#include <svkMriImageData.h>

Inheritance diagram for svkMriImageData:

Public Member Functions
	vtkTypeMacro (svkMriImageData, svkImageData)

double *	GetImagePixels (int slice)

vtkDataArray *	GetImagePixelsArray (int slice)

double *	GetImagePixel (int id)

double *	GetImagePixel (int x, int y, int z)

void	SetImagePixels (double *pixels, int slice)

void	SetImagePixel (int id, double value)

void	SetImagePixel (int x, int y, int z, double value)

virtual void	GetNumberOfVoxels (int numVoxels[3])

void	GetAutoWindowLevel (double &window, double &level, int numBins=START_NUM_BINS, double excludeFactor=EXCLUDE_FACTOR)

virtual int	GetVolumeIndexForFrame (int frame)

void	GetCenterOfMass (double centerOfMass[3], int component=0)

virtual svk4DImageData *	GetCellDataRepresentation ()

void	SyncPixelDataToCellRepresentation ()

void	SyncCellRepresentationToPixelData ()

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	GetNumberOfSlices (svkDcmHeader::Orientation sliceOrientation=svkDcmHeader::UNKNOWN_ORIENTATION)

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

virtual int	GetLastSlice (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 svkMriImageData *	New ()

static vtkObject *	NewObject ()

static void	UpdatePixelData (vtkObject subject, unsigned long eid, void thisObject, void *calldata)

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

Protected Types
enum	ActorType { PLOT_GRID }

Protected Member Functions
	svkMriImageData ()

	~svkMriImageData ()

Protected Member Functions inherited from svkImageData
	svkImageData ()

	~svkImageData ()

bool	WasModified ()

virtual void	UpdateSvkParams ()

virtual void	UpdateRange (int component)

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

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

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

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

Class that represents a MR Image data set. Contains methods for accessing MRI specific actors.

Member Enumeration Documentation

enum ActorType

protected

Enumerator
PLOT_GRID

Constructor & Destructor Documentation

svkMriImageData ( )

protected

~svkMriImageData ( )

protected

Member Function Documentation

void GetAutoWindowLevel	(	double &	window,
		double &	level,
		int	numBins = `START_NUM_BINS`,
		double	excludeFactor = `EXCLUDE_FACTOR`
	)

Method attempts to determine the best default window/level values for the dataset. It does this by:

Create a histogram with the number of bins specified at input.
Determine the mode, excluding zero, and use that as the level.
Calculate the standard deviation excluding zero.
Use the input number of standard deviations to determine the window.
If the window extends outside the range, clip the window such that it is within range.

Parameters

window	output reference
level	output reference
numBins	the number of bins used to make the histogram
excludeFactor	the percentage of pixels excluded from each end when defining the window.

References MAX_NUM_BINS, MIN_USED_BINS, and svkImageData::range.

svk4DImageData * GetCellDataRepresentation ( )

virtual

This method will return a representation of the data using cell data. This representation is used primarily for the visualization of the image volume as traces.

Returns

References svkImageData::GetDcmHeader(), svk4DImageData::New(), svkImageData::SetDcmHeader(), svkImageData::SetSourceData(), svkMriImageData::SyncCellRepresentationToPixelData(), and svkImageData::SyncVTKImageDataToDcmHeader().

Referenced by svkMRSKinetics::RequestData().

void GetCenterOfMass	(	double	centerOfMass[3],
		int	component = `0`
	)

Calculates the center of mass of a volume using the pixel intensities as 'mass'. Just a weighted average location.

References dims, svkImageData::GetIDFromIndex(), and svkImageData::GetPositionFromIndex().

double * GetImagePixel ( int id )

Returns a pointer to the data at the specified voxel ID.

Referenced by svkHSVD::GetFitSuccessStatus(), svkMriImageData::GetImagePixel(), and svkVoxelTaggingUtils::ToggleVoxelTag().

double * GetImagePixel	(	int	x,
		int	y,
		int	z
	)

Returns a pointer to the data at the specified voxel index.

References svkImageData::GetIDFromIndex(), and svkMriImageData::GetImagePixel().

double * GetImagePixels ( int slice )

Creates an array of doubles that is the pixels of image at slice "slice. Currently assumes 1 component data

Referenced by svkBurnResearchPixels::RequestData().

vtkDataArray * GetImagePixelsArray ( int slice )

Creates an array of doubles that is the pixels of image at slice "slice. Output goes into a vtkDataArray that matches the type of the pixel array in the original dataset. Currently assumes 1 component data.

void GetNumberOfVoxels ( int numVoxels[3] )

virtual

Return the number of voxels in the data set.

Implements svkImageData.

Referenced by svkBurnResearchPixels::RequestData().

int GetVolumeIndexForFrame ( int frame )

virtual

Uses the dimension index sequence to determine the volume for the frame.

References svkImageData::GetDcmHeader(), svkDcmHeader::GetDimensionIndexPosition(), svkDcmHeader::GetIntSequenceItemElement(), svkDcmHeader::GetNumberOfFramesInDimension(), and svkDcmHeader::GetNumberOfItemsInSequence().

static svkMriImageData* New ( )

static