BaseGeometry Describes the geometry of a data object. More...

#include <mitkBaseGeometry.h>

Inheritance diagram for mitk::BaseGeometry:

[legend]

Collaboration diagram for mitk::BaseGeometry:

Public Types
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

virtual const char *	GetClassName () const

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 ()

const vtkMatrix4x4 *	GetVtkMatrix () const

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=false)
	Compose new IndexToWorldTransform with a given transform. More...

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

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

void	ExecuteOperation (Operation *operation) override
	executes affine operations (translate, rotate, scale) 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 ((continuous!)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 void	ChangeImageGeometryConsideringOriginOffset (const bool isAnImageGeometry)
	When switching from an Image Geometry to a normal Geometry (and the other way around), you have to. More...

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

virtual void	SetImageGeometry (bool _arg)
	Define that this BaseGeometry is referring to an Image. More...

virtual void	ImageGeometryOn ()

virtual void	ImageGeometryOff ()

const GeometryTransformHolder *	GetGeometryTransformHolder () const

void	MapAxesToOrientations (int axes[]) const
	One to one mapping of axes to world orientations. More...

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

Static Public Member Functions
static const char *	GetStaticNameOfClass ()

Protected Member Functions
	BaseGeometry ()

	BaseGeometry (const BaseGeometry &other)

	~BaseGeometry () override

itk::LightObject::Pointer	InternalClone () const override=0

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

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	PreSetSpacing (const mitk::Vector3D &)
	PreSetSpacing. More...

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

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

Static Protected Member Functions
static const std::string	GetTransformAsString (TransformType *transformType)

Detailed Description

BaseGeometry Describes the geometry of a data object.

The class holds

a bounding box which is axes-parallel in intrinsic coordinates (often integer indices of pixels), to be accessed by GetBoundingBox()
a transform to convert intrinsic coordinates into a world-coordinate system with coordinates in millimeters and milliseconds (all are floating point values), to be accessed by GetIndexToWorldTransform()
an origin and spacing to define the geometry

BaseGeometry and its sub-classes allow converting between intrinsic coordinates (called index or unit coordinates) and world-coordinates (called world or mm coordinates), e.g. WorldToIndex. In case you need integer index coordinates, provide an mitk::Index3D (or itk::Index) as target variable to WorldToIndex, otherwise you will get a continuous index (floating point values).

An important sub-class is SlicedGeometry3D, which describes data objects consisting of slices, e.g., objects of type Image. Conversions between world coordinates (in mm) and unit coordinates (e.g., pixels in the case of an Image) can be performed.

For more information on related classes, see Geometry Classes.

BaseGeometry instances referring to an Image need a slightly different definition of corners, see SetImageGeometry. This is usually automatically called by Image.

BaseGeometry 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 itk::ProcessObject::GenerateOutputInformation(), itk::DataObject::CopyInformation() and itk::DataObject::UpdateOutputInformation().

At least, it can return the bounding box of the data object.

The BaseGeometry class is an abstract class. The most simple implementation is the subclass Geometry3D.

Rule: everything is in mm (ms) if not stated otherwise.

Definition at line 94 of file mitkBaseGeometry.h.

Member Typedef Documentation

◆ BoundingBoxPointer

typedef BoundingBoxType::Pointer mitk::BaseGeometry::BoundingBoxPointer

Definition at line 105 of file mitkBaseGeometry.h.

◆ BoundingBoxType

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

Definition at line 103 of file mitkBaseGeometry.h.

◆ BoundsArrayType

typedef BoundingBoxType::BoundsArrayType mitk::BaseGeometry::BoundsArrayType

Definition at line 104 of file mitkBaseGeometry.h.

◆ ConstPointer

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

Definition at line 97 of file mitkBaseGeometry.h.

◆ Pointer

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

Definition at line 97 of file mitkBaseGeometry.h.

◆ Self

typedef BaseGeometry mitk::BaseGeometry::Self

Definition at line 97 of file mitkBaseGeometry.h.

◆ Superclass

typedef itk::Object mitk::BaseGeometry::Superclass

Definition at line 97 of file mitkBaseGeometry.h.

◆ TransformType

typedef GeometryTransformHolder::TransformType mitk::BaseGeometry::TransformType

Definition at line 98 of file mitkBaseGeometry.h.

Constructor & Destructor Documentation

◆ BaseGeometry() [1/2]

mitk::BaseGeometry::BaseGeometry ( )

protected

◆ BaseGeometry() [2/2]

mitk::BaseGeometry::BaseGeometry ( const BaseGeometry & other )

protected

◆ ~BaseGeometry()

mitk::BaseGeometry::~BaseGeometry ( )

overrideprotected

Member Function Documentation

◆ _SetSpacing()

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

protected

◆ CalculateBoundingBoxRelativeToTransform()

mitk::BoundingBox::Pointer mitk::BaseGeometry::CalculateBoundingBoxRelativeToTransform ( const mitk::AffineTransform3D * transform ) const

Calculates a bounding-box around the geometry relative to a coordinate system defined by a transform.

◆ ChangeImageGeometryConsideringOriginOffset()

virtual void mitk::BaseGeometry::ChangeImageGeometryConsideringOriginOffset ( const bool isAnImageGeometry )

virtual

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

Reimplemented in mitk::SlicedGeometry3D.

◆ CheckBounds()

virtual void mitk::BaseGeometry::CheckBounds ( const BoundsArrayType & )

inlineprotectedvirtual

CheckBounds.

This function is called in SetBounds. Assertions can be implemented in this function (see PlaneGeometry.cpp). If you implement this function in a subclass, make sure, that all classes were your class inherits from have an implementation of CheckBounds (e.g. inheritance BaseGeometry <- A <- B. Implementation of CheckBounds in class B needs implementation in A as

Reimplemented in mitk::PlaneGeometry.

Definition at line 584 of file mitkBaseGeometry.h.

◆ CheckIndexToWorldTransform()

virtual void mitk::BaseGeometry::CheckIndexToWorldTransform ( mitk::AffineTransform3D * )

inlineprotectedvirtual

CheckIndexToWorldTransform.

This function is called in SetIndexToWorldTransform. Assertions can be implemented in this function (see

Reimplemented in mitk::PlaneGeometry.

Definition at line 592 of file mitkBaseGeometry.h.

◆ Clone()

Pointer mitk::BaseGeometry::Clone ( ) const

◆ Compose() [1/2]

void mitk::BaseGeometry::Compose	(	const TransformType *	other,
		bool	pre = `false`
	)

Compose new IndexToWorldTransform with a given transform.

This method composes m_IndexToWorldTransform with another transform, modifying self to be the composition of self and other. If the argument pre is true, then other is precomposed with self; that is, the resulting transformation consists of first applying other to the source, followed by self. If pre is false or omitted, then other is post-composed with self; that is the resulting transformation consists of first applying self to the source, followed by other. This method also changes m_spacing.

◆ Compose() [2/2]

void mitk::BaseGeometry::Compose	(	const vtkMatrix4x4 *	vtkmatrix,
		bool	pre = `false`
	)

Compose new IndexToWorldTransform with a given vtkMatrix4x4.

Converts the vtkMatrix4x4 into a itk-transform and calls the previous method.

◆ ExecuteOperation()

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

overridevirtual

executes affine operations (translate, rotate, scale)

Implements mitk::OperationActor.

Reimplemented in mitk::PlaneGeometry, and mitk::SlicedGeometry3D.

◆ GetAxisVector()

Vector3D mitk::BaseGeometry::GetAxisVector ( unsigned int direction ) const

Get vector along bounding-box in the specified direction in mm.

The length of the vector is the size of the bounding-box in the specified direction in mm

See also: GetMatrixColumn

◆ GetBoundingBox()

virtual const BoundingBoxType* mitk::BaseGeometry::GetBoundingBox ( )

virtual

Get the bounding box

Referenced by mitk::PlaneClipping::CalculateClippedPlaneBounds().

◆ GetBounds()

const BoundsArrayType mitk::BaseGeometry::GetBounds ( ) const

◆ GetCenter()

Point3D mitk::BaseGeometry::GetCenter ( ) const

Get the center of the bounding-box in mm.

◆ GetClassHierarchy()

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

inlinevirtual

Reimplemented in mitk::PlaneGeometry, mitk::SlicedGeometry3D, mitk::Geometry3D, mitk::LandmarkProjectorBasedCurvedGeometry, and mitk::ThinPlateSplineCurvedGeometry.

Definition at line 97 of file mitkBaseGeometry.h.

◆ GetClassName()

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

virtual

Reimplemented in mitk::PlaneGeometry, mitk::SlicedGeometry3D, mitk::Geometry3D, mitk::LandmarkProjectorBasedCurvedGeometry, and mitk::ThinPlateSplineCurvedGeometry.

◆ GetCornerPoint() [1/2]

Point3D mitk::BaseGeometry::GetCornerPoint	(	bool	xFront = `true`,
		bool	yFront = `true`,
		bool	zFront = `true`
	)		const

Get the position of a corner (in world coordinates)

See SetImageGeometry for how a corner is defined on images.

◆ GetCornerPoint() [2/2]

Point3D mitk::BaseGeometry::GetCornerPoint ( int id ) const

Get the position of the corner number id (in world coordinates)

See SetImageGeometry for how a corner is defined on images.

◆ GetDiagonalLength()

double mitk::BaseGeometry::GetDiagonalLength ( ) const

Get the length of the diagonal of the bounding-box in mm.

◆ GetDiagonalLength2()

double mitk::BaseGeometry::GetDiagonalLength2 ( ) const

Get the squared length of the diagonal of the bounding-box in mm.

◆ GetExtent()

ScalarType mitk::BaseGeometry::GetExtent ( unsigned int direction ) const

Set the time bounds (in ms)

Get the extent of the bounding box

◆ GetExtentInMM()

ScalarType mitk::BaseGeometry::GetExtentInMM ( int direction ) const

Get the extent of the bounding-box in the specified direction in mm.

Equals length of GetAxisVector(direction).

◆ GetFrameOfReferenceID()

virtual unsigned int mitk::BaseGeometry::GetFrameOfReferenceID ( ) const

virtual

Get the DICOM FrameOfReferenceID referring to the used world coordinate system.

◆ GetGeometryTransformHolder()

const GeometryTransformHolder* mitk::BaseGeometry::GetGeometryTransformHolder ( ) const

◆ GetImageGeometry()

virtual bool mitk::BaseGeometry::GetImageGeometry ( ) const

virtual

Is this an ImageGeometry?

For more information, see SetImageGeometry

Referenced by mitk::PlaneClipping::CalculateClippedPlaneBounds().

◆ GetIndexToWorldTransform() [1/2]

mitk::AffineTransform3D* mitk::BaseGeometry::GetIndexToWorldTransform ( )

Get the transformation used to convert from index to world coordinates.

Referenced by mitk::GetRotation(), mitk::GetWorldToItkPhysicalTransform(), and mitk::Image::InitializeByItk().

◆ GetIndexToWorldTransform() [2/2]

const mitk::AffineTransform3D* mitk::BaseGeometry::GetIndexToWorldTransform ( ) const

Get the transformation used to convert from index to world coordinates.

◆ GetIndexToWorldTransformLastModified()

virtual unsigned long mitk::BaseGeometry::GetIndexToWorldTransformLastModified ( ) const

virtual

◆ GetMatrixColumn()

VnlVector mitk::BaseGeometry::GetMatrixColumn ( unsigned int direction ) const

Get a VnlVector along bounding-box in the specified direction, length is spacing.

See also: GetAxisVector

◆ GetNDimensions()

virtual unsigned int mitk::BaseGeometry::GetNDimensions ( ) const

protectedvirtual

◆ GetOrigin()

const Point3D mitk::BaseGeometry::GetOrigin ( ) const

Get the origin, e.g. the upper-left corner of the plane.

Referenced by mitk::PlaneGeometry::SignedDistanceFromPlane().

◆ GetOriginVnl()

VnlVector mitk::BaseGeometry::GetOriginVnl ( ) const

Get the origin as VnlVector.

See also: GetOrigin

◆ GetSpacing()

const mitk::Vector3D mitk::BaseGeometry::GetSpacing ( ) const

Get the spacing (size of a pixel).

Referenced by mitk::PlaneClipping::CalculateClippedPlaneBounds(), and mitk::GetRotation().

◆ GetStaticNameOfClass()

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

inlinestatic

Definition at line 97 of file mitkBaseGeometry.h.

◆ GetTransformAsString()

static const std::string mitk::BaseGeometry::GetTransformAsString ( TransformType * transformType )

staticprotected

◆ GetVtkMatrix() [1/2]

vtkMatrix4x4* mitk::BaseGeometry::GetVtkMatrix ( )

◆ GetVtkMatrix() [2/2]

const vtkMatrix4x4* mitk::BaseGeometry::GetVtkMatrix ( ) const

◆ GetVtkTransform()

vtkLinearTransform* mitk::BaseGeometry::GetVtkTransform ( ) const

Get the m_IndexToWorldTransform as a vtkLinearTransform.

Referenced by mitk::PlaneClipping::CalculateClippedPlaneBounds().

◆ ImageGeometryOff()

virtual void mitk::BaseGeometry::ImageGeometryOff ( )

virtual

◆ ImageGeometryOn()

virtual void mitk::BaseGeometry::ImageGeometryOn ( )

virtual

◆ IndexToWorld() [1/4]

template<unsigned int VIndexDimension>

void mitk::BaseGeometry::IndexToWorld	(	const itk::Index< VIndexDimension > &	index,
		mitk::Point3D &	pt_mm
	)		const

inline

Convert (discrete) index coordinates of a point to world coordinates (in mm) For further information about coordinates types, please see the Geometry documentation.

Definition at line 298 of file mitkBaseGeometry.h.

◆ IndexToWorld() [2/4]

void mitk::BaseGeometry::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)

Deprecated:: First parameter (Point3D) is not used. If possible, please use void IndexToWorld(const

◆ IndexToWorld() [3/4]

void mitk::BaseGeometry::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.

◆ IndexToWorld() [4/4]

void mitk::BaseGeometry::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.

◆ Initialize()

void mitk::BaseGeometry::Initialize ( )

Initialize the BaseGeometry.

◆ InitializeGeometry()

void mitk::BaseGeometry::InitializeGeometry ( Self * newGeometry ) const

◆ InternalClone()

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

overrideprotectedpure virtual

Implemented in mitk::PlaneGeometry, mitk::SlicedGeometry3D, mitk::AbstractTransformGeometry, mitk::Geometry3D, mitk::LandmarkProjectorBasedCurvedGeometry, and mitk::ThinPlateSplineCurvedGeometry.

◆ Is2DConvertable()

virtual bool mitk::BaseGeometry::Is2DConvertable ( )

virtual

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.

◆ IsBoundingBoxNull()

bool mitk::BaseGeometry::IsBoundingBoxNull ( ) const

protected

◆ IsIndexInside() [1/2]

template<unsigned int VIndexDimension>

bool mitk::BaseGeometry::IsIndexInside ( const itk::Index< VIndexDimension > & index ) const

inline

Convenience method for working with ITK indices.

Definition at line 492 of file mitkBaseGeometry.h.

◆ IsIndexInside() [2/2]

bool mitk::BaseGeometry::IsIndexInside ( const mitk::Point3D & index ) const

Test whether the point p ((continuous!)index coordinates in units) is inside the bounding box.

◆ IsIndexToWorldTransformNull()

bool mitk::BaseGeometry::IsIndexToWorldTransformNull ( ) const

protected

◆ IsInside()

bool mitk::BaseGeometry::IsInside ( const mitk::Point3D & p ) const

Test whether the point p (world coordinates in mm) is inside the bounding box.

◆ IsValid()

virtual bool mitk::BaseGeometry::IsValid ( ) const

virtual

Is this BaseGeometry in a state that is valid?

This function returns always true in the BaseGeometry class. Other implementations are possible in subclasses.

Reimplemented in mitk::ThinPlateSplineCurvedGeometry.

◆ ItkPhysicalPointToWorld()

template<class TCoordRep >

void mitk::BaseGeometry::ItkPhysicalPointToWorld	(	const itk::Point< TCoordRep, 3 > &	itkPhysicalPoint,
		mitk::Point3D &	pt_mm
	)		const

inline

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)

For more information, see WorldToItkPhysicalPoint.

Definition at line 338 of file mitkBaseGeometry.h.

References mitk::vtk2itk().

◆ MapAxesToOrientations()

void mitk::BaseGeometry::MapAxesToOrientations ( int axes[] ) const

One to one mapping of axes to world orientations.

The result is stored in the output argument that must be an array of three int values. The elements of the array will be the axis indices that correspond to the sagittal, coronal and axial orientations, in this order. It is guaranteed that each axis will be mapped to different orientations.

Parameters

axes	Output argument that will store the axis indices for each orientation.

◆ Modified()

void mitk::BaseGeometry::Modified ( ) const

override

Overload of function Modified() to prohibit several calls of Modified() using the ModifiedLock class.

For the use of Modified(), see class ModifiedLock.

◆ PreSetSpacing()

virtual void mitk::BaseGeometry::PreSetSpacing ( const mitk::Vector3D & )

inlineprotectedvirtual

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 in mitk::PlaneGeometry, mitk::SlicedGeometry3D, mitk::AbstractTransformGeometry, mitk::Geometry3D, mitk::LandmarkProjectorBasedCurvedGeometry, and mitk::ThinPlateSplineCurvedGeometry.

Definition at line 574 of file mitkBaseGeometry.h.

◆ PrintSelf()

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

overrideprotected

◆ SetBounds()

void mitk::BaseGeometry::SetBounds ( const BoundsArrayType & bounds )

Set the bounding box (in index/unit coordinates)

Only possible via the BoundsArray to make clear that a copy of the bounding-box is stored, not a reference to it.

◆ SetExtentInMM()

void mitk::BaseGeometry::SetExtentInMM	(	int	direction,
		ScalarType	extentInMM
	)

Set the extent of the bounding-box in the specified direction in mm.

Note: This changes the matrix in the transform, not the bounds, which are given in units!

◆ SetFloatBounds() [1/2]

void mitk::BaseGeometry::SetFloatBounds ( const double bounds[6] )

Set the bounding box (in index/unit coordinates) via a double array.

◆ SetFloatBounds() [2/2]

void mitk::BaseGeometry::SetFloatBounds ( const float bounds[6] )

Set the bounding box (in index/unit coordinates) via a float array.

◆ SetFrameOfReferenceID()

virtual void mitk::BaseGeometry::SetFrameOfReferenceID ( unsigned int _arg )

virtual

Set the DICOM FrameOfReferenceID referring to the used world coordinate system.

◆ SetIdentity()

void mitk::BaseGeometry::SetIdentity ( )

Set the transform to identity, the spacing to 1 and origin to 0.

◆ SetImageGeometry()

virtual void mitk::BaseGeometry::SetImageGeometry ( bool _arg )

virtual

Define that this BaseGeometry is referring 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 in mitk::SlicedGeometry3D.

◆ SetIndexToWorldTransform()

void mitk::BaseGeometry::SetIndexToWorldTransform ( mitk::AffineTransform3D * transform )

◆ SetIndexToWorldTransformByVtkMatrix()

void mitk::BaseGeometry::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.

See also: SetIndexToWorldTransform

◆ SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing()

void mitk::BaseGeometry::SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing ( vtkMatrix4x4 * vtkmatrix )

Convenience method for setting the ITK transform (m_IndexToWorldTransform) via an vtkMatrix4x4. This function keeps the original spacing.

See also: SetIndexToWorldTransform

◆ SetIndexToWorldTransformWithoutChangingSpacing()

void mitk::BaseGeometry::SetIndexToWorldTransformWithoutChangingSpacing ( mitk::AffineTransform3D * transform )

◆ SetOrigin()

void mitk::BaseGeometry::SetOrigin ( const Point3D & origin )

Set the origin, i.e. the upper-left corner of the plane.

Referenced by mitk::Image::InitializeByItk().

◆ SetSpacing()

void mitk::BaseGeometry::SetSpacing	(	const mitk::Vector3D &	aSpacing,
		bool	enforceSetSpacing = `false`
	)

Set the spacing (m_Spacing).

The spacing is also changed in the IndexToWorldTransform.

Referenced by mitk::Image::InitializeByItk().

◆ SetVtkMatrixDeepCopy()

void mitk::BaseGeometry::SetVtkMatrixDeepCopy ( vtkTransform * vtktransform )

protected

◆ Translate()

void mitk::BaseGeometry::Translate ( const Vector3D & vector )

Translate the origin by a vector.

◆ WorldToIndex() [1/4]

void mitk::BaseGeometry::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.

Deprecated:: First parameter (Point3D) is not used. If possible, please use void WorldToIndex(const

◆ WorldToIndex() [2/4]

template<unsigned int VIndexDimension>

void mitk::BaseGeometry::WorldToIndex	(	const mitk::Point3D &	pt_mm,
		itk::Index< VIndexDimension > &	index
	)		const

inline

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.

Definition at line 266 of file mitkBaseGeometry.h.

◆ WorldToIndex() [3/4]

void mitk::BaseGeometry::WorldToIndex	(	const mitk::Point3D &	pt_mm,
		mitk::Point3D &	pt_units
	)		const

Convert world coordinates (in mm) of a point to (continuous!) index coordinates.

Warning: If you need (discrete) integer index coordinates (e.g., for iterating easily over an image), use WorldToIndex(const mitk::Point3D& pt_mm, itk::Index<VIndexDimension> &index). For further information about coordinates types, please see the Geometry documentation

Referenced by mitk::ImagePixelWriteAccessor< TPixel, VDimension >::GetPixelByWorldCoordinates(), and mitk::ImagePixelReadAccessor< TPixel, VDimension >::GetPixelByWorldCoordinates().

◆ WorldToIndex() [4/4]

void mitk::BaseGeometry::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.

◆ WorldToItkPhysicalPoint()

template<class TCoordRep >

void mitk::BaseGeometry::WorldToItkPhysicalPoint	(	const mitk::Point3D &	pt_mm,
		itk::Point< TCoordRep, 3 > &	itkPhysicalPoint
	)		const

inline

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)

This method is useful if you have want to access an mitk::Image via an itk::Image. ITK v3.8 and older did not support rotated (tilted) images, i.e., ITK images are always parallel to the coordinate axes. When accessing a (possibly rotated) mitk::Image via an itk::Image the rotational part of the transformation in the BaseGeometry is simply discarded; in other word: only the origin and spacing is used by ITK, not the complete matrix available in MITK. With WorldToItkPhysicalPoint you can convert an MITK world coordinate (including the rotation) into a coordinate that can be used with the ITK image as a ITK physical coordinate (excluding the rotation).

Definition at line 360 of file mitkBaseGeometry.h.

References mitk::vtk2itk().

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

mitkBaseGeometry.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Detailed Description

Member Typedef Documentation

◆ BoundingBoxPointer

◆ BoundingBoxType

◆ BoundsArrayType

◆ ConstPointer

◆ Pointer

◆ Self

◆ Superclass

◆ TransformType

Constructor & Destructor Documentation

◆ BaseGeometry() [1/2]

◆ BaseGeometry() [2/2]

◆ ~BaseGeometry()

Member Function Documentation

◆ _SetSpacing()

◆ CalculateBoundingBoxRelativeToTransform()

◆ ChangeImageGeometryConsideringOriginOffset()

◆ CheckBounds()

◆ CheckIndexToWorldTransform()

◆ Clone()

◆ Compose() [1/2]

◆ Compose() [2/2]

◆ ExecuteOperation()

◆ GetAxisVector()

◆ GetBoundingBox()

◆ GetBounds()

◆ GetCenter()

◆ GetClassHierarchy()

◆ GetClassName()

◆ GetCornerPoint() [1/2]

◆ GetCornerPoint() [2/2]

◆ GetDiagonalLength()

◆ GetDiagonalLength2()

◆ GetExtent()

◆ GetExtentInMM()

◆ GetFrameOfReferenceID()

◆ GetGeometryTransformHolder()

◆ GetImageGeometry()

◆ GetIndexToWorldTransform() [1/2]

◆ GetIndexToWorldTransform() [2/2]

◆ GetIndexToWorldTransformLastModified()

◆ GetMatrixColumn()

◆ GetNDimensions()

◆ GetOrigin()

◆ GetOriginVnl()

◆ GetSpacing()

◆ GetStaticNameOfClass()

◆ GetTransformAsString()

◆ GetVtkMatrix() [1/2]

◆ GetVtkMatrix() [2/2]

◆ GetVtkTransform()

◆ ImageGeometryOff()

◆ ImageGeometryOn()

◆ IndexToWorld() [1/4]

◆ IndexToWorld() [2/4]

◆ IndexToWorld() [3/4]

◆ IndexToWorld() [4/4]

◆ Initialize()

◆ InitializeGeometry()

◆ InternalClone()

◆ Is2DConvertable()

◆ IsBoundingBoxNull()

◆ IsIndexInside() [1/2]

◆ IsIndexInside() [2/2]

◆ IsIndexToWorldTransformNull()

◆ IsInside()

◆ IsValid()

◆ ItkPhysicalPointToWorld()

◆ MapAxesToOrientations()

◆ Modified()

◆ PreSetSpacing()

◆ PrintSelf()

◆ SetBounds()

◆ SetExtentInMM()