#include <svk4DImageData.h>

Inheritance diagram for svk4DImageData:

Public Types
enum	ActorType { PLOT_GRID, VOL_SELECTION, SAT_BANDS }

Public Types inherited from svkImageData
enum	RangeComponent { REAL = 0, IMAGINARY, MAGNITUDE }

enum	DataBasis { ROW = 0, COLUMN, SLICE, LR, PA, SI }

Public Member Functions
	vtkTypeMacro (svk4DImageData, svkImageData)

virtual void	GetNumberOfVoxels (int numVoxels[3])

virtual int	GetIDFromIndex (int indexX, int indexY, int indexZ, int *indexArray=NULL)

vtkDataArray *	GetArray (int linearIndex)

vtkDataArray *	GetArrayFromID (int index, int *indexArray=NULL)

vtkDataArray *	GetArray (int x, int y, int z, int *indexArray=NULL)

vtkDataArray *	GetArray (int *indexArray)

void	SetArrayName (vtkDataArray array, svkDcmHeader::DimensionVector dimensionVector)

virtual int	GetLastSlice (svkDcmHeader::Orientation sliceOrientation=svkDcmHeader::UNKNOWN_ORIENTATION)

void	GetTlcBrcInUserSelection (int tlcBrc[2], double userSelection[6], svkDcmHeader::Orientation orientation=svkDcmHeader::UNKNOWN_ORIENTATION, int slice=-1)

void	GetZeroImage (svkImageData *image)

virtual void	GetImage (svkImageData image, int point, int indexArray=NULL, int component=2, int vtkDataType=VTK_VOID)

virtual void	GetImage (svkImageData image, int point, svkDcmHeader::DimensionVector indexVector=NULL, int component=2, int vtkDataType=VTK_VOID)

virtual void	GetImage (svkImageData image, int point, string seriesDescription, int indexArray=NULL, int component=2, int vtkDataType=VTK_VOID)

virtual void	GetImage (svkImageData image, int point, string seriesDescription, svkDcmHeader::DimensionVector indexVector=NULL, int component=2, int vtkDataType=VTK_VOID)

void	SetImage (vtkImageData image, int point, int indexArray=NULL)

void	SetImage (vtkImageData image, int point, svkDcmHeader::DimensionVector indexVector)

void	SetImageComponent (vtkImageData image, int point, int indexArray=NULL, int component=0)

virtual void	UpdateRange (int component)

int	GetNumberOfSlices (svkDcmHeader::Orientation sliceOrientation)

virtual void	EstimateDataRange (double range[2], int minPt, int maxPt, int component, int tlcBrc=NULL, int indexArray=NULL)

virtual int	GetVolumeIndexSize (int volumeIndex)

virtual int	GetNumberOfVolumeDimensions ()

virtual void	GetPolyDataGrid (vtkPolyData *grid)

Public Member Functions inherited from svkImageData
	vtkTypeMacro (svkImageData, vtkImageData)

virtual void	PrintSelf (ostream &os, vtkIndent indent)

virtual void	DeepCopy (vtkDataObject *src)

virtual void	DeepCopy (vtkDataObject *src, svkDcmHeader::DcmPixelDataFormat castToFormat)

virtual void	ShallowCopy (vtkDataObject *src)

virtual void	ShallowCopy (vtkDataObject *src, svkDcmHeader::DcmPixelDataFormat castToFormat)

virtual void	ZeroCopy (vtkImageData *src, svkDcmHeader::DcmPixelDataFormat castToFormat=svkDcmHeader::UNDEFINED)

virtual void	CopyAndFillComponents (vtkImageData *src, double fillValue, svkDcmHeader::DcmPixelDataFormat castToFormat=svkDcmHeader::UNDEFINED)

virtual void	CastDataFormat (svkDcmHeader::DcmPixelDataFormat castToFormat)

virtual void	CopyAndCastFrom (vtkImageData *inData, int extent[6])

virtual void	CopyAndCastFrom (vtkImageData *inData, int x0, int x1, int y0, int y1, int z0, int z1)

virtual void	CopyStructure (vtkDataSet *ds)

virtual void	CopyDcos (vtkDataObject *src)

virtual void	CopyVtkImage (vtkImageData *sourceImage, double dcos[][3])

virtual double *	GetPoint (vtkIdType ptId)

virtual void	GetPoint (vtkIdType id, double x[3])

virtual vtkCell *	GetCell (vtkIdType cellId)

virtual void	GetCell (vtkIdType cellId, vtkGenericCell *cell)

virtual void	GetCellBounds (vtkIdType cellId, double bounds[6])

virtual vtkIdType	FindPoint (double x, double y, double z)

virtual vtkIdType	FindPoint (double x[3])

virtual vtkIdType	FindCell (double x[3], vtkCell cell, vtkIdType cellId, double tol2, int &subId, double pcoords[3], double weights)

virtual vtkIdType	FindCell (double x[3], vtkCell cell, vtkGenericCell gencell, vtkIdType cellId, double tol2, int &subId, double pcoords[3], double *weights)

virtual vtkCell *	FindAndGetCell (double x[3], vtkCell cell, vtkIdType cellId, double tol2, int &subId, double pcoords[3], double weights)

virtual int	GetCellType (vtkIdType cellId)

virtual void	GetCellPoints (vtkIdType cellId, vtkIdList *ptIds)

virtual void	GetPointCells (vtkIdType ptId, vtkIdList *cellIds)

virtual void	ComputeBounds ()

virtual int	ComputeStructuredCoordinates (double x[3], int ijk[3], double pcoords[3])

virtual void	GetVoxelGradient (int i, int j, int k, vtkDataArray s, vtkDataArray g)

virtual void	GetPointGradient (int i, int j, int k, vtkDataArray *s, double g[3])

virtual void	SetAxisUpdateExtent (int axis, int min, int max)

virtual void	GetAxisUpdateExtent (int axis, int &min, int &max)

virtual void	SetDcos (double x[3][3])

virtual void	GetDcos (double x[3][3])

void	SetDcmHeader (svkDcmHeader *dcmHeader)

svkDcmHeader *	GetDcmHeader ()

void	SetProvenance (svkProvenance *provenance)

svkProvenance *	GetProvenance ()

int	GetIDFromIndex (int indexX, int indexY, int indexZ)

void	GetIndexFromID (int voxelID, int indexX, int indexY, int *indexZ)

void	GetIndexFromID (int voxelID, int *index)

void	GetIndexFromPosition (double posLPS[3], int *index)

void	GetIndexFromPosition (double posLPS[3], double *index)

virtual void	GetPositionFromIndex (int index, double posLPS)

virtual void	GetSliceOrigin (int slice, double *sliceOrigin, svkDcmHeader::Orientation sliceOrientation=svkDcmHeader::UNKNOWN_ORIENTATION)

virtual void	GetSliceCenter (int slice, double *sliceCenter, svkDcmHeader::Orientation sliceOrientation=svkDcmHeader::UNKNOWN_ORIENTATION)

virtual void	GetSliceNormal (double *normal, svkDcmHeader::Orientation sliceOrientation=svkDcmHeader::UNKNOWN_ORIENTATION)

virtual int	GetClosestSlice (double *posLPS, svkDcmHeader::Orientation sliceOrientation=svkDcmHeader::UNKNOWN_ORIENTATION, double tolerance=-1)

virtual int	GetFirstSlice (svkDcmHeader::Orientation sliceOrientation=svkDcmHeader::UNKNOWN_ORIENTATION)

virtual void	GetDataBasis (double basisVector[3], DataBasis basis)

virtual int	GetOrientationIndex (svkDcmHeader::Orientation orientation)

virtual void	GetImageCenter (double *center)

void	GetDataRange (double range[2], int component)
	Getter of the data range variable. More...

void	SetDataRange (double range[2], int component)
	Setter of the data range variable. More...

void	SetSourceData (svkImageData *source)

svkImageData *	GetSourceData ()

void	SyncVTKImageDataToDcmHeader ()

	vtkSetStringMacro (SourceFileName)

	vtkGetStringMacro (SourceFileName)

Static Public Member Functions
static svk4DImageData *	New ()

static vtkObject *	NewObject ()

static string	GetArrayName (svkDcmHeader::DimensionVector *dimensionVector)

static bool	IsIndexInExtent (int extent, svkDcmHeader::DimensionVector indexVector)

Static Public Member Functions inherited from svkImageData
static void	RemoveArrays (svkImageData *data)

Protected Member Functions
	svk4DImageData ()

	~svk4DImageData ()

Protected Member Functions inherited from svkImageData
	svkImageData ()

	~svkImageData ()

bool	WasModified ()

virtual void	UpdateSvkParams ()

int	FindMatchingSlice (double posLPS, svkDcmHeader::Orientation sliceOrientation, double origin, double *spacing, double tolerance=-1)

Additional Inherited Members
Protected Attributes inherited from svkImageData
svkDcmHeader *	dcmHeader

svkProvenance *	provenance

char *	SourceFileName

svkImageData *	source

double	range [3][2]
	Range needs to be able to accomodate real, imaginary, and magnitude components. More...

Detailed Description

This class represents multi-volumentric 4D imaging data. Data is stored in its vtkCellData object and we will have one vtkDataArray per voxel/ per volume. Data can be accessed with general GetArray methods that take as input the number of volumetric indices, an array the index values, and an array of dimension sizes. From this a linear index is determined (based on the order of these afore mentioned arrays ) and the data can be accessed. As such it is extremely important not to change the order of the arrays as it implies the cell association.

Member Enumeration Documentation

enum ActorType

Enumerator
PLOT_GRID
VOL_SELECTION
SAT_BANDS

Constructor & Destructor Documentation

svk4DImageData ( )

protected

Constructor.

~svk4DImageData ( )

protected

Destructor.

Member Function Documentation

void EstimateDataRange	(	double	range[2],
		int	minPt,
		int	maxPt,
		int	component,
		int *	tlcBrc = `NULL`,
		int *	indexArray = `NULL`
	)

virtual

Attempts to estimate the data range for a given frequency range. It finds the average maximum/minimum then adds three standard deviations. This should cover around 99% of the peaks.

Parameters

range
minPt
maxPt
component
tlcBrc
indexArray

References svk4DImageData::GetArray(), svkImageData::GetIndexFromID(), and svkImageData::MAGNITUDE.

vtkDataArray * GetArray ( int linearIndex )

Gets the array by linear index.

Parameters

linearIndex

Returns

Referenced by svk4DImageData::EstimateDataRange(), svk4DImageData::GetArray(), svk4DImageData::GetArrayFromID(), svk4DImageData::GetImage(), svkMrsImageData::GetSpectrum(), svkMrsImageData::InitializeDataArrays(), svkGEPFileMapper::ReorderEPSI(), svkDSCDeltaR2::RequestData(), svkMRSKinetics::RequestData(), svkMrsImageFFT::RequestDataSpatial(), svkMrsZeroFill::RequestDataSpatial(), svk4DImageData::SetImage(), svk4DImageData::SetImageComponent(), svkMRSAutoPhase::SVKRequestDataPreExec(), and svk4DImageData::UpdateRange().

vtkDataArray * GetArray	(	int	x,
		int	y,
		int	z,
		int *	indexArray = `NULL`
	)

Gets an array based on the xyz index of the voxel and a volumetric index array.

Parameters

x
y
z
indexArray

Returns

References svk4DImageData::GetArray(), and svk4DImageData::GetIDFromIndex().

vtkDataArray* GetArray ( int * indexArray )

vtkDataArray * GetArrayFromID	(	int	index,
		int *	indexArray = `NULL`
	)

Gets a specified data array from linear index.

References svk4DImageData::GetArray(), and svkImageData::GetIndexFromID().

Referenced by svkMrsImageData::GetSpectrumFromID().

string GetArrayName ( svkDcmHeader::DimensionVector * dimensionVector )

static

Takes vector of dimension indices and constructs an array name for the cell data lookup.

References svkDcmHeader::GetDimensionVectorValue(), and svkTypeUtils::IntToString().

Referenced by svkEPSIReorder::CombineLobes(), svkMrsImageData::InitializeDataArrays(), svkImageData::RemoveArrays(), and svk4DImageData::SetArrayName().

int GetIDFromIndex	(	int	indexX,
		int	indexY,
		int	indexZ,
		int *	indexArray = `NULL`
	)

virtual

References svk4DImageData::GetNumberOfVolumeDimensions(), and svk4DImageData::GetVolumeIndexSize().

Referenced by svk4DImageData::GetArray(), svk4DImageData::GetImage(), svk4DImageData::SetImage(), and svk4DImageData::SetImageComponent().

void GetImage	(	svkImageData *	image,
		int	point,
		int *	indexArray = `NULL`,
		int	component = `2`,
		int	vtkDataType = `VTK_VOID`
	)

virtual

Method will extract a volume into a vtkImageData object representing a single point in the spectra. This is usefull for spatial FFT's.

Parameters

target	image the point image (must be initialized)
point	the point in the array you wish operate on
component	the component to operate on
timePoint	the time point to operate on
channel	the the channel to operate on
component	(0 = real, 1=im, 2=cmplx)

References svkImageData::CopyDcos(), svk4DImageData::GetArray(), and svk4DImageData::GetIDFromIndex().

Referenced by svk4DImageData::GetImage(), and svk4DImageData::GetZeroImage().

void GetImage	(	svkImageData *	image,
		int	point,
		svkDcmHeader::DimensionVector *	indexVector = `NULL`,
		int	component = `2`,
		int	vtkDataType = `VTK_VOID`
	)

virtual

Method will extract a volume into a vtkImageData object representing a single point in the spectra. This is usefull for spatial FFT's.

Parameters

target	image the point image (must be initialized)
point	the point in the array you wish operate on
component	the component to operate on
timePoint	the time point to operate on
channel	the the channel to operate on
component	(0 = real, 1=im, 2=cmplx)

References svkDcmHeader::COL_INDEX, svkImageData::CopyDcos(), svk4DImageData::GetArray(), svkDcmHeader::GetCellIDFromDimensionVectorIndex(), svkImageData::GetDcmHeader(), svkDcmHeader::GetDimensionIndexVector(), svkDcmHeader::GetSpatialCellIDFromDimensionVectorIndex(), svkDcmHeader::GetSpatialDimensions(), loopVector, svkDcmHeader::ROW_INDEX, svkDcmHeader::SetDimensionVectorValue(), and svkDcmHeader::SLICE_INDEX.

void GetImage	(	svkImageData *	image,
		int	point,
		string	seriesDescription,
		int *	indexArray = `NULL`,
		int	component = `2`,
		int	vtkDataType = `VTK_VOID`
	)

virtual

Method will extract a volume into a vtkImageData object representing a single point in the 4D representation. This is useful for spatial FFT's and map generation.

Parameters

target	image the point image (must be initialized)
point	the point in the array you wish operate on
seriesDescription	for DCM header
indexArray	is the array of non-spatial indices, e.g. channel and time point
component	(0 = real, 1=im, 2=cmplx)

References svkImageData::GetDcmHeader(), svk4DImageData::GetImage(), svkEnhancedMRIIOD::InitDcmHeader(), svkDcmHeader::InitDerivedMRIHeader(), svkEnhancedMRIIOD::New(), svkIOD::SetDcmHeader(), and svkImageData::SyncVTKImageDataToDcmHeader().

void GetImage	(	svkImageData *	image,
		int	point,
		string	seriesDescription,
		svkDcmHeader::DimensionVector *	indexVector = `NULL`,
		int	component = `2`,
		int	vtkDataType = `VTK_VOID`
	)

virtual

Method will extract a 3D volume into a vtkImageData object representing a single 3D point from the 4+D representation. This is useful for spatial FFT's and map generation.

Parameters

target	image the point image (must be initialized)
point	the point in the array you wish operate on
seriesDescription	for DCM header
indexVector	is the array of non-spatial indices, e.g. channel and time point for the image we want to get
component	(0 = real, 1=im, 2=cmplx)

References svkImageData::GetDcmHeader(), svk4DImageData::GetImage(), svkEnhancedMRIIOD::InitDcmHeader(), svkDcmHeader::InitDerivedMRIHeader(), svkEnhancedMRIIOD::New(), svkIOD::SetDcmHeader(), and svkImageData::SyncVTKImageDataToDcmHeader().

int GetLastSlice ( svkDcmHeader::Orientation sliceOrientation = svkDcmHeader::UNKNOWN_ORIENTATION )

virtual

Get the last slice index for a given orientation. This is different for cell data so that is why it is overloaded.

Parameters

sliceOrientation the orientation whose last slice you wish to get

Returns: the last slice

Reimplemented from svkImageData.

Referenced by svkMrsImageData::Get2DProjectedTlcBrcInSelectionBox(), svk4DImageData::GetTlcBrcInUserSelection(), and svkMrsImageData::IsSliceInSelectionBox().

int GetNumberOfSlices ( svkDcmHeader::Orientation sliceOrientation )

virtual

Determins the number of slices for a given orientation.

Reimplemented from svkImageData.

References svkImageData::GetDcmHeader(), svkImageData::GetOrientationIndex(), svkDcmHeader::GetOrientationType(), and svkDcmHeader::UNKNOWN_ORIENTATION.

int GetNumberOfVolumeDimensions ( )

virtual

Currently assumes one dimension. TODO: Use the header to dynamically determine the number of dimensions

Returns

Reimplemented in svkMrsImageData.

Referenced by svk4DImageData::GetIDFromIndex(), svk4DImageData::GetZeroImage(), and svkPlotLineGrid::SetInput().

void GetNumberOfVoxels ( int numVoxels[3] )

virtual

Returns the number of voxels in the data set.

Implements svkImageData.

Referenced by svkMultiCoilPhase::CalculateCenterPhase(), svkMrsImageData::GetSelectionBoxMask(), svkIntegratePeak::RequestData(), svkMrsLinearPhase::RequestData(), svkDSCDeltaR2::RequestData(), and svkMrsZeroFill::RequestInformation().

void GetPolyDataGrid ( vtkPolyData * grid )

virtual

References dims.

void GetTlcBrcInUserSelection	(	int	tlcBrc[2],
		double	userSelection[6],
		svkDcmHeader::Orientation	orientation = `svkDcmHeader::UNKNOWN_ORIENTATION`,
		int	slice = `-1`
	)

This will get the top left corner, and bottom right hand corner (low index-high index) for a given selection and slice. It assumes the userSelection defines a minimum and maximum range and that the user wishes to select all voxels within that range (for a given slice) in a regular box aligned with the dcos having corners at the minimum and maximum values. If no slice is defined

Parameters

tlcBrc	the destination for the result of the calculation
userSelection	the [minx, maxx, miny, maxy, minz, maxz] selection range
slice	the slice within which to make the selection, if slice is outside of the range then the resulting tlcBrc will span the slices in the given selection

References svkImageData::GetDcmHeader(), svkImageData::GetFirstSlice(), svkImageData::GetIndexFromPosition(), svk4DImageData::GetLastSlice(), svkImageData::GetOrientationIndex(), svkDcmHeader::GetOrientationType(), and svkDcmHeader::UNKNOWN_ORIENTATION.

int GetVolumeIndexSize ( int volumeIndex )

virtual

Gets the size of the given volume Index

Parameters

volumeIndex

Returns

Reimplemented in svkMrsImageData.

References svkImageData::dcmHeader, and svkDcmHeader::GetNumberOfCoils().

Referenced by svk4DImageData::GetIDFromIndex().

void GetZeroImage ( svkImageData * image )

Method will extract a volume into a svkImageData object that matches the geometry of the 4D Image volume with a zero value for all pixels.

Parameters

target image the zero image (must be initialized)

References svk4DImageData::GetImage(), and svk4DImageData::GetNumberOfVolumeDimensions().

Referenced by svkVoxelTaggingUtils::CreateVoxelTagData(), svkHSVD::RequestData(), and svkMRSAutoPhase::SVKRequestDataPreExec().

bool IsIndexInExtent	(	int *	extent,
		svkDcmHeader::DimensionVector *	indexVector
	)

static

References svkDcmHeader::GetDimensionVectorValue().

Referenced by svkMRSAutoPhase::AutoPhaseExecute(), and svkMrsImageFFT::RequestDataSpectral().

static svk4DImageData* New ( )

static

Referenced by svkMriImageData::GetCellDataRepresentation(), and svk4DImageData::NewObject().

vtkObject * NewObject ( )

static

This is used by vtkInstantiator and is used in svk algorithms

References svk4DImageData::New().

Referenced by svkImageAlgorithm::svkImageAlgorithm(), and svkThreadedImageAlgorithm::svkThreadedImageAlgorithm().

void SetArrayName	(	vtkDataArray *	array,
		svkDcmHeader::DimensionVector *	dimensionVector
	)

Takes vector of dimension indices and constructs an array name for the cell data (vtkDataArray). Will always be at least: "col row slice", but may have additional indices appended as well.

References svk4DImageData::GetArrayName().

Referenced by svkGEPFileMapper::ReorderEPSI().

void SetImage	(	vtkImageData *	image,
		int	point,
		int *	indexArray = `NULL`
	)

Method will set a spectral point from a vtkImageData object representing a single 3D image point in the spectra. This is usefull for spatial FFT's.

Parameters

image	the point image
point	the point in the array you wish operate on
timePoint	the time point to operate on
channel	the the channel to operate on

References svk4DImageData::GetArray(), and svk4DImageData::GetIDFromIndex().

Referenced by svkMriImageData::SyncCellRepresentationToPixelData().

void SetImage	(	vtkImageData *	image,
		int	point,
		svkDcmHeader::DimensionVector *	indexVector
	)

Method will set a spectral point from a vtkImageData object representing a single 3D image point in the spectra. This is usefull for spatial FFT's.

Parameters

image	the point image
point	the point in the array you wish operate on (point in spectral domain, frequency or time)
dimensionVector	represents non spatial volume indices to set 3D image into

References svkDcmHeader::COL_INDEX, svk4DImageData::GetArray(), svkDcmHeader::GetCellIDFromDimensionVectorIndex(), svkImageData::GetDcmHeader(), svkDcmHeader::GetDimensionIndexVector(), svkDcmHeader::GetSpatialCellIDFromDimensionVectorIndex(), svkDcmHeader::GetSpatialDimensions(), loopVector, svkDcmHeader::ROW_INDEX, svkDcmHeader::SetDimensionVectorValue(), and svkDcmHeader::SLICE_INDEX.

void SetImageComponent	(	vtkImageData *	image,
		int	point,
		int *	indexArray = `NULL`,
		int	component = `0`
	)

Method will set a spectral point from a vtkImageData object representing a single point in the spectra. This is usefull for spatial FFT's.

Parameters

image	the point image
point	the point in the array you wish operate on
timePoint	the time point to operate on
channel	the the channel to operate on
component	the component Re or Im

References svk4DImageData::GetArray(), and svk4DImageData::GetIDFromIndex().

void UpdateRange ( int component )

virtual

Makes sure the range gets updated when the object is modified. It searches all arrays for each component to determine maximum and minimums

Reimplemented from svkImageData.

References svk4DImageData::GetArray(), svkImageData::IMAGINARY, svkImageData::MAGNITUDE, svkImageData::REAL, and svkImageData::SetDataRange().

vtkTypeMacro	(	svk4DImageData	,
		svkImageData
	)

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

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation