Abstract base class describing the geometry of a data object. More...

#include <mitkBaseGeometry.h>

Inheritance diagram for mitk::BaseGeometry:

[legend]

Collaboration diagram for mitk::BaseGeometry:

Public Types
typedef GeometryTransformHolder::TransformType	TransformType
	Affine transform type used for index-to-world mapping. More...

typedef itk::BoundingBox< unsigned long, 3, ScalarType >	BoundingBoxType
	3D bounding box type parameterized with ScalarType. More...

typedef BoundingBoxType::BoundsArrayType	BoundsArrayType
	Fixed-size array of six ScalarType values representing axis-aligned bounds [xmin,xmax,ymin,ymax,zmin,zmax]. More...

typedef BoundingBoxType::Pointer	BoundingBoxPointer
	Smart-pointer type for BoundingBoxType. More...

Public Member Functions
	mitkClassMacroItkParent (BaseGeometry, itk::Object)

Pointer	Clone () const

Point3D	GetOrigin () const
	Get the origin of the geometry in world coordinates (mm). More...

void	SetOrigin (const Point3D &origin)
	Set the origin of the geometry in world coordinates (mm). More...

mitk::Vector3D	GetSpacing () const
	Get the spacing (voxel size) in mm per unit for each axis. More...

void	SetSpacing (const mitk::Vector3D &aSpacing, bool enforceSetSpacing=false)
	Set the spacing (voxel size) for each axis. More...

VnlVector	GetOriginVnl () const
	Get the origin as a VNL vector. More...

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

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

virtual unsigned long	GetIndexToWorldTransformLastModified () const
	Get the last-modified timestamp of the IndexToWorldTransform. More...

void	Modified () const override
	Overloaded Modified() to support the ModifiedLock mechanism. More...

virtual bool	IsValid () const
	Check whether this geometry is in a valid state. More...

void	Initialize ()
	Initialize the geometry to default values. More...

void	InitializeGeometry (Self *newGeometry) const
	Copy the essential geometry properties into another instance. More...

mitk::AffineTransform3D *	GetIndexToWorldTransform ()
	Get the affine transform that maps index coordinates to world coordinates. More...

const mitk::AffineTransform3D *	GetIndexToWorldTransform () const
	Get the affine transform that maps index coordinates to world coordinates (const). More...

void	SetIndexToWorldTransform (mitk::AffineTransform3D *transform)
	Set the affine transform for index-to-world coordinate mapping. More...

void	SetIndexToWorldTransformByVtkMatrix (vtkMatrix4x4 *vtkmatrix)
	Set the IndexToWorldTransform via a vtkMatrix4x4. More...

void	SetIndexToWorldTransformWithoutChangingSpacing (mitk::AffineTransform3D *transform)
	Set the IndexToWorldTransform while preserving the current spacing. More...

void	SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing (vtkMatrix4x4 *vtkmatrix)
	Set the IndexToWorldTransform via a vtkMatrix4x4 while preserving spacing. More...

vtkMatrix4x4 *	GetVtkMatrix ()
	Get the IndexToWorldTransform as a 4x4 VTK matrix. More...

const vtkMatrix4x4 *	GetVtkMatrix () const
	Get the IndexToWorldTransform as a 4x4 VTK matrix (const). More...

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

void	SetIdentity ()
	Reset the geometry to identity. More...

void	Compose (const TransformType *other, bool pre=false)
	Compose the IndexToWorldTransform with another transform. More...

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

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

void	ExecuteOperation (Operation *operation) override
	Execute an affine operation (translate, rotate, scale) on this geometry. More...

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

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

template<unsigned int VIndexDimension>
void	WorldToIndex (const mitk::Point3D &pt_mm, itk::Index< VIndexDimension > &index) const
	Convert world coordinates (mm) of a point to discrete (integer) index coordinates. More...

void	IndexToWorld (const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const
	Convert index coordinates of a vector to world coordinates (mm). 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 (mm). More...

template<unsigned int VIndexDimension>
void	IndexToWorld (const itk::Index< VIndexDimension > &index, mitk::Point3D &pt_mm) const
	Convert discrete (itk::Index) index coordinates of a point to world coordinates (mm). More...

template<class TCoordRep >
void	ItkPhysicalPointToWorld (const itk::Point< TCoordRep, 3 > &itkPhysicalPoint, mitk::Point3D &pt_mm) const
	Convert an ITK physical point to MITK world coordinates. More...

template<class TCoordRep >
void	WorldToItkPhysicalPoint (const mitk::Point3D &pt_mm, itk::Point< TCoordRep, 3 > &itkPhysicalPoint) const
	Convert MITK world coordinates to ITK physical coordinates. More...

virtual const BoundingBoxType *	GetBoundingBox ()
	Get the bounding box in index/unit coordinates. More...

const BoundsArrayType	GetBounds () const
	Get the bounding box bounds as a BoundsArrayType in index/unit coordinates. More...

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

void	SetFloatBounds (const float bounds[6])
	Set the bounding box via a float array. More...

void	SetFloatBounds (const double bounds[6])
	Set the bounding box via a double array. More...

VnlVector	GetMatrixColumn (unsigned int direction) const
	Get a column of the IndexToWorldTransform matrix as a VnlVector. More...

mitk::BoundingBox::Pointer	CalculateBoundingBoxRelativeToTransform (const mitk::AffineTransform3D *transform) const
	Calculate a bounding box relative to a given 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 mm along the specified direction. More...

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

virtual bool	Is2DConvertable ()
	Check if this geometry can be converted to 2D without information loss. More...

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

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

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

Point3D	GetCornerPoint (int id) const
	Get the position of 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 mm along the specified direction. More...

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

bool	IsIndexInside (const mitk::Point3D &index) const
	Test whether a point in continuous index coordinates lies inside the bounding box. More...

template<unsigned int VIndexDimension>
bool	IsIndexInside (const itk::Index< VIndexDimension > &index) const
	Test whether a discrete ITK index lies inside the bounding box. More...

Point3D	ClampPoint (const Point3D &point) const
	Clamp a point to lie within the geometry's world-coordinate bounds. More...

virtual void	ChangeImageGeometryConsideringOriginOffset (const bool isAnImageGeometry)
	Switch between image geometry and normal geometry with origin correction. More...

virtual bool	GetImageGeometry () const
	Query whether this geometry refers to an image. More...

virtual void	SetImageGeometry (bool _arg)
	Define that this BaseGeometry refers to an image. More...

virtual void	ImageGeometryOn ()
	Toggle macro for ImageGeometry (ImageGeometryOn/ImageGeometryOff). More...

virtual void	ImageGeometryOff ()

const GeometryTransformHolder *	GetGeometryTransformHolder () const
	Get the internal GeometryTransformHolder. More...

void	MapAxesToOrientations (int axes[]) const
	Map geometry axes to anatomical orientations (sagittal, coronal, axial). More...

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

Protected Member Functions
	BaseGeometry ()

	BaseGeometry (const BaseGeometry &other)

	~BaseGeometry () override

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

Abstract base class describing the geometry of a data object.

BaseGeometry stores the spatial metadata that maps between intrinsic (index / unit) coordinates and world coordinates (in millimeters). It holds:

An axes-parallel bounding box in intrinsic coordinates (often integer pixel indices), accessible via GetBoundingBox().
An affine transform (IndexToWorldTransform) that converts intrinsic coordinates into the world-coordinate system (floating-point values in mm), accessible via GetIndexToWorldTransform().
An origin and spacing that, together with the transform, fully define the geometry.

Coordinate conversion is provided through WorldToIndex() and IndexToWorld(). When integer index coordinates are needed (e.g. for pixel iteration), pass an itk::Index as target to WorldToIndex(); otherwise a continuous (floating-point) index is returned.

An important sub-class is SlicedGeometry3D, which describes data objects consisting of slices, e.g. objects of type Image.

BaseGeometry instances referring to an Image need a slightly different definition of corners – see SetImageGeometry(). This flag is usually set automatically by Image.

Geometries must be initialized in GenerateOutputInformation() of BaseProcess (or CopyInformation / UpdateOutputInformation of BaseData) subclasses.

This class is abstract. The simplest concrete implementation is Geometry3D.

Note: All spatial values are in millimeters (mm) and all temporal values in milliseconds (ms) unless stated otherwise.

See also: Geometry3D, SlicedGeometry3D, PlaneGeometry, TimeGeometry

Definition at line 93 of file mitkBaseGeometry.h.

Member Typedef Documentation

◆ BoundingBoxPointer

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

Smart-pointer type for BoundingBoxType.

Definition at line 108 of file mitkBaseGeometry.h.

◆ BoundingBoxType

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

3D bounding box type parameterized with ScalarType.

Definition at line 104 of file mitkBaseGeometry.h.

◆ BoundsArrayType

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

Fixed-size array of six ScalarType values representing axis-aligned bounds [xmin,xmax,ymin,ymax,zmin,zmax].

Definition at line 106 of file mitkBaseGeometry.h.

◆ TransformType

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

Affine transform type used for index-to-world mapping.

Definition at line 102 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

Calculate a bounding box relative to a given transform.

Transforms all eight corner points of this geometry by the inverse of transform and computes an axis-aligned bounding box around the results. If transform is nullptr, the corner points in world coordinates are used directly.

Parameters

[in] transform The coordinate system transform (may be nullptr).

Returns: Smart pointer to the computed bounding box.

◆ ChangeImageGeometryConsideringOriginOffset()

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

virtual

Switch between image geometry and normal geometry with origin correction.

Image geometries use center-based voxel coordinates (origin is at voxel center), so switching to or from image geometry requires a half-voxel offset on the origin. This method toggles the ImageGeometry flag and adjusts the origin accordingly.

Parameters

[in] isAnImageGeometry true to switch to image geometry, false to switch to normal geometry.

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 835 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 843 of file mitkBaseGeometry.h.

◆ ClampPoint()

Point3D mitk::BaseGeometry::ClampPoint ( const Point3D & point ) const

Clamp a point to lie within the geometry's world-coordinate bounds.

If the given point lies outside the geometry's bounds it is projected onto the nearest boundary. If the point is already inside, it is returned unchanged.

Parameters

[in] point The point to clamp (world coordinates, mm).

Returns: The clamped point, guaranteed to lie within the bounds.

◆ Clone()

Pointer mitk::BaseGeometry::Clone ( ) const

◆ Compose() [1/2]

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

Compose the IndexToWorldTransform with another transform.

Modifies this geometry so its transform becomes the composition of itself and other.

Parameters

[in]	other	The transform to compose with.
[in]	pre	If true, other is pre-composed (applied first, then self). If false (default), other is post-composed (self first, then other).

Note: This also updates the internally stored spacing.

◆ Compose() [2/2]

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

Compose the IndexToWorldTransform with a vtkMatrix4x4.

Converts the VTK matrix into an ITK transform and calls Compose(const TransformType*, bool).

Parameters

[in]	vtkmatrix	The 4x4 VTK matrix to compose with.
[in]	pre	If true, pre-compose; if false (default), post-compose.

◆ ExecuteOperation()

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

overridevirtual

Execute an affine operation (translate, rotate, scale) on this geometry.

Supported operation types include OpMOVE, OpSCALE, OpROTATE, OpRESTOREPLANEPOSITION, and OpAPPLYTRANSFORMMATRIX.

Parameters

[in] operation The operation to execute.

See also: OperationActor

Implements mitk::OperationActor.

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

◆ GetAxisVector()

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

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

The vector's direction is the transform matrix column for that axis, and its length equals the bounding-box extent in that direction (in mm).

Parameters

[in] direction The axis (0=x, 1=y, 2=z).

Returns: The axis vector in mm.

See also: GetMatrixColumn

◆ GetBoundingBox()

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

virtual

Get the bounding box in index/unit coordinates.

Returns: Const pointer to the BoundingBoxType.

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

◆ GetBounds()

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

Get the bounding box bounds as a BoundsArrayType in index/unit coordinates.

Returns: An array of six ScalarType values [xmin,xmax,ymin,ymax,zmin,zmax].

◆ GetCenter()

Point3D mitk::BaseGeometry::GetCenter ( ) const

Get the center of the bounding box in world coordinates (mm).

For image geometries the center accounts for the half-voxel offset.

Returns: The center point.

◆ 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.

Parameters

[in]	xFront	If true, use the minimum x-bound; otherwise maximum.
[in]	yFront	If true, use the minimum y-bound; otherwise maximum.
[in]	zFront	If true, use the minimum z-bound; otherwise maximum.

Returns: The corner point in mm.

See also: SetImageGeometry

◆ GetCornerPoint() [2/2]

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

Get the position of corner number id in world coordinates.

Corners are numbered 0–7 corresponding to the eight vertices of the axis-aligned bounding box. For image geometries a half-voxel offset is applied.

Parameters

[in] id Corner index (0–7).

Returns: The corner point in mm.

Exceptions

itk::ExceptionObject if id is out of range.

See also: SetImageGeometry

◆ GetDiagonalLength()

double mitk::BaseGeometry::GetDiagonalLength ( ) const

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

Returns: Diagonal length.

See also: GetDiagonalLength2

◆ GetDiagonalLength2()

double mitk::BaseGeometry::GetDiagonalLength2 ( ) const

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

Returns: Squared diagonal length.

See also: GetDiagonalLength

◆ GetExtent()

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

Set the time bounds (in ms)

Get the extent of the bounding box in index/unit coordinates.

Parameters

[in] direction The axis (0=x, 1=y, 2=z).

Returns: Extent in units along the specified direction.

Exceptions

mitk::Exception if direction >= 3.

See also: GetExtentInMM

◆ GetExtentInMM()

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

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

This equals the length of the axis vector in that direction: GetAxisVector(direction).GetNorm().

Parameters

[in] direction The axis (0=x, 1=y, 2=z).

Returns: Extent in millimeters.

See also: GetAxisVector

◆ GetFrameOfReferenceID()

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

virtual

Get the DICOM FrameOfReferenceID referring to the world coordinate system.

Returns: The frame of reference identifier.

◆ GetGeometryTransformHolder()

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

Get the internal GeometryTransformHolder.

Returns: Const pointer to the GeometryTransformHolder.

◆ GetImageGeometry()

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

virtual

Query whether this geometry refers to an image.

Returns: true if this is an image geometry.

See also: SetImageGeometry

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

◆ GetIndexToWorldTransform() [1/2]

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

Get the affine transform that maps index coordinates to world coordinates.

Returns: Non-const pointer to the IndexToWorldTransform.

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

◆ GetIndexToWorldTransform() [2/2]

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

Get the affine transform that maps index coordinates to world coordinates (const).

Returns: Const pointer to the IndexToWorldTransform.

◆ GetIndexToWorldTransformLastModified()

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

virtual

Get the last-modified timestamp of the IndexToWorldTransform.

Returns: The modification time as an unsigned long.

◆ GetMatrixColumn()

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

Get a column of the IndexToWorldTransform matrix as a VnlVector.

The returned vector points along the bounding box in the specified direction and has the length of the spacing in that direction.

Parameters

[in] direction The column index (0, 1, or 2).

Returns: VnlVector representing the matrix column.

See also: GetAxisVector

◆ GetNDimensions()

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

protectedvirtual

◆ GetOrigin()

Point3D mitk::BaseGeometry::GetOrigin ( ) const

Get the origin of the geometry in world coordinates (mm).

For a plane, this is typically the upper-left corner.

Returns: The origin as a 3D point in mm.

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

◆ GetOriginVnl()

VnlVector mitk::BaseGeometry::GetOriginVnl ( ) const

Get the origin as a VNL vector.

Returns: The origin as a VnlVector.

See also: GetOrigin

◆ GetSpacing()

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

Get the spacing (voxel size) in mm per unit for each axis.

Returns: A 3D vector with spacing values along each axis.

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

◆ GetTransformAsString()

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

staticprotected

◆ GetVtkMatrix() [1/2]

vtkMatrix4x4* mitk::BaseGeometry::GetVtkMatrix ( )

Get the IndexToWorldTransform as a 4x4 VTK matrix.

Returns: Pointer to the vtkMatrix4x4.

◆ GetVtkMatrix() [2/2]

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

Get the IndexToWorldTransform as a 4x4 VTK matrix (const).

Returns: Const pointer to the vtkMatrix4x4.

◆ GetVtkTransform()

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

Get the IndexToWorldTransform as a vtkLinearTransform.

Returns: Pointer to the vtkLinearTransform representation.

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

◆ ImageGeometryOff()

virtual void mitk::BaseGeometry::ImageGeometryOff ( )

virtual

◆ ImageGeometryOn()

virtual void mitk::BaseGeometry::ImageGeometryOn ( )

virtual

Toggle macro for ImageGeometry (ImageGeometryOn/ImageGeometryOff).

◆ IndexToWorld() [1/3]

template<unsigned int VIndexDimension>

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

inline

Convert discrete (itk::Index) index coordinates of a point to world coordinates (mm).

Template Parameters

VIndexDimension Dimension of the ITK index (dimensions beyond 3 are ignored).

Parameters

[in]	index	Discrete index coordinates.
[out]	pt_mm	Point in world coordinates (mm).

Definition at line 423 of file mitkBaseGeometry.h.

◆ IndexToWorld() [2/3]

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 (mm).

Parameters

[in]	pt_units	Point in index coordinates.
[out]	pt_mm	Point in world coordinates (mm).

◆ IndexToWorld() [3/3]

void mitk::BaseGeometry::IndexToWorld	(	const mitk::Vector3D &	vec_units,
		mitk::Vector3D &	vec_mm
	)		const

Convert index coordinates of a vector to world coordinates (mm).

Parameters

[in]	vec_units	Vector in index (unit) coordinates.
[out]	vec_mm	Vector in world coordinates (mm).

◆ Initialize()

void mitk::BaseGeometry::Initialize ( )

Initialize the geometry to default values.

Resets the bounding box to [0,1] in each dimension, sets the IndexToWorldTransform to identity, clears the FrameOfReferenceID, and sets ImageGeometry to false.

◆ InitializeGeometry()

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

Copy the essential geometry properties into another instance.

Copies bounding box, FrameOfReferenceID, the transform holder, and the ImageGeometry flag from this geometry into newGeometry.

Parameters

[in,out] newGeometry Target geometry to initialize.

◆ Is2DConvertable()

virtual bool mitk::BaseGeometry::Is2DConvertable ( )

virtual

Check if this geometry can be converted to 2D without information loss.

When a 2D image is saved, the 3x3 matrix is typically cropped to 2x2. This method checks whether such a reduction would discard geometric information (non-trivial z-spacing, z-origin, or off-axis components).

Returns: true if conversion to 2D is lossless, false otherwise.

◆ 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

Test whether a discrete ITK index lies inside the bounding box.

Convenience overload that converts itk::Index to Point3D and delegates to IsIndexInside(const Point3D&).

Template Parameters

VIndexDimension Dimension of the ITK index.

Parameters

[in] index The discrete index to test.

Returns: true if the index is inside.

Definition at line 713 of file mitkBaseGeometry.h.

◆ IsIndexInside() [2/2]

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

Test whether a point in continuous index coordinates lies inside the bounding box.

For image geometries the index is rounded before the check so that discrete pixel semantics apply.

Parameters

[in] index The point in continuous index coordinates.

Returns: true if the point is inside.

◆ IsIndexToWorldTransformNull()

bool mitk::BaseGeometry::IsIndexToWorldTransformNull ( ) const

protected

◆ IsInside()

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

Test whether a point (world coordinates, mm) lies inside the bounding box.

Converts the point to index coordinates and delegates to IsIndexInside().

Parameters

[in] p The point in world coordinates.

Returns: true if the point is inside the bounding box.

◆ IsValid()

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

virtual

Check whether this geometry is in a valid state.

The base implementation always returns true. Subclasses may override this to implement specific validity checks.

Returns: true if the geometry is valid, false otherwise.

Reimplemented in mitk::ThinPlateSplineCurvedGeometry.

◆ ItkPhysicalPointToWorld()

template<class TCoordRep >

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

inline

Convert an ITK physical point to MITK world coordinates.

Since ITK 3.10, ITK physical coordinates and MITK world coordinates are equivalent, so this is a plain coordinate copy.

Template Parameters

TCoordRep Coordinate representation type of the ITK point.

Parameters

[in]	itkPhysicalPoint	Point in ITK physical coordinates (mm).
[out]	pt_mm	Point in MITK world coordinates (mm).

See also: WorldToItkPhysicalPoint

Definition at line 453 of file mitkBaseGeometry.h.

References mitk::FillArray().

◆ MapAxesToOrientations()

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

Map geometry axes to anatomical orientations (sagittal, coronal, axial).

Determines which geometry axis (0, 1, 2) most closely aligns with each of the three anatomical orientations. The result is stored in the output array where element [0] is the axis index for sagittal, [1] for coronal, and [2] for axial. Each axis is mapped to exactly one orientation.

Parameters

[out] axes Array of three ints receiving the axis index for each orientation (sagittal, coronal, axial).

◆ mitkClassMacroItkParent()

mitk::BaseGeometry::mitkClassMacroItkParent	(	BaseGeometry	,
		itk::Object
	)

◆ Modified()

void mitk::BaseGeometry::Modified ( ) const

override

Overloaded Modified() to support the ModifiedLock mechanism.

When a ModifiedLock is active, calls to Modified() are deferred until the lock is released, preventing redundant notifications during multi-step geometry updates.

See also: 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::ThinPlateSplineCurvedGeometry, mitk::SlicedGeometry3D, mitk::PlaneGeometry, mitk::LandmarkProjectorBasedCurvedGeometry, mitk::Geometry3D, and mitk::AbstractTransformGeometry.

Definition at line 825 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.

A copy of the bounds array is stored, not a reference.

Parameters

[in] bounds The bounds array [xmin,xmax,ymin,ymax,zmin,zmax].

◆ SetExtentInMM()

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

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

This modifies the IndexToWorldTransform matrix by scaling the corresponding column, but does not change the bounding-box bounds (which are in index/unit coordinates).

Parameters

[in]	direction	The axis (0=x, 1=y, 2=z).
[in]	extentInMM	The new extent in mm.

◆ SetFloatBounds() [1/2]

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

Set the bounding box via a double array.

Parameters

[in] bounds Six doubles [xmin,xmax,ymin,ymax,zmin,zmax] in index coordinates.

◆ SetFloatBounds() [2/2]

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

Set the bounding box via a float array.

Parameters

[in] bounds Six floats [xmin,xmax,ymin,ymax,zmin,zmax] in index coordinates.

◆ SetFrameOfReferenceID()

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

virtual

Set the DICOM FrameOfReferenceID referring to the world coordinate system.

Parameters

[in] _arg The frame of reference identifier to set.

◆ SetIdentity()

void mitk::BaseGeometry::SetIdentity ( )

Reset the geometry to identity.

Sets the IndexToWorldTransform to identity, the spacing to 1.0 in all directions, and the origin to (0, 0, 0).

◆ SetImageGeometry()

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

virtual

Define that this BaseGeometry refers to an image.

An image geometry uses center-based voxel positions: the origin is at the center of the first voxel, and corner points are offset by half a voxel. This flag enables that correction in GetCornerPoint(), GetCenter(), IsIndexInside(), etc.

Parameters

[in] _arg true if this geometry refers to an image.

See also: GetImageGeometry, ImageGeometryOn, ImageGeometryOff

Reimplemented in mitk::SlicedGeometry3D.

◆ SetIndexToWorldTransform()

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

Set the affine transform for index-to-world coordinate mapping.

The spacing stored in the geometry is updated to match the column magnitudes of the new transform's matrix.

Parameters

[in] transform The new affine transform.

◆ SetIndexToWorldTransformByVtkMatrix()

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

Set the IndexToWorldTransform via a vtkMatrix4x4.

The matrix is converted to an ITK affine transform and the spacing is updated accordingly.

Parameters

[in] vtkmatrix A 4x4 VTK matrix describing the transform.

See also: SetIndexToWorldTransform

◆ SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing()

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

Set the IndexToWorldTransform via a vtkMatrix4x4 while preserving spacing.

Parameters

[in] vtkmatrix A 4x4 VTK matrix describing the transform.

See also: SetIndexToWorldTransform, SetIndexToWorldTransformWithoutChangingSpacing

◆ SetIndexToWorldTransformWithoutChangingSpacing()

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

Set the IndexToWorldTransform while preserving the current spacing.

Unlike SetIndexToWorldTransform(), this method keeps the original spacing values unchanged. The transform matrix columns are adjusted to maintain the previous spacing.

Parameters

[in] transform The new affine transform.

◆ SetOrigin()

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

Set the origin of the geometry in world coordinates (mm).

Parameters

[in] origin The new origin point in mm.

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

◆ SetSpacing()

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

Set the spacing (voxel size) for each axis.

Updates the IndexToWorldTransform accordingly so that the matrix columns reflect the new spacing.

Parameters

[in]	aSpacing	The new spacing vector in mm per unit.
[in]	enforceSetSpacing	If true, forces the spacing to be set even if subclass-specific constraints would normally prevent it.

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 given vector.

No action is taken if the vector is zero.

Parameters

[in] vector The translation vector in mm.

◆ WorldToIndex() [1/3]

template<unsigned int VIndexDimension>

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

inline

Convert world coordinates (mm) of a point to discrete (integer) index coordinates.

The continuous index values are rounded to the nearest integer using half-integer-up rounding.

Template Parameters

VIndexDimension Dimension of the ITK index (must be <= 3).

Parameters

[in]	pt_mm	Point in world coordinates (mm).
[out]	index	Discrete index coordinates; dimensions beyond 3 are set to 0.

Definition at line 382 of file mitkBaseGeometry.h.

◆ WorldToIndex() [2/3]

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

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

Parameters

[in]	pt_mm	Point in world coordinates (mm).
[out]	pt_units	Point in continuous (floating-point) index coordinates.

Warning: For discrete (integer) index coordinates use the overload accepting an itk::Index instead.

See also: IndexToWorld

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

◆ WorldToIndex() [3/3]

void mitk::BaseGeometry::WorldToIndex	(	const mitk::Vector3D &	vec_mm,
		mitk::Vector3D &	vec_units
	)		const

Convert world coordinates (mm) of a vector to continuous index coordinates.

Parameters

[in]	vec_mm	Vector in world coordinates (mm).
[out]	vec_units	Vector in continuous index coordinates.

◆ WorldToItkPhysicalPoint()

template<class TCoordRep >

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

inline

Convert MITK world coordinates to ITK physical coordinates.

Since ITK 3.10, ITK physical coordinates and MITK world coordinates are equivalent, so this is a plain coordinate copy. Historically, ITK did not support rotated images; only origin and spacing were used, and this method performed the full rotation-aware conversion.

Template Parameters

TCoordRep Coordinate representation type of the ITK point.

Parameters

[in]	pt_mm	Point in MITK world coordinates (mm).
[out]	itkPhysicalPoint	Point in ITK physical coordinates (mm).

See also: ItkPhysicalPointToWorld

Definition at line 473 of file mitkBaseGeometry.h.

References mitk::FillArray().

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

mitkBaseGeometry.h

Public Types

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Detailed Description

Member Typedef Documentation

◆ BoundingBoxPointer

◆ BoundingBoxType

◆ BoundsArrayType

◆ TransformType

Constructor & Destructor Documentation

◆ BaseGeometry() [1/2]

◆ BaseGeometry() [2/2]

◆ ~BaseGeometry()

Member Function Documentation

◆ _SetSpacing()

◆ CalculateBoundingBoxRelativeToTransform()

◆ ChangeImageGeometryConsideringOriginOffset()

◆ CheckBounds()

◆ CheckIndexToWorldTransform()

◆ ClampPoint()

◆ Clone()

◆ Compose() [1/2]

◆ Compose() [2/2]

◆ ExecuteOperation()

◆ GetAxisVector()

◆ GetBoundingBox()

◆ GetBounds()

◆ GetCenter()

◆ 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()

◆ GetTransformAsString()

◆ GetVtkMatrix() [1/2]

◆ GetVtkMatrix() [2/2]

◆ GetVtkTransform()

◆ ImageGeometryOff()

◆ ImageGeometryOn()

◆ IndexToWorld() [1/3]

◆ IndexToWorld() [2/3]

◆ IndexToWorld() [3/3]

◆ Initialize()

◆ InitializeGeometry()

◆ Is2DConvertable()

◆ IsBoundingBoxNull()

◆ IsIndexInside() [1/2]

◆ IsIndexInside() [2/2]

◆ IsIndexToWorldTransformNull()

◆ IsInside()

◆ IsValid()

◆ ItkPhysicalPointToWorld()

◆ MapAxesToOrientations()

◆ mitkClassMacroItkParent()

◆ Modified()

◆ PreSetSpacing()

◆ PrintSelf()

◆ SetBounds()

◆ SetExtentInMM()

◆ SetFloatBounds() [1/2]

◆ SetFloatBounds() [2/2]

◆ SetFrameOfReferenceID()

◆ SetIdentity()

◆ SetImageGeometry()

◆ SetIndexToWorldTransform()

◆ SetIndexToWorldTransformByVtkMatrix()

◆ SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing()