Describes the geometry of a data object consisting of slices. More...

#include <mitkSlicedGeometry3D.h>

Inheritance diagram for mitk::SlicedGeometry3D:

Collaboration diagram for mitk::SlicedGeometry3D:

Public Types
typedef SlicedGeometry3D	Self

typedef BaseGeometry	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

Public Types inherited from mitk::BaseGeometry
typedef BaseGeometry	Self

typedef itk::Object	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef GeometryTransformHolder::TransformType	TransformType

typedef itk::BoundingBox< unsigned long, 3, ScalarType >	BoundingBoxType

typedef BoundingBoxType::BoundsArrayType	BoundsArrayType

typedef BoundingBoxType::Pointer	BoundingBoxPointer

Public Member Functions
virtual std::vector< std::string >	GetClassHierarchy () const override

virtual const char *	GetClassName () const

Pointer	Clone () const

virtual mitk::PlaneGeometry *	GetPlaneGeometry (int s) const
	Returns the PlaneGeometry of the slice (s). More...

const PlaneGeometry *	GetGeometry2D (int s)

void	SetGeometry2D (PlaneGeometry *geo, int s)

virtual void	ChangeImageGeometryConsideringOriginOffset (const bool isAnImageGeometry) override
	When switching from an Image Geometry to a normal Geometry (and the other way around), you have to. More...

virtual const mitk::BoundingBox *	GetBoundingBox () const override

virtual unsigned int	GetSlices () const
	Get the number of slices. More...

virtual bool	SetPlaneGeometry (mitk::PlaneGeometry *geometry2D, int s)
	Set PlaneGeometry of slice s. More...

virtual bool	IsValidSlice (int s=0) const
	Check whether a slice exists. More...

virtual const BaseGeometry *	GetReferenceGeometry () const

virtual void	SetReferenceGeometry (const BaseGeometry *referenceGeometry)

bool	HasReferenceGeometry () const

virtual void	SetSliceNavigationController (mitk::SliceNavigationController *snc)
	Set the SliceNavigationController corresponding to this sliced geometry. More...

mitk::SliceNavigationController *	GetSliceNavigationController ()

virtual bool	GetEvenlySpaced () const
	Set/Get whether the SlicedGeometry3D is evenly-spaced (m_EvenlySpaced) More...

virtual void	SetEvenlySpaced (bool on=true)

virtual void	SetDirectionVector (const mitk::Vector3D &directionVector)
	Set/Get the vector between slices for the evenly-spaced case (m_EvenlySpaced==true). More...

virtual const mitk::Vector3D &	GetDirectionVector () const

virtual itk::LightObject::Pointer	InternalClone () const override
	clones the geometry More...

virtual void	InitializeSlicedGeometry (unsigned int slices)
	Tell this instance how many PlaneGeometries it shall manage. Bounding box and the PlaneGeometries must be set additionally by calling the respective methods! More...

virtual void	InitializeEvenlySpaced (mitk::PlaneGeometry *geometry2D, unsigned int slices)
	Completely initialize this instance as evenly-spaced with slices parallel to the provided PlaneGeometry that is used as the first slice and for spacing calculation. More...

virtual void	InitializeEvenlySpaced (mitk::PlaneGeometry *geometry2D, mitk::ScalarType zSpacing, unsigned int slices)
	Completely initialize this instance as evenly-spaced with slices parallel to the provided PlaneGeometry that is used as the first slice and for spacing calculation (except z-spacing). More...

virtual void	InitializePlanes (const mitk::BaseGeometry *geometry3D, mitk::PlaneGeometry::PlaneOrientation planeorientation, bool top=true, bool frontside=true, bool rotated=false)
	Completely initialize this instance as evenly-spaced plane slices parallel to a side of the provided BaseGeometry and using its spacing information. More...

virtual void	SetImageGeometry (const bool isAnImageGeometry) override
	Define that this BaseGeometry is refering to an Image. More...

virtual void	ExecuteOperation (Operation *operation) override
	executes affine operations (translate, rotate, scale) More...

Public Member Functions inherited from mitk::BaseGeometry
Pointer	Clone () const

const Point3D	GetOrigin () const
	Get the origin, e.g. the upper-left corner of the plane. More...

void	SetOrigin (const Point3D &origin)
	Set the origin, i.e. the upper-left corner of the plane. More...

const mitk::Vector3D	GetSpacing () const
	Get the spacing (size of a pixel). More...

void	SetSpacing (const mitk::Vector3D &aSpacing, bool enforceSetSpacing=false)
	Set the spacing (m_Spacing). More...

VnlVector	GetOriginVnl () const
	Get the origin as VnlVector. More...

virtual unsigned int	GetFrameOfReferenceID () const
	Get the DICOM FrameOfReferenceID referring to the used world coordinate system. More...

virtual void	SetFrameOfReferenceID (unsigned int _arg)
	Set the DICOM FrameOfReferenceID referring to the used world coordinate system. More...

virtual unsigned long	GetIndexToWorldTransformLastModified () const

void	Modified () const override
	Overload of function Modified() to prohibit several calls of Modified() using the ModifiedLock class. More...

virtual bool	IsValid () const
	Is this BaseGeometry in a state that is valid? More...

void	Initialize ()
	Initialize the BaseGeometry. More...

void	InitializeGeometry (Self *newGeometry) const

mitk::AffineTransform3D *	GetIndexToWorldTransform ()
	Get the transformation used to convert from index to world coordinates. More...

const mitk::AffineTransform3D *	GetIndexToWorldTransform () const
	Get the transformation used to convert from index to world coordinates. More...

void	SetIndexToWorldTransform (mitk::AffineTransform3D *transform)

void	SetIndexToWorldTransformByVtkMatrix (vtkMatrix4x4 *vtkmatrix)
	Convenience method for setting the ITK transform (m_IndexToWorldTransform) via an vtkMatrix4x4.The spacing of the new transform is copied to m_spacing. More...

void	SetIndexToWorldTransformWithoutChangingSpacing (mitk::AffineTransform3D *transform)

void	SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing (vtkMatrix4x4 *vtkmatrix)
	Convenience method for setting the ITK transform (m_IndexToWorldTransform) via an vtkMatrix4x4. This function keeps the original spacing. More...

vtkMatrix4x4 *	GetVtkMatrix ()

vtkLinearTransform *	GetVtkTransform () const
	Get the m_IndexToWorldTransform as a vtkLinearTransform. More...

void	SetIdentity ()
	Set the transform to identity, the spacing to 1 and origin to 0. More...

void	Compose (const TransformType *other, bool pre=0)
	Compose new IndexToWorldTransform with a given transform. More...

void	Compose (const vtkMatrix4x4 *vtkmatrix, bool pre=0)
	Compose new IndexToWorldTransform with a given vtkMatrix4x4. More...

void	Translate (const Vector3D &vector)
	Translate the origin by a vector. More...

void	WorldToIndex (const mitk::Point3D &pt_mm, mitk::Point3D &pt_units) const
	Convert world coordinates (in mm) of a point to (continuous!) index coordinates. More...

void	WorldToIndex (const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const
	Convert world coordinates (in mm) of a vector vec_mm to (continuous!) index coordinates. For further information about coordinates types, please see the Geometry documentation. More...

template<unsigned int VIndexDimension>
void	WorldToIndex (const mitk::Point3D &pt_mm, itk::Index< VIndexDimension > &index) const
	Convert world coordinates (in mm) of a point to (discrete!) index coordinates. This method rounds to integer indices! For further information about coordinates types, please see the Geometry documentation. More...

void	IndexToWorld (const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const
	Convert (continuous or discrete) index coordinates of a vector vec_units to world coordinates (in mm) For further information about coordinates types, please see the Geometry documentation. More...

void	IndexToWorld (const mitk::Point3D &pt_units, mitk::Point3D &pt_mm) const
	Convert (continuous or discrete) index coordinates of a point to world coordinates (in mm) For further information about coordinates types, please see the Geometry documentation. More...

template<unsigned int VIndexDimension>
void	IndexToWorld (const itk::Index< VIndexDimension > &index, mitk::Point3D &pt_mm) const
	Convert (discrete) index coordinates of a point to world coordinates (in mm) For further information about coordinates types, please see the Geometry documentation. More...

void	IndexToWorld (const mitk::Point3D &atPt3d_units, const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const
	Convert (continuous or discrete) index coordinates of a vector vec_units to world coordinates (in mm) More...

void	WorldToIndex (const mitk::Point3D &atPt3d_mm, const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const
	Convert world coordinates (in mm) of a vector vec_mm to (continuous!) index coordinates. More...

template<class TCoordRep >
void	ItkPhysicalPointToWorld (const itk::Point< TCoordRep, 3 > &itkPhysicalPoint, mitk::Point3D &pt_mm) const
	Deprecated for use with ITK version 3.10 or newer. Convert ITK physical coordinates of a point (in mm, but without a rotation) into MITK world coordinates (in mm) More...

template<class TCoordRep >
void	WorldToItkPhysicalPoint (const mitk::Point3D &pt_mm, itk::Point< TCoordRep, 3 > &itkPhysicalPoint) const
	Deprecated for use with ITK version 3.10 or newer. Convert world coordinates (in mm) of a point to ITK physical coordinates (in mm, but without a possible rotation) More...

virtual const BoundingBoxType *	GetBoundingBox ()

const BoundsArrayType	GetBounds () const

void	SetBounds (const BoundsArrayType &bounds)
	Set the bounding box (in index/unit coordinates) More...

void	SetFloatBounds (const float bounds[6])
	Set the bounding box (in index/unit coordinates) via a float array. More...

void	SetFloatBounds (const double bounds[6])
	Set the bounding box (in index/unit coordinates) via a double array. More...

VnlVector	GetMatrixColumn (unsigned int direction) const
	Get a VnlVector along bounding-box in the specified direction, length is spacing. More...

mitk::BoundingBox::Pointer	CalculateBoundingBoxRelativeToTransform (const mitk::AffineTransform3D *transform) const
	Calculates a bounding-box around the geometry relative to a coordinate system defined by a transform. More...

ScalarType	GetExtent (unsigned int direction) const
	Set the time bounds (in ms) More...

ScalarType	GetExtentInMM (int direction) const
	Get the extent of the bounding-box in the specified direction in mm. More...

Vector3D	GetAxisVector (unsigned int direction) const
	Get vector along bounding-box in the specified direction in mm. More...

virtual bool	Is2DConvertable ()
	Checks, if the given geometry can be converted to 2D without information loss e.g. when a 2D image is saved, the matrix is usually cropped to 2x2, and when you load it back to MITK it will be filled with standard values. This function checks, if information would be lost during this procedure. More...

Point3D	GetCenter () const
	Get the center of the bounding-box in mm. More...

double	GetDiagonalLength2 () const
	Get the squared length of the diagonal of the bounding-box in mm. More...

double	GetDiagonalLength () const
	Get the length of the diagonal of the bounding-box in mm. More...

Point3D	GetCornerPoint (int id) const
	Get the position of the corner number id (in world coordinates) More...

Point3D	GetCornerPoint (bool xFront=true, bool yFront=true, bool zFront=true) const
	Get the position of a corner (in world coordinates) More...

void	SetExtentInMM (int direction, ScalarType extentInMM)
	Set the extent of the bounding-box in the specified direction in mm. More...

bool	IsInside (const mitk::Point3D &p) const
	Test whether the point p (world coordinates in mm) is inside the bounding box. More...

bool	IsIndexInside (const mitk::Point3D &index) const
	Test whether the point p ((continous!)index coordinates in units) is inside the bounding box. More...

template<unsigned int VIndexDimension>
bool	IsIndexInside (const itk::Index< VIndexDimension > &index) const
	Convenience method for working with ITK indices. More...

virtual bool	GetImageGeometry () const
	Is this an ImageGeometry? More...

virtual void	ImageGeometryOn ()

virtual void	ImageGeometryOff ()

const GeometryTransformHolder *	GetGeometryTransformHolder () const

Public Member Functions inherited from mitk::OperationActor
	itkTypeMacroNoParent (OperationActor) virtual ~OperationActor()

Static Public Member Functions
static const char *	GetStaticNameOfClass ()

static Pointer	New ()

static double	CalculateSpacing (const mitk::Vector3D &spacing, const mitk::Vector3D &d)

Static Public Member Functions inherited from mitk::BaseGeometry
static const char *	GetStaticNameOfClass ()

Static Public Attributes
static const std::string	SLICES

static const std::string	DIRECTION_VECTOR

static const std::string	EVENLY_SPACED

Protected Member Functions
	SlicedGeometry3D ()

	SlicedGeometry3D (const SlicedGeometry3D &other)

virtual	~SlicedGeometry3D ()

virtual void	ReinitializePlanes (const Point3D &center, const Point3D &referencePoint)

ScalarType	GetLargestExtent (const BaseGeometry *geometry)

void	PrintSelf (std::ostream &os, itk::Indent indent) const override

double	CalculateSpacing (const mitk::Vector3D &direction) const

mitk::Vector3D	AdjustNormal (const mitk::Vector3D &normal) const

virtual void	PreSetSpacing (const mitk::Vector3D &aSpacing) override
	PreSetSpacing. More...

Protected Member Functions inherited from mitk::BaseGeometry
	BaseGeometry ()

	BaseGeometry (const BaseGeometry &other)

virtual	~BaseGeometry ()

virtual unsigned int	GetNDimensions () const

bool	IsBoundingBoxNull () const

bool	IsIndexToWorldTransformNull () const

void	SetVtkMatrixDeepCopy (vtkTransform *vtktransform)

void	_SetSpacing (const mitk::Vector3D &aSpacing, bool enforceSetSpacing=false)

virtual void	CheckBounds (const BoundsArrayType &)
	CheckBounds. More...

virtual void	CheckIndexToWorldTransform (mitk::AffineTransform3D *)
	CheckIndexToWorldTransform. More...

Protected Attributes
std::vector< PlaneGeometry::Pointer >	m_PlaneGeometries

bool	m_EvenlySpaced

mitk::Vector3D	m_DirectionVector

unsigned int	m_Slices

const mitk::BaseGeometry *	m_ReferenceGeometry

mitk::SliceNavigationController *	m_SliceNavigationController

Additional Inherited Members
Static Protected Member Functions inherited from mitk::BaseGeometry
static const std::string	GetTransformAsString (TransformType *transformType)

Detailed Description

Describes the geometry of a data object consisting of slices.

A PlaneGeometry can be requested for each slice. In the case of evenly-spaced, plane geometries (m_EvenlySpaced==true), only the 2D-geometry of the first slice has to be set (to an instance of PlaneGeometry). The 2D geometries of the other slices are calculated by shifting the first slice in the direction m_DirectionVector by m_Spacing.z * sliceNumber. The m_Spacing member (which is only relevant in the case m_EvenlySpaced==true) descibes the size of a voxel (in mm), i.e., m_Spacing.x is the voxel width in the x-direction of the plane. It is derived from the reference geometry of this SlicedGeometry3D, which usually would be the global geometry describing how datasets are to be resliced.

By default, slices are oriented in the direction of one of the main axes (x, y, z). However, by means of rotation, it is possible to realign the slices in any possible direction. In case of an inclined plane, the spacing is derived as a product of the (regular) geometry spacing and the direction vector of the plane.

SlicedGeometry3D and the associated PlaneGeometries have to be initialized in the method GenerateOutputInformation() of BaseProcess (or CopyInformation / UpdateOutputInformation of BaseData, if possible, e.g., by analyzing pic tags in Image) subclasses. See also

See also: itk::ProcessObject::GenerateOutputInformation(),; itk::DataObject::CopyInformation() and itk::DataObject::UpdateOutputInformation().

Rule: everything is in mm (or ms for temporal information) if not stated otherwise.

Warning: The hull (i.e., transform, bounding-box and time-bounds) is only guaranteed to be up-to-date after calling UpdateInformation().

Definition at line 66 of file mitkSlicedGeometry3D.h.

Member Typedef Documentation

typedef itk::SmartPointer<const Self> mitk::SlicedGeometry3D::ConstPointer

Definition at line 69 of file mitkSlicedGeometry3D.h.

typedef itk::SmartPointer<Self> mitk::SlicedGeometry3D::Pointer

Definition at line 69 of file mitkSlicedGeometry3D.h.

typedef SlicedGeometry3D mitk::SlicedGeometry3D::Self

Definition at line 69 of file mitkSlicedGeometry3D.h.

typedef BaseGeometry mitk::SlicedGeometry3D::Superclass

Definition at line 69 of file mitkSlicedGeometry3D.h.

Constructor & Destructor Documentation

mitk::SlicedGeometry3D::SlicedGeometry3D ( )

protected

Definition at line 31 of file mitkSlicedGeometry3D.cpp.

References InitializeSlicedGeometry(), m_DirectionVector, and m_Slices.

mitk::SlicedGeometry3D::SlicedGeometry3D ( const SlicedGeometry3D & other )

protected

Definition at line 38 of file mitkSlicedGeometry3D.cpp.

References GetDirectionVector(), mitk::BaseGeometry::GetSpacing(), m_DirectionVector, m_EvenlySpaced, m_PlaneGeometries, m_Slices, SetDirectionVector(), SetPlaneGeometry(), and mitk::BaseGeometry::SetSpacing().

mitk::SlicedGeometry3D::~SlicedGeometry3D ( )

protectedvirtual

Definition at line 76 of file mitkSlicedGeometry3D.cpp.

Member Function Documentation

mitk::Vector3D mitk::SlicedGeometry3D::AdjustNormal ( const mitk::Vector3D & normal ) const

protected

The extent of the slice stack, i.e. the number of slices, depends on the plane normal. For rotated geometries, the geometry's transform needs to be accounted in this calculation.

Definition at line 417 of file mitkSlicedGeometry3D.cpp.

References mitk::New().

double mitk::SlicedGeometry3D::CalculateSpacing	(	const mitk::Vector3D &	spacing,
		const mitk::Vector3D &	d
	)

static

Definition at line 400 of file mitkSlicedGeometry3D.cpp.

Referenced by CalculateSpacing(), and mitk::PlaneGeometryDataMapper2D::CreateVtkCrosshair().

double mitk::SlicedGeometry3D::CalculateSpacing ( const mitk::Vector3D & direction ) const

protected

Calculate "directed spacing", i.e. the spacing in directions non-orthogonal to the coordinate axes. This is done via the ellipsoid equation.

Definition at line 388 of file mitkSlicedGeometry3D.cpp.

References CalculateSpacing().

void mitk::SlicedGeometry3D::ChangeImageGeometryConsideringOriginOffset ( const bool isAnImageGeometry )

overridevirtual

When switching from an Image Geometry to a normal Geometry (and the other way around), you have to.

Reimplemented from mitk::BaseGeometry.

Definition at line 443 of file mitkSlicedGeometry3D.cpp.

References mitk::BaseGeometry::ChangeImageGeometryConsideringOriginOffset().

Pointer mitk::SlicedGeometry3D::Clone ( ) const

Referenced by mitk::DiffSliceOperation::DiffSliceOperation().

void mitk::SlicedGeometry3D::ExecuteOperation ( Operation * operation )

overridevirtual

executes affine operations (translate, rotate, scale)

Reimplemented from mitk::BaseGeometry.

Definition at line 635 of file mitkSlicedGeometry3D.cpp.

References mitk::PlaneOperation::AreAxisDefined(), mitk::eps, mitk::BaseGeometry::ExecuteOperation(), mitk::RotationOperation::GetAngleOfRotation(), mitk::PlaneOperation::GetAxisVec0(), mitk::PlaneOperation::GetAxisVec1(), mitk::RotationOperation::GetCenterOfRotation(), mitk::RestorePlanePositionOperation::GetDirectionVector(), mitk::PlaneOperation::GetNormal(), mitk::Operation::GetOperationType(), mitk::PointOperation::GetPoint(), mitk::RestorePlanePositionOperation::GetPos(), mitk::ApplyTransformMatrixOperation::GetReferencePoint(), mitk::RestorePlanePositionOperation::GetSpacing(), mitk::RotationOperation::GetVectorOfRotation(), mitk::OpAPPLYTRANSFORMMATRIX, mitk::OpNOTHING, mitk::OpORIENT, mitk::OpRESTOREPLANEPOSITION, mitk::OpROTATE, and PI.

const mitk::BoundingBox * mitk::SlicedGeometry3D::GetBoundingBox ( ) const

overridevirtual

Definition at line 126 of file mitkSlicedGeometry3D.cpp.

virtual std::vector<std::string> mitk::SlicedGeometry3D::GetClassHierarchy ( ) const

inlineoverridevirtual

Reimplemented from mitk::BaseGeometry.

Definition at line 69 of file mitkSlicedGeometry3D.h.

virtual const char* mitk::SlicedGeometry3D::GetClassName ( ) const

virtual

Reimplemented from mitk::BaseGeometry.

virtual const mitk::Vector3D& mitk::SlicedGeometry3D::GetDirectionVector ( ) const

virtual

Referenced by mitk::SliceNavigationController::AdjustSliceStepperRange(), mitk::SliceNavigationController::SelectSliceByPoint(), and SlicedGeometry3D().

virtual bool mitk::SlicedGeometry3D::GetEvenlySpaced ( ) const

virtual

Set/Get whether the SlicedGeometry3D is evenly-spaced (m_EvenlySpaced)

If (a) m_EvenlySpaced==true, (b) we don't have a PlaneGeometry stored for the requested slice, and (c) the first slice (s=0) is a PlaneGeometry instance, then we calculate the geometry of the requested as the plane of the first slice shifted by m_Spacing.z * s in the direction of m_DirectionVector.

See also: GetPlaneGeometry

Referenced by mitk::SliceNavigationController::SelectSliceByPoint(), and mitk::SlicedData::SetOrigin().

const PlaneGeometry* mitk::SlicedGeometry3D::GetGeometry2D ( int s )

inline

Deprecated:: (as of 2014_10) Please use GetPlaneGeometry

Definition at line 99 of file mitkSlicedGeometry3D.h.

ScalarType mitk::SlicedGeometry3D::GetLargestExtent ( const BaseGeometry * geometry )

protected

mitk::PlaneGeometry * mitk::SlicedGeometry3D::GetPlaneGeometry ( int s ) const

virtual

Returns the PlaneGeometry of the slice (s).

If (a) m_EvenlySpaced==true, (b) we don't have a PlaneGeometry stored for the requested slice, and (c) the first slice (s=0) is a PlaneGeometry instance, then we calculate the geometry of the requested as the plane of the first slice shifted by m_Spacing[3]*s in the direction of m_DirectionVector.

Warning: The PlaneGeometries are not necessarily up-to-date and not even initialized.

The PlaneGeometries have to be initialized in the method GenerateOutputInformation() of BaseProcess (or CopyInformation / UpdateOutputInformation of BaseData, if possible, e.g., by analyzing pic tags in Image) subclasses. See also

See also: itk::ProcessObject::GenerateOutputInformation(),; itk::DataObject::CopyInformation() and; itk::DataObject::UpdateOutputInformation().

Definition at line 80 of file mitkSlicedGeometry3D.cpp.

References mitk::PlaneGeometry::Clone(), and mitk::PlaneGeometry::GetNormal().

Referenced by mitk::SliceNavigationController::GetCurrentPlaneGeometry(), mitk::Image::Initialize(), mitk::SliceNavigationController::SelectSliceByPoint(), mitk::SlicedData::SetOrigin(), mitk::BaseRenderer::SetSlice(), mitk::BaseRenderer::SetTimeStep(), mitk::BaseRenderer::SetWorldGeometry3D(), QmitkSliceBasedInterpolatorWidget::TranslateAndInterpolateChangedSlice(), QmitkSlicesInterpolator::TranslateAndInterpolateChangedSlice(), mitk::ClippedSurfaceBoundsCalculator::Update(), and mitk::BaseRenderer::UpdateGeometry().

const mitk::BaseGeometry * mitk::SlicedGeometry3D::GetReferenceGeometry ( ) const

virtual

Definition at line 463 of file mitkSlicedGeometry3D.cpp.

mitk::SliceNavigationController * mitk::SlicedGeometry3D::GetSliceNavigationController ( )

Definition at line 565 of file mitkSlicedGeometry3D.cpp.

virtual unsigned int mitk::SlicedGeometry3D::GetSlices ( ) const

virtual

Get the number of slices.

Referenced by mitk::ItkImageIO::GetWriterConfidenceLevel(), mitk::SliceNavigationController::SelectSliceByPoint(), mitk::SlicedData::SetOrigin(), mitk::BaseRenderer::SetSlice(), mitk::BaseRenderer::SetWorldGeometry3D(), and mitk::ClippedSurfaceBoundsCalculator::Update().

static const char* mitk::SlicedGeometry3D::GetStaticNameOfClass ( )

inlinestatic

Definition at line 69 of file mitkSlicedGeometry3D.h.

bool mitk::SlicedGeometry3D::HasReferenceGeometry ( ) const

Definition at line 480 of file mitkSlicedGeometry3D.cpp.

void mitk::SlicedGeometry3D::InitializeEvenlySpaced	(	mitk::PlaneGeometry *	geometry2D,
		unsigned int	slices
	)

virtual

Completely initialize this instance as evenly-spaced with slices parallel to the provided PlaneGeometry that is used as the first slice and for spacing calculation.

Initializes the bounding box according to the width/height of the PlaneGeometry and slices. The spacing is calculated from the PlaneGeometry.

Definition at line 158 of file mitkSlicedGeometry3D.cpp.

References mitk::BaseGeometry::GetExtent(), and mitk::BaseGeometry::GetExtentInMM().

Referenced by mitk::ItkImageFileReader::GenerateData(), mitk::NrrdTbssRoiImageReader::GenerateData(), mitk::AutoCropImageFilter::GenerateOutputInformation(), mitk::Image::InitializeByItk(), mitk::ItkImageIO::Read(), mitk::LabelSetImageIO::Read(), and mitk::SlicedData::SetOrigin().

void mitk::SlicedGeometry3D::InitializeEvenlySpaced	(	mitk::PlaneGeometry *	geometry2D,
		mitk::ScalarType	zSpacing,
		unsigned int	slices
	)

virtual

Completely initialize this instance as evenly-spaced with slices parallel to the provided PlaneGeometry that is used as the first slice and for spacing calculation (except z-spacing).

Initializes the bounding box according to the width/height of the PlaneGeometry and slices. The x-/y-spacing is calculated from the PlaneGeometry.

Definition at line 164 of file mitkSlicedGeometry3D.cpp.

References mitk::FillVector3D(), mitk::BaseGeometry::GetAxisVector(), mitk::BaseGeometry::GetBounds(), mitk::BaseGeometry::GetExtent(), mitk::BaseGeometry::GetExtentInMM(), mitk::BaseGeometry::GetFrameOfReferenceID(), mitk::BaseGeometry::GetImageGeometry(), and mitk::BaseGeometry::GetIndexToWorldTransform().

void mitk::SlicedGeometry3D::InitializePlanes	(	const mitk::BaseGeometry *	geometry3D,
		mitk::PlaneGeometry::PlaneOrientation	planeorientation,
		bool	top = `true`,
		bool	frontside = `true`,
		bool	rotated = `false`
	)

virtual

Completely initialize this instance as evenly-spaced plane slices parallel to a side of the provided BaseGeometry and using its spacing information.

Initializes the bounding box according to the width/height of the BaseGeometry and the number of slices according to BaseGeometry::GetExtent(2).

Parameters

planeorientation	side parallel to which the slices will be oriented
top	if true, create plane at top, otherwise at bottom (for PlaneOrientation Axial, for other plane locations respectively)
frontside	defines the side of the plane (the definition of front/back is somewhat arbitrary)
rotate	rotates the plane by 180 degree around its normal (the definition of rotated vs not rotated is somewhat arbitrary)

Although the double value returned by GetExtent() holds a round number, you need to add 0.5 to safely convert it to unsigned it. I have seen a case when the result was less by one without this.

The normal vector of an imaginary plane that points from the world origin (bottom left back corner or the world, with the lowest physical coordinates) towards the inside of the volume, along the renderer axis. Length is the slice thickness.

The normal of the standard plane geometry just created.

The standard plane must be parallel to the 'world plane'. The normal of the standard plane must point against the world plane if and only if 'top' is 'false'. The length of the standard plane normal must be equal to the slice thickness.

The standard plane normal and the z axis vector of the sliced geometry must point in the same direction.

You can use this test is to check the handedness of the coordinate system of the current geometry. In principle, you can use either left- or right-handed coordinate systems, but you normally want it to be consistent, that is the handedness should be the same across the renderers of the same viewer.

Definition at line 221 of file mitkSlicedGeometry3D.cpp.

References mitk::PlaneGeometry::Frontal, mitk::BaseGeometry::GetExtent(), mitk::BaseGeometry::GetIndexToWorldTransform(), mitk::BaseGeometry::GetSpacing(), mitk::PlaneGeometry::New(), and mitk::PlaneGeometry::Sagittal.

void mitk::SlicedGeometry3D::InitializeSlicedGeometry ( unsigned int slices )

virtual

Tell this instance how many PlaneGeometries it shall manage. Bounding box and the PlaneGeometries must be set additionally by calling the respective methods!

Warning: Bounding box and the 2D-geometries must be set additionally: use SetBounds(), SetGeometry().

Definition at line 143 of file mitkSlicedGeometry3D.cpp.

Referenced by SlicedGeometry3D().

itk::LightObject::Pointer mitk::SlicedGeometry3D::InternalClone ( ) const

overridevirtual

clones the geometry

Overwrite in all sub-classes. Normally looks like:

//##  Self::Pointer newGeometry = new Self(*this);
//##  newGeometry->UnRegister();
//##  return newGeometry.GetPointer();
//## 

Implements mitk::BaseGeometry.

Definition at line 606 of file mitkSlicedGeometry3D.cpp.

bool mitk::SlicedGeometry3D::IsValidSlice ( int s = 0 ) const

virtual

Check whether a slice exists.

Definition at line 458 of file mitkSlicedGeometry3D.cpp.

static Pointer mitk::SlicedGeometry3D::New ( )

static

Method for creation through the object factory.

Referenced by CheckIntersectionWithRotatedGeometry(), CheckIntersectionWithRotatedGeometry90(), createEvenlySpacedSlicedGeometry(), createSlicedGeometry(), mitk::Image::Initialize(), mitkClippedSurfaceBoundsCalculatorTest(), mitk::SlicedData::SetGeometry(), and mitk::SliceNavigationController::Update().

void mitk::SlicedGeometry3D::PreSetSpacing ( const mitk::Vector3D & aSpacing )

overrideprotectedvirtual

PreSetSpacing.

These virtual function allows a different beahiour in subclasses. Do implement them in every subclass of BaseGeometry. If not needed, use {Superclass::PreSetSpacing();};

Reimplemented from mitk::BaseGeometry.

Definition at line 485 of file mitkSlicedGeometry3D.cpp.

References mitk::BaseGeometry::_SetSpacing(), mitk::BaseGeometry::GetAxisVector(), mitk::BaseGeometry::GetBounds(), mitk::BaseGeometry::GetOrigin(), mitkThrow, and mitk::PlaneGeometry::New().

void mitk::SlicedGeometry3D::PrintSelf	(	std::ostream &	os,
		itk::Indent	indent
	)		const

overrideprotectedvirtual

Reimplemented from mitk::BaseGeometry.

Definition at line 613 of file mitkSlicedGeometry3D.cpp.

void mitk::SlicedGeometry3D::ReinitializePlanes	(	const Point3D &	center,
		const Point3D &	referencePoint
	)

protectedvirtual

Reinitialize plane stack after rotation. More precisely, the first plane of the stack needs to spatially aligned, in two respects:

Re-alignment with respect to the dataset center; this is necessary since the distance from the first plane to the center could otherwise continuously decrease or increase.
Re-alignment with respect to a given reference point; the reference point is a location which the user wants to be exactly touched by one plane of the plane stack. The first plane is minimally shifted to ensure this touching. Usually, the reference point would be the point around which the geometry is rotated.

Definition at line 292 of file mitkSlicedGeometry3D.cpp.

References mitk::BaseGeometry::GetAxisVector(), mitk::PlaneGeometry::GetNormal(), mitk::BaseGeometry::GetOrigin(), mitk::BaseGeometry::SetOrigin(), and mitk::PlaneGeometry::SignedDistanceFromPlane().

void mitk::SlicedGeometry3D::SetDirectionVector ( const mitk::Vector3D & directionVector )

virtual

Set/Get the vector between slices for the evenly-spaced case (m_EvenlySpaced==true).

If the direction-vector is (0,0,0) (the default) and the first 2D geometry is a PlaneGeometry, then the direction-vector will be calculated from the plane normal.

See also: m_DirectionVector

Definition at line 579 of file mitkSlicedGeometry3D.cpp.

Referenced by SlicedGeometry3D().

void mitk::SlicedGeometry3D::SetEvenlySpaced ( bool on = true )

virtual

Definition at line 570 of file mitkSlicedGeometry3D.cpp.

void mitk::SlicedGeometry3D::SetGeometry2D	(	PlaneGeometry *	geo,
		int	s
	)

inline

Deprecated:: (as of 2014_10) Please use SetPlaneGeometry

Definition at line 103 of file mitkSlicedGeometry3D.h.

void mitk::SlicedGeometry3D::SetImageGeometry ( const bool _arg )

overridevirtual

Define that this BaseGeometry is refering to an Image.

A geometry referring to an Image needs a slightly different definition of the position of the corners (see GetCornerPoint). The position of a voxel is defined by the position of its center. If we would use the origin (position of the (center of) the first voxel) as a corner and display this point, it would seem to be not at the corner but a bit within the image. Even worse for the opposite corner of the image: here the corner would appear outside the image (by half of the voxel diameter). Thus, we have to correct for this and to be able to do that, we need to know that the BaseGeometry is referring to an Image.

Reimplemented from mitk::BaseGeometry.

Definition at line 428 of file mitkSlicedGeometry3D.cpp.

References mitk::BaseGeometry::SetImageGeometry().

bool mitk::SlicedGeometry3D::SetPlaneGeometry	(	mitk::PlaneGeometry *	geometry2D,
		int	s
	)

virtual

Set PlaneGeometry of slice s.

Definition at line 132 of file mitkSlicedGeometry3D.cpp.

References mitk::PlaneGeometry::SetReferenceGeometry().

Referenced by SlicedGeometry3D().

void mitk::SlicedGeometry3D::SetReferenceGeometry ( const BaseGeometry * referenceGeometry )

virtual

Definition at line 468 of file mitkSlicedGeometry3D.cpp.

void mitk::SlicedGeometry3D::SetSliceNavigationController ( mitk::SliceNavigationController * snc )

virtual

Set the SliceNavigationController corresponding to this sliced geometry.

The SNC needs to be informed when the number of slices in the geometry changes, which can occur whenthe slices are re-oriented by rotation.

Definition at line 560 of file mitkSlicedGeometry3D.cpp.

Member Data Documentation

const std::string mitk::SlicedGeometry3D::DIRECTION_VECTOR

static

Definition at line 177 of file mitkSlicedGeometry3D.h.

const std::string mitk::SlicedGeometry3D::EVENLY_SPACED

static

Definition at line 178 of file mitkSlicedGeometry3D.h.

mitk::Vector3D mitk::SlicedGeometry3D::m_DirectionVector

mutableprotected

Vector between slices for the evenly-spaced case (m_EvenlySpaced==true). If the direction-vector is (0,0,0) (the default) and the first 2D geometry is a PlaneGeometry, then the direction-vector will be calculated from the plane normal.

Definition at line 303 of file mitkSlicedGeometry3D.h.

Referenced by SlicedGeometry3D().

bool mitk::SlicedGeometry3D::m_EvenlySpaced

protected

If (a) m_EvenlySpaced==true, (b) we don't have a PlaneGeometry stored for the requested slice, and (c) the first slice (s=0) is a PlaneGeometry instance, then we calculate the geometry of the requested as the plane of the first slice shifted by m_Spacing.z*s in the direction of m_DirectionVector.

See also: GetPlaneGeometry

Definition at line 295 of file mitkSlicedGeometry3D.h.

Referenced by SlicedGeometry3D().

std::vector<PlaneGeometry::Pointer> mitk::SlicedGeometry3D::m_PlaneGeometries

mutableprotected

Container for the 2D-geometries contained within this SliceGeometry3D.

Definition at line 284 of file mitkSlicedGeometry3D.h.

Referenced by SlicedGeometry3D().

const mitk::BaseGeometry* mitk::SlicedGeometry3D::m_ReferenceGeometry

protected

Underlying BaseGeometry for this SlicedGeometry

Definition at line 309 of file mitkSlicedGeometry3D.h.

mitk::SliceNavigationController* mitk::SlicedGeometry3D::m_SliceNavigationController

protected

SNC correcsponding to this geometry; used to reflect changes in the number of slices due to rotation.

Definition at line 314 of file mitkSlicedGeometry3D.h.

unsigned int mitk::SlicedGeometry3D::m_Slices

protected

Number of slices this SliceGeometry3D is descibing.

Definition at line 306 of file mitkSlicedGeometry3D.h.

Referenced by SlicedGeometry3D().

const std::string mitk::SlicedGeometry3D::SLICES

static

Definition at line 176 of file mitkSlicedGeometry3D.h.

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

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation