImageReader::MINCImageTypeSigned
protected

Definition at line 163 of file vtkMINCImageReader.h.

double vtkMINCImageReader::ValidRange[2]
protected

Definition at line 165 of file vtkMINCImageReader.h.

double vtkMINCImageReader::ImageRange[2]
protected

Definition at line 166 of file vtkMINCImageReader.h.

double vtkMINCImageReader::DataRange[2]
protected

Definition at line 167 of file vtkMINCImageReader.h.

int vtkMINCImageReader::NumberOfTimeSteps
protected

Definition at line 169 of file vtkMINCImageReader.h.

int vtkMINCImageReader::TimeStep
protected

Definition at line 170 of file vtkMINCImageReader.h.

vtkMatrix4x4* vtkMINCImageReader::DirectionCosines
protected

Definition at line 171 of file vtkMINCImageReader.h.

double vtkMINCImageReader::RescaleSlope
protected

Definition at line 172 of file vtkMINCImageReader.h.

double vtkMINCImageReader::RescaleIntercept
protected

Definition at line 173 of file vtkMINCImageReader.h.

int vtkMINCImageReader::RescaleRealValues
protected

Definition at line 174 of file vtkMINCImageReader.h.

vtkMINCImageAttributes* vtkMINCImageReader::ImageAttributes
protected

Definition at line 175 of file vtkMINCImageReader.h.

int vtkMINCImageReader::FileNameHasChanged
protected

Definition at line 177 of file vtkMINCImageReader.h.


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