vtkDICOMReader Class Reference

Read DICOM image files. More...

#include <vtkDICOMReader.h>

Inheritance diagram for vtkDICOMReader:

Collaboration diagram for vtkDICOMReader:

Public Types
enum	RowOrder { FileNative , TopDown , BottomUp }
	Enumeration for top-down vs. bottom-up ordering.
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 }
typedef vtkObject	Superclass

Public Member Functions
virtual vtkTypeBool	IsA (const char *type)
vtkDICOMReader *	NewInstance () const
void	PrintSelf (ostream &os, vtkIndent indent) VTK_DICOM_OVERRIDE
	Print information about this object.
const char *	GetFileExtensions () VTK_DICOM_OVERRIDE
	Valid extensions for this file type.
const char *	GetDescriptiveName () VTK_DICOM_OVERRIDE
	Return a descriptive name that might be useful in a GUI.
int	CanReadFile (const char *filename) VTK_DICOM_OVERRIDE
	Return true if this reader can read the given file.
void	SetDesiredStackID (const char *stackId)
	Set the Stack ID of the stack to load, for named stacks. More...
const char *	GetDesiredStackID ()
vtkStringArray *	GetStackIDs ()
	Get a list of the stacks that are present in the input files. More...
vtkIntArray *	GetFileIndexArray ()
	Get an array that converts slice index to input file index. More...
vtkIntArray *	GetFrameIndexArray ()
	Get an array that converts slice index to frame index. More...
vtkDICOMMetaData *	GetMetaData ()
	Get the meta data for the DICOM files. More...
void	SetDefaultCharacterSet (vtkDICOMCharacterSet cs)
	Set the character set to use if SpecificCharacterSet is missing. More...
vtkDICOMCharacterSet	GetDefaultCharacterSet ()
virtual void	SetOverrideCharacterSet (bool)
	Override the value stored in SpecificCharacterSet. More...
virtual void	OverrideCharacterSetOn ()
virtual void	OverrideCharacterSetOff ()
bool	GetOverrideCharacterSet ()
virtual int	GetSorting ()
	If the files have been pre-sorted, the sorting can be disabled.
virtual void	SetSorting (int)
virtual void	SortingOn ()
virtual void	SortingOff ()
void	SetSorter (vtkDICOMSliceSorter *sorter)
	Set a custom sorter to be used to sort files and frames into slices. More...
vtkDICOMSliceSorter *	GetSorter ()
virtual int	GetTimeAsVector ()
	Read the time dimension as scalar components (default: Off). More...
virtual void	SetTimeAsVector (int)
virtual void	TimeAsVectorOn ()
virtual void	TimeAsVectorOff ()
int	GetTimeDimension ()
	Get the time dimension if the DICOM series has one.
double	GetTimeSpacing ()
virtual void	SetDesiredTimeIndex (int)
	Set the desired time index (set to -1 for all).
virtual int	GetDesiredTimeIndex ()
virtual int	GetAutoYBRToRGB ()
	Turn off automatic conversion of YBR images to RGB. More...
virtual void	SetAutoYBRToRGB (int)
virtual void	AutoYBRToRGBOn ()
virtual void	AutoYBRToRGBOff ()
virtual int	GetAutoRescale ()
	Turn off automatic rescaling of stored pixel values. More...
virtual void	SetAutoRescale (int)
virtual void	AutoRescaleOn ()
virtual void	AutoRescaleOff ()
double	GetRescaleSlope ()
	Get the slope and intercept for rescaling the scalar values. More...
double	GetRescaleIntercept ()
vtkMatrix4x4 *	GetPatientMatrix ()
	Get a matrix to place the image within DICOM patient coords. More...
vtkImageData *	GetOverlayOutput ()
	Get the overlay. More...
vtkAlgorithmOutput *	GetOverlayOutputPort ()
void	SetOverlayOutput (vtkImageData *data)
bool	HasOverlay ()
	Returns true if any overlays are present.
unsigned short	GetOverlayBitfield ()
	Returns a bitfield that indicates which overlays are present.
vtkMedicalImageProperties *	GetMedicalImageProperties ()
	Get a MedicalImageProperties object for this file.
void	SetMemoryRowOrder (int order)
	Set the ordering of the image rows in memory. More...
void	SetMemoryRowOrderToFileNative ()
void	SetMemoryRowOrderToTopDown ()
void	SetMemoryRowOrderToBottomUp ()
int	GetMemoryRowOrder ()
const char *	GetMemoryRowOrderAsString ()
virtual void	SetOutputScalarType (int)
	Set the scalar type of the output. More...
virtual int	GetOutputScalarType ()
void	Update () VTK_DICOM_OVERRIDE
	Update both the image and, if present, the overlay.
Public Member Functions inherited from vtkImageReader2
vtkImageReader2 *	NewInstance () const
void	PrintSelf (ostream &os, vtkIndent indent)
virtual void	SetFileName (const char *)
virtual char *	GetFileName ()
virtual void	SetFileNames (vtkStringArray *)
virtual vtkStringArray *	GetFileNames ()
virtual void	SetFilePrefix (const char *)
virtual char *	GetFilePrefix ()
virtual void	SetFilePattern (const char *)
virtual char *	GetFilePattern ()
virtual void	SetMemoryBuffer (void *)
virtual void *	GetMemoryBuffer ()
virtual void	SetMemoryBufferLength (vtkIdType buflen)
vtkIdType	GetMemoryBufferLength ()
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	SetHeaderSize (unsigned long size)
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 ()
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 ()
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
vtkImageAlgorithm *	NewInstance () const
vtkImageData *	GetOutput ()
vtkImageData *	GetOutput (int)
virtual void	SetOutput (vtkDataObject *d)
int	ProcessRequest (vtkInformation *, vtkInformationVector **, vtkInformationVector *) VTK_OVERRIDE
void	SetInputData (vtkDataObject *)
void	SetInputData (int, vtkDataObject *)
vtkDataObject *	GetInput (int port)
vtkDataObject *	GetInput ()
vtkImageData *	GetImageDataInput (int port)
virtual void	AddInputData (vtkDataObject *)
virtual void	AddInputData (int, vtkDataObject *)
Public Member Functions inherited from vtkAlgorithm
vtkAlgorithm *	NewInstance () const
int	HasExecutive ()
vtkExecutive *	GetExecutive ()
virtual void	SetExecutive (vtkExecutive *executive)
int	ProcessRequest (vtkInformation *request, vtkCollection *inInfo, vtkInformationVector *outInfo)
virtual int	ComputePipelineMTime (vtkInformation *request, vtkInformationVector **inInfoVec, vtkInformationVector *outInfoVec, int requestFromOutputPort, vtkMTimeType *mtime)
virtual int	ModifyRequest (vtkInformation *request, int when)
vtkInformation *	GetInputPortInformation (int port)
vtkInformation *	GetOutputPortInformation (int port)
virtual vtkInformation *	GetInformation ()
virtual void	SetInformation (vtkInformation *)
int	GetNumberOfInputPorts ()
int	GetNumberOfOutputPorts ()
void	Register (vtkObjectBase *o) VTK_OVERRIDE
void	UnRegister (vtkObjectBase *o) VTK_OVERRIDE
virtual void	SetAbortExecute (int)
virtual int	GetAbortExecute ()
virtual void	AbortExecuteOn ()
virtual void	AbortExecuteOff ()
virtual void	SetProgress (double)
virtual double	GetProgress ()
void	UpdateProgress (double amount)
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)
vtkInformation *	GetInputArrayInformation (int idx)
void	RemoveAllInputs ()
vtkDataObject *	GetOutputDataObject (int port)
vtkDataObject *	GetInputDataObject (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)
virtual void	RemoveInputConnection (int port, vtkAlgorithmOutput *input)
virtual void	RemoveInputConnection (int port, int idx)
virtual void	RemoveAllInputConnections (int port)
virtual void	SetInputDataObject (int port, vtkDataObject *data)
virtual void	SetInputDataObject (vtkDataObject *data)
virtual void	AddInputDataObject (int port, vtkDataObject *data)
virtual void	AddInputDataObject (vtkDataObject *data)
vtkAlgorithmOutput *	GetOutputPort (int index)
vtkAlgorithmOutput *	GetOutputPort ()
int	GetNumberOfInputConnections (int port)
int	GetTotalNumberOfInputConnections ()
vtkAlgorithmOutput *	GetInputConnection (int port, int index)
vtkAlgorithm *	GetInputAlgorithm (int port, int index, int &algPort)
vtkAlgorithm *	GetInputAlgorithm (int port, int index)
vtkAlgorithm *	GetInputAlgorithm ()
vtkExecutive *	GetInputExecutive (int port, int index)
vtkExecutive *	GetInputExecutive ()
vtkInformation *	GetInputInformation (int port, int index)
vtkInformation *	GetInputInformation ()
vtkInformation *	GetOutputInformation (int port)
virtual void	Update (int port)
virtual int	Update (int port, vtkInformationVector *requests)
virtual int	Update (vtkInformation *requests)
virtual int	UpdatePiece (int piece, int numPieces, int ghostLevels, const int extents[6]=0)
virtual int	UpdateExtent (const int extents[6])
virtual int	UpdateTimeStep (double time, int piece=-1, int numPieces=1, int ghostLevels=0, const int extents[6]=0)
virtual void	UpdateInformation ()
virtual void	UpdateDataObject ()
virtual void	PropagateUpdateExtent ()
virtual void	UpdateWholeExtent ()
void	ConvertTotalInputToPortConnection (int ind, int &port, int &conn)
virtual void	SetReleaseDataFlag (int)
virtual int	GetReleaseDataFlag ()
void	ReleaseDataFlagOn ()
void	ReleaseDataFlagOff ()
int	UpdateExtentIsEmpty (vtkInformation *pinfo, vtkDataObject *output)
int	UpdateExtentIsEmpty (vtkInformation *pinfo, int extentType)
int	SetUpdateExtentToWholeExtent (int port)
int	SetUpdateExtentToWholeExtent ()
void	SetUpdateExtent (int port, int piece, int numPieces, int ghostLevel)
void	SetUpdateExtent (int piece, int numPieces, int ghostLevel)
void	SetUpdateExtent (int port, int extent[6])
void	SetUpdateExtent (int extent[6])
int *	GetUpdateExtent ()
int *	GetUpdateExtent (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 ()
int	GetUpdatePiece (int port)
int	GetUpdateNumberOfPieces ()
int	GetUpdateNumberOfPieces (int port)
int	GetUpdateGhostLevel ()
int	GetUpdateGhostLevel (int port)
void	SetProgressObserver (vtkProgressObserver *)
virtual vtkProgressObserver *	GetProgressObserver ()
Public Member Functions inherited from vtkObject
	vtkBaseTypeMacro (vtkObject, vtkObjectBase)
virtual void	DebugOn ()
virtual void	DebugOff ()
bool	GetDebug ()
void	SetDebug (bool debugFlag)
virtual void	Modified ()
virtual vtkMTimeType	GetMTime ()
void	PrintSelf (ostream &os, vtkIndent indent) VTK_OVERRIDE
unsigned long	AddObserver (unsigned long event, vtkCommand *, float priority=0.0f)
unsigned long	AddObserver (const char *event, vtkCommand *, float priority=0.0f)
vtkCommand *	GetCommand (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)
template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, bool(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	InitializeObjectBase ()
void	Print (ostream &os)
virtual void	PrintHeader (ostream &os, vtkIndent indent)
virtual void	PrintTrailer (ostream &os, vtkIndent indent)
int	GetReferenceCount ()
void	SetReferenceCount (int)
void	PrintRevisions (ostream &)

Static Public Member Functions
static vtkTypeBool	IsTypeOf (const char *type)
static vtkDICOMReader *	SafeDownCast (vtkObjectBase *o)
static vtkDICOMReader *	New ()
	Static method for construction.
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 ()
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 ()
static vtkInformationIntegerKey *	CAN_HANDLE_PIECE_REQUEST ()
static void	SetDefaultExecutivePrototype (vtkExecutive *proto)
Static Public Member Functions inherited from vtkObject
static vtkObject *	New ()
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 vtkTypeBool	IsTypeOf (const char *name)
static vtkObjectBase *	New ()

Protected Member Functions
virtual vtkObjectBase *	NewInstanceInternal () const
vtkTypeBool	ProcessRequest (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector) VTK_DICOM_OVERRIDE
	Entry point for all pipeline requests.
int	RequestInformation (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector) VTK_DICOM_OVERRIDE
	Read the header information.
int	RequestData (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector) VTK_DICOM_OVERRIDE
	Read the voxel data.
virtual bool	ReadOverlays (vtkImageData *data)
	Read the overlays into an allocated vtkImageData object.
void	UnpackOverlay (const void *filePtr, vtkIdType bitskip, vtkIdType count, void *buffer, vtkIdType incr, int bit)
	Unpack overlay bits to build the overlay image.
virtual bool	ReadOneFile (const char *filename, int idx, unsigned char *buffer, vtkIdType bufferSize)
	Read one file. Specify the offset to the PixelData.
void	MaskBits (void *buffer, vtkIdType bufferSize, int scalarSize, int bitsStored, int pixelRepresentation)
	Clear or sign-extend any bits beyond BitsStored.
void	UnpackBits (const void *source, void *buffer, vtkIdType bufferSize, int bits)
	Unpack 1 bit to 8 bits or 12 bits to 16 bits.
void	UnpackYBR422 (const void *source, void *buffer, vtkIdType bufferSize, vtkIdType rowlen)
	Unpack 4:2:2 color data.
virtual bool	ReadFileNative (const char *filename, int idx, unsigned char *buffer, vtkIdType bufferSize)
	Read an DICOM file directly.
virtual bool	ReadFileDelegated (const char *filename, int idx, unsigned char *buffer, vtkIdType bufferSize)
	Read a DICOM file via DCMTK or GDCM.
virtual int	ComputeRescaledScalarType (int scalarType, int bitsStored, int pixelRepresentation)
	Check if rescaling will change scalar type.
virtual void	RescaleBuffer (int fileIdx, int frameIdx, int fileType, int outputType, int numFileComponents, int numComponents, void *fileBuffer, void *outputBuffer, vtkIdType bufferSize)
	Rescale the data in the buffer.
virtual void	YBRToRGB (int fileIdx, int frameIdx, void *buffer, vtkIdType bufferSize)
	Convert buffer from YUV to RGB.
void	RelayError (vtkObject *o, unsigned long e, void *data)
	Convert parser errors into reader errors.
virtual bool	ValidateStructure (vtkIntArray *fileArray, vtkIntArray *frameArray)
	Verify that the files can be composed into a volume. More...
virtual void	SortFiles (vtkIntArray *fileArray, vtkIntArray *frameArray)
	Sort the input files, put the sort in the supplied arrays.
void	NoSortFiles (vtkIntArray *fileArray, vtkIntArray *frameArray)
	Do not sort the files, just build the arrays.
virtual void	UpdateMedicalImageProperties ()
	Update the medical image properties;.
Protected Member Functions inherited from vtkImageReader2
virtual void	ExecuteInformation ()
virtual void	ExecuteDataWithInformation (vtkDataObject *data, vtkInformation *outInfo)
virtual void	ComputeDataIncrements ()
Protected Member Functions inherited from vtkImageAlgorithm
virtual int	RequestUpdateExtent (vtkInformation *, vtkInformationVector **, vtkInformationVector *)
virtual void	CopyInputArrayAttributesToOutput (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector)
virtual void	ExecuteData (vtkDataObject *output)
virtual void	Execute ()
virtual void	AllocateOutputData (vtkImageData *out, vtkInformation *outInfo, int *uExtent)
virtual vtkImageData *	AllocateOutputData (vtkDataObject *out, vtkInformation *outInfo)
virtual void	CopyAttributeData (vtkImageData *in, vtkImageData *out, vtkInformationVector **inputVector)
int	FillOutputPortInformation (int port, vtkInformation *info) VTK_OVERRIDE
int	FillInputPortInformation (int port, vtkInformation *info) VTK_OVERRIDE
Protected Member Functions inherited from 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)
int	GetInputArrayAssociation (int idx, int connection, vtkInformationVector **inputVector)
int	GetInputArrayAssociation (int idx, vtkDataObject *input)
vtkDataArray *	GetInputArrayToProcess (int idx, vtkInformationVector **inputVector)
vtkDataArray *	GetInputArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
vtkDataArray *	GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
vtkDataArray *	GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
vtkDataArray *	GetInputArrayToProcess (int idx, vtkDataObject *input)
vtkDataArray *	GetInputArrayToProcess (int idx, vtkDataObject *input, int &association)
vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector)
vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkDataObject *input)
vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkDataObject *input, int &association)
vtkInformation *	GetInputArrayFieldInformation (int idx, vtkInformationVector **inputVector)
virtual vtkExecutive *	CreateDefaultExecutive ()
virtual void	SetErrorCode (unsigned long)
void	ReportReferences (vtkGarbageCollector *) VTK_OVERRIDE
virtual void	SetNthInputConnection (int port, int index, vtkAlgorithmOutput *input)
virtual void	SetNumberOfInputConnections (int port, int n)
void	SetInputDataInternal (int port, vtkDataObject *input)
void	AddInputDataInternal (int port, vtkDataObject *input)
Protected Member Functions inherited from vtkObject
void	RegisterInternal (vtkObjectBase *, vtkTypeBool check) VTK_OVERRIDE
void	UnRegisterInternal (vtkObjectBase *, vtkTypeBool check) VTK_OVERRIDE
void	InternalGrabFocus (vtkCommand *mouseEvents, vtkCommand *keypressEvents=NULL)
void	InternalReleaseFocus ()
Protected Member Functions inherited from vtkObjectBase
virtual void	CollectRevisions (ostream &)
	vtkObjectBase (const vtkObjectBase &)
void	operator= (const vtkObjectBase &)

Protected Attributes
int	Sorting
	Select whether to sort the files.
double	RescaleIntercept
	Information for rescaling data to quantitative units.
double	RescaleSlope
vtkMatrix4x4 *	PatientMatrix
	The orientation matrix for the DICOM file.
vtkDICOMMetaData *	MetaData
	The meta data for the image.
vtkMedicalImageProperties *	MedicalImageProperties
	The MedicalImageProperties, for compatibility with other readers.
vtkDICOMCharacterSet	DefaultCharacterSet
	The default character set to use while parsing the file.
bool	OverrideCharacterSet
	Whether the default should override SpecificCharacterSet.
vtkDICOMParser *	Parser
	The parser that is used to read the file.
vtkDICOMSliceSorter *	Sorter
	The sorter that orders the slices within the volume.
vtkTypeInt64Array *	FileOffsetArray
	The offsets to the pixel data in each file.
vtkIntArray *	FileIndexArray
	An array to convert slice indices to input files.
vtkIntArray *	FrameIndexArray
	An array to convert slice indices to input frames.
vtkStringArray *	StackIDs
	An array that holds the stack IDs.
int	MemoryRowOrder
	The row order to use when storing the data in memory.
int	NeedsRescale
	This indicates that the data must be rescaled.
int	AutoRescale
int	FileScalarType
int	OutputScalarType
int	NeedsYBRToRGB
	This indicates that the data must be converted to RGB.
int	AutoYBRToRGB
int	NumberOfPackedComponents
	The number of packed pixel components in the input file. More...
int	NumberOfPlanarComponents
	The number of color planes in the file.
int	TimeAsVector
	Time dimension variables.
int	TimeDimension
int	DesiredTimeIndex
double	TimeSpacing
char	DesiredStackID [20]
	The stack to load.
unsigned short	OverlayBitfield
	Bitfield that says what overlays are present.
bool	UpdateOverlayFlag
Protected Attributes inherited from vtkImageReader2
vtkStringArray *	FileNames
char *	InternalFileName
char *	FileName
char *	FilePrefix
char *	FilePattern
int	NumberOfScalarComponents
int	FileLowerLeft
void *	MemoryBuffer
vtkIdType	MemoryBufferLength
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
vtkInformation *	Information
unsigned long	ErrorCode
double	Progress
char *	ProgressText
vtkProgressObserver *	ProgressObserver
Protected Attributes inherited from vtkObject
bool	Debug
vtkTimeStamp	MTime
vtkSubjectHelper *	SubjectHelper
Protected Attributes inherited from vtkObjectBase
vtkAtomicInt32	ReferenceCount
vtkWeakPointerBase **	WeakPointers

Additional Inherited Members
Public Attributes inherited from vtkAlgorithm
int	AbortExecute
Static Protected Member Functions inherited from vtkAlgorithm
static vtkInformationIntegerKey *	PORT_REQUIREMENTS_FILLED ()
Static Protected Attributes inherited from vtkAlgorithm
static vtkExecutive *	DefaultExecutivePrototype

Detailed Description

Read DICOM image files.

This class reads a series of DICOM files into a vtkImageData object, and also provides access to the DICOM meta data for each file.

Member Function Documentation

GetAutoRescale()

virtual int vtkDICOMReader::GetAutoRescale ( )

virtual

Turn off automatic rescaling of stored pixel values.

By default, if the RescaleSlope and RescaleIntercept attributes are present in the DICOM data set, they will be used to rescale stored pixel values according to the DICOM modality LUT operation. The resulting values will be stored as 16-bit integers if possible, but single-precision floats will be used if the potential output range is greater than can be stored in 16 bits, or if either the RescaleSlope or the RescaleIntercept is not an integer. If AutoRescale is off, then the data is not rescaled.

GetAutoYBRToRGB()

virtual int vtkDICOMReader::GetAutoYBRToRGB ( )

virtual

Turn off automatic conversion of YBR images to RGB.

By default, YBR images are always converted to RGB (though the photometric interpretation in the metadata will remain the same).

GetFileIndexArray()

vtkIntArray* vtkDICOMReader::GetFileIndexArray ( )

inline

Get an array that converts slice index to input file index.

If the reader has generated scalar components, then this will be a two-dimensional array and calling array->GetComponent(i,j) will return the file index for slice i and scalar component j for monochrome images, or for slice i and scalar component 3*j for RGB images (or more precisely, at scalar component N*j where N is the SamplesPerPixel value from the DICOM metadata). If the data has just one component, then use j=0. If you used SetFileNames() to provide a list of files to the reader, then use this array to find out which file provided which slice, or to index into the MetaData object to get the metadata for a particular slice.

GetFrameIndexArray()

vtkIntArray* vtkDICOMReader::GetFrameIndexArray ( )

inline

Get an array that converts slice index to frame index.

The purpose of this array is to identify individual frames in multi-frame DICOM files. The dimensions of this array are identical to the FileIndexArray. Use FileIndexArray to identify the file, then use FrameIndexArray to identify the frame within that file.

GetMetaData()

vtkDICOMMetaData* vtkDICOMReader::GetMetaData ( )

inline

Get the meta data for the DICOM files.

The Get() method of vtkDICOMMataData takes optional file and frame indices, which specify the file and the frame within that file to get the attribute from. If you have a slice index rather than a file index and frame index, then use the FileIndexArray and FrameIndexArray to convert the slice index into file and frame indices.

GetOverlayOutput()

vtkImageData* vtkDICOMReader::GetOverlayOutput

(

)

Get the overlay.

The extent of the overlay will be the same as the main image. For multiple overlays, each overlay will be stored in a different bit. An 8-bit image will be used if there are eight or fewer overlays, and an unsigned 16-bit image will be used if there are more than eight overlays.

GetPatientMatrix()

vtkMatrix4x4* vtkDICOMReader::GetPatientMatrix ( )

inline

Get a matrix to place the image within DICOM patient coords.

This matrix is constructed from the ImageOrientationPatient and ImagePositionPatient meta data attributes. See the SetMemoryRowOrder method for additional information.

GetRescaleSlope()

double vtkDICOMReader::GetRescaleSlope ( )

inline

Get the slope and intercept for rescaling the scalar values.

If AutoRescale in On (which is the default), then GetRescaleSlope() will return 1 and GetRescaleIntercept() will return zero. Otherwise, they will return the RescaleSlope and RescaleIntercept for the data set. Use the equation v = u*RescaleSlope + RescaleIntercept.

Note that the returned values might not be valid if these attributes are not the same for all slices in the series. Use the meta data to retrieve the per-slice slope and intercept.

GetStackIDs()

vtkStringArray* vtkDICOMReader::GetStackIDs ( )

inline

Get a list of the stacks that are present in the input files.

A stack is a contiguous array of slices that form a volume.

GetTimeAsVector()

virtual int vtkDICOMReader::GetTimeAsVector ( )

virtual

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

If this is on, then each time point will be stored as a scalar component in the image data. If the data 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, one vector for each time point.

IsA()

virtual vtkTypeBool vtkDICOMReader::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.

SetDefaultCharacterSet()

void vtkDICOMReader::SetDefaultCharacterSet

(

vtkDICOMCharacterSet

cs

)

Set the character set to use if SpecificCharacterSet is missing.

Some DICOM files do not list a SpecificCharacterSet attribute, but nevertheless use a non-ASCII character encoding. This method can be used to specify the character set in absence of SpecificCharacterSet. This method will not take effect unless is is called before the image is read. If SpecificCharacterSet is present, the default will not override it unless OverrideCharacterSet is true.

SetDesiredStackID()

void vtkDICOMReader::SetDesiredStackID

(

const char *

stackId

)

Set the Stack ID of the stack to load, for named stacks.

If the series has multiple stacks, then by default the reader will only load the first stack. This method allows you to select a different stack, if you know the DICOM StackID for the stack.

SetMemoryRowOrder()

void vtkDICOMReader::SetMemoryRowOrder

(

int

order

)

Set the ordering of the image rows in memory.

If the order is BottomUp (which is the default) then the images will be flipped when they are read from disk. The native orientation of DICOM images is top-to-bottom.

SetOutputScalarType()

virtual void vtkDICOMReader::SetOutputScalarType ( int  )

virtual

Set the scalar type of the output.

The default value is -1, which means that the input scalar type will be used to set the output scalar type (accounting for any type changes required by AutoRescale). Allowed output scalar types are VTK_SIGNED_CHAR, VTK_UNSIGNED_CHAR, VTK_SHORT, VTK_UNSIGNED_SHORT, VTK_INT, VTK_UNSIGNED_INT, VTK_FLOAT, or VTK_DOUBLE. The output data values will be clamped to the limits of the output type.

SetOverrideCharacterSet()

virtual void vtkDICOMReader::SetOverrideCharacterSet ( bool  )

virtual

Override the value stored in SpecificCharacterSet.

This method can be used if the SpecificCharacterSet attribute of a file is incorrect. It overrides the SpecificCharacterSet with the DefaultCharacterSet.

SetSorter()

void vtkDICOMReader::SetSorter

(

vtkDICOMSliceSorter *

sorter

)

Set a custom sorter to be used to sort files and frames into slices.

The default sorter uses the attributes "ImagePositionPatient" and "ImageOrientationPatient" to spatially arrange the slices.

ValidateStructure()

virtual bool vtkDICOMReader::ValidateStructure ( vtkIntArray *  fileArray, vtkIntArray *  frameArray  )

protectedvirtual

Verify that the files can be composed into a volume.

This is called after SortFiles has been called. It should invoke an error event and return zero upon failure.

Member Data Documentation

NumberOfPackedComponents

int vtkDICOMReader::NumberOfPackedComponents

protected

The number of packed pixel components in the input file.

This is for packed, rather than planar, components.

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

• vtkDICOMReader.h