diff --git a/Modules/Core/include/mitkAbstractTransformGeometry.h b/Modules/Core/include/mitkAbstractTransformGeometry.h index aa2c384fc6..a94d60e844 100644 --- a/Modules/Core/include/mitkAbstractTransformGeometry.h +++ b/Modules/Core/include/mitkAbstractTransformGeometry.h @@ -1,231 +1,224 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef MITKVTKABSTRACTTRANSFORMPLANEGEOMETRY_H_HEADER_INCLUDED_C1C68A2C #define MITKVTKABSTRACTTRANSFORMPLANEGEOMETRY_H_HEADER_INCLUDED_C1C68A2C #include #include "mitkPlaneGeometry.h" #include "itkVtkAbstractTransform.h" class vtkAbstractTransform; namespace mitk { //##Documentation //## @brief Describes a geometry defined by an vtkAbstractTransform and a plane //## //## vtkAbstractTransform is the most general transform in vtk (superclass for //## all vtk geometric transformations). It defines an arbitrary 3D transformation, //## i.e., a transformation of 3D space into 3D space. In contrast, //## AbstractTransformGeometry (since it is a subclass of PlaneGeometry) describes a //## 2D manifold in 3D space. The 2D manifold is defined as the manifold that results //## from transforming a rectangle (given in m_Plane as a PlaneGeometry) by the //## vtkAbstractTransform (given in m_VtkAbstractTransform). //## The PlaneGeometry m_Plane is used to define the parameter space. 2D coordinates are //## first mapped by the PlaneGeometry and the resulting 3D coordinates are put into //## the vtkAbstractTransform. //## @note This class is the superclass of concrete geometries. Since there is no //## write access to the vtkAbstractTransform and m_Plane, this class is somehow //## abstract. For full write access from extern, use ExternAbstractTransformGeometry. //## @note The bounds of the PlaneGeometry are used as the parametric bounds. //## @sa ExternAbstractTransformGeometry //## @ingroup Geometry class MITKCORE_EXPORT AbstractTransformGeometry : public PlaneGeometry { public: mitkClassMacro(AbstractTransformGeometry, PlaneGeometry); itkFactorylessNewMacro(Self) itkCloneMacro(Self) //##Documentation //## @brief Get the vtkAbstractTransform (stored in m_VtkAbstractTransform) virtual vtkAbstractTransform* GetVtkAbstractTransform() const; virtual unsigned long GetMTime() const; //##Documentation //## @brief Get the rectangular area that is used for transformation by //## m_VtkAbstractTransform and therewith defines the 2D manifold described by //## AbstractTransformGeometry itkGetConstObjectMacro(Plane, PlaneGeometry); /** * \brief projects the given point onto the curved plane */ virtual bool Project(const mitk::Point3D &pt3d_mm, mitk::Point3D &projectedPt3d_mm) const; /** * \brief projects a given vector starting from given point onto the curved plane * \warning no satisfiyng implementation existing yet */ virtual bool Project(const mitk::Point3D & atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const; /** * \brief projects a given vector starting from standard point onto the curved plane * \warning no satisfying implementation existing yet */ virtual bool Project(const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const; virtual bool Map(const mitk::Point3D &pt3d_mm, mitk::Point2D &pt2d_mm) const; virtual void Map(const mitk::Point2D &pt2d_mm, mitk::Point3D &pt3d_mm) const; virtual bool Map(const mitk::Point3D & atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector2D &vec2d_mm) const; virtual void Map(const mitk::Point2D & atPt2d_mm, const mitk::Vector2D &vec2d_mm, mitk::Vector3D &vec3d_mm) const; virtual void IndexToWorld(const mitk::Point2D &pt_units, mitk::Point2D &pt_mm) const; virtual void WorldToIndex(const mitk::Point2D &pt_mm, mitk::Point2D &pt_units) const; //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em vector //## \a vec_units to world coordinates (in mm) //## @deprecated First parameter (Point2D) is not used. If possible, please use void IndexToWorld(const mitk::Vector2D& vec_units, mitk::Vector2D& vec_mm) const. //## For further information about coordinates types, please see the Geometry documentation virtual void IndexToWorld(const mitk::Point2D &atPt2d_units, const mitk::Vector2D &vec_units, mitk::Vector2D &vec_mm) const; //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em vector //## \a vec_units to world coordinates (in mm) //## For further information about coordinates types, please see the Geometry documentation virtual void IndexToWorld(const mitk::Vector2D &vec_units, mitk::Vector2D &vec_mm) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em vector //## \a vec_mm to (continuous!) index coordinates. //## @deprecated First parameter (Point2D) is not used. If possible, please use void WorldToIndex(const mitk::Vector2D& vec_mm, mitk::Vector2D& vec_units) const. //## For further information about coordinates types, please see the Geometry documentation virtual void WorldToIndex(const mitk::Point2D &atPt2d_mm, const mitk::Vector2D &vec_mm, mitk::Vector2D &vec_units) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em vector //## \a vec_mm to (continuous!) index coordinates. //## For further information about coordinates types, please see the Geometry documentation virtual void WorldToIndex(const mitk::Vector2D &vec_mm, mitk::Vector2D &vec_units) const; - virtual bool IsAbove(const Point3D& pt3d_mm, bool considerBoundingBox=false) const; + virtual bool IsAbove(const Point3D& pt3d_mm, bool considerBoundingBox = false) const; virtual mitk::ScalarType GetParametricExtentInMM(int direction) const; - virtual const itk::Transform* GetParametricTransform() const; + virtual const itk::Transform* GetParametricTransform() const; //##Documentation //## @brief Change the parametric bounds to @a oversampling times //## the bounds of m_Plane. //## //## The change is done once (immediately). Later changes of the bounds //## of m_Plane will not influence the parametric bounds. (Consequently, //## there is no method to get the oversampling.) virtual void SetOversampling(mitk::ScalarType oversampling); //##Documentation //## @brief Calculates the standard part of a BaseGeometry //## (IndexToWorldTransform and bounding box) around the //## curved geometry. Has to be implemented in subclasses. //## //## \sa SetFrameGeometry virtual void CalculateFrameGeometry(); //##Documentation //## @brief Set the frame geometry which is used as the standard //## part of an BaseGeometry (IndexToWorldTransform and bounding box) //## //## Maybe used as a hint within which the interpolation shall occur //## by concrete sub-classes. //## \sa CalculateFrameGeometry virtual void SetFrameGeometry(const mitk::BaseGeometry* frameGeometry); virtual itk::LightObject::Pointer InternalClone() const; //##Documentation //## @brief Get the parametric bounding-box //## //## See AbstractTransformGeometry for an example usage of this. itkGetConstObjectMacro(ParametricBoundingBox, BoundingBox); //##Documentation //## @brief Get the parametric bounds //## //## See AbstractTransformGeometry for an example usage of this. const BoundingBox::BoundsArrayType& GetParametricBounds() const; //##Documentation //## @brief Get the parametric extent //## //## See AbstractTransformGeometry for an example usage of this. mitk::ScalarType GetParametricExtent(int direction) const; protected: AbstractTransformGeometry(); AbstractTransformGeometry(const AbstractTransformGeometry& other); virtual ~AbstractTransformGeometry(); //##Documentation //## @brief Set the vtkAbstractTransform (stored in m_VtkAbstractTransform) //## //## Protected in this class, made public in ExternAbstractTransformGeometry. virtual void SetVtkAbstractTransform(vtkAbstractTransform* aVtkAbstractTransform); //##Documentation //## @brief Set the rectangular area that is used for transformation by //## m_VtkAbstractTransform and therewith defines the 2D manifold described by //## ExternAbstractTransformGeometry //## //## Protected in this class, made public in ExternAbstractTransformGeometry. //## @note The bounds of the PlaneGeometry are used as the parametric bounds. //## @note The PlaneGeometry is cloned, @em not linked/referenced. virtual void SetPlane(const mitk::PlaneGeometry* aPlane); //##Documentation //## @brief The rectangular area that is used for transformation by //## m_VtkAbstractTransform and therewith defines the 2D manifold described by //## AbstractTransformGeometry. mitk::PlaneGeometry::Pointer m_Plane; itk::VtkAbstractTransform::Pointer m_ItkVtkAbstractTransform; mitk::BaseGeometry::Pointer m_FrameGeometry; //##Documentation //## @brief Set the parametric bounds //## //## Protected in this class, made public in some sub-classes, e.g., //## ExternAbstractTransformGeometry. virtual void SetParametricBounds(const BoundingBox::BoundsArrayType& bounds); mutable mitk::BoundingBox::Pointer m_ParametricBoundingBox; //##Documentation - //## @brief Pre- and Post-functions are empty in BaseGeometry + //## @brief PreSetSpacing //## - //## These virtual functions allow for a different beahiour in subclasses. - //## Do implement them in every subclass of BaseGeometry. If not needed, use {}. - //## If this class is inherited from a subclass of BaseGeometry, call {Superclass::Pre...();};, example: DisplayGeometry class - virtual void PostInitializeGeometry(mitk::BaseGeometry::Self * newGeometry) const{Superclass::PostInitializeGeometry(newGeometry);}; - virtual void PreSetSpacing(const mitk::Vector3D& aSpacing){Superclass::PreSetSpacing(aSpacing);}; - virtual void PreSetBounds( const BoundingBox::BoundsArrayType &bounds ){Superclass::PreSetBounds(bounds);}; - virtual void PreSetIndexToWorldTransform( AffineTransform3D *transform){Superclass::PreSetIndexToWorldTransform(transform);}; - virtual void PostSetExtentInMM(int direction, ScalarType extentInMM){Superclass::PostSetExtentInMM(direction,extentInMM);}; - virtual void PostSetIndexToWorldTransform(mitk::AffineTransform3D* transform){Superclass::PostSetIndexToWorldTransform(transform);}; - - virtual void PostInitialize(); + //## These virtual function allows a different beahiour in subclasses. + //## Do implement them in every subclass of BaseGeometry. If not needed, use + //## {Superclass::PreSetSpacing();}; + virtual void PreSetSpacing(const mitk::Vector3D& aSpacing){ Superclass::PreSetSpacing(aSpacing); }; }; } // namespace mitk #endif /* MITKVTKABSTRACTTRANSFORMPLANEGEOMETRY_H_HEADER_INCLUDED_C1C68A2C */ diff --git a/Modules/Core/include/mitkBaseGeometry.h b/Modules/Core/include/mitkBaseGeometry.h index daf92fcd83..7aa0b9f1b7 100644 --- a/Modules/Core/include/mitkBaseGeometry.h +++ b/Modules/Core/include/mitkBaseGeometry.h @@ -1,744 +1,745 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef BaseGeometry_H_HEADER_INCLUDED #define BaseGeometry_H_HEADER_INCLUDED #include #include #include "mitkOperationActor.h" #include #include "mitkNumericTypes.h" #include #include #include "itkScalableAffineTransform.h" #include #include #include #include class vtkMatrix4x4; class vtkMatrixToLinearTransform; class vtkLinearTransform; namespace mitk { //##Documentation //## @brief Standard 3D-BoundingBox typedef //## //## Standard 3D-BoundingBox typedef to get rid of template arguments (3D, type). typedef itk::BoundingBox BoundingBox; //##Documentation //## @brief Standard typedef for time-bounds - typedef itk::FixedArray TimeBounds; + typedef itk::FixedArray TimeBounds; typedef itk::FixedArray FixedArrayType; typedef itk::AffineGeometryFrame AffineGeometryFrame3D; //##Documentation //## @brief BaseGeometry Describes the geometry of a data object //## //## The class holds //## \li a bounding box which is axes-parallel in intrinsic coordinates //## (often integer indices of pixels), to be accessed by //## GetBoundingBox() //## \li 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() //## \li 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 descibes //## 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 \ref Geometry. //## //## BaseGeometry instances referring to an Image need a slightly //## different definition of corners, see SetImageGeometry. This //## is usualy 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 sublass Geometry3D. //## //## Rule: everything is in mm (ms) if not stated otherwise. //## @ingroup Geometry class MITKCORE_EXPORT BaseGeometry : public itk::Object, public OperationActor { public: mitkClassMacro(BaseGeometry, itk::Object); itkCloneMacro(Self) // ********************************** TypeDef ********************************** typedef GeometryTransformHolder::TransformType TransformType; typedef itk::BoundingBox BoundingBoxType; typedef BoundingBoxType::BoundsArrayType BoundsArrayType; typedef BoundingBoxType::Pointer BoundingBoxPointer; // ********************************** Origin, Spacing ********************************** //##Documentation //## @brief Get the origin, e.g. the upper-left corner of the plane const Point3D GetOrigin() const; //##Documentation //## @brief Set the origin, i.e. the upper-left corner of the plane //## void SetOrigin(const Point3D& origin); //##Documentation //## @brief Get the spacing (size of a pixel). //## const mitk::Vector3D GetSpacing() const; //##Documentation //## @brief Set the spacing (m_Spacing). //## //##The spacing is also changed in the IndexToWorldTransform. void SetSpacing(const mitk::Vector3D& aSpacing, bool enforceSetSpacing = false); //##Documentation //## @brief Get the origin as VnlVector //## //## \sa GetOrigin VnlVector GetOriginVnl() const; // ********************************** other functions ********************************** //##Documentation //## @brief Get the DICOM FrameOfReferenceID referring to the //## used world coordinate system itkGetConstMacro(FrameOfReferenceID, unsigned int); //##Documentation //## @brief Set the DICOM FrameOfReferenceID referring to the //## used world coordinate system itkSetMacro(FrameOfReferenceID, unsigned int); itkGetConstMacro(IndexToWorldTransformLastModified, unsigned long); //##Documentation //## @brief Overload of function Modified() to prohibit several calls of Modified() using the ModifiedLock class. //## //## For the use of Modified(), see class ModifiedLock. void Modified() const; friend class ModifiedLock; //##Documentation //## @brief Is this BaseGeometry in a state that is valid? //## //## This function returns always true in the BaseGeometry class. Other implementations are possible in subclasses. virtual bool IsValid() const; // ********************************** Initialize ********************************** //##Documentation //## @brief Initialize the BaseGeometry void Initialize(); void InitializeGeometry(Self * newGeometry) const; // ********************************** Transformations Set/Get ********************************** //##Documentation //## @brief Get the transformation used to convert from index //## to world coordinates mitk::AffineTransform3D* GetIndexToWorldTransform(); //##Documentation //## @brief Get the transformation used to convert from index //## to world coordinates const mitk::AffineTransform3D* GetIndexToWorldTransform() const; //## @brief Set the transformation used to convert from index //## to world coordinates. The spacing of the new transform is //## copied to m_spacing. void SetIndexToWorldTransform(mitk::AffineTransform3D* transform); //##Documentation //## @brief Convenience method for setting the ITK transform //## (m_IndexToWorldTransform) via an vtkMatrix4x4.The spacing of //## the new transform is copied to m_spacing. //## \sa SetIndexToWorldTransform - virtual void SetIndexToWorldTransformByVtkMatrix(vtkMatrix4x4* vtkmatrix); + void SetIndexToWorldTransformByVtkMatrix(vtkMatrix4x4* vtkmatrix); //## @brief Set the transformation used to convert from index //## to world coordinates.This function keeps the original spacing. void SetIndexToWorldTransformWithoutChangingSpacing(mitk::AffineTransform3D* transform); //##Documentation //## @brief Convenience method for setting the ITK transform //## (m_IndexToWorldTransform) via an vtkMatrix4x4. This function keeps the original spacing. //## \sa SetIndexToWorldTransform void SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing(vtkMatrix4x4* vtkmatrix); //## Get the Vtk Matrix which describes the transform. vtkMatrix4x4* GetVtkMatrix(); //##Documentation //## @brief Get the m_IndexToWorldTransform as a vtkLinearTransform vtkLinearTransform* GetVtkTransform() const; //##Documentation //## @brief Set the transform to identity, the spacing to 1 and origin to 0 //## - virtual void SetIdentity(); + void SetIdentity(); // ********************************** Transformations ********************************** //##Documentation //## @brief 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. - void Compose( const TransformType * other, bool pre = 0 ); + void Compose(const TransformType * other, bool pre = 0); //##Documentation //## @brief Compose new IndexToWorldTransform with a given vtkMatrix4x4. //## //## Converts the vtkMatrix4x4 into a itk-transform and calls the previous method. - void Compose( const vtkMatrix4x4 * vtkmatrix, bool pre = 0 ); + void Compose(const vtkMatrix4x4 * vtkmatrix, bool pre = 0); //##Documentation //## @brief Translate the origin by a vector //## void Translate(const Vector3D& vector); //##Documentation //##@brief executes affine operations (translate, rotate, scale) virtual void ExecuteOperation(Operation* operation); //##Documentation //## @brief Convert world coordinates (in mm) of a \em 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 &index). //## For further information about coordinates types, please see the Geometry documentation void WorldToIndex(const mitk::Point3D& pt_mm, mitk::Point3D& pt_units) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em vector //## \a vec_mm to (continuous!) index coordinates. //## For further information about coordinates types, please see the Geometry documentation void WorldToIndex(const mitk::Vector3D& vec_mm, mitk::Vector3D& vec_units) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em point to (discrete!) index coordinates. //## This method rounds to integer indices! //## For further information about coordinates types, please see the Geometry documentation template void WorldToIndex(const mitk::Point3D& pt_mm, itk::Index &index) const { typedef itk::Index IndexType; mitk::Point3D pt_units; this->WorldToIndex(pt_mm, pt_units); - int i, dim=index.GetIndexDimension(); - if(dim>3) + int i, dim = index.GetIndexDimension(); + if (dim > 3) { index.Fill(0); - dim=3; + dim = 3; } - for(i=0;i( pt_units[i] ); + for (i = 0; i < dim; ++i){ + index[i] = itk::Math::RoundHalfIntegerUp(pt_units[i]); } } //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em vector //## \a vec_units to world coordinates (in mm) //## For further information about coordinates types, please see the Geometry documentation void IndexToWorld(const mitk::Vector3D& vec_units, mitk::Vector3D& vec_mm) const; //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em point to world coordinates (in mm) //## For further information about coordinates types, please see the Geometry documentation void IndexToWorld(const mitk::Point3D& pt_units, mitk::Point3D& pt_mm) const; //##Documentation //## @brief Convert (discrete) index coordinates of a \em point to world coordinates (in mm) //## For further information about coordinates types, please see the Geometry documentation template - void IndexToWorld(const itk::Index &index, mitk::Point3D& pt_mm ) const + void IndexToWorld(const itk::Index &index, mitk::Point3D& pt_mm) const { mitk::Point3D pt_units; pt_units.Fill(0); - int i, dim=index.GetIndexDimension(); - if(dim>3) + int i, dim = index.GetIndexDimension(); + if (dim > 3) { - dim=3; + dim = 3; } - for(i=0;i void ItkPhysicalPointToWorld(const itk::Point& itkPhysicalPoint, mitk::Point3D& pt_mm) const { mitk::vtk2itk(itkPhysicalPoint, pt_mm); } //##Documentation //## @brief Deprecated for use with ITK version 3.10 or newer. //## Convert world coordinates (in mm) of a \em 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). template void WorldToItkPhysicalPoint(const mitk::Point3D& pt_mm, itk::Point& itkPhysicalPoint) const { mitk::vtk2itk(pt_mm, itkPhysicalPoint); } // ********************************** BoundingBox ********************************** /** Get the bounding box */ itkGetConstObjectMacro(BoundingBox, BoundingBoxType); //##Documentation //## @brief Get the time bounds (in ms) //itkGetConstReferenceMacro(TimeBounds, TimeBounds); // a bit of a misuse, but we want only doxygen to see the following: #ifdef DOXYGEN_SKIP //##Documentation //## @brief Get bounding box (in index/unit coordinates) itkGetConstObjectMacro(BoundingBox, BoundingBoxType); //##Documentation //## @brief Get bounding box (in index/unit coordinates) as a BoundsArrayType const BoundsArrayType GetBounds() const; #endif const BoundsArrayType GetBounds() const; //##Documentation //## \brief 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. void SetBounds(const BoundsArrayType& bounds); //##Documentation //## @brief Set the bounding box (in index/unit coordinates) via a float array void SetFloatBounds(const float bounds[6]); //##Documentation //## @brief Set the bounding box (in index/unit coordinates) via a double array void SetFloatBounds(const double bounds[6]); //##Documentation //## @brief Get a VnlVector along bounding-box in the specified //## @a direction, length is spacing //## //## \sa GetAxisVector VnlVector GetMatrixColumn(unsigned int direction) const; //##Documentation //## @brief Calculates a bounding-box around the geometry relative //## to a coordinate system defined by a transform //## mitk::BoundingBox::Pointer CalculateBoundingBoxRelativeToTransform(const mitk::AffineTransform3D* transform) const; //##Documentation //## @brief Set the time bounds (in ms) //void SetTimeBounds(const TimeBounds& timebounds); // ********************************** Geometry ********************************** #ifdef DOXYGEN_SKIP //##Documentation //## @brief Get the extent of the bounding box (in index/unit coordinates) //## //## To access the extent in mm use GetExtentInMM ScalarType GetExtent(unsigned int direction) const; #endif /** Get the extent of the bounding box */ ScalarType GetExtent(unsigned int direction) const; //##Documentation //## @brief Get the extent of the bounding-box in the specified @a direction in mm //## //## Equals length of GetAxisVector(direction). ScalarType GetExtentInMM(int direction) const; //##Documentation //## @brief Get vector along bounding-box in the specified @a direction in mm //## //## The length of the vector is the size of the bounding-box in the //## specified @a direction in mm //## \sa GetMatrixColumn Vector3D GetAxisVector(unsigned int direction) const; //##Documentation //## @brief 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 virtual bool Is2DConvertable(); //##Documentation //## @brief Get the center of the bounding-box in mm //## Point3D GetCenter() const; //##Documentation //## @brief Get the squared length of the diagonal of the bounding-box in mm //## double GetDiagonalLength2() const; //##Documentation //## @brief Get the length of the diagonal of the bounding-box in mm //## double GetDiagonalLength() const; //##Documentation //## @brief Get the position of the corner number \a id (in world coordinates) //## //## See SetImageGeometry for how a corner is defined on images. Point3D GetCornerPoint(int id) const; //##Documentation //## @brief Get the position of a corner (in world coordinates) //## //## See SetImageGeometry for how a corner is defined on images. - Point3D GetCornerPoint(bool xFront=true, bool yFront=true, bool zFront=true) const; + Point3D GetCornerPoint(bool xFront = true, bool yFront = true, bool zFront = true) const; //##Documentation //## @brief Set the extent of the bounding-box in the specified @a direction in mm //## //## @note This changes the matrix in the transform, @a not the bounds, which are given in units! void SetExtentInMM(int direction, ScalarType extentInMM); //##Documentation //## @brief Test whether the point \a p (world coordinates in mm) is //## inside the bounding box bool IsInside(const mitk::Point3D& p) const; //##Documentation //## @brief Test whether the point \a p ((continous!)index coordinates in units) is //## inside the bounding box bool IsIndexInside(const mitk::Point3D& index) const; //##Documentation //## @brief Convenience method for working with ITK indices template bool IsIndexInside(const itk::Index &index) const { - int i, dim=index.GetIndexDimension(); + int i, dim = index.GetIndexDimension(); Point3D pt_index; pt_index.Fill(0); - for ( i = 0; i < dim; ++i ) + for (i = 0; i < dim; ++i) { pt_index[i] = index[i]; } return IsIndexInside(pt_index); } // ********************************* Image Geometry ******************************** //##Documentation //## @brief When switching from an Image Geometry to a normal Geometry (and the other way around), you have to change the origin as well (See Geometry Documentation)! This function will change the "isImageGeometry" bool flag and changes the origin respectively. - virtual void ChangeImageGeometryConsideringOriginOffset( const bool isAnImageGeometry ); + virtual void ChangeImageGeometryConsideringOriginOffset(const bool isAnImageGeometry); //##Documentation //## @brief Is this an ImageGeometry? //## //## For more information, see SetImageGeometry itkGetConstMacro(ImageGeometry, bool) - //##Documentation - //## @brief 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 - //## \em 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. - itkSetMacro(ImageGeometry, bool) - itkBooleanMacro(ImageGeometry) - - const GeometryTransformHolder* GetGeometryTransformHolder() const; + //##Documentation + //## @brief 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 + //## \em 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. + itkSetMacro(ImageGeometry, bool) + itkBooleanMacro(ImageGeometry) + + const GeometryTransformHolder* GetGeometryTransformHolder() const; protected: // ********************************** Constructor ********************************** BaseGeometry(); BaseGeometry(const BaseGeometry& other); virtual ~BaseGeometry(); //##Documentation //## @brief clones the geometry //## //## Overwrite in all sub-classes. //## Normally looks like: //## \code //## Self::Pointer newGeometry = new Self(*this); //## newGeometry->UnRegister(); //## return newGeometry.GetPointer(); //## \endcode - virtual itk::LightObject::Pointer InternalClone() const =0; + virtual itk::LightObject::Pointer InternalClone() const = 0; virtual void PrintSelf(std::ostream& os, itk::Indent indent) const; - void BackTransform(const mitk::Point3D& in, mitk::Point3D& out) const; - - //Without redundant parameter Point3D - void BackTransform(const mitk::Vector3D& in, mitk::Vector3D& out) const; - - //##Documentation - //## @brief Deprecated - void BackTransform(const mitk::Point3D& at, const mitk::Vector3D& in, mitk::Vector3D& out) const; - - static const std::string GetTransformAsString( TransformType* transformType ); + static const std::string GetTransformAsString(TransformType* transformType); itkGetConstMacro(NDimensions, unsigned int) - bool IsBoundingBoxNull() const; + bool IsBoundingBoxNull() const; bool IsIndexToWorldTransformNull() const; void SetVtkMatrixDeepCopy(vtkTransform *vtktransform); void _SetSpacing(const mitk::Vector3D& aSpacing, bool enforceSetSpacing = false); //##Documentation - //## @brief Pre- and Post-functions are empty in BaseGeometry + //## @brief PreSetSpacing + //## + //## These virtual function allows a different beahiour in subclasses. + //## Do implement them in every subclass of BaseGeometry. If not needed, use + //## {Superclass::PreSetSpacing();}; + virtual void PreSetSpacing(const mitk::Vector3D& /*aSpacing*/) {}; + + //##Documentation + //## @brief 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 well!) + virtual void CheckBounds(const BoundsArrayType& bounds){}; + + //##Documentation + //## @brief CheckIndexToWorldTransform //## - //## These virtual functions allow for a different beahiour in subclasses. - //## Do implement them in every subclass of BaseGeometry. If not needed, use {}. - //## If this class is inherited from a subclass of BaseGeometry, call {Superclass::Pre...();};, example: DisplayGeometry class - virtual void PreSetBounds(const BoundsArrayType& /*bounds*/) {} - virtual void PostInitialize() {} - virtual void PostInitializeGeometry(mitk::BaseGeometry::Self * /*newGeometry*/) const {} - virtual void PostSetExtentInMM(int /*direction*/, ScalarType /*extentInMM*/) {} - virtual void PreSetIndexToWorldTransform(mitk::AffineTransform3D* /*transform*/) {} - virtual void PostSetIndexToWorldTransform(mitk::AffineTransform3D* /*transform*/) {} - virtual void PreSetSpacing(const mitk::Vector3D& /*aSpacing*/) {} + //## This function is called in SetIndexToWorldTransform. Assertions can be implemented in this function (see PlaneGeometry.cpp). + //## In Subclasses of BaseGeometry, implement own conditions or call Superclass::CheckBounds(bounds);. + virtual void CheckIndexToWorldTransform(mitk::AffineTransform3D* transform){}; private: GeometryTransformHolder* m_GeometryTransform; void InitializeGeometryTransformHolder(const BaseGeometry* otherGeometry); //##Documentation //## @brief Bounding Box, which is axes-parallel in intrinsic coordinates //## (often integer indices of pixels) BoundingBoxPointer m_BoundingBox; unsigned int m_FrameOfReferenceID; //mitk::TimeBounds m_TimeBounds; static const unsigned int m_NDimensions = 3; mutable TransformType::Pointer m_InvertedTransform; mutable unsigned long m_IndexToWorldTransformLastModified; bool m_ImageGeometry; //##Documentation //## @brief ModifiedLockFlag is used to prohibit the call of Modified() //## //## For the use of this Flag, see class ModifiedLock. This flag should only be set //## by the ModifiedLock class! bool m_ModifiedLockFlag; //##Documentation //## @brief ModifiedcalledFlag is used to collect calls of Modified(). //## //## For the use of this Flag, see class ModifiedLock. This flag should only be set //## by the Modified() function! mutable bool m_ModifiedCalledFlag; }; // ********************************** Equal Functions ********************************** // // Static compare functions mainly for testing // /** * @brief Equal A function comparing two geometries for beeing identical. * @warning This method is deprecated and will not be available in the future. Use the \a bool mitk::Equal(const mitk::mitk::BaseGeometry& g1, const mitk::BaseGeometry& g2) instead. * * @ingroup MITKTestingAPI * * The function compares the spacing, origin, axisvectors, extents, the matrix of the * IndexToWorldTransform (elementwise), the bounding (elementwise) and the ImageGeometry flag. * * The parameter eps is a tolarence value for all methods which are internally used for comparion. * If you want to use different tolarance values for different parts of the geometry, feel free to use * the other comparison methods and write your own implementation of Equal. * @param rightHandSide Compare this against leftHandSide. * @param leftHandSide Compare this against rightHandSide. * @param eps Tolarence for comparison. You can use mitk::eps in most cases. * @param verbose Flag indicating if the user wants detailed console output or not. * @return True, if all comparison are true. False in any other case. */ - DEPRECATED( MITKCORE_EXPORT bool Equal(const mitk::BaseGeometry* leftHandSide, const mitk::BaseGeometry* rightHandSide, ScalarType eps, bool verbose)); + DEPRECATED(MITKCORE_EXPORT bool Equal(const mitk::BaseGeometry* leftHandSide, const mitk::BaseGeometry* rightHandSide, ScalarType eps, bool verbose)); /** * @brief Equal A function comparing two geometries for beeing identical. * * @ingroup MITKTestingAPI * * The function compares the spacing, origin, axisvectors, extents, the matrix of the * IndexToWorldTransform (elementwise), the bounding (elementwise) and the ImageGeometry flag. * * The parameter eps is a tolarence value for all methods which are internally used for comparion. * If you want to use different tolarance values for different parts of the geometry, feel free to use * the other comparison methods and write your own implementation of Equal. * @param rightHandSide Compare this against leftHandSide. * @param leftHandSide Compare this against rightHandSide. * @param eps Tolarence for comparison. You can use mitk::eps in most cases. * @param verbose Flag indicating if the user wants detailed console output or not. * @return True, if all comparison are true. False in any other case. */ MITKCORE_EXPORT bool Equal(const mitk::BaseGeometry& leftHandSide, const mitk::BaseGeometry& rightHandSide, ScalarType eps, bool verbose); /** * @brief Equal A function comparing two transforms (TransformType) for beeing identical. * @warning This method is deprecated and will not be available in the future. Use the \a bool mitk::Equal(const mitk::mitk::BaseGeometry::TransformType& t1, const mitk::BaseGeometry::TransformType& t2) instead. * * @ingroup MITKTestingAPI * * The function compares the IndexToWorldTransform (elementwise). * * The parameter eps is a tolarence value for all methods which are internally used for comparion. * @param rightHandSide Compare this against leftHandSide. * @param leftHandSide Compare this against rightHandSide. * @param eps Tolarence for comparison. You can use mitk::eps in most cases. * @param verbose Flag indicating if the user wants detailed console output or not. * @return True, if all comparison are true. False in any other case. */ - DEPRECATED( MITKCORE_EXPORT bool Equal(const mitk::BaseGeometry::TransformType *leftHandSide, const mitk::BaseGeometry::TransformType *rightHandSide, ScalarType eps, bool verbose)); + DEPRECATED(MITKCORE_EXPORT bool Equal(const mitk::BaseGeometry::TransformType *leftHandSide, const mitk::BaseGeometry::TransformType *rightHandSide, ScalarType eps, bool verbose)); /** * @brief Equal A function comparing two transforms (TransformType) for beeing identical. * * @ingroup MITKTestingAPI * * The function compares the IndexToWorldTransform (elementwise). * * The parameter eps is a tolarence value for all methods which are internally used for comparion. * @param rightHandSide Compare this against leftHandSide. * @param leftHandSide Compare this against rightHandSide. * @param eps Tolarence for comparison. You can use mitk::eps in most cases. * @param verbose Flag indicating if the user wants detailed console output or not. * @return True, if all comparison are true. False in any other case. */ MITKCORE_EXPORT bool Equal(const mitk::BaseGeometry::TransformType& leftHandSide, const mitk::BaseGeometry::TransformType& rightHandSide, ScalarType eps, bool verbose); /** * @brief Equal A function comparing two bounding boxes (BoundingBoxType) for beeing identical. * @warning This method is deprecated and will not be available in the future. Use the \a bool mitk::Equal(const mitk::mitk::BaseGeometry::BoundingBoxType& b1, const mitk::BaseGeometry::BoundingBoxType& b2) instead. * * @ingroup MITKTestingAPI * * The function compares the bounds (elementwise). * * The parameter eps is a tolarence value for all methods which are internally used for comparion. * @param rightHandSide Compare this against leftHandSide. * @param leftHandSide Compare this against rightHandSide. * @param eps Tolarence for comparison. You can use mitk::eps in most cases. * @param verbose Flag indicating if the user wants detailed console output or not. * @return True, if all comparison are true. False in any other case. */ - DEPRECATED( MITKCORE_EXPORT bool Equal( const mitk::BaseGeometry::BoundingBoxType *leftHandSide, const mitk::BaseGeometry::BoundingBoxType *rightHandSide, ScalarType eps, bool verbose)); + DEPRECATED(MITKCORE_EXPORT bool Equal(const mitk::BaseGeometry::BoundingBoxType *leftHandSide, const mitk::BaseGeometry::BoundingBoxType *rightHandSide, ScalarType eps, bool verbose)); /** * @brief Equal A function comparing two bounding boxes (BoundingBoxType) for beeing identical. * * @ingroup MITKTestingAPI * * The function compares the bounds (elementwise). * * The parameter eps is a tolarence value for all methods which are internally used for comparion. * @param rightHandSide Compare this against leftHandSide. * @param leftHandSide Compare this against rightHandSide. * @param eps Tolarence for comparison. You can use mitk::eps in most cases. * @param verbose Flag indicating if the user wants detailed console output or not. * @return True, if all comparison are true. False in any other case. */ - MITKCORE_EXPORT bool Equal( const mitk::BaseGeometry::BoundingBoxType& leftHandSide, const mitk::BaseGeometry::BoundingBoxType& rightHandSide, ScalarType eps, bool verbose); + MITKCORE_EXPORT bool Equal(const mitk::BaseGeometry::BoundingBoxType& leftHandSide, const mitk::BaseGeometry::BoundingBoxType& rightHandSide, ScalarType eps, bool verbose); } // namespace mitk #endif /* BaseGeometry_H_HEADER_INCLUDED */ diff --git a/Modules/Core/include/mitkDisplayGeometry.h b/Modules/Core/include/mitkDisplayGeometry.h index 3b06b46c4e..cf1735c841 100644 --- a/Modules/Core/include/mitkDisplayGeometry.h +++ b/Modules/Core/include/mitkDisplayGeometry.h @@ -1,245 +1,238 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef mitkDisplayGeometry_h #define mitkDisplayGeometry_h #include "mitkPlaneGeometry.h" namespace mitk { /** \brief Describes the geometry on the display/screen for 2D display. The main purpose of this class is to convert between display coordinates (in display-units) and world coordinates (in mm). DisplayGeometry depends on the size of the display area (widget width and - height, m_SizeInDisplayUnits) and on a PlaneGeometry (m_WoldGeometry). It + height, m_SizeInDisplayUnits) and on a PlaneGeometry (m_WoldGeometry). It represents a recangular view on this world-geometry. E.g., you can tell the DisplayGeometry to fit the world-geometry in the display area by calling Fit(). Provides methods for zooming and panning. Zooming and panning can be restricted within reasonable bounds by setting the ConstrainZoomingAndPanning flag. In these cases you can re-define what bounds you accept as "reasonable" by calling \warning \em Units refers to the units of the underlying world-geometry. Take care, whether these are really the units you want to convert to. E.g., when you want to convert a point \a pt_display (which is 2D) given in display coordinates into a point in units of a BaseData-object @a datum (the requested point is 3D!), use \code displaygeometry->DisplayToWorld(pt_display, pt2d_mm); displaygeometry->Map(pt2d_mm, pt3d_mm); datum->GetGeometry()->WorldToIndex(pt3d_mm, pt3d_datum_units); \endcode Even, if you want to convert the 2D point \a pt_display into a 2D point in units on a certain 2D geometry \a certaingeometry, it is safer to use \code displaygeometry->DisplayToWorld(pt_display, pt_mm); certaingeometry->WorldToIndex(pt_mm, pt_certain_geometry_units); \endcode unless you can be sure that the underlying geometry of \a displaygeometry is really the \a certaingeometry. \ingroup Geometry - */ + */ class MITKCORE_EXPORT DisplayGeometry : public PlaneGeometry { public: - mitkClassMacro(DisplayGeometry,PlaneGeometry); + mitkClassMacro(DisplayGeometry, PlaneGeometry); /// Method for creation through the object factory. itkFactorylessNewMacro(Self) - itkCloneMacro(Self) + itkCloneMacro(Self) - /// \brief duplicates the geometry, NOT useful for this sub-class - virtual itk::LightObject::Pointer InternalClone() const; + /// \brief duplicates the geometry, NOT useful for this sub-class + virtual itk::LightObject::Pointer InternalClone() const; /// \return this objects modified time. virtual unsigned long GetMTime() const; //virtual const TimeBounds& GetTimeBounds() const; // size definition methods virtual void SetWorldGeometry(const PlaneGeometry* aWorldGeometry); itkGetConstObjectMacro(WorldGeometry, PlaneGeometry); /// \return if new origin was within accepted limits virtual bool SetOriginInMM(const Vector2D& origin_mm); virtual Vector2D GetOriginInMM() const; virtual Vector2D GetOriginInDisplayUnits() const; /** \brief Set the size of the display in display units. This method must be called every time the display is resized (normally, the GUI-toolkit informs about resizing). \param keepDisplayedRegion: if \a true (the default), the displayed contents is zoomed/shrinked so that the displayed region is (approximately) the same as before: The point at the center will be kept at the center and the length of the diagonal of the displayed region \em in \em units will also be kept. When the aspect ration changes, the displayed region includes the old displayed region, but cannot be exaclty the same. */ - virtual void SetSizeInDisplayUnits(unsigned int width, unsigned int height, bool keepDisplayedRegion=true); + virtual void SetSizeInDisplayUnits(unsigned int width, unsigned int height, bool keepDisplayedRegion = true); virtual Vector2D GetSizeInDisplayUnits() const; virtual Vector2D GetSizeInMM() const; unsigned int GetDisplayWidth() const; unsigned int GetDisplayHeight() const; // zooming, panning, restriction of both virtual void SetConstrainZoomingAndPanning(bool constrain); virtual bool GetConstrainZommingAndPanning() const; /// what percentage of the world should be visible at maximum zoom out (default 1.0, i.e. 100% of width or height) itkGetMacro(MaxWorldViewPercentage, float); itkSetMacro(MaxWorldViewPercentage, float); /// what percentage of the world should be visible at maximum zoom in (default 0.1, i.e. 10% of width or height) itkGetMacro(MinWorldViewPercentage, float); itkSetMacro(MinWorldViewPercentage, float); virtual bool SetScaleFactor(ScalarType mmPerDisplayUnit); ScalarType GetScaleFactorMMPerDisplayUnit() const; /** * \brief Zooms with a factor (1.0=identity) to/from the specified center in display units * \return true if zoom request was within accepted limits */ virtual bool Zoom(ScalarType factor, const Point2D& centerInDisplayUnits); /** * \brief Zooms with a factor (1.0=identity) to/from the specified center, trying to preserve the center of zoom in world coordiantes * * Same zoom as mentioned above but tries (if it's within view contraints) to match the center in display units with the center in world coordinates. * * \return true if zoom request was within accepted limits */ - virtual bool ZoomWithFixedWorldCoordinates(ScalarType factor, const Point2D& focusDisplayUnits, const Point2D& focusUnitsInMM ); + virtual bool ZoomWithFixedWorldCoordinates(ScalarType factor, const Point2D& focusDisplayUnits, const Point2D& focusUnitsInMM); // \return true if move request was within accepted limits virtual bool MoveBy(const Vector2D& shiftInDisplayUnits); // \brief align display with world, make world completely visible virtual void Fit(); // conversion methods virtual void DisplayToWorld(const Point2D &pt_display, Point2D &pt_mm) const; virtual void WorldToDisplay(const Point2D &pt_mm, Point2D &pt_display) const; virtual void DisplayToWorld(const Vector2D &vec_display, Vector2D &vec_mm) const; virtual void WorldToDisplay(const Vector2D &vec_mm, Vector2D &vec_display) const; virtual void ULDisplayToMM(const Point2D &pt_ULdisplay, Point2D &pt_mm) const; virtual void MMToULDisplay(const Point2D &pt_mm, Point2D &pt_ULdisplay) const; virtual void ULDisplayToMM(const Vector2D &vec_ULdisplay, Vector2D &vec_mm) const; virtual void MMToULDisplay(const Vector2D &vec_mm, Vector2D &vec_ULdisplay) const; virtual void ULDisplayToDisplay(const Point2D &pt_ULdisplay, Point2D &pt_display) const; virtual void DisplayToULDisplay(const Point2D &pt_display, Point2D &pt_ULdisplay) const; virtual void ULDisplayToDisplay(const Vector2D &vec_ULdisplay, Vector2D &vec_display) const; virtual void DisplayToULDisplay(const Vector2D &vec_display, Vector2D &vec_ULdisplay) const; /** * \brief projects the given point onto current 2D world geometry plane */ virtual bool Project(const Point3D &pt3d_mm, Point3D &projectedPt3d_mm) const; /** * \brief projects the given vector onto current 2D world geometry plane. * \warning DEPRECATED, please use Project(const Vector3D &vec3d_mm, Vector3D &projectedVec3d_mm) instead */ virtual bool Project(const Point3D & atPt3d_mm, const Vector3D &vec3d_mm, Vector3D &projectedVec3d_mm) const; /** * \brief projects the given vector onto current 2D world geometry plane */ virtual bool Project(const Vector3D &vec3d_mm, Vector3D &projectedVec3d_mm) const; virtual bool Map(const Point3D &pt3d_mm, Point2D &pt2d_mm) const; virtual void Map(const Point2D &pt2d_mm, Point3D &pt3d_mm) const; virtual bool Map(const Point3D & atPt3d_mm, const Vector3D &vec3d_mm, Vector2D &vec2d_mm) const; virtual void Map(const Point2D & atPt2d_mm, const Vector2D &vec2d_mm, Vector3D &vec3d_mm) const; virtual bool IsValid() const; - virtual bool IsAbove( const Point3D &pt3d_mm , bool /*considerBoundingBox=false*/) const { return Superclass::IsAbove(pt3d_mm, true);}; + virtual bool IsAbove(const Point3D &pt3d_mm, bool /*considerBoundingBox=false*/) const { return Superclass::IsAbove(pt3d_mm, true); }; protected: DisplayGeometry(); virtual ~DisplayGeometry(); /** \brief Called after zooming/panning to restrict these operations to sensible measures. \return true if a correction in either zooming or panning was made Enforces a couple of constraints on the relation of the current viewport and the current world geometry. The basic logic in this lengthy method is:
  1. Make display region big enough (in case of too large zoom factors)
  2. Make display region small enough (so that the image cannot be scaled into a single screen pixel
  3. Correct panning for each border (left, right, bottom, top)
The little more complicated implementation is illustrated in the code itself. - */ + */ virtual bool RefitVisibleRect(); virtual void PrintSelf(std::ostream& os, itk::Indent indent) const; Vector2D m_OriginInMM; Vector2D m_OriginInDisplayUnits; ScalarType m_ScaleFactorMMPerDisplayUnit; Vector2D m_SizeInMM; Vector2D m_SizeInDisplayUnits; PlaneGeometry::ConstPointer m_WorldGeometry; bool m_ConstrainZoomingAndPanning; float m_MaxWorldViewPercentage; float m_MinWorldViewPercentage; //##Documentation - //## @brief Pre- and Post-functions are empty in BaseGeometry + //## @brief PreSetSpacing //## - //## These virtual functions allow for a different beahiour in subclasses. - //## Do implement them in every subclass of BaseGeometry. If not needed, use {}. - //## If this class is inherited from a subclass of BaseGeometry, call {Superclass::Pre...();};, example: DisplayGeometry class - virtual void PostInitialize(){Superclass::PostInitialize();}; - virtual void PostInitializeGeometry(mitk::BaseGeometry::Self * newGeometry) const{Superclass::PostInitializeGeometry(newGeometry);}; - virtual void PreSetSpacing(const mitk::Vector3D& aSpacing){Superclass::PreSetSpacing(aSpacing);}; - virtual void PreSetBounds( const BoundingBox::BoundsArrayType &bounds ){Superclass::PreSetBounds(bounds);}; - virtual void PreSetIndexToWorldTransform( AffineTransform3D *transform){Superclass::PreSetIndexToWorldTransform(transform);}; - virtual void PostSetExtentInMM(int direction, ScalarType extentInMM){Superclass::PostSetExtentInMM(direction,extentInMM);}; - virtual void PostSetIndexToWorldTransform(mitk::AffineTransform3D* transform){Superclass::PostSetIndexToWorldTransform(transform);}; - + //## These virtual function allows a different beahiour in subclasses. + //## Do implement them in every subclass of BaseGeometry. If not needed, use + //## {Superclass::PreSetSpacing();}; + virtual void PreSetSpacing(const mitk::Vector3D& aSpacing){ Superclass::PreSetSpacing(aSpacing); }; }; } // namespace #endif // include guard diff --git a/Modules/Core/include/mitkGeometry3D.h b/Modules/Core/include/mitkGeometry3D.h index f561276232..25959e6c76 100644 --- a/Modules/Core/include/mitkGeometry3D.h +++ b/Modules/Core/include/mitkGeometry3D.h @@ -1,87 +1,81 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef GEOMETRY3D_H_HEADER_INCLUDED_C1EBD0AD #define GEOMETRY3D_H_HEADER_INCLUDED_C1EBD0AD #include #include #include "mitkNumericTypes.h" #include "itkScalableAffineTransform.h" #include #include "mitkBaseGeometry.h" class vtkLinearTransform; namespace mitk { //##Documentation //## @brief Standard implementation of BaseGeometry. //## //## @ingroup Geometry class MITKCORE_EXPORT Geometry3D : public BaseGeometry { public: mitkClassMacro(Geometry3D, mitk::BaseGeometry) - typedef itk::QuaternionRigidTransform< ScalarType > QuaternionTransformType; + typedef itk::QuaternionRigidTransform< ScalarType > QuaternionTransformType; typedef QuaternionTransformType::VnlQuaternionType VnlQuaternionType; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self) - mitkNewMacro1Param(Self, const Self&) + mitkNewMacro1Param(Self, const Self&) - itkCloneMacro(Self) + itkCloneMacro(Self) //itkGetConstReferenceMacro(TimeBounds, TimeBounds); //virtual void SetTimeBounds(const TimeBounds& timebounds); protected: Geometry3D(); - Geometry3D(const Geometry3D& ); + Geometry3D(const Geometry3D&); //##Documentation //## @brief clones the geometry //## //## Overwrite in all sub-classes. //## Normally looks like: //## \code //## Self::Pointer newGeometry = new Self(*this); //## newGeometry->UnRegister(); //## return newGeometry.GetPointer(); //## \endcode virtual itk::LightObject::Pointer InternalClone() const; virtual ~Geometry3D(); //##Documentation - //## @brief Pre- and Post-functions are empty in BaseGeometry + //## @brief PreSetSpacing //## - //## These virtual functions allow for a different beahiour in subclasses. - //## Do implement them in every subclass of BaseGeometry. If not needed, use {}. - //## If this class is inherited from a subclass of BaseGeometry, call {Superclass::Pre...();};, example: DisplayGeometry class - virtual void PreSetBounds(const BoundsArrayType& /*bounds*/) {} - virtual void PostInitialize() {} - virtual void PostInitializeGeometry(mitk::BaseGeometry::Self * /*newGeometry*/) const {} - virtual void PostSetExtentInMM(int /*direction*/, ScalarType /*extentInMM*/) {} - virtual void PreSetIndexToWorldTransform(mitk::AffineTransform3D* /*transform*/) {} - virtual void PostSetIndexToWorldTransform(mitk::AffineTransform3D* /*transform*/) {} - virtual void PreSetSpacing(const mitk::Vector3D& /*aSpacing*/) {} + //## These virtual function allows a different beahiour in subclasses. + //## Do implement them in every subclass of BaseGeometry. If not needed, use + //## {Superclass::PreSetSpacing();}; + virtual void PreSetSpacing(const mitk::Vector3D& aSpacing){ Superclass::PreSetSpacing(aSpacing); }; }; } // namespace mitk #endif /* GEOMETRY3D_H_HEADER_INCLUDED_C1EBD0AD */ diff --git a/Modules/Core/include/mitkLandmarkProjectorBasedCurvedGeometry.h b/Modules/Core/include/mitkLandmarkProjectorBasedCurvedGeometry.h index db9fe634f2..886e3f5fb0 100644 --- a/Modules/Core/include/mitkLandmarkProjectorBasedCurvedGeometry.h +++ b/Modules/Core/include/mitkLandmarkProjectorBasedCurvedGeometry.h @@ -1,83 +1,77 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef MITKLANDMARKPROJECTORBASEDCURVEDGEOMETRY_H_HEADER_INCLUDED_C1C68A2C #define MITKLANDMARKPROJECTORBASEDCURVEDGEOMETRY_H_HEADER_INCLUDED_C1C68A2C #include "mitkLandmarkProjector.h" #include "mitkAbstractTransformGeometry.h" #include "mitkPointSet.h" namespace mitk { //##Documentation //## @brief Superclass of AbstractTransformGeometry sub-classes defined //## by a set of landmarks. //## //## @ingroup Geometry class MITKCORE_EXPORT LandmarkProjectorBasedCurvedGeometry : public AbstractTransformGeometry { public: mitkClassMacro(LandmarkProjectorBasedCurvedGeometry, AbstractTransformGeometry); void SetLandmarkProjector(mitk::LandmarkProjector* aLandmarkProjector); itkGetConstObjectMacro(LandmarkProjector, mitk::LandmarkProjector); virtual void SetFrameGeometry(const mitk::BaseGeometry* frameGeometry); virtual void ComputeGeometry(); itkGetConstMacro(InterpolatingAbstractTransform, vtkAbstractTransform*); itk::LightObject::Pointer InternalClone() const; //##Documentation //## @brief Set the landmarks through which the geometry shall pass itkSetConstObjectMacro(TargetLandmarks, mitk::PointSet::DataType::PointsContainer); //##Documentation //## @brief Get the landmarks through which the geometry shall pass itkGetConstObjectMacro(TargetLandmarks, mitk::PointSet::DataType::PointsContainer); protected: LandmarkProjectorBasedCurvedGeometry(); LandmarkProjectorBasedCurvedGeometry(const LandmarkProjectorBasedCurvedGeometry& other); virtual ~LandmarkProjectorBasedCurvedGeometry(); mitk::LandmarkProjector::Pointer m_LandmarkProjector; vtkAbstractTransform* m_InterpolatingAbstractTransform; mitk::PointSet::DataType::PointsContainer::ConstPointer m_TargetLandmarks; //##Documentation - //## @brief Pre- and Post-functions are empty in BaseGeometry + //## @brief PreSetSpacing //## - //## These virtual functions allow for a different beahiour in subclasses. - //## Do implement them in every subclass of BaseGeometry. If not needed, use {}. - //## If this class is inherited from a subclass of BaseGeometry, call {Superclass::Pre...();};, example: DisplayGeometry class - virtual void PostInitialize(){Superclass::PostInitialize();}; - virtual void PostInitializeGeometry(mitk::BaseGeometry::Self * newGeometry) const{Superclass::PostInitializeGeometry(newGeometry);}; - virtual void PreSetSpacing(const mitk::Vector3D& aSpacing){Superclass::PreSetSpacing(aSpacing);}; - virtual void PreSetBounds( const BoundingBox::BoundsArrayType &bounds ){Superclass::PreSetBounds(bounds);}; - virtual void PreSetIndexToWorldTransform( AffineTransform3D *transform){Superclass::PreSetIndexToWorldTransform(transform);}; - virtual void PostSetExtentInMM(int direction, ScalarType extentInMM){Superclass::PostSetExtentInMM(direction,extentInMM);}; - virtual void PostSetIndexToWorldTransform(mitk::AffineTransform3D* transform){Superclass::PostSetIndexToWorldTransform(transform);}; + //## These virtual function allows a different beahiour in subclasses. + //## Do implement them in every subclass of BaseGeometry. If not needed, use + //## {Superclass::PreSetSpacing();}; + virtual void PreSetSpacing(const mitk::Vector3D& aSpacing){ Superclass::PreSetSpacing(aSpacing); }; }; } // namespace mitk #endif /* MITKLANDMARKPROJECTORBASEDCURVEDGEOMETRY_H_HEADER_INCLUDED_C1C68A2C */ diff --git a/Modules/Core/include/mitkPlaneGeometry.h b/Modules/Core/include/mitkPlaneGeometry.h index 9c687f83c0..2dce78dc7a 100644 --- a/Modules/Core/include/mitkPlaneGeometry.h +++ b/Modules/Core/include/mitkPlaneGeometry.h @@ -1,567 +1,571 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ /** * \brief Describes the geometry of a plane object * * Describes a two-dimensional manifold, i.e., to put it simply, * an object that can be described using a 2D coordinate-system. * * PlaneGeometry can map points between 3D world coordinates * (in mm) and the described 2D coordinate-system (in mm) by first projecting * the 3D point onto the 2D manifold and then calculating the 2D-coordinates * (in mm). These 2D-mm-coordinates can be further converted into * 2D-unit-coordinates (e.g., pixels), giving a parameter representation of * the object with parameter values inside a rectangle * (e.g., [0,0]..[width, height]), which is the bounding box (bounding range * in z-direction always [0]..[1]). * * A PlaneGeometry describes the 2D representation within a 3D object (derived from BaseGeometry). For example, * a single CT-image (slice) is 2D in the sense that you can access the * pixels using 2D-coordinates, but is also 3D, as the pixels are really * voxels, thus have an extension (thickness) in the 3rd dimension. * * * Optionally, a reference BaseGeometry can be specified, which usually would * be the geometry associated with the underlying dataset. This is currently * used for calculating the intersection of inclined / rotated planes * (represented as PlaneGeometry) with the bounding box of the associated * BaseGeometry. * * \warning The PlaneGeometry are not necessarily up-to-date and not even * initialized. As described in the previous paragraph, one of the * Generate-/Copy-/UpdateOutputInformation methods have to initialize it. * mitk::BaseData::GetPlaneGeometry() makes sure, that the PlaneGeometry is * up-to-date before returning it (by setting the update extent appropriately * and calling UpdateOutputInformation). * * Rule: everything is in mm (or ms for temporal information) if not * stated otherwise. * \ingroup Geometry */ #ifndef PLANEGEOMETRY_H_HEADER_INCLUDED_C1C68A2C #define PLANEGEOMETRY_H_HEADER_INCLUDED_C1C68A2C #include #include "mitkBaseGeometry.h" #include "mitkRestorePlanePositionOperation.h" #include namespace mitk { template < class TCoordRep, unsigned int NPointDimension > class Line; typedef Line Line3D; class PlaneGeometry; /** \deprecatedSince{2014_10} This class is deprecated. Please use PlaneGeometry instead. */ - DEPRECATED( typedef PlaneGeometry Geometry2D); + DEPRECATED(typedef PlaneGeometry Geometry2D); /** * \brief Describes a two-dimensional, rectangular plane * * \ingroup Geometry */ class MITKCORE_EXPORT PlaneGeometry : public BaseGeometry { public: - mitkClassMacro(PlaneGeometry,BaseGeometry); + mitkClassMacro(PlaneGeometry, BaseGeometry); /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self) itkCloneMacro(Self) - enum PlaneOrientation + enum PlaneOrientation { Axial, Sagittal, Frontal }; virtual void IndexToWorld(const Point2D &pt_units, Point2D &pt_mm) const; virtual void WorldToIndex(const Point2D &pt_mm, Point2D &pt_units) const; //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em vector //## \a vec_units to world coordinates (in mm) //## @deprecated First parameter (Point2D) is not used. If possible, please use void IndexToWorld(const mitk::Vector2D& vec_units, mitk::Vector2D& vec_mm) const. //## For further information about coordinates types, please see the Geometry documentation virtual void IndexToWorld(const mitk::Point2D &atPt2d_untis, const mitk::Vector2D &vec_units, mitk::Vector2D &vec_mm) const; //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em vector //## \a vec_units to world coordinates (in mm) //## For further information about coordinates types, please see the Geometry documentation virtual void IndexToWorld(const mitk::Vector2D &vec_units, mitk::Vector2D &vec_mm) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em vector //## \a vec_mm to (continuous!) index coordinates. //## @deprecated First parameter (Point2D) is not used. If possible, please use void WorldToIndex(const mitk::Vector2D& vec_mm, mitk::Vector2D& vec_units) const. //## For further information about coordinates types, please see the Geometry documentation virtual void WorldToIndex(const mitk::Point2D &atPt2d_mm, const mitk::Vector2D &vec_mm, mitk::Vector2D &vec_units) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em vector //## \a vec_mm to (continuous!) index coordinates. //## For further information about coordinates types, please see the Geometry documentation virtual void WorldToIndex(const mitk::Vector2D &vec_mm, mitk::Vector2D &vec_units) const; /** * \brief Initialize a plane with orientation \a planeorientation * (default: axial) with respect to \a BaseGeometry (default: identity). * Spacing also taken from \a BaseGeometry. * * \warning A former version of this method created a geometry with unit * spacing. For unit spacing use * * \code * // for in-plane unit spacing: * thisgeometry->SetSizeInUnits(thisgeometry->GetExtentInMM(0), * thisgeometry->GetExtentInMM(1)); * // additionally, for unit spacing in normal direction (former version * // did not do this): * thisgeometry->SetExtentInMM(2, 1.0); * \endcode */ - virtual void InitializeStandardPlane( const BaseGeometry* geometry3D, + virtual void InitializeStandardPlane(const BaseGeometry* geometry3D, PlaneOrientation planeorientation = Axial, ScalarType zPosition = 0, - bool frontside=true, bool rotated=false ); + bool frontside = true, bool rotated = false); /** * \brief Initialize a plane with orientation \a planeorientation * (default: axial) with respect to \a BaseGeometry (default: identity). * Spacing also taken from \a BaseGeometry. * * \param top if \a true, create plane at top, otherwise at bottom * (for PlaneOrientation Axial, for other plane locations respectively) */ - virtual void InitializeStandardPlane( const BaseGeometry* geometry3D, bool top, + virtual void InitializeStandardPlane(const BaseGeometry* geometry3D, bool top, PlaneOrientation planeorientation = Axial, - bool frontside=true, bool rotated=false ); + bool frontside = true, bool rotated = false); /** * \brief Initialize a plane with orientation \a planeorientation * (default: axial) with respect to \a transform (default: identity) * given width and height in units. * */ - virtual void InitializeStandardPlane( ScalarType width, ScalarType height, + virtual void InitializeStandardPlane(ScalarType width, ScalarType height, const AffineTransform3D* transform = NULL, PlaneOrientation planeorientation = Axial, - ScalarType zPosition = 0, bool frontside=true, bool rotated=false ); + ScalarType zPosition = 0, bool frontside = true, bool rotated = false); /** * \brief Initialize plane with orientation \a planeorientation * (default: axial) given width, height and spacing. * */ - virtual void InitializeStandardPlane( ScalarType width, ScalarType height, + virtual void InitializeStandardPlane(ScalarType width, ScalarType height, const Vector3D & spacing, PlaneOrientation planeorientation = Axial, - ScalarType zPosition = 0, bool frontside = true, bool rotated = false ); + ScalarType zPosition = 0, bool frontside = true, bool rotated = false); /** * \brief Initialize plane by width and height in pixels, right-/down-vector * (itk) to describe orientation in world-space (vectors will be normalized) * and spacing (default: 1.0 mm in all directions). * * The vectors are normalized and multiplied by the respective spacing before * they are set in the matrix. */ - virtual void InitializeStandardPlane( ScalarType width, ScalarType height, + virtual void InitializeStandardPlane(ScalarType width, ScalarType height, const Vector3D& rightVector, const Vector3D& downVector, - const Vector3D *spacing = NULL ); + const Vector3D *spacing = NULL); /** * \brief Initialize plane by width and height in pixels, * right-/down-vector (vnl) to describe orientation in world-space (vectors * will be normalized) and spacing (default: 1.0 mm in all directions). * * The vectors are normalized and multiplied by the respective spacing * before they are set in the matrix. */ - virtual void InitializeStandardPlane( ScalarType width, ScalarType height, + virtual void InitializeStandardPlane(ScalarType width, ScalarType height, const VnlVector& rightVector, const VnlVector& downVector, - const Vector3D * spacing = NULL ); + const Vector3D * spacing = NULL); /** * \brief Initialize plane by right-/down-vector (itk) and spacing * (default: 1.0 mm in all directions). * * The length of the right-/-down-vector is used as width/height in units, * respectively. Then, the vectors are normalized and multiplied by the * respective spacing before they are set in the matrix. */ - virtual void InitializeStandardPlane( const Vector3D& rightVector, - const Vector3D& downVector, const Vector3D * spacing = NULL ); + virtual void InitializeStandardPlane(const Vector3D& rightVector, + const Vector3D& downVector, const Vector3D * spacing = NULL); /** * \brief Initialize plane by right-/down-vector (vnl) and spacing * (default: 1.0 mm in all directions). * * The length of the right-/-down-vector is used as width/height in units, * respectively. Then, the vectors are normalized and multiplied by the * respective spacing before they are set in the matrix. */ - virtual void InitializeStandardPlane( const VnlVector& rightVector, - const VnlVector& downVector, const Vector3D * spacing = NULL ); + virtual void InitializeStandardPlane(const VnlVector& rightVector, + const VnlVector& downVector, const Vector3D * spacing = NULL); /** * \brief Initialize plane by origin and normal (size is 1.0 mm in * all directions, direction of right-/down-vector valid but * undefined). * */ - virtual void InitializePlane( const Point3D& origin, const Vector3D& normal); + virtual void InitializePlane(const Point3D& origin, const Vector3D& normal); /** * \brief Initialize plane by right-/down-vector. * * \warning The vectors are set into the matrix as they are, * \em without normalization! */ - void SetMatrixByVectors( const VnlVector& rightVector, - const VnlVector& downVector, ScalarType thickness=1.0 ); + void SetMatrixByVectors(const VnlVector& rightVector, + const VnlVector& downVector, ScalarType thickness = 1.0); /** * \brief Change \a transform so that the third column of the * transform-martix is perpendicular to the first two columns * */ - static void EnsurePerpendicularNormal( AffineTransform3D* transform ); + static void EnsurePerpendicularNormal(AffineTransform3D* transform); /** * \brief Normal of the plane * */ Vector3D GetNormal() const; /** * \brief Normal of the plane as VnlVector * */ VnlVector GetNormalVnl() const; - virtual ScalarType SignedDistance( const Point3D& pt3d_mm ) const; + virtual ScalarType SignedDistance(const Point3D& pt3d_mm) const; /** * \brief Calculates, whether a point is below or above the plane. There are two different *calculation methods, with or without consideration of the bounding box. */ - virtual bool IsAbove( const Point3D& pt3d_mm , bool considerBoundingBox=false) const; + virtual bool IsAbove(const Point3D& pt3d_mm, bool considerBoundingBox = false) const; /** * \brief Distance of the point from the plane * (bounding-box \em not considered) * */ - ScalarType DistanceFromPlane( const Point3D& pt3d_mm ) const ; + ScalarType DistanceFromPlane(const Point3D& pt3d_mm) const; /** * \brief Signed distance of the point from the plane * (bounding-box \em not considered) * * > 0 : point is in the direction of the direction vector. */ - inline ScalarType SignedDistanceFromPlane( const Point3D& pt3d_mm ) const + inline ScalarType SignedDistanceFromPlane(const Point3D& pt3d_mm) const { ScalarType len = GetNormalVnl().two_norm(); - if( len == 0 ) + if (len == 0) return 0; - return (pt3d_mm-GetOrigin())*GetNormal() / len; + return (pt3d_mm - GetOrigin())*GetNormal() / len; } /** * \brief Distance of the plane from another plane * (bounding-box \em not considered) * * Result is 0 if planes are not parallel. */ ScalarType DistanceFromPlane(const PlaneGeometry* plane) const { return fabs(SignedDistanceFromPlane(plane)); } /** * \brief Signed distance of the plane from another plane * (bounding-box \em not considered) * * Result is 0 if planes are not parallel. */ - inline ScalarType SignedDistanceFromPlane( const PlaneGeometry *plane ) const + inline ScalarType SignedDistanceFromPlane(const PlaneGeometry *plane) const { - if(IsParallel(plane)) + if (IsParallel(plane)) { return SignedDistance(plane->GetOrigin()); } return 0; } /** * \brief Calculate the intersecting line of two planes * * \return \a true planes are intersecting * \return \a false planes do not intersect */ - bool IntersectionLine( const PlaneGeometry *plane, Line3D &crossline ) const; + bool IntersectionLine(const PlaneGeometry *plane, Line3D &crossline) const; /** * \brief Calculate two points where another plane intersects the border of this plane * * \return number of intersection points (0..2). First interection point (if existing) * is returned in \a lineFrom, second in \a lineTo. */ unsigned int IntersectWithPlane2D(const PlaneGeometry *plane, - Point2D &lineFrom, Point2D &lineTo ) const ; + Point2D &lineFrom, Point2D &lineTo) const; /** * \brief Calculate the angle between two planes * * \return angle in radiants */ - double Angle( const PlaneGeometry *plane ) const; + double Angle(const PlaneGeometry *plane) const; /** * \brief Calculate the angle between the plane and a line * * \return angle in radiants */ - double Angle( const Line3D &line ) const; + double Angle(const Line3D &line) const; /** * \brief Calculate intersection point between the plane and a line * * \param intersectionPoint intersection point * \return \a true if \em unique intersection exists, i.e., if line * is \em not on or parallel to the plane */ - bool IntersectionPoint( const Line3D &line, - Point3D &intersectionPoint ) const; + bool IntersectionPoint(const Line3D &line, + Point3D &intersectionPoint) const; /** * \brief Calculate line parameter of intersection point between the * plane and a line * * \param t parameter of line: intersection point is * line.GetPoint()+t*line.GetDirection() * \return \a true if \em unique intersection exists, i.e., if line * is \em not on or parallel to the plane */ - bool IntersectionPointParam( const Line3D &line, double &t ) const; + bool IntersectionPointParam(const Line3D &line, double &t) const; /** * \brief Returns whether the plane is parallel to another plane * * @return true iff the normal vectors both point to the same or exactly oposit direction */ - bool IsParallel( const PlaneGeometry *plane ) const; + bool IsParallel(const PlaneGeometry *plane) const; /** * \brief Returns whether the point is on the plane * (bounding-box \em not considered) */ - bool IsOnPlane( const Point3D &point ) const; + bool IsOnPlane(const Point3D &point) const; /** * \brief Returns whether the line is on the plane * (bounding-box \em not considered) */ - bool IsOnPlane( const Line3D &line ) const; + bool IsOnPlane(const Line3D &line) const; /** * \brief Returns whether the plane is on the plane * (bounding-box \em not considered) * * @return true iff the normal vector of the planes point to the same or the exactly oposit direction and * the distance of the planes is < eps * */ - bool IsOnPlane( const PlaneGeometry *plane ) const; + bool IsOnPlane(const PlaneGeometry *plane) const; /** * \brief Returns the lot from the point to the plane */ - Point3D ProjectPointOntoPlane( const Point3D &pt ) const; + Point3D ProjectPointOntoPlane(const Point3D &pt) const; virtual itk::LightObject::Pointer InternalClone() const; /** Implements operation to re-orient the plane */ - virtual void ExecuteOperation( Operation *operation ); + virtual void ExecuteOperation(Operation *operation); /** * \brief Project a 3D point given in mm (\a pt3d_mm) onto the 2D * geometry. The result is a 2D point in mm (\a pt2d_mm). * * The result is a 2D point in mm (\a pt2d_mm) relative to the upper-left * corner of the geometry. To convert this point into units (e.g., pixels * in case of an image), use WorldToIndex. * \return true projection was possible * \sa Project(const mitk::Point3D &pt3d_mm, mitk::Point3D * &projectedPt3d_mm) */ virtual bool Map(const mitk::Point3D &pt3d_mm, mitk::Point2D &pt2d_mm) const; /** * \brief Converts a 2D point given in mm (\a pt2d_mm) relative to the * upper-left corner of the geometry into the corresponding * world-coordinate (a 3D point in mm, \a pt3d_mm). * * To convert a 2D point given in units (e.g., pixels in case of an * image) into a 2D point given in mm (as required by this method), use * IndexToWorld. */ virtual void Map(const mitk::Point2D &pt2d_mm, mitk::Point3D &pt3d_mm) const; /** * \brief Set the width and height of this 2D-geometry in units by calling * SetBounds. This does \a not change the extent in mm! * * For an image, this is the number of pixels in x-/y-direction. * \note In contrast to calling SetBounds directly, this does \a not change * the extent in mm! */ virtual void SetSizeInUnits(mitk::ScalarType width, mitk::ScalarType height); /** * \brief Project a 3D point given in mm (\a pt3d_mm) onto the 2D * geometry. The result is a 3D point in mm (\a projectedPt3d_mm). * * \return true projection was possible */ virtual bool Project(const mitk::Point3D &pt3d_mm, mitk::Point3D &projectedPt3d_mm) const; /** * \brief Project a 3D vector given in mm (\a vec3d_mm) onto the 2D * geometry. The result is a 2D vector in mm (\a vec2d_mm). * * The result is a 2D vector in mm (\a vec2d_mm) relative to the * upper-left * corner of the geometry. To convert this point into units (e.g., pixels * in case of an image), use WorldToIndex. * \return true projection was possible * \sa Project(const mitk::Vector3D &vec3d_mm, mitk::Vector3D * &projectedVec3d_mm) */ virtual bool Map(const mitk::Point3D & atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector2D &vec2d_mm) const; /** * \brief Converts a 2D vector given in mm (\a vec2d_mm) relative to the * upper-left corner of the geometry into the corresponding * world-coordinate (a 3D vector in mm, \a vec3d_mm). * * To convert a 2D vector given in units (e.g., pixels in case of an * image) into a 2D vector given in mm (as required by this method), use * IndexToWorld. */ virtual void Map(const mitk::Point2D & atPt2d_mm, const mitk::Vector2D &vec2d_mm, mitk::Vector3D &vec3d_mm) const; /** * \brief Project a 3D vector given in mm (\a vec3d_mm) onto the 2D * geometry. The result is a 3D vector in mm (\a projectedVec3d_mm). * * DEPRECATED. Use Project(vector,vector) instead * * \return true projection was possible */ virtual bool Project(const mitk::Point3D & atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const; /** * \brief Project a 3D vector given in mm (\a vec3d_mm) onto the 2D * geometry. The result is a 3D vector in mm (\a projectedVec3d_mm). * * \return true projection was possible */ - virtual bool Project( const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const; + virtual bool Project(const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const; /** * \brief Distance of the point from the geometry * (bounding-box \em not considered) * */ inline ScalarType Distance(const Point3D& pt3d_mm) const { return fabs(SignedDistance(pt3d_mm)); } /** * \brief Set the geometrical frame of reference in which this PlaneGeometry * is placed. * * This would usually be the BaseGeometry of the underlying dataset, but * setting it is optional. */ - void SetReferenceGeometry( mitk::BaseGeometry *geometry ); + void SetReferenceGeometry(mitk::BaseGeometry *geometry); /** * \brief Get the geometrical frame of reference for this PlaneGeometry. */ BaseGeometry *GetReferenceGeometry() const; bool HasReferenceGeometry() const; protected: PlaneGeometry(); PlaneGeometry(const PlaneGeometry& other); virtual ~PlaneGeometry(); - virtual void PrintSelf( std::ostream &os, itk::Indent indent ) const; + virtual void PrintSelf(std::ostream &os, itk::Indent indent) const; mitk::BaseGeometry *m_ReferenceGeometry; - - - - //##Documentation - //## @brief Pre- and Post-functions are empty in BaseGeometry + //## @brief PreSetSpacing //## - //## These virtual functions allow for a different beahiour in subclasses. - //## Do implement them in every subclass. If not needed, use {}. - virtual void PostInitialize() {} - virtual void PostInitializeGeometry(mitk::BaseGeometry::Self * /*newGeometry*/) const {} - virtual void PreSetSpacing(const mitk::Vector3D& /*aSpacing*/) {} - - virtual void PostSetExtentInMM(int /*direction*/, ScalarType /*extentInMM*/) {} - virtual void PostSetIndexToWorldTransform(mitk::AffineTransform3D* /*transform*/) {} + //## These virtual function allows a different beahiour in subclasses. + //## Do implement them in every subclass of BaseGeometry. If not needed, use + //## {Superclass::PreSetSpacing();}; + virtual void PreSetSpacing(const mitk::Vector3D& aSpacing){ Superclass::PreSetSpacing(aSpacing); }; - virtual void PreSetBounds(const BoundsArrayType& bounds); - virtual void PreSetIndexToWorldTransform( AffineTransform3D * transform); + //##Documentation + //## @brief 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 well!) + virtual void CheckBounds(const BoundsArrayType& bounds); + //##Documentation + //## @brief CheckIndexToWorldTransform + //## + //## This function is called in SetIndexToWorldTransform. Assertions can be implemented in this function (see PlaneGeometry.cpp). + //## In Subclasses of BaseGeometry, implement own conditions or call Superclass::CheckBounds(bounds);. + virtual void CheckIndexToWorldTransform(mitk::AffineTransform3D* transform); private: /** * \brief Compares plane with another plane: \a true if IsOnPlane * (bounding-box \em not considered) */ - virtual bool operator==( const PlaneGeometry * ) const { return false; }; + virtual bool operator==(const PlaneGeometry *) const { return false; }; /** * \brief Compares plane with another plane: \a false if IsOnPlane * (bounding-box \em not considered) */ - virtual bool operator!=( const PlaneGeometry * ) const { return false; }; + virtual bool operator!=(const PlaneGeometry *) const { return false; }; }; } // namespace mitk #endif /* PLANEGEOMETRY_H_HEADER_INCLUDED_C1C68A2C */ diff --git a/Modules/Core/include/mitkSlicedGeometry3D.h b/Modules/Core/include/mitkSlicedGeometry3D.h index 7bf25fc880..690cdd88d9 100644 --- a/Modules/Core/include/mitkSlicedGeometry3D.h +++ b/Modules/Core/include/mitkSlicedGeometry3D.h @@ -1,335 +1,321 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef MITKSLICEDGEOMETRY3D_H_HEADER_INCLUDED_C1EBD0AD #define MITKSLICEDGEOMETRY3D_H_HEADER_INCLUDED_C1EBD0AD #include "mitkBaseGeometry.h" #include "mitkPlaneGeometry.h" namespace mitk { class SliceNavigationController; class NavigationController; /** \brief Describes the geometry of a data object consisting of slices. * * A PlaneGeometry can be requested for each slice. In the case of * \em evenly-spaced, \em 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 * * \sa itk::ProcessObject::GenerateOutputInformation(), * \sa itk::DataObject::CopyInformation() and * \a 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(). * * \ingroup Geometry */ class MITKCORE_EXPORT SlicedGeometry3D : public mitk::BaseGeometry { public: mitkClassMacro(SlicedGeometry3D, BaseGeometry) - /** Method for creation through the object factory. */ - itkFactorylessNewMacro(Self) + /** Method for creation through the object factory. */ + itkFactorylessNewMacro(Self) itkCloneMacro(Self) /** * \brief Returns the PlaneGeometry of the slice (\a 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 * * \sa itk::ProcessObject::GenerateOutputInformation(), * \sa itk::DataObject::CopyInformation() and * \sa itk::DataObject::UpdateOutputInformation(). */ - virtual mitk::PlaneGeometry* GetPlaneGeometry( int s ) const; - /** - * \deprecatedSince{2014_10} Please use GetPlaneGeometry - */ - DEPRECATED(const PlaneGeometry* GetGeometry2D(int s)){return GetPlaneGeometry(s);} - + virtual mitk::PlaneGeometry* GetPlaneGeometry(int s) const; + /** +* \deprecatedSince{2014_10} Please use GetPlaneGeometry +*/ + DEPRECATED(const PlaneGeometry* GetGeometry2D(int s)){ return GetPlaneGeometry(s); } /** * \deprecatedSince{2014_10} Please use SetPlaneGeometry */ - DEPRECATED(void SetGeometry2D(PlaneGeometry* geo, int s)){SetPlaneGeometry(geo, s);} + DEPRECATED(void SetGeometry2D(PlaneGeometry* geo, int s)){ SetPlaneGeometry(geo, s); } //##Documentation //## @brief When switching from an Image Geometry to a normal Geometry (and the other way around), you have to change the origin as well (See Geometry Documentation)! This function will change the "isImageGeometry" bool flag and changes the origin respectively. - virtual void ChangeImageGeometryConsideringOriginOffset( const bool isAnImageGeometry ); + virtual void ChangeImageGeometryConsideringOriginOffset(const bool isAnImageGeometry); - //virtual void SetTimeBounds( const mitk::TimeBounds& timebounds ); + //virtual void SetTimeBounds( const mitk::TimeBounds& timebounds ); virtual const mitk::BoundingBox* GetBoundingBox() const; /** * \brief Get the number of slices */ - itkGetConstMacro( Slices, unsigned int ) - - /** - * \brief Set PlaneGeometry of slice \a s. - */ - virtual bool SetPlaneGeometry( mitk::PlaneGeometry *geometry2D, int s ); + itkGetConstMacro(Slices, unsigned int) + /** + * \brief Set PlaneGeometry of slice \a s. + */ + virtual bool SetPlaneGeometry(mitk::PlaneGeometry *geometry2D, int s); /** * \brief Check whether a slice exists */ - virtual bool IsValidSlice( int s = 0 ) const; + virtual bool IsValidSlice(int s = 0) const; - virtual void SetReferenceGeometry( BaseGeometry *referenceGeometry ); + virtual void SetReferenceGeometry(BaseGeometry *referenceGeometry); /** * \brief 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. */ virtual void SetSliceNavigationController( - mitk::SliceNavigationController *snc ); + mitk::SliceNavigationController *snc); mitk::SliceNavigationController *GetSliceNavigationController(); /** * \brief 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. * * \sa GetPlaneGeometry */ itkGetConstMacro(EvenlySpaced, bool) - virtual void SetEvenlySpaced(bool on = true); + virtual void SetEvenlySpaced(bool on = true); /** * \brief 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. * * \sa m_DirectionVector */ virtual void SetDirectionVector(const mitk::Vector3D& directionVector); itkGetConstMacro(DirectionVector, const mitk::Vector3D&) - virtual itk::LightObject::Pointer InternalClone() const; + virtual itk::LightObject::Pointer InternalClone() const; static const std::string SLICES; const static std::string DIRECTION_VECTOR; const static std::string EVENLY_SPACED; /** * \brief 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(). */ - virtual void InitializeSlicedGeometry( unsigned int slices ); + virtual void InitializeSlicedGeometry(unsigned int slices); /** * \brief 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 \a slices. The spacing is calculated from the PlaneGeometry. */ - virtual void InitializeEvenlySpaced( mitk::PlaneGeometry *geometry2D, - unsigned int slices, bool flipped=false ); + virtual void InitializeEvenlySpaced(mitk::PlaneGeometry *geometry2D, + unsigned int slices, bool flipped = false); /** * \brief 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 \a slices. The x-/y-spacing is calculated from the * PlaneGeometry. */ - virtual void InitializeEvenlySpaced( mitk::PlaneGeometry *geometry2D, - mitk::ScalarType zSpacing, unsigned int slices, bool flipped=false ); + virtual void InitializeEvenlySpaced(mitk::PlaneGeometry *geometry2D, + mitk::ScalarType zSpacing, unsigned int slices, bool flipped = false); /** * \brief 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). * * \param planeorientation side parallel to which the slices will be oriented * \param top if \a true, create plane at top, otherwise at bottom * (for PlaneOrientation Axial, for other plane locations respectively) * \param frontside defines the side of the plane (the definition of * front/back is somewhat arbitrary) * * \param rotate rotates the plane by 180 degree around its normal (the * definition of rotated vs not rotated is somewhat arbitrary) */ - virtual void InitializePlanes( const mitk::BaseGeometry *geometry3D, - mitk::PlaneGeometry::PlaneOrientation planeorientation, bool top=true, - bool frontside=true, bool rotated=false ); + virtual void InitializePlanes(const mitk::BaseGeometry *geometry3D, + mitk::PlaneGeometry::PlaneOrientation planeorientation, bool top = true, + bool frontside = true, bool rotated = false); virtual void SetImageGeometry(const bool isAnImageGeometry); virtual void ExecuteOperation(Operation* operation); - static double CalculateSpacing( const mitk::Vector3D spacing, const mitk::Vector3D &d ); + static double CalculateSpacing(const mitk::Vector3D spacing, const mitk::Vector3D &d); protected: SlicedGeometry3D(); SlicedGeometry3D(const SlicedGeometry3D& other); virtual ~SlicedGeometry3D(); /** * Reinitialize plane stack after rotation. More precisely, the first plane * of the stack needs to spatially aligned, in two respects: * * 1. 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. * 2. 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. */ - virtual void ReinitializePlanes( const Point3D ¢er, - const Point3D &referencePoint ); + virtual void ReinitializePlanes(const Point3D ¢er, + const Point3D &referencePoint); - ScalarType GetLargestExtent( const BaseGeometry *geometry ); + ScalarType GetLargestExtent(const BaseGeometry *geometry); void PrintSelf(std::ostream& os, itk::Indent indent) const; /** Calculate "directed spacing", i.e. the spacing in directions * non-orthogonal to the coordinate axes. This is done via the * ellipsoid equation. */ - double CalculateSpacing( const mitk::Vector3D &direction ) const; + double CalculateSpacing(const mitk::Vector3D &direction) const; /** 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. */ - mitk::Vector3D AdjustNormal( const mitk::Vector3D &normal ) const; + mitk::Vector3D AdjustNormal(const mitk::Vector3D &normal) const; /** * Container for the 2D-geometries contained within this SliceGeometry3D. */ mutable std::vector m_PlaneGeometries; /** * 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. * * \sa GetPlaneGeometry */ bool m_EvenlySpaced; /** * 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. */ mutable mitk::Vector3D m_DirectionVector; /** Number of slices this SliceGeometry3D is descibing. */ unsigned int m_Slices; /** Underlying BaseGeometry for this SlicedGeometry */ mitk::BaseGeometry *m_ReferenceGeometry; /** SNC correcsponding to this geometry; used to reflect changes in the * number of slices due to rotation. */ //mitk::NavigationController *m_NavigationController; mitk::SliceNavigationController *m_SliceNavigationController; - - - /** - * @brief Pre- and Post-functions are empty in BaseGeometry - * - * These virtual functions allow for a different beahiour in subclasses. - * Do implement them in every subclass. If not needed, use {}. - */ - virtual void PostInitialize() {} - virtual void PostInitializeGeometry(mitk::BaseGeometry::Self * /*newGeometry*/) const {} - virtual void PostSetExtentInMM(int /*direction*/, ScalarType /*extentInMM*/) {} - virtual void PreSetIndexToWorldTransform(mitk::AffineTransform3D* /*transform*/) {} - virtual void PostSetIndexToWorldTransform(mitk::AffineTransform3D* /*transform*/) {} - virtual void PreSetBounds(const BoundsArrayType& /*bounds*/) {} - - /** - * \brief Set the spacing (m_Spacing), in direction of the plane normal. - */ - virtual void PreSetSpacing( const mitk::Vector3D &aSpacing ); + //##Documentation + //## @brief PreSetSpacing + //## + //## These virtual function allows a different beahiour in subclasses. + //## Do implement them in every subclass of BaseGeometry. If not needed, use + //## {Superclass::PreSetSpacing();}; + virtual void PreSetSpacing(const mitk::Vector3D& aSpacing); }; } // namespace mitk #endif /* MITKSLICEDGEOMETRY3D_H_HEADER_INCLUDED_C1EBD0AD */ diff --git a/Modules/Core/include/mitkThinPlateSplineCurvedGeometry.h b/Modules/Core/include/mitkThinPlateSplineCurvedGeometry.h index cb650c092f..f1b19e1042 100644 --- a/Modules/Core/include/mitkThinPlateSplineCurvedGeometry.h +++ b/Modules/Core/include/mitkThinPlateSplineCurvedGeometry.h @@ -1,79 +1,73 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef MITKTHINPLATESPLINECURVEDGEOMETRY_H_HEADER_INCLUDED_C1C68A2C #define MITKTHINPLATESPLINECURVEDGEOMETRY_H_HEADER_INCLUDED_C1C68A2C #include "mitkLandmarkProjectorBasedCurvedGeometry.h" class vtkPoints; class vtkThinPlateSplineTransform; namespace mitk { //##Documentation //## @brief Thin-plate-spline-based landmark-based curved geometry //## //## @ingroup Geometry class MITKCORE_EXPORT ThinPlateSplineCurvedGeometry : public LandmarkProjectorBasedCurvedGeometry { public: mitkClassMacro(ThinPlateSplineCurvedGeometry, LandmarkProjectorBasedCurvedGeometry); itkFactorylessNewMacro(Self) itkCloneMacro(Self) virtual void ComputeGeometry(); virtual itk::LightObject::Pointer InternalClone() const; vtkThinPlateSplineTransform* GetThinPlateSplineTransform() const { return m_ThinPlateSplineTransform; } virtual void SetSigma(double sigma); virtual double GetSigma() const; virtual bool IsValid() const; protected: ThinPlateSplineCurvedGeometry(); - ThinPlateSplineCurvedGeometry(const ThinPlateSplineCurvedGeometry& other ); + ThinPlateSplineCurvedGeometry(const ThinPlateSplineCurvedGeometry& other); virtual ~ThinPlateSplineCurvedGeometry(); vtkThinPlateSplineTransform* m_ThinPlateSplineTransform; vtkPoints* m_VtkTargetLandmarks; vtkPoints* m_VtkProjectedLandmarks; //##Documentation - //## @brief Pre- and Post-functions are empty in BaseGeometry + //## @brief PreSetSpacing //## - //## These virtual functions allow for a different beahiour in subclasses. - //## Do implement them in every subclass of BaseGeometry. If not needed, use {}. - //## If this class is inherited from a subclass of BaseGeometry, call {Superclass::Pre...();};, example: DisplayGeometry class - virtual void PostInitialize(){Superclass::PostInitialize();}; - virtual void PostInitializeGeometry(mitk::BaseGeometry::Self * newGeometry) const{Superclass::PostInitializeGeometry(newGeometry);}; - virtual void PreSetSpacing(const mitk::Vector3D& aSpacing){Superclass::PreSetSpacing(aSpacing);}; - virtual void PreSetBounds( const BoundingBox::BoundsArrayType &bounds ){Superclass::PreSetBounds(bounds);}; - virtual void PreSetIndexToWorldTransform( AffineTransform3D *transform){Superclass::PreSetIndexToWorldTransform(transform);}; - virtual void PostSetExtentInMM(int direction, ScalarType extentInMM){Superclass::PostSetExtentInMM(direction,extentInMM);}; - virtual void PostSetIndexToWorldTransform(mitk::AffineTransform3D* transform){Superclass::PostSetIndexToWorldTransform(transform);}; + //## These virtual function allows a different beahiour in subclasses. + //## Do implement them in every subclass of BaseGeometry. If not needed, use + //## {Superclass::PreSetSpacing();}; + virtual void PreSetSpacing(const mitk::Vector3D& aSpacing){ Superclass::PreSetSpacing(aSpacing); }; }; } // namespace mitk #endif /* MITKTHINPLATESPLINECURVEDGEOMETRY_H_HEADER_INCLUDED_C1C68A2C */ diff --git a/Modules/Core/src/DataManagement/mitkAbstractTransformGeometry.cpp b/Modules/Core/src/DataManagement/mitkAbstractTransformGeometry.cpp index 62560923e6..6344b37b57 100644 --- a/Modules/Core/src/DataManagement/mitkAbstractTransformGeometry.cpp +++ b/Modules/Core/src/DataManagement/mitkAbstractTransformGeometry.cpp @@ -1,319 +1,315 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkAbstractTransformGeometry.h" #include mitk::AbstractTransformGeometry::AbstractTransformGeometry() : Superclass(), m_Plane(NULL), m_FrameGeometry(NULL) { Initialize(); + m_ItkVtkAbstractTransform = itk::VtkAbstractTransform::New(); } mitk::AbstractTransformGeometry::AbstractTransformGeometry(const AbstractTransformGeometry& other) : Superclass(other), m_ParametricBoundingBox(other.m_ParametricBoundingBox) { - if(other.m_ParametricBoundingBox.IsNotNull()) + if (other.m_ParametricBoundingBox.IsNotNull()) { m_ParametricBoundingBox = other.m_ParametricBoundingBox->DeepCopy(); this->SetParametricBounds(m_ParametricBoundingBox->GetBounds()); } this->SetPlane(other.m_Plane); this->SetFrameGeometry(other.m_FrameGeometry); + m_ItkVtkAbstractTransform = itk::VtkAbstractTransform::New(); } mitk::AbstractTransformGeometry::~AbstractTransformGeometry() { } -void mitk::AbstractTransformGeometry::PostInitialize() -{ - m_ItkVtkAbstractTransform = itk::VtkAbstractTransform::New(); - Superclass::PostInitialize(); -} - vtkAbstractTransform* mitk::AbstractTransformGeometry::GetVtkAbstractTransform() const { return m_ItkVtkAbstractTransform->GetVtkAbstractTransform(); } mitk::ScalarType mitk::AbstractTransformGeometry::GetParametricExtentInMM(int direction) const { - if(m_Plane.IsNull()) + if (m_Plane.IsNull()) { - itkExceptionMacro(<<"m_Plane is NULL."); + itkExceptionMacro(<< "m_Plane is NULL."); } return m_Plane->GetExtentInMM(direction); } const itk::Transform* mitk::AbstractTransformGeometry::GetParametricTransform() const { return m_ItkVtkAbstractTransform; } bool mitk::AbstractTransformGeometry::Project(const mitk::Point3D &pt3d_mm, mitk::Point3D &projectedPt3d_mm) const { - assert(this->IsBoundingBoxNull()==false); + assert(this->IsBoundingBoxNull() == false); mitk::Point2D pt2d_mm; bool isInside; isInside = Map(pt3d_mm, pt2d_mm); Map(pt2d_mm, projectedPt3d_mm); return isInside; //Point3D pt3d_units; //pt3d_units = m_ItkVtkAbstractTransform->BackTransform(pt3d_mm); //pt3d_units[2] = 0; //projectedPt3d_mm = m_ItkVtkAbstractTransform->TransformPoint(pt3d_units); //return const_cast(m_BoundingBox.GetPointer())->IsInside(pt3d_units); } bool mitk::AbstractTransformGeometry::Map(const mitk::Point3D &pt3d_mm, mitk::Point2D &pt2d_mm) const { assert((m_ItkVtkAbstractTransform.IsNotNull()) && (m_Plane.IsNotNull())); Point3D pt3d_units; pt3d_units = m_ItkVtkAbstractTransform->BackTransform(pt3d_mm); return m_Plane->Map(pt3d_units, pt2d_mm); } void mitk::AbstractTransformGeometry::Map(const mitk::Point2D &pt2d_mm, mitk::Point3D &pt3d_mm) const { assert((m_ItkVtkAbstractTransform.IsNotNull()) && (m_Plane.IsNotNull())); m_Plane->Map(pt2d_mm, pt3d_mm); pt3d_mm = m_ItkVtkAbstractTransform->TransformPoint(pt3d_mm); } bool mitk::AbstractTransformGeometry::Project(const mitk::Point3D & atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const { itkExceptionMacro("not implemented yet - replace GetIndexToWorldTransform by m_ItkVtkAbstractTransform->GetInverseVtkAbstractTransform()"); - assert(this->IsBoundingBoxNull()==false); + assert(this->IsBoundingBoxNull() == false); Vector3D vec3d_units; vec3d_units = GetIndexToWorldTransform()->GetInverseMatrix() * vec3d_mm; vec3d_units[2] = 0; projectedVec3d_mm = GetIndexToWorldTransform()->TransformVector(vec3d_units); Point3D pt3d_units; mitk::ScalarType temp[3]; unsigned int i, j; for (j = 0; j < 3; ++j) temp[j] = atPt3d_mm[j] - GetIndexToWorldTransform()->GetOffset()[j]; for (i = 0; i < 3; ++i) { pt3d_units[i] = 0.0; for (j = 0; j < 3; ++j) pt3d_units[i] += GetIndexToWorldTransform()->GetInverseMatrix()[i][j] * temp[j]; } return const_cast(this->GetBoundingBox())->IsInside(pt3d_units); } bool mitk::AbstractTransformGeometry::Project(const mitk::Vector3D &/*vec3d_mm*/, mitk::Vector3D &/*projectedVec3d_mm*/) const { MITK_WARN << "Need additional point! No standard value defined. Please use Project(const mitk::Point3D & atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm). Unfortunatley this one is not implemented at the moment. Sorry :("; itkExceptionMacro("not implemented yet - replace GetIndexToWorldTransform by m_ItkVtkAbstractTransform->GetInverseVtkAbstractTransform()"); return false; } bool mitk::AbstractTransformGeometry::Map(const mitk::Point3D & atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector2D &vec2d_mm) const { assert((m_ItkVtkAbstractTransform.IsNotNull()) && (m_Plane.IsNotNull())); ScalarType vtkpt[3], vtkvec[3]; itk2vtk(atPt3d_mm, vtkpt); itk2vtk(vec3d_mm, vtkvec); m_ItkVtkAbstractTransform->GetInverseVtkAbstractTransform()->TransformVectorAtPoint(vtkpt, vtkvec, vtkvec); mitk::Vector3D vec3d_units; vtk2itk(vtkvec, vec3d_units); return m_Plane->Map(atPt3d_mm, vec3d_units, vec2d_mm); } void mitk::AbstractTransformGeometry::Map(const mitk::Point2D & atPt2d_mm, const mitk::Vector2D &vec2d_mm, mitk::Vector3D &vec3d_mm) const { m_Plane->Map(atPt2d_mm, vec2d_mm, vec3d_mm); Point3D atPt3d_mm; Map(atPt2d_mm, atPt3d_mm); float vtkpt[3], vtkvec[3]; itk2vtk(atPt3d_mm, vtkpt); itk2vtk(vec3d_mm, vtkvec); m_ItkVtkAbstractTransform->GetVtkAbstractTransform()->TransformVectorAtPoint(vtkpt, vtkvec, vtkvec); vtk2itk(vtkvec, vec3d_mm); } void mitk::AbstractTransformGeometry::IndexToWorld(const mitk::Point2D &pt_units, mitk::Point2D &pt_mm) const { m_Plane->IndexToWorld(pt_units, pt_mm); } void mitk::AbstractTransformGeometry::WorldToIndex(const mitk::Point2D &pt_mm, mitk::Point2D &pt_units) const { m_Plane->WorldToIndex(pt_mm, pt_units); } void mitk::AbstractTransformGeometry::IndexToWorld(const mitk::Point2D & /*atPt2d_units*/, const mitk::Vector2D &vec_units, mitk::Vector2D &vec_mm) const { - MITK_WARN<<"Warning! Call of the deprecated function AbstractTransformGeometry::IndexToWorld(point, vec, vec). Use AbstractTransformGeometry::IndexToWorld(vec, vec) instead!"; + MITK_WARN << "Warning! Call of the deprecated function AbstractTransformGeometry::IndexToWorld(point, vec, vec). Use AbstractTransformGeometry::IndexToWorld(vec, vec) instead!"; this->IndexToWorld(vec_units, vec_mm); } void mitk::AbstractTransformGeometry::IndexToWorld(const mitk::Vector2D &vec_units, mitk::Vector2D &vec_mm) const { m_Plane->IndexToWorld(vec_units, vec_mm); } void mitk::AbstractTransformGeometry::WorldToIndex(const mitk::Point2D & /*atPt2d_mm*/, const mitk::Vector2D &vec_mm, mitk::Vector2D &vec_units) const { - MITK_WARN<<"Warning! Call of the deprecated function AbstractTransformGeometry::WorldToIndex(point, vec, vec). Use AbstractTransformGeometry::WorldToIndex(vec, vec) instead!"; + MITK_WARN << "Warning! Call of the deprecated function AbstractTransformGeometry::WorldToIndex(point, vec, vec). Use AbstractTransformGeometry::WorldToIndex(vec, vec) instead!"; this->WorldToIndex(vec_mm, vec_units); } void mitk::AbstractTransformGeometry::WorldToIndex(const mitk::Vector2D &vec_mm, mitk::Vector2D &vec_units) const { m_Plane->WorldToIndex(vec_mm, vec_units); } bool mitk::AbstractTransformGeometry::IsAbove(const mitk::Point3D& pt3d_mm, bool /*considerBoundingBox*/) const { assert((m_ItkVtkAbstractTransform.IsNotNull()) && (m_Plane.IsNotNull())); Point3D pt3d_ParametricWorld; pt3d_ParametricWorld = m_ItkVtkAbstractTransform->BackTransform(pt3d_mm); Point3D pt3d_ParametricUnits; ((BaseGeometry*)m_Plane)->WorldToIndex(pt3d_ParametricWorld, pt3d_ParametricUnits); return (pt3d_ParametricUnits[2] > m_ParametricBoundingBox->GetBounds()[4]); } void mitk::AbstractTransformGeometry::SetVtkAbstractTransform(vtkAbstractTransform* aVtkAbstractTransform) { m_ItkVtkAbstractTransform->SetVtkAbstractTransform(aVtkAbstractTransform); } void mitk::AbstractTransformGeometry::SetPlane(const mitk::PlaneGeometry* aPlane) { - if(aPlane!=NULL) + if (aPlane != NULL) { m_Plane = static_cast(aPlane->Clone().GetPointer()); - BoundingBox::BoundsArrayType b=m_Plane->GetBoundingBox()->GetBounds(); + BoundingBox::BoundsArrayType b = m_Plane->GetBoundingBox()->GetBounds(); SetParametricBounds(b); CalculateFrameGeometry(); } else { - if(m_Plane.IsNull()) + if (m_Plane.IsNull()) return; - m_Plane=NULL; + m_Plane = NULL; } Modified(); } void mitk::AbstractTransformGeometry::CalculateFrameGeometry() { - if((m_Plane.IsNull()) || (m_FrameGeometry.IsNotNull())) + if ((m_Plane.IsNull()) || (m_FrameGeometry.IsNotNull())) return; //@warning affine-transforms and bounding-box should be set by specific sub-classes! SetBounds(m_Plane->GetBoundingBox()->GetBounds()); } void mitk::AbstractTransformGeometry::SetFrameGeometry(const mitk::BaseGeometry* frameGeometry) { - if((frameGeometry != NULL) && (frameGeometry->IsValid())) + if ((frameGeometry != NULL) && (frameGeometry->IsValid())) { m_FrameGeometry = static_cast(frameGeometry->Clone().GetPointer()); SetIndexToWorldTransform(m_FrameGeometry->GetIndexToWorldTransform()); SetBounds(m_FrameGeometry->GetBounds()); } else { m_FrameGeometry = NULL; } } unsigned long mitk::AbstractTransformGeometry::GetMTime() const { - if(Superclass::GetMTime()GetMTime()) + if (Superclass::GetMTime() < m_ItkVtkAbstractTransform->GetMTime()) return m_ItkVtkAbstractTransform->GetMTime(); return Superclass::GetMTime(); } void mitk::AbstractTransformGeometry::SetOversampling(mitk::ScalarType oversampling) { - if(m_Plane.IsNull()) + if (m_Plane.IsNull()) { itkExceptionMacro(<< "m_Plane is not set."); } mitk::BoundingBox::BoundsArrayType bounds = m_Plane->GetBounds(); - bounds[1]*=oversampling; bounds[3]*=oversampling; bounds[5]*=oversampling; + bounds[1] *= oversampling; bounds[3] *= oversampling; bounds[5] *= oversampling; SetParametricBounds(bounds); } itk::LightObject::Pointer mitk::AbstractTransformGeometry::InternalClone() const { Self::Pointer newGeometry = new AbstractTransformGeometry(*this); newGeometry->UnRegister(); return newGeometry.GetPointer(); } void mitk::AbstractTransformGeometry::SetParametricBounds(const BoundingBox::BoundsArrayType& bounds) { m_ParametricBoundingBox = BoundingBoxType::New(); BoundingBoxType::PointsContainer::Pointer pointscontainer = BoundingBoxType::PointsContainer::New(); BoundingBoxType::PointType p; BoundingBoxType::PointIdentifier pointid; - for(pointid=0; pointid<2;++pointid) + for (pointid = 0; pointid < 2; ++pointid) { unsigned int i; - for(i=0; iInsertElement(pointid, p); } m_ParametricBoundingBox->SetPoints(pointscontainer); m_ParametricBoundingBox->ComputeBoundingBox(); this->Modified(); } const mitk::BoundingBox::BoundsArrayType& mitk::AbstractTransformGeometry::GetParametricBounds() const { assert(m_ParametricBoundingBox.IsNotNull()); return m_ParametricBoundingBox->GetBounds(); } mitk::ScalarType mitk::AbstractTransformGeometry::GetParametricExtent(int direction) const { - if (direction < 0 || direction>=3) + if (direction < 0 || direction >= 3) mitkThrow() << "Invalid direction. Must be between either 0, 1 or 2. "; assert(m_ParametricBoundingBox.IsNotNull()); BoundingBoxType::BoundsArrayType bounds = m_ParametricBoundingBox->GetBounds(); - return bounds[direction*2+1]-bounds[direction*2]; -} + return bounds[direction * 2 + 1] - bounds[direction * 2]; +} \ No newline at end of file diff --git a/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp b/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp index ceeaaa5324..2f8b5ea52f 100644 --- a/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp +++ b/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp @@ -1,955 +1,929 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include "mitkBaseGeometry.h" #include "mitkVector.h" #include "mitkMatrixConvert.h" #include #include #include "mitkRotationOperation.h" #include "mitkRestorePlanePositionOperation.h" #include "mitkApplyTransformMatrixOperation.h" #include "mitkPointOperation.h" #include "mitkInteractionConst.h" #include "mitkModifiedLock.h" #include "mitkGeometryTransformHolder.h" -mitk::BaseGeometry::BaseGeometry(): Superclass(), mitk::OperationActor(), - m_FrameOfReferenceID(0), m_IndexToWorldTransformLastModified(0), m_ImageGeometry(false), m_ModifiedLockFlag(false), m_ModifiedCalledFlag(false) +mitk::BaseGeometry::BaseGeometry() : Superclass(), mitk::OperationActor(), +m_FrameOfReferenceID(0), m_IndexToWorldTransformLastModified(0), m_ImageGeometry(false), m_ModifiedLockFlag(false), m_ModifiedCalledFlag(false) { m_GeometryTransform = new GeometryTransformHolder(); Initialize(); } -mitk::BaseGeometry::BaseGeometry(const BaseGeometry& other): Superclass(), mitk::OperationActor(), //m_TimeBounds(other.m_TimeBounds), - m_FrameOfReferenceID(other.m_FrameOfReferenceID), m_IndexToWorldTransformLastModified(other.m_IndexToWorldTransformLastModified), - m_ImageGeometry(other.m_ImageGeometry), m_ModifiedLockFlag(false), m_ModifiedCalledFlag(false) +mitk::BaseGeometry::BaseGeometry(const BaseGeometry& other) : Superclass(), mitk::OperationActor(), +m_FrameOfReferenceID(other.m_FrameOfReferenceID), m_IndexToWorldTransformLastModified(other.m_IndexToWorldTransformLastModified), +m_ImageGeometry(other.m_ImageGeometry), m_ModifiedLockFlag(false), m_ModifiedCalledFlag(false) { m_GeometryTransform = new GeometryTransformHolder(*other.GetGeometryTransformHolder()); other.InitializeGeometry(this); } mitk::BaseGeometry::~BaseGeometry() { delete m_GeometryTransform; } void mitk::BaseGeometry::SetVtkMatrixDeepCopy(vtkTransform *vtktransform) { m_GeometryTransform->SetVtkMatrixDeepCopy(vtktransform); } const mitk::Point3D mitk::BaseGeometry::GetOrigin() const { return m_GeometryTransform->GetOrigin(); } void mitk::BaseGeometry::SetOrigin(const Point3D & origin) { mitk::ModifiedLock lock(this); - if(origin!=GetOrigin()) + if (origin != GetOrigin()) { m_GeometryTransform->SetOrigin(origin); Modified(); } } const mitk::Vector3D mitk::BaseGeometry::GetSpacing() const { return m_GeometryTransform->GetSpacing(); } void mitk::BaseGeometry::Initialize() { - float b[6] = {0,1,0,1,0,1}; + float b[6] = { 0, 1, 0, 1, 0, 1 }; SetFloatBounds(b); m_GeometryTransform->Initialize(); m_FrameOfReferenceID = 0; m_ImageGeometry = false; - - this->PostInitialize(); } void mitk::BaseGeometry::SetFloatBounds(const float bounds[6]) { mitk::BoundingBox::BoundsArrayType b; const float *input = bounds; - int i=0; - for(mitk::BoundingBox::BoundsArrayType::Iterator it = b.Begin(); i < 6 ;++i) *it++ = (mitk::ScalarType)*input++; + int i = 0; + for (mitk::BoundingBox::BoundsArrayType::Iterator it = b.Begin(); i < 6; ++i) *it++ = (mitk::ScalarType)*input++; SetBounds(b); } void mitk::BaseGeometry::SetFloatBounds(const double bounds[6]) { mitk::BoundingBox::BoundsArrayType b; const double *input = bounds; - int i=0; - for(mitk::BoundingBox::BoundsArrayType::Iterator it = b.Begin(); i < 6 ;++i) *it++ = (mitk::ScalarType)*input++; + int i = 0; + for (mitk::BoundingBox::BoundsArrayType::Iterator it = b.Begin(); i < 6; ++i) *it++ = (mitk::ScalarType)*input++; SetBounds(b); } /** Initialize the geometry */ void - mitk::BaseGeometry::InitializeGeometry(BaseGeometry* newGeometry) const +mitk::BaseGeometry::InitializeGeometry(BaseGeometry* newGeometry) const { newGeometry->SetBounds(m_BoundingBox->GetBounds()); newGeometry->SetFrameOfReferenceID(GetFrameOfReferenceID()); newGeometry->InitializeGeometryTransformHolder(this); newGeometry->m_ImageGeometry = m_ImageGeometry; - - this->PostInitializeGeometry(newGeometry); } void mitk::BaseGeometry::InitializeGeometryTransformHolder(const BaseGeometry* otherGeometry) { this->m_GeometryTransform->Initialize(otherGeometry->GetGeometryTransformHolder()); } /** Set the bounds */ void mitk::BaseGeometry::SetBounds(const BoundsArrayType& bounds) { mitk::ModifiedLock lock(this); - this->PreSetBounds(bounds); + this->CheckBounds(bounds); m_BoundingBox = BoundingBoxType::New(); BoundingBoxType::PointsContainer::Pointer pointscontainer = BoundingBoxType::PointsContainer::New(); BoundingBoxType::PointType p; BoundingBoxType::PointIdentifier pointid; - for(pointid=0; pointid<2;++pointid) + for (pointid = 0; pointid < 2; ++pointid) { unsigned int i; - for(i=0; iInsertElement(pointid, p); } m_BoundingBox->SetPoints(pointscontainer); m_BoundingBox->ComputeBoundingBox(); this->Modified(); } void mitk::BaseGeometry::SetIndexToWorldTransform(mitk::AffineTransform3D* transform) { mitk::ModifiedLock lock(this); - PreSetIndexToWorldTransform(transform); + CheckIndexToWorldTransform(transform); m_GeometryTransform->SetIndexToWorldTransform(transform); Modified(); - - PostSetIndexToWorldTransform(transform); } void mitk::BaseGeometry::SetIndexToWorldTransformWithoutChangingSpacing(mitk::AffineTransform3D* transform) { //security check mitk::Vector3D originalSpacing = this->GetSpacing(); mitk::ModifiedLock lock(this); - PreSetIndexToWorldTransform(transform); + CheckIndexToWorldTransform(transform); m_GeometryTransform->SetIndexToWorldTransformWithoutChangingSpacing(transform); Modified(); - PostSetIndexToWorldTransform(transform); - //Security check. Spacig must not have changed - if(!mitk::Equal(originalSpacing,this->GetSpacing())) + if (!mitk::Equal(originalSpacing, this->GetSpacing())) { MITK_WARN << "Spacing has changed in a method, where the spacing must not change."; assert(false); } } const mitk::BaseGeometry::BoundsArrayType mitk::BaseGeometry::GetBounds() const { assert(m_BoundingBox.IsNotNull()); return m_BoundingBox->GetBounds(); } bool mitk::BaseGeometry::IsValid() const { return true; } -void mitk::BaseGeometry::SetSpacing(const mitk::Vector3D& aSpacing, bool enforceSetSpacing ) +void mitk::BaseGeometry::SetSpacing(const mitk::Vector3D& aSpacing, bool enforceSetSpacing) { PreSetSpacing(aSpacing); _SetSpacing(aSpacing, enforceSetSpacing); } void mitk::BaseGeometry::_SetSpacing(const mitk::Vector3D& aSpacing, bool enforceSetSpacing){ m_GeometryTransform->SetSpacing(aSpacing, enforceSetSpacing); } mitk::Vector3D mitk::BaseGeometry::GetAxisVector(unsigned int direction) const { Vector3D frontToBack; frontToBack.SetVnlVector(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(direction)); frontToBack *= GetExtent(direction); return frontToBack; } mitk::ScalarType mitk::BaseGeometry::GetExtent(unsigned int direction) const { assert(m_BoundingBox.IsNotNull()); - if (direction>=m_NDimensions) + if (direction >= m_NDimensions) mitkThrow() << "Direction is too big. This geometry is for 3D Data"; BoundsArrayType bounds = m_BoundingBox->GetBounds(); - return bounds[direction*2+1]-bounds[direction*2]; + return bounds[direction * 2 + 1] - bounds[direction * 2]; } bool mitk::BaseGeometry::Is2DConvertable() { bool isConvertableWithoutLoss = true; do { if (this->GetSpacing()[2] != 1) { isConvertableWithoutLoss = false; break; } if (this->GetOrigin()[2] != 0) { isConvertableWithoutLoss = false; break; } mitk::Vector3D col0, col1, col2; col0.SetVnlVector(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(0)); col1.SetVnlVector(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(1)); col2.SetVnlVector(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(2)); if ((col0[2] != 0) || (col1[2] != 0) || (col2[0] != 0) || (col2[1] != 0) || (col2[2] != 1)) { isConvertableWithoutLoss = false; break; } } while (0); return isConvertableWithoutLoss; } mitk::Point3D mitk::BaseGeometry::GetCenter() const { assert(m_BoundingBox.IsNotNull()); return this->GetIndexToWorldTransform()->TransformPoint(m_BoundingBox->GetCenter()); } double mitk::BaseGeometry::GetDiagonalLength2() const { - Vector3D diagonalvector = GetCornerPoint()-GetCornerPoint(false, false, false); + Vector3D diagonalvector = GetCornerPoint() - GetCornerPoint(false, false, false); return diagonalvector.GetSquaredNorm(); } double mitk::BaseGeometry::GetDiagonalLength() const { return sqrt(GetDiagonalLength2()); } mitk::Point3D mitk::BaseGeometry::GetCornerPoint(int id) const { assert(id >= 0); - assert(this->IsBoundingBoxNull()==false); + assert(this->IsBoundingBoxNull() == false); BoundingBox::BoundsArrayType bounds = this->GetBoundingBox()->GetBounds(); Point3D cornerpoint; - switch(id) - { - case 0: FillVector3D(cornerpoint, bounds[0],bounds[2],bounds[4]); break; - case 1: FillVector3D(cornerpoint, bounds[0],bounds[2],bounds[5]); break; - case 2: FillVector3D(cornerpoint, bounds[0],bounds[3],bounds[4]); break; - case 3: FillVector3D(cornerpoint, bounds[0],bounds[3],bounds[5]); break; - case 4: FillVector3D(cornerpoint, bounds[1],bounds[2],bounds[4]); break; - case 5: FillVector3D(cornerpoint, bounds[1],bounds[2],bounds[5]); break; - case 6: FillVector3D(cornerpoint, bounds[1],bounds[3],bounds[4]); break; - case 7: FillVector3D(cornerpoint, bounds[1],bounds[3],bounds[5]); break; + switch (id) + { + case 0: FillVector3D(cornerpoint, bounds[0], bounds[2], bounds[4]); break; + case 1: FillVector3D(cornerpoint, bounds[0], bounds[2], bounds[5]); break; + case 2: FillVector3D(cornerpoint, bounds[0], bounds[3], bounds[4]); break; + case 3: FillVector3D(cornerpoint, bounds[0], bounds[3], bounds[5]); break; + case 4: FillVector3D(cornerpoint, bounds[1], bounds[2], bounds[4]); break; + case 5: FillVector3D(cornerpoint, bounds[1], bounds[2], bounds[5]); break; + case 6: FillVector3D(cornerpoint, bounds[1], bounds[3], bounds[4]); break; + case 7: FillVector3D(cornerpoint, bounds[1], bounds[3], bounds[5]); break; default: - { - itkExceptionMacro(<<"A cube only has 8 corners. These are labeled 0-7."); - } + { + itkExceptionMacro(<< "A cube only has 8 corners. These are labeled 0-7."); } - if(m_ImageGeometry) + } + if (m_ImageGeometry) { // Here i have to adjust the 0.5 offset manually, because the cornerpoint is the corner of the // bounding box. The bounding box itself is no image, so it is corner-based - FillVector3D(cornerpoint, cornerpoint[0]-0.5, cornerpoint[1]-0.5, cornerpoint[2]-0.5); + FillVector3D(cornerpoint, cornerpoint[0] - 0.5, cornerpoint[1] - 0.5, cornerpoint[2] - 0.5); } return this->GetIndexToWorldTransform()->TransformPoint(cornerpoint); } mitk::Point3D mitk::BaseGeometry::GetCornerPoint(bool xFront, bool yFront, bool zFront) const { - assert(this->IsBoundingBoxNull()==false); + assert(this->IsBoundingBoxNull() == false); BoundingBox::BoundsArrayType bounds = this->GetBoundingBox()->GetBounds(); Point3D cornerpoint; cornerpoint[0] = (xFront ? bounds[0] : bounds[1]); cornerpoint[1] = (yFront ? bounds[2] : bounds[3]); cornerpoint[2] = (zFront ? bounds[4] : bounds[5]); - if(m_ImageGeometry) + if (m_ImageGeometry) { // Here i have to adjust the 0.5 offset manually, because the cornerpoint is the corner of the // bounding box. The bounding box itself is no image, so it is corner-based - FillVector3D(cornerpoint, cornerpoint[0]-0.5, cornerpoint[1]-0.5, cornerpoint[2]-0.5); + FillVector3D(cornerpoint, cornerpoint[0] - 0.5, cornerpoint[1] - 0.5, cornerpoint[2] - 0.5); } return this->GetIndexToWorldTransform()->TransformPoint(cornerpoint); } mitk::ScalarType mitk::BaseGeometry::GetExtentInMM(int direction) const { return this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(direction).magnitude()*GetExtent(direction); } void mitk::BaseGeometry::SetExtentInMM(int direction, ScalarType extentInMM) { mitk::ModifiedLock lock(this); ScalarType len = GetExtentInMM(direction); - if(fabs(len - extentInMM)>=mitk::eps) + if (fabs(len - extentInMM) >= mitk::eps) { AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; vnlmatrix = m_GeometryTransform->GetVnlMatrix(); - if(len>extentInMM) - vnlmatrix.set_column(direction, vnlmatrix.get_column(direction)/len*extentInMM); + if (len > extentInMM) + vnlmatrix.set_column(direction, vnlmatrix.get_column(direction) / len*extentInMM); else - vnlmatrix.set_column(direction, vnlmatrix.get_column(direction)*extentInMM/len); + vnlmatrix.set_column(direction, vnlmatrix.get_column(direction)*extentInMM / len); Matrix3D matrix; matrix = vnlmatrix; m_GeometryTransform->SetMatrix(matrix); Modified(); } - PostSetExtentInMM(direction,extentInMM); } bool mitk::BaseGeometry::IsInside(const mitk::Point3D& p) const { mitk::Point3D index; WorldToIndex(p, index); return IsIndexInside(index); } bool mitk::BaseGeometry::IsIndexInside(const mitk::Point3D& index) const { bool inside = false; //if it is an image geometry, we need to convert the index to discrete values //this is done by applying the rounding function also used in WorldToIndex (see line 323) if (m_ImageGeometry) { mitk::Point3D discretIndex; - discretIndex[0]=itk::Math::RoundHalfIntegerUp( index[0] ); - discretIndex[1]=itk::Math::RoundHalfIntegerUp( index[1] ); - discretIndex[2]=itk::Math::RoundHalfIntegerUp( index[2] ); + discretIndex[0] = itk::Math::RoundHalfIntegerUp(index[0]); + discretIndex[1] = itk::Math::RoundHalfIntegerUp(index[1]); + discretIndex[2] = itk::Math::RoundHalfIntegerUp(index[2]); inside = this->GetBoundingBox()->IsInside(discretIndex); //we have to check if the index is at the upper border of each dimension, // because the boundingbox is not centerbased if (inside) { const BoundingBox::BoundsArrayType& bounds = this->GetBoundingBox()->GetBounds(); - if((discretIndex[0] == bounds[1]) || + if ((discretIndex[0] == bounds[1]) || (discretIndex[1] == bounds[3]) || (discretIndex[2] == bounds[5])) inside = false; } } else inside = this->GetBoundingBox()->IsInside(index); return inside; } void mitk::BaseGeometry::WorldToIndex(const mitk::Point3D &pt_mm, mitk::Point3D &pt_units) const { - BackTransform(pt_mm, pt_units); -} + mitk::Vector3D tempIn, tempOut; + const TransformType::OffsetType& offset = this->GetIndexToWorldTransform()->GetOffset(); + tempIn = pt_mm.GetVectorFromOrigin() - offset; -void mitk::BaseGeometry::WorldToIndex( const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const -{ - BackTransform( vec_mm, vec_units); + WorldToIndex(tempIn, tempOut); + + pt_units = tempOut; } -void mitk::BaseGeometry::BackTransform(const mitk::Vector3D& in, mitk::Vector3D& out) const +void mitk::BaseGeometry::WorldToIndex(const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const { // Get WorldToIndex transform if (m_IndexToWorldTransformLastModified != this->GetIndexToWorldTransform()->GetMTime()) { if (!m_InvertedTransform) { m_InvertedTransform = TransformType::New(); } - if (!this->GetIndexToWorldTransform()->GetInverse( m_InvertedTransform.GetPointer() )) + if (!this->GetIndexToWorldTransform()->GetInverse(m_InvertedTransform.GetPointer())) { - itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed." ); + itkExceptionMacro("Internal ITK matrix inversion error, cannot proceed."); } m_IndexToWorldTransformLastModified = this->GetIndexToWorldTransform()->GetMTime(); } // Check for valid matrix inversion const TransformType::MatrixType& inverse = m_InvertedTransform->GetMatrix(); - if(inverse.GetVnlMatrix().has_nans()) + if (inverse.GetVnlMatrix().has_nans()) { - itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed. Matrix was: " << std::endl + itkExceptionMacro("Internal ITK matrix inversion error, cannot proceed. Matrix was: " << std::endl << this->GetIndexToWorldTransform()->GetMatrix() << "Suggested inverted matrix is:" << std::endl - << inverse ); + << inverse); } - out = inverse * in; + vec_units = inverse * vec_mm; } -void mitk::BaseGeometry::BackTransform(const mitk::Point3D &in, mitk::Point3D& out) const +void mitk::BaseGeometry::WorldToIndex(const mitk::Point3D & /*atPt3d_mm*/, const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const { - mitk::Vector3D tempIn, tempOut; - const TransformType::OffsetType& offset = this->GetIndexToWorldTransform()->GetOffset(); - tempIn = in.GetVectorFromOrigin() - offset; - - BackTransform(tempIn, tempOut); - - out = tempOut; + MITK_WARN << "Warning! Call of the deprecated function BaseGeometry::WorldToIndex(point, vec, vec). Use BaseGeometry::WorldToIndex(vec, vec) instead!"; + this->WorldToIndex(vec_mm, vec_units); } mitk::VnlVector mitk::BaseGeometry::GetOriginVnl() const { return const_cast(this)->GetOrigin().GetVnlVector(); } vtkLinearTransform* mitk::BaseGeometry::GetVtkTransform() const { return m_GeometryTransform->GetVtkTransform(); } void mitk::BaseGeometry::SetIdentity() { mitk::ModifiedLock lock(this); m_GeometryTransform->SetIdentity(); Modified(); } -void mitk::BaseGeometry::Compose( const mitk::BaseGeometry::TransformType * other, bool pre ) +void mitk::BaseGeometry::Compose(const mitk::BaseGeometry::TransformType * other, bool pre) { mitk::ModifiedLock lock(this); - m_GeometryTransform->Compose(other,pre); + m_GeometryTransform->Compose(other, pre); Modified(); } -void mitk::BaseGeometry::Compose( const vtkMatrix4x4 * vtkmatrix, bool pre ) +void mitk::BaseGeometry::Compose(const vtkMatrix4x4 * vtkmatrix, bool pre) { mitk::BaseGeometry::TransformType::Pointer itkTransform = mitk::BaseGeometry::TransformType::New(); TransferVtkMatrixToItkTransform(vtkmatrix, itkTransform.GetPointer()); Compose(itkTransform, pre); } void mitk::BaseGeometry::Translate(const Vector3D & vector) { - if((vector[0] != 0) || (vector[1] != 0) || (vector[2] != 0)) + if ((vector[0] != 0) || (vector[1] != 0) || (vector[2] != 0)) { this->SetOrigin(this->GetOrigin() + vector); } } void mitk::BaseGeometry::IndexToWorld(const mitk::Point3D &pt_units, mitk::Point3D &pt_mm) const { pt_mm = this->GetIndexToWorldTransform()->TransformPoint(pt_units); } void mitk::BaseGeometry::IndexToWorld(const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const { vec_mm = this->GetIndexToWorldTransform()->TransformVector(vec_units); } void mitk::BaseGeometry::ExecuteOperation(Operation* operation) { mitk::ModifiedLock lock(this); vtkTransform *vtktransform = vtkTransform::New(); vtktransform->SetMatrix(this->GetVtkMatrix()); switch (operation->GetOperationType()) { case OpNOTHING: break; case OpMOVE: + { + mitk::PointOperation *pointOp = dynamic_cast(operation); + if (pointOp == NULL) { - mitk::PointOperation *pointOp = dynamic_cast(operation); - if (pointOp == NULL) - { - //mitk::StatusBar::GetInstance()->DisplayText("received wrong type of operation!See mitkAffineInteractor.cpp", 10000); - return; - } - mitk::Point3D newPos = pointOp->GetPoint(); - ScalarType data[3]; - vtktransform->GetPosition(data); - vtktransform->PostMultiply(); - vtktransform->Translate(newPos[0], newPos[1], newPos[2]); - vtktransform->PreMultiply(); - break; + //mitk::StatusBar::GetInstance()->DisplayText("received wrong type of operation!See mitkAffineInteractor.cpp", 10000); + return; } + mitk::Point3D newPos = pointOp->GetPoint(); + ScalarType data[3]; + vtktransform->GetPosition(data); + vtktransform->PostMultiply(); + vtktransform->Translate(newPos[0], newPos[1], newPos[2]); + vtktransform->PreMultiply(); + break; + } case OpSCALE: + { + mitk::PointOperation *pointOp = dynamic_cast(operation); + if (pointOp == NULL) { - mitk::PointOperation *pointOp = dynamic_cast(operation); - if (pointOp == NULL) - { - //mitk::StatusBar::GetInstance()->DisplayText("received wrong type of operation!See mitkAffineInteractor.cpp", 10000); - return; - } - mitk::Point3D newScale = pointOp->GetPoint(); - ScalarType data[3]; - /* calculate new scale: newscale = oldscale * (oldscale + scaletoadd)/oldscale */ - data[0] = 1 + (newScale[0] / GetMatrixColumn(0).magnitude()); - data[1] = 1 + (newScale[1] / GetMatrixColumn(1).magnitude()); - data[2] = 1 + (newScale[2] / GetMatrixColumn(2).magnitude()); - - mitk::Point3D center = const_cast(m_BoundingBox.GetPointer())->GetCenter(); - ScalarType pos[3]; - vtktransform->GetPosition(pos); - vtktransform->PostMultiply(); - vtktransform->Translate(-pos[0], -pos[1], -pos[2]); - vtktransform->Translate(-center[0], -center[1], -center[2]); - vtktransform->PreMultiply(); - vtktransform->Scale(data[0], data[1], data[2]); - vtktransform->PostMultiply(); - vtktransform->Translate(+center[0], +center[1], +center[2]); - vtktransform->Translate(pos[0], pos[1], pos[2]); - vtktransform->PreMultiply(); - break; + //mitk::StatusBar::GetInstance()->DisplayText("received wrong type of operation!See mitkAffineInteractor.cpp", 10000); + return; } + mitk::Point3D newScale = pointOp->GetPoint(); + ScalarType data[3]; + /* calculate new scale: newscale = oldscale * (oldscale + scaletoadd)/oldscale */ + data[0] = 1 + (newScale[0] / GetMatrixColumn(0).magnitude()); + data[1] = 1 + (newScale[1] / GetMatrixColumn(1).magnitude()); + data[2] = 1 + (newScale[2] / GetMatrixColumn(2).magnitude()); + + mitk::Point3D center = const_cast(m_BoundingBox.GetPointer())->GetCenter(); + ScalarType pos[3]; + vtktransform->GetPosition(pos); + vtktransform->PostMultiply(); + vtktransform->Translate(-pos[0], -pos[1], -pos[2]); + vtktransform->Translate(-center[0], -center[1], -center[2]); + vtktransform->PreMultiply(); + vtktransform->Scale(data[0], data[1], data[2]); + vtktransform->PostMultiply(); + vtktransform->Translate(+center[0], +center[1], +center[2]); + vtktransform->Translate(pos[0], pos[1], pos[2]); + vtktransform->PreMultiply(); + break; + } case OpROTATE: + { + mitk::RotationOperation *rotateOp = dynamic_cast(operation); + if (rotateOp == NULL) { - mitk::RotationOperation *rotateOp = dynamic_cast(operation); - if (rotateOp == NULL) - { - //mitk::StatusBar::GetInstance()->DisplayText("received wrong type of operation!See mitkAffineInteractor.cpp", 10000); - return; - } - Vector3D rotationVector = rotateOp->GetVectorOfRotation(); - Point3D center = rotateOp->GetCenterOfRotation(); - ScalarType angle = rotateOp->GetAngleOfRotation(); - vtktransform->PostMultiply(); - vtktransform->Translate(-center[0], -center[1], -center[2]); - vtktransform->RotateWXYZ(angle, rotationVector[0], rotationVector[1], rotationVector[2]); - vtktransform->Translate(center[0], center[1], center[2]); - vtktransform->PreMultiply(); - break; + //mitk::StatusBar::GetInstance()->DisplayText("received wrong type of operation!See mitkAffineInteractor.cpp", 10000); + return; } + Vector3D rotationVector = rotateOp->GetVectorOfRotation(); + Point3D center = rotateOp->GetCenterOfRotation(); + ScalarType angle = rotateOp->GetAngleOfRotation(); + vtktransform->PostMultiply(); + vtktransform->Translate(-center[0], -center[1], -center[2]); + vtktransform->RotateWXYZ(angle, rotationVector[0], rotationVector[1], rotationVector[2]); + vtktransform->Translate(center[0], center[1], center[2]); + vtktransform->PreMultiply(); + break; + } case OpRESTOREPLANEPOSITION: - { - //Copy necessary to avoid vtk warning - vtkMatrix4x4* matrix = vtkMatrix4x4::New(); - TransferItkTransformToVtkMatrix(dynamic_cast(operation)->GetTransform().GetPointer(), matrix); - vtktransform->SetMatrix(matrix); - matrix->Delete(); - break; - } + { + //Copy necessary to avoid vtk warning + vtkMatrix4x4* matrix = vtkMatrix4x4::New(); + TransferItkTransformToVtkMatrix(dynamic_cast(operation)->GetTransform().GetPointer(), matrix); + vtktransform->SetMatrix(matrix); + matrix->Delete(); + break; + } case OpAPPLYTRANSFORMMATRIX: - { - ApplyTransformMatrixOperation *applyMatrixOp = dynamic_cast< ApplyTransformMatrixOperation* >( operation ); - vtktransform->SetMatrix(applyMatrixOp->GetMatrix()); - break; - } + { + ApplyTransformMatrixOperation *applyMatrixOp = dynamic_cast(operation); + vtktransform->SetMatrix(applyMatrixOp->GetMatrix()); + break; + } default: vtktransform->Delete(); return; } this->SetVtkMatrixDeepCopy(vtktransform); Modified(); vtktransform->Delete(); } mitk::VnlVector mitk::BaseGeometry::GetMatrixColumn(unsigned int direction) const { return this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(direction); } mitk::BoundingBox::Pointer mitk::BaseGeometry::CalculateBoundingBoxRelativeToTransform(const mitk::AffineTransform3D* transform) const { - mitk::BoundingBox::PointsContainer::Pointer pointscontainer=mitk::BoundingBox::PointsContainer::New(); + mitk::BoundingBox::PointsContainer::Pointer pointscontainer = mitk::BoundingBox::PointsContainer::New(); - mitk::BoundingBox::PointIdentifier pointid=0; + mitk::BoundingBox::PointIdentifier pointid = 0; unsigned char i; - if(transform!=NULL) + if (transform != NULL) { mitk::AffineTransform3D::Pointer inverse = mitk::AffineTransform3D::New(); transform->GetInverse(inverse); - for(i=0; i<8; ++i) - pointscontainer->InsertElement( pointid++, inverse->TransformPoint( GetCornerPoint(i) )); + for (i = 0; i < 8; ++i) + pointscontainer->InsertElement(pointid++, inverse->TransformPoint(GetCornerPoint(i))); } else { - for(i=0; i<8; ++i) - pointscontainer->InsertElement( pointid++, GetCornerPoint(i) ); + for (i = 0; i < 8; ++i) + pointscontainer->InsertElement(pointid++, GetCornerPoint(i)); } mitk::BoundingBox::Pointer result = mitk::BoundingBox::New(); result->SetPoints(pointscontainer); result->ComputeBoundingBox(); return result; } -const std::string mitk::BaseGeometry::GetTransformAsString( TransformType* transformType ) +const std::string mitk::BaseGeometry::GetTransformAsString(TransformType* transformType) { std::ostringstream out; out << '['; - for( int i=0; i<3; ++i ) + for (int i = 0; i < 3; ++i) { out << '['; - for( int j=0; j<3; ++j ) + for (int j = 0; j < 3; ++j) out << transformType->GetMatrix().GetVnlMatrix().get(i, j) << ' '; out << ']'; } out << "]["; - for( int i=0; i<3; ++i ) + for (int i = 0; i < 3; ++i) out << transformType->GetOffset()[i] << ' '; out << "]\0"; return out.str(); } void mitk::BaseGeometry::SetIndexToWorldTransformByVtkMatrix(vtkMatrix4x4* vtkmatrix) { m_GeometryTransform->SetIndexToWorldTransformByVtkMatrix(vtkmatrix); } void mitk::BaseGeometry::SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing(vtkMatrix4x4* vtkmatrix) { m_GeometryTransform->SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing(vtkmatrix); } -void mitk::BaseGeometry::WorldToIndex(const mitk::Point3D & /*atPt3d_mm*/, const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const -{ - MITK_WARN<<"Warning! Call of the deprecated function BaseGeometry::WorldToIndex(point, vec, vec). Use BaseGeometry::WorldToIndex(vec, vec) instead!"; - //BackTransform(atPt3d_mm, vec_mm, vec_units); - this->WorldToIndex(vec_mm, vec_units); -} - void mitk::BaseGeometry::IndexToWorld(const mitk::Point3D &/*atPt3d_units*/, const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const { - MITK_WARN<<"Warning! Call of the deprecated function BaseGeometry::IndexToWorld(point, vec, vec). Use BaseGeometry::IndexToWorld(vec, vec) instead!"; + MITK_WARN << "Warning! Call of the deprecated function BaseGeometry::IndexToWorld(point, vec, vec). Use BaseGeometry::IndexToWorld(vec, vec) instead!"; //vec_mm = m_IndexToWorldTransform->TransformVector(vec_units); this->IndexToWorld(vec_units, vec_mm); } -void mitk::BaseGeometry::BackTransform(const mitk::Point3D &/*at*/, const mitk::Vector3D &in, mitk::Vector3D& out) const -{ - MITK_INFO<<"Warning! Call of the deprecated function BaseGeometry::BackTransform(point, vec, vec). Use BaseGeometry::BackTransform(vec, vec) instead!"; - this->BackTransform(in, out); -} - vtkMatrix4x4* mitk::BaseGeometry::GetVtkMatrix(){ return m_GeometryTransform->GetVtkMatrix(); } bool mitk::BaseGeometry::IsBoundingBoxNull() const{ return m_BoundingBox.IsNull(); } bool mitk::BaseGeometry::IsIndexToWorldTransformNull() const{ return m_GeometryTransform->IsIndexToWorldTransformNull(); } void - mitk::BaseGeometry::ChangeImageGeometryConsideringOriginOffset( const bool isAnImageGeometry ) +mitk::BaseGeometry::ChangeImageGeometryConsideringOriginOffset(const bool isAnImageGeometry) { // If Geometry is switched to ImageGeometry, you have to put an offset to the origin, because // imageGeometries origins are pixel-center-based // ... and remove the offset, if you switch an imageGeometry back to a normal geometry // For more information please see the Geometry documentation page - if(m_ImageGeometry == isAnImageGeometry) + if (m_ImageGeometry == isAnImageGeometry) return; const BoundingBox::BoundsArrayType& boundsarray = this->GetBoundingBox()->GetBounds(); Point3D originIndex; - FillVector3D(originIndex, boundsarray[0], boundsarray[2], boundsarray[4]); + FillVector3D(originIndex, boundsarray[0], boundsarray[2], boundsarray[4]); - if(isAnImageGeometry == true) - FillVector3D( originIndex, + if (isAnImageGeometry == true) + FillVector3D(originIndex, originIndex[0] + 0.5, originIndex[1] + 0.5, - originIndex[2] + 0.5 ); + originIndex[2] + 0.5); else - FillVector3D( originIndex, + FillVector3D(originIndex, originIndex[0] - 0.5, originIndex[1] - 0.5, - originIndex[2] - 0.5 ); + originIndex[2] - 0.5); Point3D originWorld; originWorld = GetIndexToWorldTransform() - ->TransformPoint( originIndex ); + ->TransformPoint(originIndex); // instead could as well call IndexToWorld(originIndex,originWorld); SetOrigin(originWorld); this->SetImageGeometry(isAnImageGeometry); } void mitk::BaseGeometry::PrintSelf(std::ostream& os, itk::Indent indent) const { os << indent << " IndexToWorldTransform: "; - if(this->IsIndexToWorldTransformNull()) + if (this->IsIndexToWorldTransformNull()) os << "NULL" << std::endl; else { // from itk::MatrixOffsetTransformBase unsigned int i, j; os << std::endl; os << indent << "Matrix: " << std::endl; for (i = 0; i < 3; i++) { os << indent.GetNextIndent(); for (j = 0; j < 3; j++) { os << this->GetIndexToWorldTransform()->GetMatrix()[i][j] << " "; } os << std::endl; } os << indent << "Offset: " << this->GetIndexToWorldTransform()->GetOffset() << std::endl; os << indent << "Center: " << this->GetIndexToWorldTransform()->GetCenter() << std::endl; os << indent << "Translation: " << this->GetIndexToWorldTransform()->GetTranslation() << std::endl; os << indent << "Inverse: " << std::endl; for (i = 0; i < 3; i++) { os << indent.GetNextIndent(); for (j = 0; j < 3; j++) { os << this->GetIndexToWorldTransform()->GetInverseMatrix()[i][j] << " "; } os << std::endl; } // from itk::ScalableAffineTransform os << indent << "Scale : "; for (i = 0; i < 3; i++) { os << this->GetIndexToWorldTransform()->GetScale()[i] << " "; } os << std::endl; } os << indent << " BoundingBox: "; - if(this->IsBoundingBoxNull()) + if (this->IsBoundingBoxNull()) os << "NULL" << std::endl; else { os << indent << "( "; - for (unsigned int i=0; i<3; i++) + for (unsigned int i = 0; i < 3; i++) { - os << this->GetBoundingBox()->GetBounds()[2*i] << "," << this->GetBoundingBox()->GetBounds()[2*i+1] << " "; + os << this->GetBoundingBox()->GetBounds()[2 * i] << "," << this->GetBoundingBox()->GetBounds()[2 * i + 1] << " "; } os << " )" << std::endl; } os << indent << " Origin: " << this->GetOrigin() << std::endl; os << indent << " ImageGeometry: " << this->GetImageGeometry() << std::endl; os << indent << " Spacing: " << this->GetSpacing() << std::endl; } void mitk::BaseGeometry::Modified() const{ - if(!m_ModifiedLockFlag) + if (!m_ModifiedLockFlag) Superclass::Modified(); else m_ModifiedCalledFlag = true; } mitk::AffineTransform3D* mitk::BaseGeometry::GetIndexToWorldTransform() { return m_GeometryTransform->GetIndexToWorldTransform(); } const mitk::AffineTransform3D* mitk::BaseGeometry::GetIndexToWorldTransform() const { return m_GeometryTransform->GetIndexToWorldTransform(); } const mitk::GeometryTransformHolder* - mitk::BaseGeometry::GetGeometryTransformHolder() const +mitk::BaseGeometry::GetGeometryTransformHolder() const { return m_GeometryTransform; } -bool mitk::Equal( const mitk::BaseGeometry::BoundingBoxType *leftHandSide, const mitk::BaseGeometry::BoundingBoxType *rightHandSide, ScalarType eps, bool verbose ) +bool mitk::Equal(const mitk::BaseGeometry::BoundingBoxType *leftHandSide, const mitk::BaseGeometry::BoundingBoxType *rightHandSide, ScalarType eps, bool verbose) { - if(( leftHandSide == NULL) || ( rightHandSide == NULL )) + if ((leftHandSide == NULL) || (rightHandSide == NULL)) { MITK_ERROR << "mitk::Equal( const mitk::Geometry3D::BoundingBoxType *leftHandSide, const mitk::Geometry3D::BoundingBoxType *rightHandSide, ScalarType eps, bool verbose ) does not with NULL pointer input."; return false; } - return Equal( *leftHandSide, *rightHandSide, eps, verbose); + return Equal(*leftHandSide, *rightHandSide, eps, verbose); } -bool mitk::Equal( const mitk::BaseGeometry::BoundingBoxType& leftHandSide, const mitk::BaseGeometry::BoundingBoxType& rightHandSide, ScalarType eps, bool verbose ) +bool mitk::Equal(const mitk::BaseGeometry::BoundingBoxType& leftHandSide, const mitk::BaseGeometry::BoundingBoxType& rightHandSide, ScalarType eps, bool verbose) { bool result = true; BaseGeometry::BoundsArrayType rightBounds = rightHandSide.GetBounds(); BaseGeometry::BoundsArrayType leftBounds = leftHandSide.GetBounds(); BaseGeometry::BoundsArrayType::Iterator itLeft = leftBounds.Begin(); - for( BaseGeometry::BoundsArrayType::Iterator itRight = rightBounds.Begin(); itRight != rightBounds.End(); ++itRight) + for (BaseGeometry::BoundsArrayType::Iterator itRight = rightBounds.Begin(); itRight != rightBounds.End(); ++itRight) { - if(( !mitk::Equal( *itLeft, *itRight, eps )) ) + if ((!mitk::Equal(*itLeft, *itRight, eps))) { - if(verbose) + if (verbose) { MITK_INFO << "[( Geometry3D::BoundingBoxType )] bounds are not equal."; MITK_INFO << "rightHandSide is " << setprecision(12) << *itRight << " : leftHandSide is " << *itLeft << " and tolerance is " << eps; } result = false; } itLeft++; } return result; } bool mitk::Equal(const mitk::BaseGeometry *leftHandSide, const mitk::BaseGeometry *rightHandSide, ScalarType eps, bool verbose) { - if(( leftHandSide == NULL) || ( rightHandSide == NULL )) + if ((leftHandSide == NULL) || (rightHandSide == NULL)) { MITK_ERROR << "mitk::Equal(const mitk::Geometry3D *leftHandSide, const mitk::Geometry3D *rightHandSide, ScalarType eps, bool verbose) does not with NULL pointer input."; return false; } - return Equal( *leftHandSide, *rightHandSide, eps, verbose); + return Equal(*leftHandSide, *rightHandSide, eps, verbose); } bool mitk::Equal(const mitk::BaseGeometry& leftHandSide, const mitk::BaseGeometry& rightHandSide, ScalarType eps, bool verbose) { bool result = true; //Compare spacings - if( !mitk::Equal( leftHandSide.GetSpacing(), rightHandSide.GetSpacing(), eps ) ) + if (!mitk::Equal(leftHandSide.GetSpacing(), rightHandSide.GetSpacing(), eps)) { - if(verbose) + if (verbose) { MITK_INFO << "[( Geometry3D )] Spacing differs."; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetSpacing() << " : leftHandSide is " << leftHandSide.GetSpacing() << " and tolerance is " << eps; } result = false; } //Compare Origins - if( !mitk::Equal( leftHandSide.GetOrigin(), rightHandSide.GetOrigin(), eps ) ) + if (!mitk::Equal(leftHandSide.GetOrigin(), rightHandSide.GetOrigin(), eps)) { - if(verbose) + if (verbose) { MITK_INFO << "[( Geometry3D )] Origin differs."; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetOrigin() << " : leftHandSide is " << leftHandSide.GetOrigin() << " and tolerance is " << eps; } result = false; } //Compare Axis and Extents - for( unsigned int i=0; i<3; ++i) + for (unsigned int i = 0; i < 3; ++i) { - if( !mitk::Equal( leftHandSide.GetAxisVector(i), rightHandSide.GetAxisVector(i), eps)) + if (!mitk::Equal(leftHandSide.GetAxisVector(i), rightHandSide.GetAxisVector(i), eps)) { - if(verbose) + if (verbose) { MITK_INFO << "[( Geometry3D )] AxisVector #" << i << " differ"; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetAxisVector(i) << " : leftHandSide is " << leftHandSide.GetAxisVector(i) << " and tolerance is " << eps; } - result = false; + result = false; } - if( !mitk::Equal( leftHandSide.GetExtent(i), rightHandSide.GetExtent(i), eps) ) + if (!mitk::Equal(leftHandSide.GetExtent(i), rightHandSide.GetExtent(i), eps)) { - if(verbose) + if (verbose) { MITK_INFO << "[( Geometry3D )] Extent #" << i << " differ"; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetExtent(i) << " : leftHandSide is " << leftHandSide.GetExtent(i) << " and tolerance is " << eps; } result = false; } } //Compare ImageGeometry Flag - if( rightHandSide.GetImageGeometry() != leftHandSide.GetImageGeometry() ) + if (rightHandSide.GetImageGeometry() != leftHandSide.GetImageGeometry()) { - if(verbose) + if (verbose) { MITK_INFO << "[( Geometry3D )] GetImageGeometry is different."; MITK_INFO << "rightHandSide is " << rightHandSide.GetImageGeometry() << " : leftHandSide is " << leftHandSide.GetImageGeometry(); } result = false; } //Compare BoundingBoxes - if( !mitk::Equal( *leftHandSide.GetBoundingBox(), *rightHandSide.GetBoundingBox(), eps, verbose) ) + if (!mitk::Equal(*leftHandSide.GetBoundingBox(), *rightHandSide.GetBoundingBox(), eps, verbose)) { result = false; } //Compare IndexToWorldTransform Matrix - if( !mitk::Equal( *leftHandSide.GetIndexToWorldTransform(), *rightHandSide.GetIndexToWorldTransform(), eps, verbose) ) + if (!mitk::Equal(*leftHandSide.GetIndexToWorldTransform(), *rightHandSide.GetIndexToWorldTransform(), eps, verbose)) { result = false; } return result; } -bool mitk::Equal(const mitk::BaseGeometry::TransformType *leftHandSide, const mitk::BaseGeometry::TransformType *rightHandSide, ScalarType eps, bool verbose ) +bool mitk::Equal(const mitk::BaseGeometry::TransformType *leftHandSide, const mitk::BaseGeometry::TransformType *rightHandSide, ScalarType eps, bool verbose) { - if(( leftHandSide == NULL) || ( rightHandSide == NULL )) + if ((leftHandSide == NULL) || (rightHandSide == NULL)) { MITK_ERROR << "mitk::Equal(const Geometry3D::TransformType *leftHandSide, const Geometry3D::TransformType *rightHandSide, ScalarType eps, bool verbose ) does not with NULL pointer input."; return false; } - return Equal( *leftHandSide, *rightHandSide, eps, verbose); + return Equal(*leftHandSide, *rightHandSide, eps, verbose); } -bool mitk::Equal(const mitk::BaseGeometry::TransformType& leftHandSide, const mitk::BaseGeometry::TransformType& rightHandSide, ScalarType eps, bool verbose ) +bool mitk::Equal(const mitk::BaseGeometry::TransformType& leftHandSide, const mitk::BaseGeometry::TransformType& rightHandSide, ScalarType eps, bool verbose) { //Compare IndexToWorldTransform Matrix - if( !mitk::MatrixEqualElementWise( leftHandSide.GetMatrix(), - rightHandSide.GetMatrix() ) ) + if (!mitk::MatrixEqualElementWise(leftHandSide.GetMatrix(), + rightHandSide.GetMatrix())) { - if(verbose) + if (verbose) { MITK_INFO << "[( Geometry3D::TransformType )] Index to World Transformation matrix differs."; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetMatrix() << " : leftHandSide is " << leftHandSide.GetMatrix() << " and tolerance is " << eps; } return false; } return true; } \ No newline at end of file diff --git a/Modules/Core/src/DataManagement/mitkPlaneGeometry.cpp b/Modules/Core/src/DataManagement/mitkPlaneGeometry.cpp index cfcea89df2..af8a3393b4 100644 --- a/Modules/Core/src/DataManagement/mitkPlaneGeometry.cpp +++ b/Modules/Core/src/DataManagement/mitkPlaneGeometry.cpp @@ -1,900 +1,896 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkPlaneGeometry.h" #include "mitkPlaneOperation.h" #include "mitkInteractionConst.h" #include "mitkLine.h" #include #include namespace mitk { PlaneGeometry::PlaneGeometry() : Superclass(), m_ReferenceGeometry( NULL ) { Initialize(); } PlaneGeometry::~PlaneGeometry() { } PlaneGeometry::PlaneGeometry(const PlaneGeometry& other) : Superclass(other), m_ReferenceGeometry( other.m_ReferenceGeometry ) { } void PlaneGeometry::EnsurePerpendicularNormal(mitk::AffineTransform3D *transform) { //ensure row(2) of transform to be perpendicular to plane, keep length. VnlVector normal = vnl_cross_3d( transform->GetMatrix().GetVnlMatrix().get_column(0), transform->GetMatrix().GetVnlMatrix().get_column(1) ); normal.normalize(); ScalarType len = transform->GetMatrix() .GetVnlMatrix().get_column(2).two_norm(); if (len==0) len = 1; normal*=len; Matrix3D matrix = transform->GetMatrix(); matrix.GetVnlMatrix().set_column(2, normal); transform->SetMatrix(matrix); } - void - PlaneGeometry::PreSetIndexToWorldTransform(mitk::AffineTransform3D *transform) + void PlaneGeometry::CheckIndexToWorldTransform(mitk::AffineTransform3D* transform) { EnsurePerpendicularNormal(transform); } void - PlaneGeometry::PreSetBounds(const BoundingBox::BoundsArrayType &bounds) + PlaneGeometry::CheckBounds(const BoundingBox::BoundsArrayType &bounds) { // error: unused parameter 'bounds' // this happens in release mode, where the assert macro is defined empty // hence we "use" the parameter: (void)bounds; //currently the unit rectangle must be starting at the origin [0,0] assert(bounds[0]==0); assert(bounds[2]==0); //the unit rectangle must be two-dimensional assert(bounds[1]>0); assert(bounds[3]>0); } void PlaneGeometry::IndexToWorld( const Point2D &pt_units, Point2D &pt_mm ) const { pt_mm[0] = GetExtentInMM(0) / GetExtent(0)*pt_units[0]; pt_mm[1] = GetExtentInMM(1) / GetExtent(1)*pt_units[1]; } void PlaneGeometry::WorldToIndex( const Point2D &pt_mm, Point2D &pt_units ) const { pt_units[0] = pt_mm[0] * (1.0 / (GetExtentInMM(0) / GetExtent(0))); pt_units[1] = pt_mm[1] * (1.0 / (GetExtentInMM(1) / GetExtent(1))); } void PlaneGeometry::IndexToWorld( const Point2D & /*atPt2d_units*/, const Vector2D &vec_units, Vector2D &vec_mm) const { MITK_WARN<<"Warning! Call of the deprecated function PlaneGeometry::IndexToWorld(point, vec, vec). Use PlaneGeometry::IndexToWorld(vec, vec) instead!"; this->IndexToWorld(vec_units, vec_mm); } void PlaneGeometry::IndexToWorld(const Vector2D &vec_units, Vector2D &vec_mm) const { vec_mm[0] = (GetExtentInMM(0) / GetExtent(0)) * vec_units[0]; vec_mm[1] = (GetExtentInMM(1) / GetExtent(1)) * vec_units[1]; } void PlaneGeometry::WorldToIndex( const Point2D & /*atPt2d_mm*/, const Vector2D &vec_mm, Vector2D &vec_units) const { MITK_WARN<<"Warning! Call of the deprecated function PlaneGeometry::WorldToIndex(point, vec, vec). Use PlaneGeometry::WorldToIndex(vec, vec) instead!"; this->WorldToIndex(vec_mm, vec_units); } void PlaneGeometry::WorldToIndex( const Vector2D &vec_mm, Vector2D &vec_units) const { vec_units[0] = vec_mm[0] * (1.0 / (GetExtentInMM(0) / GetExtent(0))); vec_units[1] = vec_mm[1] * (1.0 / (GetExtentInMM(1) / GetExtent(1))); } void PlaneGeometry::InitializeStandardPlane( mitk::ScalarType width, ScalarType height, const Vector3D & spacing, PlaneGeometry::PlaneOrientation planeorientation, ScalarType zPosition, bool frontside, bool rotated ) { AffineTransform3D::Pointer transform; transform = AffineTransform3D::New(); AffineTransform3D::MatrixType matrix; AffineTransform3D::MatrixType::InternalMatrixType &vnlmatrix = matrix.GetVnlMatrix(); vnlmatrix.set_identity(); vnlmatrix(0,0) = spacing[0]; vnlmatrix(1,1) = spacing[1]; vnlmatrix(2,2) = spacing[2]; transform->SetIdentity(); transform->SetMatrix(matrix); InitializeStandardPlane(width, height, transform.GetPointer(), planeorientation, zPosition, frontside, rotated); } void PlaneGeometry::InitializeStandardPlane( mitk::ScalarType width, ScalarType height, const AffineTransform3D* transform, PlaneGeometry::PlaneOrientation planeorientation, ScalarType zPosition, bool frontside, bool rotated ) { Superclass::Initialize(); //construct standard view Point3D origin; VnlVector rightDV(3), bottomDV(3); origin.Fill(0); int normalDirection; switch(planeorientation) { case Axial: if(frontside) { if(rotated==false) { FillVector3D(origin, 0, 0, zPosition); FillVector3D(rightDV, 1, 0, 0); FillVector3D(bottomDV, 0, 1, 0); } else { FillVector3D(origin, width, height, zPosition); FillVector3D(rightDV, -1, 0, 0); FillVector3D(bottomDV, 0, -1, 0); } } else { if(rotated==false) { FillVector3D(origin, width, 0, zPosition); FillVector3D(rightDV, -1, 0, 0); FillVector3D(bottomDV, 0, 1, 0); } else { FillVector3D(origin, 0, height, zPosition); FillVector3D(rightDV, 1, 0, 0); FillVector3D(bottomDV, 0, -1, 0); } } normalDirection = 2; break; case Frontal: if(frontside) { if(rotated==false) { FillVector3D(origin, 0, zPosition, 0); FillVector3D(rightDV, 1, 0, 0); FillVector3D(bottomDV, 0, 0, 1); } else { FillVector3D(origin, width, zPosition, height); FillVector3D(rightDV, -1, 0, 0); FillVector3D(bottomDV, 0, 0, -1); } } else { if(rotated==false) { FillVector3D(origin, width, zPosition, 0); FillVector3D(rightDV, -1, 0, 0); FillVector3D(bottomDV, 0, 0, 1); } else { FillVector3D(origin, 0, zPosition, height); FillVector3D(rightDV, 1, 0, 0); FillVector3D(bottomDV, 0, 0, -1); } } normalDirection = 1; break; case Sagittal: if(frontside) { if(rotated==false) { FillVector3D(origin, zPosition, 0, 0); FillVector3D(rightDV, 0, 1, 0); FillVector3D(bottomDV, 0, 0, 1); } else { FillVector3D(origin, zPosition, width, height); FillVector3D(rightDV, 0, -1, 0); FillVector3D(bottomDV, 0, 0, -1); } } else { if(rotated==false) { FillVector3D(origin, zPosition, width, 0); FillVector3D(rightDV, 0, -1, 0); FillVector3D(bottomDV, 0, 0, 1); } else { FillVector3D(origin, zPosition, 0, height); FillVector3D(rightDV, 0, 1, 0); FillVector3D(bottomDV, 0, 0, -1); } } normalDirection = 0; break; default: itkExceptionMacro("unknown PlaneOrientation"); } if ( transform != NULL ) { origin = transform->TransformPoint( origin ); rightDV = transform->TransformVector( rightDV ); bottomDV = transform->TransformVector( bottomDV ); } ScalarType bounds[6]= { 0, width, 0, height, 0, 1 }; this->SetBounds( bounds ); if ( transform == NULL ) { this->SetMatrixByVectors( rightDV, bottomDV ); } else { this->SetMatrixByVectors( rightDV, bottomDV, transform->GetMatrix().GetVnlMatrix() .get_column(normalDirection).magnitude() ); } this->SetOrigin(origin); } void PlaneGeometry::InitializeStandardPlane( const BaseGeometry *geometry3D, PlaneOrientation planeorientation, ScalarType zPosition, bool frontside, bool rotated ) { this->SetReferenceGeometry( const_cast< BaseGeometry * >( geometry3D ) ); ScalarType width, height; const BoundingBox::BoundsArrayType& boundsarray = geometry3D->GetBoundingBox()->GetBounds(); Vector3D originVector; FillVector3D(originVector, boundsarray[0], boundsarray[2], boundsarray[4]); if(geometry3D->GetImageGeometry()) { FillVector3D( originVector, originVector[0] - 0.5, originVector[1] - 0.5, originVector[2] - 0.5 ); } switch(planeorientation) { case Axial: width = geometry3D->GetExtent(0); height = geometry3D->GetExtent(1); break; case Frontal: width = geometry3D->GetExtent(0); height = geometry3D->GetExtent(2); break; case Sagittal: width = geometry3D->GetExtent(1); height = geometry3D->GetExtent(2); break; default: itkExceptionMacro("unknown PlaneOrientation"); } InitializeStandardPlane( width, height, geometry3D->GetIndexToWorldTransform(), planeorientation, zPosition, frontside, rotated ); ScalarType bounds[6]= { 0, width, 0, height, 0, 1 }; this->SetBounds( bounds ); Point3D origin; originVector = geometry3D->GetIndexToWorldTransform() ->TransformVector( originVector ); origin = GetOrigin() + originVector; SetOrigin(origin); } void PlaneGeometry::InitializeStandardPlane( const BaseGeometry *geometry3D, bool top, PlaneOrientation planeorientation, bool frontside, bool rotated ) { ScalarType zPosition; switch(planeorientation) { case Axial: zPosition = (top ? 0.5 : geometry3D->GetExtent(2)-1+0.5); break; case Frontal: zPosition = (top ? 0.5 : geometry3D->GetExtent(1)-1+0.5); break; case Sagittal: zPosition = (top ? 0.5 : geometry3D->GetExtent(0)-1+0.5); break; default: itkExceptionMacro("unknown PlaneOrientation"); } InitializeStandardPlane( geometry3D, planeorientation, zPosition, frontside, rotated ); } void PlaneGeometry::InitializeStandardPlane( const Vector3D &rightVector, const Vector3D &downVector, const Vector3D *spacing ) { InitializeStandardPlane( rightVector.GetVnlVector(), downVector.GetVnlVector(), spacing ); } void PlaneGeometry::InitializeStandardPlane( const VnlVector& rightVector, const VnlVector &downVector, const Vector3D *spacing ) { ScalarType width = rightVector.magnitude(); ScalarType height = downVector.magnitude(); InitializeStandardPlane( width, height, rightVector, downVector, spacing ); } void PlaneGeometry::InitializeStandardPlane( mitk::ScalarType width, ScalarType height, const Vector3D &rightVector, const Vector3D &downVector, const Vector3D *spacing ) { InitializeStandardPlane( width, height, rightVector.GetVnlVector(), downVector.GetVnlVector(), spacing ); } void PlaneGeometry::InitializeStandardPlane( mitk::ScalarType width, ScalarType height, const VnlVector &rightVector, const VnlVector &downVector, const Vector3D *spacing ) { assert(width > 0); assert(height > 0); VnlVector rightDV = rightVector; rightDV.normalize(); VnlVector downDV = downVector; downDV.normalize(); VnlVector normal = vnl_cross_3d(rightVector, downVector); normal.normalize(); if(spacing!=NULL) { rightDV *= (*spacing)[0]; downDV *= (*spacing)[1]; normal *= (*spacing)[2]; } AffineTransform3D::Pointer transform = AffineTransform3D::New(); Matrix3D matrix; matrix.GetVnlMatrix().set_column(0, rightDV); matrix.GetVnlMatrix().set_column(1, downDV); matrix.GetVnlMatrix().set_column(2, normal); transform->SetMatrix(matrix); transform->SetOffset(this->GetIndexToWorldTransform()->GetOffset()); ScalarType bounds[6] = { 0, width, 0, height, 0, 1 }; this->SetBounds( bounds ); this->SetIndexToWorldTransform( transform ); } void PlaneGeometry::InitializePlane( const Point3D &origin, const Vector3D &normal ) { VnlVector rightVectorVnl(3), downVectorVnl; if( Equal( normal[1], 0.0f ) == false ) { FillVector3D( rightVectorVnl, 1.0f, -normal[0]/normal[1], 0.0f ); rightVectorVnl.normalize(); } else { FillVector3D( rightVectorVnl, 0.0f, 1.0f, 0.0f ); } downVectorVnl = vnl_cross_3d( normal.GetVnlVector(), rightVectorVnl ); downVectorVnl.normalize(); InitializeStandardPlane( rightVectorVnl, downVectorVnl ); SetOrigin(origin); } void PlaneGeometry::SetMatrixByVectors( const VnlVector &rightVector, const VnlVector &downVector, ScalarType thickness ) { VnlVector normal = vnl_cross_3d(rightVector, downVector); normal.normalize(); normal *= thickness; AffineTransform3D::Pointer transform = AffineTransform3D::New(); Matrix3D matrix; matrix.GetVnlMatrix().set_column(0, rightVector); matrix.GetVnlMatrix().set_column(1, downVector); matrix.GetVnlMatrix().set_column(2, normal); transform->SetMatrix(matrix); transform->SetOffset(this->GetIndexToWorldTransform()->GetOffset()); SetIndexToWorldTransform(transform); } Vector3D PlaneGeometry::GetNormal() const { Vector3D frontToBack; frontToBack.SetVnlVector( this->GetIndexToWorldTransform() ->GetMatrix().GetVnlMatrix().get_column(2) ); return frontToBack; } VnlVector PlaneGeometry::GetNormalVnl() const { return this->GetIndexToWorldTransform() ->GetMatrix().GetVnlMatrix().get_column(2); } ScalarType PlaneGeometry::DistanceFromPlane( const Point3D &pt3d_mm ) const { return fabs(SignedDistance( pt3d_mm )); } ScalarType PlaneGeometry::SignedDistance( const Point3D &pt3d_mm ) const { return SignedDistanceFromPlane(pt3d_mm); } //Function from Geometry2D // mitk::ScalarType // PlaneGeometry::SignedDistance(const mitk::Point3D& pt3d_mm) const //{ // Point3D projectedPoint; // Project(pt3d_mm, projectedPoint); // Vector3D direction = pt3d_mm-projectedPoint; // ScalarType distance = direction.GetNorm(); // if(IsAbove(pt3d_mm) == false) // distance*=-1.0; // return distance; //} bool PlaneGeometry::IsAbove( const Point3D &pt3d_mm , bool considerBoundingBox) const { if(considerBoundingBox) { Point3D pt3d_units; BaseGeometry::WorldToIndex(pt3d_mm, pt3d_units); return (pt3d_units[2] > this->GetBoundingBox()->GetBounds()[4]); } else return SignedDistanceFromPlane(pt3d_mm) > 0; } bool PlaneGeometry::IntersectionLine( const PlaneGeometry* plane, Line3D& crossline ) const { Vector3D normal = this->GetNormal(); normal.Normalize(); Vector3D planeNormal = plane->GetNormal(); planeNormal.Normalize(); Vector3D direction = itk::CrossProduct( normal, planeNormal ); if ( direction.GetSquaredNorm() < eps ) return false; crossline.SetDirection( direction ); double N1dN2 = normal * planeNormal; double determinant = 1.0 - N1dN2 * N1dN2; Vector3D origin = this->GetOrigin().GetVectorFromOrigin(); Vector3D planeOrigin = plane->GetOrigin().GetVectorFromOrigin(); double d1 = normal * origin; double d2 = planeNormal * planeOrigin; double c1 = ( d1 - d2 * N1dN2 ) / determinant; double c2 = ( d2 - d1 * N1dN2 ) / determinant; Vector3D p = normal * c1 + planeNormal * c2; crossline.GetPoint().GetVnlVector() = p.GetVnlVector(); return true; } unsigned int PlaneGeometry::IntersectWithPlane2D( const PlaneGeometry* plane, Point2D& lineFrom, Point2D &lineTo ) const { Line3D crossline; if ( this->IntersectionLine( plane, crossline ) == false ) return 0; Point2D point2; Vector2D direction2; this->Map( crossline.GetPoint(), point2 ); this->Map( crossline.GetPoint(), crossline.GetDirection(), direction2 ); return Line3D::RectangleLineIntersection( 0, 0, GetExtentInMM(0), GetExtentInMM(1), point2, direction2, lineFrom, lineTo ); } double PlaneGeometry::Angle( const PlaneGeometry *plane ) const { return angle(plane->GetMatrixColumn(2), GetMatrixColumn(2)); } double PlaneGeometry::Angle( const Line3D &line ) const { return vnl_math::pi_over_2 - angle( line.GetDirection().GetVnlVector(), GetMatrixColumn(2) ); } bool PlaneGeometry::IntersectionPoint( const Line3D &line, Point3D &intersectionPoint ) const { Vector3D planeNormal = this->GetNormal(); planeNormal.Normalize(); Vector3D lineDirection = line.GetDirection(); lineDirection.Normalize(); double t = planeNormal * lineDirection; if ( fabs( t ) < eps ) { return false; } Vector3D diff; diff = this->GetOrigin() - line.GetPoint(); t = ( planeNormal * diff ) / t; intersectionPoint = line.GetPoint() + lineDirection * t; return true; } bool PlaneGeometry::IntersectionPointParam( const Line3D &line, double &t ) const { Vector3D planeNormal = this->GetNormal(); Vector3D lineDirection = line.GetDirection(); t = planeNormal * lineDirection; if ( fabs( t ) < eps ) { return false; } Vector3D diff; diff = this->GetOrigin() - line.GetPoint(); t = ( planeNormal * diff ) / t; return true; } bool PlaneGeometry::IsParallel( const PlaneGeometry *plane ) const { return ( (Angle(plane) < 10.0 * mitk::sqrteps ) || ( Angle(plane) > ( vnl_math::pi - 10.0 * sqrteps ) ) ) ; } bool PlaneGeometry::IsOnPlane( const Point3D &point ) const { return Distance(point) < eps; } bool PlaneGeometry::IsOnPlane( const Line3D &line ) const { return ( (Distance( line.GetPoint() ) < eps) && (Distance( line.GetPoint2() ) < eps) ); } bool PlaneGeometry::IsOnPlane( const PlaneGeometry *plane ) const { return ( IsParallel( plane ) && (Distance( plane->GetOrigin() ) < eps) ); } Point3D PlaneGeometry::ProjectPointOntoPlane( const Point3D& pt ) const { ScalarType len = this->GetNormalVnl().two_norm(); return pt - this->GetNormal() * this->SignedDistanceFromPlane( pt ) / len; } itk::LightObject::Pointer PlaneGeometry::InternalClone() const { Self::Pointer newGeometry = new PlaneGeometry(*this); newGeometry->UnRegister(); return newGeometry.GetPointer(); } void PlaneGeometry::ExecuteOperation( Operation *operation ) { vtkTransform *transform = vtkTransform::New(); transform->SetMatrix( this->GetVtkMatrix()); switch ( operation->GetOperationType() ) { case OpORIENT: { mitk::PlaneOperation *planeOp = dynamic_cast< mitk::PlaneOperation * >( operation ); if ( planeOp == NULL ) { return; } Point3D center = planeOp->GetPoint(); Vector3D orientationVector = planeOp->GetNormal(); Vector3D defaultVector; FillVector3D( defaultVector, 0.0, 0.0, 1.0 ); Vector3D rotationAxis = itk::CrossProduct( orientationVector, defaultVector ); //double rotationAngle = acos( orientationVector[2] / orientationVector.GetNorm() ); double rotationAngle = atan2( (double) rotationAxis.GetNorm(), (double) (orientationVector * defaultVector) ); rotationAngle *= 180.0 / vnl_math::pi; transform->PostMultiply(); transform->Identity(); transform->Translate( center[0], center[1], center[2] ); transform->RotateWXYZ( rotationAngle, rotationAxis[0], rotationAxis[1], rotationAxis[2] ); transform->Translate( -center[0], -center[1], -center[2] ); break; } case OpRESTOREPLANEPOSITION: { RestorePlanePositionOperation *op = dynamic_cast< mitk::RestorePlanePositionOperation* >(operation); if(op == NULL) { return; } AffineTransform3D::Pointer transform2 = AffineTransform3D::New(); Matrix3D matrix; matrix.GetVnlMatrix().set_column(0, op->GetTransform()->GetMatrix().GetVnlMatrix().get_column(0)); matrix.GetVnlMatrix().set_column(1, op->GetTransform()->GetMatrix().GetVnlMatrix().get_column(1)); matrix.GetVnlMatrix().set_column(2, op->GetTransform()->GetMatrix().GetVnlMatrix().get_column(2)); transform2->SetMatrix(matrix); Vector3D offset = op->GetTransform()->GetOffset(); transform2->SetOffset(offset); this->SetIndexToWorldTransform(transform2); ScalarType bounds[6] = {0, op->GetWidth(), 0, op->GetHeight(), 0 ,1 }; this->SetBounds(bounds); this->Modified(); transform->Delete(); return; } default: Superclass::ExecuteOperation( operation ); transform->Delete(); return; } this->SetVtkMatrixDeepCopy(transform); this->Modified(); transform->Delete(); } void PlaneGeometry::PrintSelf( std::ostream& os, itk::Indent indent ) const { Superclass::PrintSelf(os,indent); os << indent << " ScaleFactorMMPerUnitX: " << GetExtentInMM(0) / GetExtent(0) << std::endl; os << indent << " ScaleFactorMMPerUnitY: " << GetExtentInMM(1) / GetExtent(1) << std::endl; os << indent << " Normal: " << GetNormal() << std::endl; } - bool PlaneGeometry::Map(const mitk::Point3D &pt3d_mm, mitk::Point2D &pt2d_mm) const { assert(this->IsBoundingBoxNull()==false); Point3D pt3d_units; - BackTransform(pt3d_mm, pt3d_units); + Superclass::WorldToIndex(pt3d_mm, pt3d_units); pt2d_mm[0] = pt3d_units[0] * GetExtentInMM(0) / GetExtent(0); pt2d_mm[1] = pt3d_units[1] * GetExtentInMM(1) / GetExtent(1); pt3d_units[2]=0; return const_cast(this->GetBoundingBox())->IsInside(pt3d_units); } void PlaneGeometry::Map(const mitk::Point2D &pt2d_mm, mitk::Point3D &pt3d_mm) const { //pt2d_mm is measured from the origin of the world geometry (at leats it called form BaseRendere::Mouse...Event) Point3D pt3d_units; pt3d_units[0] = pt2d_mm[0] / (GetExtentInMM(0) / GetExtent(0)); pt3d_units[1] = pt2d_mm[1] / (GetExtentInMM(1) / GetExtent(1)); pt3d_units[2]=0; //pt3d_units is a continuos index. We divided it with the Scale Factor (= spacing in x and y) to convert it from mm to index units. // pt3d_mm = GetIndexToWorldTransform()->TransformPoint(pt3d_units); //now we convert the 3d index to a 3D world point in mm. We could have used IndexToWorld as well as GetITW->Transform... } void PlaneGeometry::SetSizeInUnits(mitk::ScalarType width, mitk::ScalarType height) { ScalarType bounds[6]={0, width, 0, height, 0, 1}; ScalarType extent, newextentInMM; if(GetExtent(0)>0) { extent = GetExtent(0); if(width>extent) newextentInMM = GetExtentInMM(0)/width*extent; else newextentInMM = GetExtentInMM(0)*extent/width; SetExtentInMM(0, newextentInMM); } if(GetExtent(1)>0) { extent = GetExtent(1); if(width>extent) newextentInMM = GetExtentInMM(1)/height*extent; else newextentInMM = GetExtentInMM(1)*extent/height; SetExtentInMM(1, newextentInMM); } SetBounds(bounds); } bool PlaneGeometry::Project( const mitk::Point3D &pt3d_mm, mitk::Point3D &projectedPt3d_mm) const { assert(this->IsBoundingBoxNull()==false); Point3D pt3d_units; - BackTransform(pt3d_mm, pt3d_units); + Superclass::WorldToIndex(pt3d_mm, pt3d_units); pt3d_units[2] = 0; projectedPt3d_mm = GetIndexToWorldTransform()->TransformPoint(pt3d_units); return const_cast(this->GetBoundingBox())->IsInside(pt3d_units); } bool PlaneGeometry::Project(const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const { assert(this->IsBoundingBoxNull()==false); Vector3D vec3d_units; - BackTransform(vec3d_mm, vec3d_units); + Superclass::WorldToIndex(vec3d_mm, vec3d_units); vec3d_units[2] = 0; projectedVec3d_mm = GetIndexToWorldTransform()->TransformVector(vec3d_units); return true; } bool PlaneGeometry::Project(const mitk::Point3D & atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const { MITK_WARN << "Deprecated function! Call Project(vec3D,vec3D) instead."; assert(this->IsBoundingBoxNull()==false); Vector3D vec3d_units; - BackTransform(atPt3d_mm, vec3d_mm, vec3d_units); + Superclass::WorldToIndex(atPt3d_mm, vec3d_mm, vec3d_units); vec3d_units[2] = 0; projectedVec3d_mm = GetIndexToWorldTransform()->TransformVector(vec3d_units); Point3D pt3d_units; - BackTransform(atPt3d_mm, pt3d_units); + Superclass::WorldToIndex(atPt3d_mm, pt3d_units); return const_cast(this->GetBoundingBox())->IsInside(pt3d_units); } bool PlaneGeometry::Map(const mitk::Point3D & atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector2D &vec2d_mm) const { Point2D pt2d_mm_start, pt2d_mm_end; Point3D pt3d_mm_end; bool inside=Map(atPt3d_mm, pt2d_mm_start); pt3d_mm_end = atPt3d_mm+vec3d_mm; inside&=Map(pt3d_mm_end, pt2d_mm_end); vec2d_mm=pt2d_mm_end-pt2d_mm_start; return inside; } void PlaneGeometry::Map(const mitk::Point2D &/*atPt2d_mm*/, const mitk::Vector2D &/*vec2d_mm*/, mitk::Vector3D &/*vec3d_mm*/) const { //@todo implement parallel to the other Map method! assert(false); } - - void PlaneGeometry::SetReferenceGeometry( mitk::BaseGeometry *geometry ) { m_ReferenceGeometry = geometry; } mitk::BaseGeometry * PlaneGeometry::GetReferenceGeometry() const { return m_ReferenceGeometry; } bool PlaneGeometry::HasReferenceGeometry() const { return ( m_ReferenceGeometry != NULL ); } -} // namespace +} // namespace \ No newline at end of file diff --git a/Modules/Core/src/DataManagement/mitkSlicedGeometry3D.cpp b/Modules/Core/src/DataManagement/mitkSlicedGeometry3D.cpp index 5b649d0121..241288f891 100644 --- a/Modules/Core/src/DataManagement/mitkSlicedGeometry3D.cpp +++ b/Modules/Core/src/DataManagement/mitkSlicedGeometry3D.cpp @@ -1,1032 +1,1032 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkSlicedGeometry3D.h" #include "mitkPlaneGeometry.h" #include "mitkRotationOperation.h" #include "mitkPlaneOperation.h" #include "mitkRestorePlanePositionOperation.h" #include "mitkApplyTransformMatrixOperation.h" #include "mitkInteractionConst.h" #include "mitkSliceNavigationController.h" #include "mitkAbstractTransformGeometry.h" const mitk::ScalarType PI = 3.14159265359; mitk::SlicedGeometry3D::SlicedGeometry3D() : m_EvenlySpaced( true ), m_Slices( 0 ), m_ReferenceGeometry( NULL ), m_SliceNavigationController( NULL ) { m_DirectionVector.Fill(0); this->InitializeSlicedGeometry( m_Slices ); } mitk::SlicedGeometry3D::SlicedGeometry3D(const SlicedGeometry3D& other) : Superclass(other), m_EvenlySpaced( other.m_EvenlySpaced ), m_Slices( other.m_Slices ), m_ReferenceGeometry( other.m_ReferenceGeometry ), m_SliceNavigationController( other.m_SliceNavigationController ) { m_DirectionVector.Fill(0); SetSpacing( other.GetSpacing() ); SetDirectionVector( other.GetDirectionVector() ); if ( m_EvenlySpaced ) { PlaneGeometry::Pointer geometry = other.m_PlaneGeometries[0]->Clone(); assert(geometry.IsNotNull()); SetPlaneGeometry(geometry, 0); } else { unsigned int s; for ( s = 0; s < other.m_Slices; ++s ) { if ( other.m_PlaneGeometries[s].IsNull() ) { assert(other.m_EvenlySpaced); m_PlaneGeometries[s] = NULL; } else { PlaneGeometry* geometry2D = other.m_PlaneGeometries[s]->Clone(); assert(geometry2D!=NULL); SetPlaneGeometry(geometry2D, s); } } } } mitk::SlicedGeometry3D::~SlicedGeometry3D() { } mitk::PlaneGeometry * mitk::SlicedGeometry3D::GetPlaneGeometry( int s ) const { mitk::PlaneGeometry::Pointer geometry2D = NULL; if ( this->IsValidSlice(s) ) { geometry2D = m_PlaneGeometries[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[2]*s // in the direction of m_DirectionVector. if ( (m_EvenlySpaced) && (geometry2D.IsNull()) ) { PlaneGeometry *firstSlice = m_PlaneGeometries[0]; if ( firstSlice != NULL && dynamic_cast(m_PlaneGeometries[0].GetPointer() )==NULL) { if ( (m_DirectionVector[0] == 0.0) && (m_DirectionVector[1] == 0.0) && (m_DirectionVector[2] == 0.0) ) { m_DirectionVector = firstSlice->GetNormal(); m_DirectionVector.Normalize(); } Vector3D direction; direction = m_DirectionVector * this->GetSpacing()[2]; mitk::PlaneGeometry::Pointer requestedslice; requestedslice = static_cast< mitk::PlaneGeometry * >( firstSlice->Clone().GetPointer() ); requestedslice->SetOrigin( requestedslice->GetOrigin() + direction * s ); geometry2D = requestedslice; m_PlaneGeometries[s] = geometry2D; } } return geometry2D; } else { return NULL; } } const mitk::BoundingBox * mitk::SlicedGeometry3D::GetBoundingBox() const { assert(this->IsBoundingBoxNull()==false); return Superclass::GetBoundingBox(); } bool mitk::SlicedGeometry3D::SetPlaneGeometry( mitk::PlaneGeometry *geometry2D, int s ) { if ( this->IsValidSlice(s) ) { m_PlaneGeometries[s] = geometry2D; m_PlaneGeometries[s]->SetReferenceGeometry( m_ReferenceGeometry ); return true; } return false; } void mitk::SlicedGeometry3D::InitializeSlicedGeometry( unsigned int slices ) { Superclass::Initialize(); m_Slices = slices; PlaneGeometry::Pointer gnull = NULL; m_PlaneGeometries.assign( m_Slices, gnull ); Vector3D spacing; spacing.Fill( 1.0 ); this->SetSpacing( spacing ); m_DirectionVector.Fill( 0 ); } void mitk::SlicedGeometry3D::InitializeEvenlySpaced( mitk::PlaneGeometry* geometry2D, unsigned int slices, bool flipped ) { assert( geometry2D != NULL ); this->InitializeEvenlySpaced( geometry2D, geometry2D->GetExtentInMM(2)/geometry2D->GetExtent(2), slices, flipped ); } void mitk::SlicedGeometry3D::InitializeEvenlySpaced( mitk::PlaneGeometry* geometry2D, mitk::ScalarType zSpacing, unsigned int slices, bool flipped ) { assert( geometry2D != NULL ); assert( geometry2D->GetExtent(0) > 0 ); assert( geometry2D->GetExtent(1) > 0 ); geometry2D->Register(); Superclass::Initialize(); m_Slices = slices; BoundingBox::BoundsArrayType bounds = geometry2D->GetBounds(); bounds[4] = 0; bounds[5] = slices; // clear and reserve PlaneGeometry::Pointer gnull = NULL; m_PlaneGeometries.assign( m_Slices, gnull ); Vector3D directionVector = geometry2D->GetAxisVector(2); directionVector.Normalize(); directionVector *= zSpacing; if ( flipped == false ) { // Normally we should use the following four lines to create a copy of // the transform contrained in geometry2D, because it may not be changed // by us. But we know that SetSpacing creates a new transform without // changing the old (coming from geometry2D), so we can use the fifth // line instead. We check this at (**). // // AffineTransform3D::Pointer transform = AffineTransform3D::New(); // transform->SetMatrix(geometry2D->GetIndexToWorldTransform()->GetMatrix()); // transform->SetOffset(geometry2D->GetIndexToWorldTransform()->GetOffset()); // SetIndexToWorldTransform(transform); this->SetIndexToWorldTransform( const_cast< AffineTransform3D * >( geometry2D->GetIndexToWorldTransform() )); } else { directionVector *= -1.0; this->SetIndexToWorldTransform( AffineTransform3D::New()); this->GetIndexToWorldTransform()->SetMatrix( geometry2D->GetIndexToWorldTransform()->GetMatrix() ); AffineTransform3D::OutputVectorType scaleVector; FillVector3D(scaleVector, 1.0, 1.0, -1.0); this->GetIndexToWorldTransform()->Scale(scaleVector, true); this->GetIndexToWorldTransform()->SetOffset( geometry2D->GetIndexToWorldTransform()->GetOffset() ); } mitk::Vector3D spacing; FillVector3D( spacing, geometry2D->GetExtentInMM(0) / bounds[1], geometry2D->GetExtentInMM(1) / bounds[3], zSpacing ); this->SetDirectionVector( directionVector ); this->SetBounds( bounds ); this->SetPlaneGeometry( geometry2D, 0 ); this->SetSpacing( spacing, true); this->SetEvenlySpaced(); //this->SetTimeBounds( geometry2D->GetTimeBounds() ); assert(this->GetIndexToWorldTransform() != geometry2D->GetIndexToWorldTransform()); // (**) see above. this->SetFrameOfReferenceID( geometry2D->GetFrameOfReferenceID() ); this->SetImageGeometry( geometry2D->GetImageGeometry() ); geometry2D->UnRegister(); } void mitk::SlicedGeometry3D::InitializePlanes( const mitk::BaseGeometry *geometry3D, mitk::PlaneGeometry::PlaneOrientation planeorientation, bool top, bool frontside, bool rotated ) { m_ReferenceGeometry = const_cast< BaseGeometry * >( geometry3D ); PlaneGeometry::Pointer planeGeometry = mitk::PlaneGeometry::New(); planeGeometry->InitializeStandardPlane( geometry3D, top, planeorientation, frontside, rotated ); ScalarType viewSpacing = 1; unsigned int slices = 1; switch ( planeorientation ) { case PlaneGeometry::Axial: viewSpacing = geometry3D->GetSpacing()[2]; slices = (unsigned int) geometry3D->GetExtent( 2 ); break; case PlaneGeometry::Frontal: viewSpacing = geometry3D->GetSpacing()[1]; slices = (unsigned int) geometry3D->GetExtent( 1 ); break; case PlaneGeometry::Sagittal: viewSpacing = geometry3D->GetSpacing()[0]; slices = (unsigned int) geometry3D->GetExtent( 0 ); break; default: itkExceptionMacro("unknown PlaneOrientation"); } mitk::Vector3D normal = this->AdjustNormal( planeGeometry->GetNormal() ); ScalarType directedExtent = std::abs( m_ReferenceGeometry->GetExtentInMM( 0 ) * normal[0] ) + std::abs( m_ReferenceGeometry->GetExtentInMM( 1 ) * normal[1] ) + std::abs( m_ReferenceGeometry->GetExtentInMM( 2 ) * normal[2] ); if ( directedExtent >= viewSpacing ) { slices = static_cast< int >(directedExtent / viewSpacing + 0.5); } else { slices = 1; } bool flipped = (top == false); if ( frontside == false ) { flipped = !flipped; } if ( planeorientation == PlaneGeometry::Frontal ) { flipped = !flipped; } this->InitializeEvenlySpaced( planeGeometry, viewSpacing, slices, flipped ); } void mitk::SlicedGeometry3D ::ReinitializePlanes( const Point3D ¢er, const Point3D &referencePoint ) { // Need a reference frame to align the rotated planes if ( !m_ReferenceGeometry ) { return; } // Get first plane of plane stack PlaneGeometry *firstPlane = m_PlaneGeometries[0]; // If plane stack is empty, exit if ( !firstPlane || dynamic_cast(firstPlane) ) { return; } // Calculate the "directed" spacing when taking the plane (defined by its axes // vectors and normal) as the reference coordinate frame. // // This is done by calculating the radius of the ellipsoid defined by the // original volume spacing axes, in the direction of the respective axis of the // reference frame. mitk::Vector3D axis0 = firstPlane->GetAxisVector(0); mitk::Vector3D axis1 = firstPlane->GetAxisVector(1); mitk::Vector3D normal = firstPlane->GetNormal(); normal.Normalize(); Vector3D spacing; spacing[0] = this->CalculateSpacing( axis0 ); spacing[1] = this->CalculateSpacing( axis1 ); spacing[2] = this->CalculateSpacing( normal ); Superclass::SetSpacing( spacing ); // Now we need to calculate the number of slices in the plane's normal // direction, so that the entire volume is covered. This is done by first // calculating the dot product between the volume diagonal (the maximum // distance inside the volume) and the normal, and dividing this value by // the directed spacing calculated above. ScalarType directedExtent = std::abs( m_ReferenceGeometry->GetExtentInMM( 0 ) * normal[0] ) + std::abs( m_ReferenceGeometry->GetExtentInMM( 1 ) * normal[1] ) + std::abs( m_ReferenceGeometry->GetExtentInMM( 2 ) * normal[2] ); if ( directedExtent >= spacing[2] ) { m_Slices = static_cast< unsigned int >(directedExtent / spacing[2] + 0.5); } else { m_Slices = 1; } // The origin of our "first plane" needs to be adapted to this new extent. // To achieve this, we first calculate the current distance to the volume's // center, and then shift the origin in the direction of the normal by the // difference between this distance and half of the new extent. double centerOfRotationDistance = firstPlane->SignedDistanceFromPlane( center ); if ( centerOfRotationDistance > 0 ) { firstPlane->SetOrigin( firstPlane->GetOrigin() + normal * (centerOfRotationDistance - directedExtent / 2.0) ); m_DirectionVector = normal; } else { firstPlane->SetOrigin( firstPlane->GetOrigin() + normal * (directedExtent / 2.0 + centerOfRotationDistance) ); m_DirectionVector = -normal; } // Now we adjust this distance according with respect to the given reference // point: we need to make sure that the point is touched by one slice of the // new slice stack. double referencePointDistance = firstPlane->SignedDistanceFromPlane( referencePoint ); int referencePointSlice = static_cast< int >( referencePointDistance / spacing[2]); double alignmentValue = referencePointDistance / spacing[2] - referencePointSlice; firstPlane->SetOrigin( firstPlane->GetOrigin() + normal * alignmentValue * spacing[2] ); // Finally, we can clear the previous geometry stack and initialize it with // our re-initialized "first plane". m_PlaneGeometries.assign( m_Slices, PlaneGeometry::Pointer( NULL ) ); if ( m_Slices > 0 ) { m_PlaneGeometries[0] = firstPlane; } // Reinitialize SNC with new number of slices m_SliceNavigationController->GetSlice()->SetSteps( m_Slices ); this->Modified(); } double mitk::SlicedGeometry3D::CalculateSpacing( const mitk::Vector3D &d ) const { // Need the spacing of the underlying dataset / geometry if ( !m_ReferenceGeometry ) { return 1.0; } const mitk::Vector3D &spacing = m_ReferenceGeometry->GetSpacing(); return SlicedGeometry3D::CalculateSpacing( spacing, d ); } double mitk::SlicedGeometry3D::CalculateSpacing( const mitk::Vector3D spacing, const mitk::Vector3D &d ) { // The following can be derived from the ellipsoid equation // // 1 = x^2/a^2 + y^2/b^2 + z^2/c^2 // // where (a,b,c) = spacing of original volume (ellipsoid radii) // and (x,y,z) = scaled coordinates of vector d (according to ellipsoid) // double scaling = d[0]*d[0] / (spacing[0] * spacing[0]) + d[1]*d[1] / (spacing[1] * spacing[1]) + d[2]*d[2] / (spacing[2] * spacing[2]); scaling = sqrt( scaling ); return ( sqrt( d[0]*d[0] + d[1]*d[1] + d[2]*d[2] ) / scaling ); } mitk::Vector3D mitk::SlicedGeometry3D::AdjustNormal( const mitk::Vector3D &normal ) const { TransformType::Pointer inverse = TransformType::New(); m_ReferenceGeometry->GetIndexToWorldTransform()->GetInverse( inverse ); Vector3D transformedNormal = inverse->TransformVector( normal ); transformedNormal.Normalize(); return transformedNormal; } void mitk::SlicedGeometry3D::SetImageGeometry( const bool isAnImageGeometry ) { Superclass::SetImageGeometry( isAnImageGeometry ); mitk::BaseGeometry* geometry; unsigned int s; for ( s = 0; s < m_Slices; ++s ) { geometry = m_PlaneGeometries[s]; if ( geometry!=NULL ) { geometry->SetImageGeometry( isAnImageGeometry ); } } } void mitk::SlicedGeometry3D::ChangeImageGeometryConsideringOriginOffset( const bool isAnImageGeometry ) { mitk::BaseGeometry* geometry; unsigned int s; for ( s = 0; s < m_Slices; ++s ) { geometry = m_PlaneGeometries[s]; if ( geometry!=NULL ) { geometry->ChangeImageGeometryConsideringOriginOffset( isAnImageGeometry ); } } Superclass::ChangeImageGeometryConsideringOriginOffset( isAnImageGeometry ); } bool mitk::SlicedGeometry3D::IsValidSlice( int s ) const { return ((s >= 0) && (s < (int)m_Slices)); } void mitk::SlicedGeometry3D::SetReferenceGeometry( BaseGeometry *referenceGeometry ) { m_ReferenceGeometry = referenceGeometry; std::vector::iterator it; for ( it = m_PlaneGeometries.begin(); it != m_PlaneGeometries.end(); ++it ) { (*it)->SetReferenceGeometry( referenceGeometry ); } } void mitk::SlicedGeometry3D::PreSetSpacing( const mitk::Vector3D &aSpacing ) { bool hasEvenlySpacedPlaneGeometry = false; mitk::Point3D origin; mitk::Vector3D rightDV, bottomDV; BoundingBox::BoundsArrayType bounds; // Check for valid spacing if(!(aSpacing[0]>0 && aSpacing[1]>0 && aSpacing[2]>0)) { mitkThrow() << "You try to set a spacing with at least one element equal or " "smaller to \"0\". This might lead to a crash during rendering. Please double" " check your data!"; } // In case of evenly-spaced data: re-initialize instances of PlaneGeometry, // since the spacing influences them if ((m_EvenlySpaced) && (m_PlaneGeometries.size() > 0)) { const PlaneGeometry *planeGeometry = m_PlaneGeometries[0]; if ( planeGeometry && !dynamic_cast( planeGeometry ) ) { this->WorldToIndex( planeGeometry->GetOrigin(), origin ); this->WorldToIndex( planeGeometry->GetAxisVector(0), rightDV ); this->WorldToIndex( planeGeometry->GetAxisVector(1), bottomDV ); bounds = planeGeometry->GetBounds(); hasEvenlySpacedPlaneGeometry = true; } } BaseGeometry::_SetSpacing(aSpacing); mitk::PlaneGeometry::Pointer firstGeometry; // In case of evenly-spaced data: re-initialize instances of PlaneGeometry, // since the spacing influences them if ( hasEvenlySpacedPlaneGeometry ) { //create planeGeometry according to new spacing this->IndexToWorld( origin, origin ); this->IndexToWorld( rightDV, rightDV ); this->IndexToWorld( bottomDV, bottomDV ); mitk::PlaneGeometry::Pointer planeGeometry = mitk::PlaneGeometry::New(); planeGeometry->SetImageGeometry( this->GetImageGeometry() ); planeGeometry->SetReferenceGeometry( m_ReferenceGeometry ); //Store spacing, as Initialize... needs a pointer mitk::Vector3D lokalSpacing = this->GetSpacing(); planeGeometry->InitializeStandardPlane( rightDV.GetVnlVector(), bottomDV.GetVnlVector(), &lokalSpacing ); planeGeometry->SetOrigin(origin); planeGeometry->SetBounds(bounds); firstGeometry = planeGeometry; } else if ( (m_EvenlySpaced) && (m_PlaneGeometries.size() > 0) ) { firstGeometry = m_PlaneGeometries[0].GetPointer(); } //clear and reserve PlaneGeometry::Pointer gnull=NULL; m_PlaneGeometries.assign(m_Slices, gnull); if ( m_Slices > 0 ) { m_PlaneGeometries[0] = firstGeometry; } this->Modified(); } void mitk::SlicedGeometry3D ::SetSliceNavigationController( SliceNavigationController *snc ) { m_SliceNavigationController = snc; } mitk::SliceNavigationController * mitk::SlicedGeometry3D::GetSliceNavigationController() { return m_SliceNavigationController; } void mitk::SlicedGeometry3D::SetEvenlySpaced(bool on) { if(m_EvenlySpaced!=on) { m_EvenlySpaced=on; this->Modified(); } } void mitk::SlicedGeometry3D ::SetDirectionVector( const mitk::Vector3D& directionVector ) { Vector3D newDir = directionVector; newDir.Normalize(); if ( newDir != m_DirectionVector ) { m_DirectionVector = newDir; this->Modified(); } } //void //mitk::SlicedGeometry3D::SetTimeBounds( const mitk::TimeBounds& timebounds ) //{ // Superclass::SetTimeBounds( timebounds ); // // unsigned int s; // for ( s = 0; s < m_Slices; ++s ) // { // if(m_Geometry2Ds[s].IsNotNull()) // { // m_Geometry2Ds[s]->SetTimeBounds( timebounds ); // } // } // m_TimeBounds = timebounds; //} itk::LightObject::Pointer mitk::SlicedGeometry3D::InternalClone() const { Self::Pointer newGeometry = new SlicedGeometry3D(*this); newGeometry->UnRegister(); return newGeometry.GetPointer(); } void mitk::SlicedGeometry3D::PrintSelf( std::ostream& os, itk::Indent indent ) const { Superclass::PrintSelf(os,indent); os << indent << " EvenlySpaced: " << m_EvenlySpaced << std::endl; if ( m_EvenlySpaced ) { os << indent << " DirectionVector: " << m_DirectionVector << std::endl; } os << indent << " Slices: " << m_Slices << std::endl; os << std::endl; os << indent << " GetPlaneGeometry(0): "; if ( this->GetPlaneGeometry(0) == NULL ) { os << "NULL" << std::endl; } else { this->GetPlaneGeometry(0)->Print(os, indent); } } void mitk::SlicedGeometry3D::ExecuteOperation(Operation* operation) { switch ( operation->GetOperationType() ) { case OpNOTHING: break; case OpROTATE: if ( m_EvenlySpaced ) { // Need a reference frame to align the rotation if ( m_ReferenceGeometry ) { // Clear all generated geometries and then rotate only the first slice. // The other slices will be re-generated on demand // Save first slice PlaneGeometry::Pointer geometry2D = m_PlaneGeometries[0]; RotationOperation *rotOp = dynamic_cast< RotationOperation * >( operation ); // Generate a RotationOperation using the dataset center instead of // the supplied rotation center. This is necessary so that the rotated // zero-plane does not shift away. The supplied center is instead used // to adjust the slice stack afterwards. Point3D center = m_ReferenceGeometry->GetCenter(); RotationOperation centeredRotation( rotOp->GetOperationType(), center, rotOp->GetVectorOfRotation(), rotOp->GetAngleOfRotation() ); // Rotate first slice geometry2D->ExecuteOperation( ¢eredRotation ); // Clear the slice stack and adjust it according to the center of // the dataset and the supplied rotation center (see documentation of // ReinitializePlanes) this->ReinitializePlanes( center, rotOp->GetCenterOfRotation() ); geometry2D->SetSpacing(this->GetSpacing()); if ( m_SliceNavigationController ) { m_SliceNavigationController->SelectSliceByPoint( rotOp->GetCenterOfRotation() ); m_SliceNavigationController->AdjustSliceStepperRange(); } BaseGeometry::ExecuteOperation( ¢eredRotation ); } else { // we also have to consider the case, that there is no reference geometry available. if ( m_PlaneGeometries.size() > 0 ) { // Reach through to all slices in my container for (std::vector::iterator iter = m_PlaneGeometries.begin(); iter != m_PlaneGeometries.end(); ++iter) { // Test for empty slices, which can happen if evenly spaced geometry if ((*iter).IsNotNull()) { (*iter)->ExecuteOperation(operation); } } // rotate overall geometry RotationOperation *rotOp = dynamic_cast< RotationOperation * >( operation ); BaseGeometry::ExecuteOperation( rotOp); } } } else { // Reach through to all slices for (std::vector::iterator iter = m_PlaneGeometries.begin(); iter != m_PlaneGeometries.end(); ++iter) { (*iter)->ExecuteOperation(operation); } } break; case OpORIENT: if ( m_EvenlySpaced ) { // get operation data PlaneOperation *planeOp = dynamic_cast< PlaneOperation * >( operation ); // Get first slice PlaneGeometry::Pointer planeGeometry = m_PlaneGeometries[0]; // Need a PlaneGeometry, a PlaneOperation and a reference frame to // carry out the re-orientation. If not all avaialble, stop here if ( !m_ReferenceGeometry || ( !planeGeometry || dynamic_cast(planeGeometry.GetPointer()) ) || !planeOp ) { break; } // General Behavior: // Clear all generated geometries and then rotate only the first slice. // The other slices will be re-generated on demand // // 1st Step: Reorient Normal Vector of first plane // Point3D center = planeOp->GetPoint(); //m_ReferenceGeometry->GetCenter(); mitk::Vector3D currentNormal = planeGeometry->GetNormal(); mitk::Vector3D newNormal; if (planeOp->AreAxisDefined()) { // If planeOp was defined by one centerpoint and two axis vectors newNormal = CrossProduct(planeOp->GetAxisVec0(), planeOp->GetAxisVec1()); } else { // If planeOp was defined by one centerpoint and one normal vector newNormal = planeOp->GetNormal(); } // Get Rotation axis und angle currentNormal.Normalize(); newNormal.Normalize(); ScalarType rotationAngle = angle(currentNormal.GetVnlVector(),newNormal.GetVnlVector()); rotationAngle *= 180.0 / vnl_math::pi; // from rad to deg Vector3D rotationAxis = itk::CrossProduct( currentNormal, newNormal ); if (std::abs(rotationAngle-180) < mitk::eps ) { // current Normal and desired normal are not linear independent!!(e.g 1,0,0 and -1,0,0). // Rotation Axis should be ANY vector that is 90� to current Normal mitk::Vector3D helpNormal; helpNormal = currentNormal; helpNormal[0] += 1; helpNormal[1] -= 1; helpNormal[2] += 1; helpNormal.Normalize(); rotationAxis = itk::CrossProduct( helpNormal, currentNormal ); } RotationOperation centeredRotation( mitk::OpROTATE, center, rotationAxis, rotationAngle ); // Rotate first slice planeGeometry->ExecuteOperation( ¢eredRotation ); // Reinitialize planes and select slice, if my rotations are all done. if (!planeOp->AreAxisDefined()) { // Clear the slice stack and adjust it according to the center of // rotation and plane position (see documentation of ReinitializePlanes) this->ReinitializePlanes( center, planeOp->GetPoint() ); if ( m_SliceNavigationController ) { m_SliceNavigationController->SelectSliceByPoint( planeOp->GetPoint() ); m_SliceNavigationController->AdjustSliceStepperRange(); } } // Also apply rotation on the slicedGeometry - Geometry3D (Bounding geometry) BaseGeometry::ExecuteOperation( ¢eredRotation ); // // 2nd step. If axis vectors were defined, rotate the plane around its normal to fit these // if (planeOp->AreAxisDefined()) { mitk::Vector3D vecAxixNew = planeOp->GetAxisVec0(); vecAxixNew.Normalize(); mitk::Vector3D VecAxisCurr = planeGeometry->GetAxisVector(0); VecAxisCurr.Normalize(); ScalarType rotationAngle = angle(VecAxisCurr.GetVnlVector(),vecAxixNew.GetVnlVector()); rotationAngle = rotationAngle * 180 / PI; // Rad to Deg // we rotate around the normal of the plane, but we do not know, if we need to rotate clockwise // or anti-clockwise. So we rotate around the crossproduct of old and new Axisvector. // Since both axis vectors lie in the plane, the crossproduct is the planes normal or the negative planes normal rotationAxis = itk::CrossProduct( VecAxisCurr, vecAxixNew ); if (std::abs(rotationAngle-180) < mitk::eps ) { // current axisVec and desired axisVec are not linear independent!!(e.g 1,0,0 and -1,0,0). // Rotation Axis can be just plane Normal. (have to rotate by 180�) rotationAxis = newNormal; } // Perfom Rotation mitk::RotationOperation op(mitk::OpROTATE, center, rotationAxis, rotationAngle); planeGeometry->ExecuteOperation( &op ); // Apply changes on first slice to whole slice stack this->ReinitializePlanes( center, planeOp->GetPoint() ); if ( m_SliceNavigationController ) { m_SliceNavigationController->SelectSliceByPoint( planeOp->GetPoint() ); m_SliceNavigationController->AdjustSliceStepperRange(); } // Also apply rotation on the slicedGeometry - Geometry3D (Bounding geometry) BaseGeometry::ExecuteOperation( &op ); } } else { // Reach through to all slices for (std::vector::iterator iter = m_PlaneGeometries.begin(); iter != m_PlaneGeometries.end(); ++iter) { (*iter)->ExecuteOperation(operation); } } break; case OpRESTOREPLANEPOSITION: if ( m_EvenlySpaced ) { // Save first slice PlaneGeometry::Pointer planeGeometry = m_PlaneGeometries[0]; RestorePlanePositionOperation *restorePlaneOp = dynamic_cast< RestorePlanePositionOperation* >( operation ); // Need a PlaneGeometry, a PlaneOperation and a reference frame to // carry out the re-orientation if ( m_ReferenceGeometry && (planeGeometry && dynamic_cast(planeGeometry.GetPointer()) == NULL) && restorePlaneOp ) { // Clear all generated geometries and then rotate only the first slice. // The other slices will be re-generated on demand // Rotate first slice planeGeometry->ExecuteOperation( restorePlaneOp ); m_DirectionVector = restorePlaneOp->GetDirectionVector(); double centerOfRotationDistance = planeGeometry->SignedDistanceFromPlane( m_ReferenceGeometry->GetCenter() ); if ( centerOfRotationDistance > 0 ) { m_DirectionVector = m_DirectionVector; } else { m_DirectionVector = -m_DirectionVector; } Vector3D spacing = restorePlaneOp->GetSpacing(); Superclass::SetSpacing( spacing ); // /*Now we need to calculate the number of slices in the plane's normal // direction, so that the entire volume is covered. This is done by first // calculating the dot product between the volume diagonal (the maximum // distance inside the volume) and the normal, and dividing this value by // the directed spacing calculated above.*/ ScalarType directedExtent = std::abs( m_ReferenceGeometry->GetExtentInMM( 0 ) * m_DirectionVector[0] ) + std::abs( m_ReferenceGeometry->GetExtentInMM( 1 ) * m_DirectionVector[1] ) + std::abs( m_ReferenceGeometry->GetExtentInMM( 2 ) * m_DirectionVector[2] ); if ( directedExtent >= spacing[2] ) { m_Slices = static_cast< unsigned int >(directedExtent / spacing[2] + 0.5); } else { m_Slices = 1; } m_PlaneGeometries.assign( m_Slices, PlaneGeometry::Pointer( NULL ) ); if ( m_Slices > 0 ) { m_PlaneGeometries[0] = planeGeometry; } m_SliceNavigationController->GetSlice()->SetSteps( m_Slices ); this->Modified(); //End Reinitialization if ( m_SliceNavigationController ) { m_SliceNavigationController->GetSlice()->SetPos( restorePlaneOp->GetPos() ); m_SliceNavigationController->AdjustSliceStepperRange(); } BaseGeometry::ExecuteOperation(restorePlaneOp); } } else { // Reach through to all slices for (std::vector::iterator iter = m_PlaneGeometries.begin(); iter != m_PlaneGeometries.end(); ++iter) { (*iter)->ExecuteOperation(operation); } } break; case OpAPPLYTRANSFORMMATRIX: // Clear all generated geometries and then transform only the first slice. // The other slices will be re-generated on demand // Save first slice PlaneGeometry::Pointer geometry2D = m_PlaneGeometries[0]; ApplyTransformMatrixOperation *applyMatrixOp = dynamic_cast< ApplyTransformMatrixOperation* >( operation ); // Apply transformation to first plane geometry2D->ExecuteOperation( applyMatrixOp ); // Generate a ApplyTransformMatrixOperation using the dataset center instead of // the supplied rotation center. The supplied center is instead used to adjust the // slice stack afterwards (see OpROTATE). Point3D center = m_ReferenceGeometry->GetCenter(); // Clear the slice stack and adjust it according to the center of // the dataset and the supplied rotation center (see documentation of // ReinitializePlanes) this->ReinitializePlanes( center, applyMatrixOp->GetReferencePoint() ); BaseGeometry::ExecuteOperation( applyMatrixOp ); break; } this->Modified(); -} +} \ No newline at end of file diff --git a/Modules/Core/test/mitkBaseGeometryTest.cpp b/Modules/Core/test/mitkBaseGeometryTest.cpp index 1e6d16b4b1..9cf4436011 100644 --- a/Modules/Core/test/mitkBaseGeometryTest.cpp +++ b/Modules/Core/test/mitkBaseGeometryTest.cpp @@ -1,1288 +1,1282 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkTestingMacros.h" #include #include #include #include #include #include "mitkOperationActor.h" #include #include "mitkVector.h" #include #include #include "itkScalableAffineTransform.h" #include #include #include #include "mitkRotationOperation.h" #include "mitkInteractionConst.h" #include #include class vtkMatrix4x4; class vtkMatrixToLinearTransform; class vtkLinearTransform; typedef itk::BoundingBox BoundingBox; typedef itk::BoundingBox BoundingBoxType; typedef BoundingBoxType::BoundsArrayType BoundsArrayType; typedef BoundingBoxType::Pointer BoundingBoxPointer; // Dummy instance of abstract base class class DummyTestClass : public mitk::BaseGeometry { public: DummyTestClass(){}; DummyTestClass(const DummyTestClass& other) : BaseGeometry(other){}; ~DummyTestClass(){}; mitkClassMacro(DummyTestClass, mitk::BaseGeometry); itkNewMacro(Self); mitkNewMacro1Param(Self, const Self&); itk::LightObject::Pointer InternalClone() const { Self::Pointer newGeometry = new Self(*this); newGeometry->UnRegister(); return newGeometry.GetPointer(); } protected: virtual void PrintSelf(std::ostream& /*os*/, itk::Indent /*indent*/) const{}; //##Documentation //## @brief Pre- and Post-functions are empty in BaseGeometry //## //## These virtual functions allow for a different beahiour in subclasses. //## Do implement them in every subclass of BaseGeometry. If not needed, use {}. //## If this class is inherited from a subclass of BaseGeometry, call {Superclass::Pre...();};, example: DisplayGeometry class - virtual void PreSetBounds(const BoundsArrayType& bounds){}; - virtual void PostInitialize(){}; - virtual void PostInitializeGeometry(mitk::BaseGeometry::Self * newGeometry) const{}; - virtual void PostSetExtentInMM(int direction, mitk::ScalarType extentInMM){}; - virtual void PreSetIndexToWorldTransform(mitk::AffineTransform3D* transform){}; - virtual void PostSetIndexToWorldTransform(mitk::AffineTransform3D* transform){}; virtual void PreSetSpacing(const mitk::Vector3D& aSpacing){}; }; class mitkBaseGeometryTestSuite : public mitk::TestFixture { // List of Tests CPPUNIT_TEST_SUITE(mitkBaseGeometryTestSuite); //Constructor MITK_TEST(TestConstructors); MITK_TEST(TestInitialize); //Set MITK_TEST(TestSetOrigin); MITK_TEST(TestSetBounds); MITK_TEST(TestSetFloatBounds); MITK_TEST(TestSetFloatBoundsDouble); MITK_TEST(TestSetFrameOfReferenceID); MITK_TEST(TestSetIndexToWorldTransform); MITK_TEST(TestSetIndexToWorldTransformWithoutChangingSpacing); MITK_TEST(TestSetIndexToWorldTransform_WithPointerToSameTransform); MITK_TEST(TestSetSpacing); MITK_TEST(TestTransferItkToVtkTransform); MITK_TEST(TestSetIndexToWorldTransformByVtkMatrix); MITK_TEST(TestSetIdentity); MITK_TEST(TestSetImageGeometry); //Equal MITK_TEST(Equal_CloneAndOriginal_ReturnsTrue); MITK_TEST(Equal_DifferentOrigin_ReturnsFalse); MITK_TEST(Equal_DifferentIndexToWorldTransform_ReturnsFalse); MITK_TEST(Equal_DifferentSpacing_ReturnsFalse); MITK_TEST(Equal_InputIsNull_ReturnsFalse); MITK_TEST(Equal_DifferentBoundingBox_ReturnsFalse); //other Functions MITK_TEST(TestComposeTransform); MITK_TEST(TestComposeVtkMatrix); MITK_TEST(TestTranslate); MITK_TEST(TestIndexToWorld); MITK_TEST(TestExecuteOperation); MITK_TEST(TestCalculateBoundingBoxRelToTransform); //MITK_TEST(TestSetTimeBounds); MITK_TEST(TestIs2DConvertable); MITK_TEST(TestGetCornerPoint); MITK_TEST(TestExtentInMM); MITK_TEST(TestGetAxisVector); MITK_TEST(TestGetCenter); MITK_TEST(TestGetDiagonalLength); MITK_TEST(TestGetExtent); MITK_TEST(TestIsInside); MITK_TEST(TestGetMatrixColumn); CPPUNIT_TEST_SUITE_END(); // Used Variables private: mitk::Point3D aPoint; float aFloatSpacing[3]; mitk::Vector3D aSpacing; mitk::AffineTransform3D::Pointer aTransform; BoundingBoxPointer aBoundingBox; mitk::AffineTransform3D::MatrixType aMatrix; mitk::Point3D anotherPoint; mitk::Vector3D anotherSpacing; BoundingBoxPointer anotherBoundingBox; BoundingBoxPointer aThirdBoundingBox; mitk::AffineTransform3D::Pointer anotherTransform; mitk::AffineTransform3D::Pointer aThirdTransform; mitk::AffineTransform3D::MatrixType anotherMatrix; mitk::AffineTransform3D::MatrixType aThirdMatrix; DummyTestClass::Pointer aDummyGeometry; DummyTestClass::Pointer anotherDummyGeometry; public: // Set up for variables void setUp() { mitk::FillVector3D(aFloatSpacing, 1,1,1); mitk::FillVector3D(aSpacing, 1,1,1); mitk::FillVector3D(aPoint, 0,0,0); //Transform aTransform = mitk::AffineTransform3D::New(); aTransform->SetIdentity(); aMatrix.SetIdentity(); anotherTransform = mitk::AffineTransform3D::New(); anotherMatrix.SetIdentity(); anotherMatrix(1,1) = 2; anotherTransform->SetMatrix( anotherMatrix ); aThirdTransform = mitk::AffineTransform3D::New(); aThirdMatrix.SetIdentity(); aThirdMatrix(1,1) = 7; aThirdTransform->SetMatrix( aThirdMatrix ); //Bounding Box float bounds[6] = {0,1,0,1,0,1}; mitk::BoundingBox::BoundsArrayType b; const float *input = bounds; int j=0; for(mitk::BoundingBox::BoundsArrayType::Iterator it = b.Begin(); j < 6 ;++j) *it++ = (mitk::ScalarType)*input++; aBoundingBox = BoundingBoxType::New(); BoundingBoxType::PointsContainer::Pointer pointscontainer = BoundingBoxType::PointsContainer::New(); BoundingBoxType::PointType p; BoundingBoxType::PointIdentifier pointid; for(pointid=0; pointid<2;++pointid) { unsigned int i; for(i=0; i<3; ++i) { p[i] = bounds[2*i+pointid]; } pointscontainer->InsertElement(pointid, p); } aBoundingBox->SetPoints(pointscontainer); aBoundingBox->ComputeBoundingBox(); anotherBoundingBox = BoundingBoxType::New(); p[0]=11; p[1]=12; p[2]=13; pointscontainer->InsertElement(1, p); anotherBoundingBox->SetPoints(pointscontainer); anotherBoundingBox->ComputeBoundingBox(); aThirdBoundingBox = BoundingBoxType::New(); p[0]=22; p[1]=23; p[2]=24; pointscontainer->InsertElement(1, p); aThirdBoundingBox->SetPoints(pointscontainer); aThirdBoundingBox->ComputeBoundingBox(); mitk::FillVector3D(anotherPoint, 2,3,4); mitk::FillVector3D(anotherSpacing, 5,6.5,7); aDummyGeometry = DummyTestClass::New(); aDummyGeometry->Initialize(); anotherDummyGeometry = aDummyGeometry->Clone(); } void tearDown() { aDummyGeometry = NULL; anotherDummyGeometry = NULL; } // Test functions void TestSetOrigin() { DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetOrigin(anotherPoint); CPPUNIT_ASSERT(mitk::Equal(anotherPoint,dummy->GetOrigin())); //undo changes, new and changed object need to be the same! dummy->SetOrigin(aPoint); DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy, newDummy, "TestSetOrigin"); } void TestSetImageGeometry() { DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetImageGeometry(true); CPPUNIT_ASSERT(dummy->GetImageGeometry()); //undo changes, new and changed object need to be the same! dummy->SetImageGeometry(false); CPPUNIT_ASSERT(dummy->GetImageGeometry()==false); DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy,newDummy, "TestSetImageGeometry"); } void TestSetFloatBounds(){ float bounds[6] = {0,11,0,12,0,13}; DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetFloatBounds(bounds); MITK_ASSERT_EQUAL(BoundingBox::ConstPointer(dummy->GetBoundingBox()), anotherBoundingBox, "BoundingBox equality"); //Wrong bounds, test needs to fail bounds[1]=7; dummy->SetFloatBounds(bounds); MITK_ASSERT_NOT_EQUAL(BoundingBox::ConstPointer(dummy->GetBoundingBox()), anotherBoundingBox, "BoundingBox not equal"); //undo changes, new and changed object need to be the same! float originalBounds[6] = {0,1,0,1,0,1}; dummy->SetFloatBounds(originalBounds); DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy,newDummy, "Undo and equal"); } void TestSetBounds(){ DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetBounds(anotherBoundingBox->GetBounds()); MITK_ASSERT_EQUAL(BoundingBox::ConstPointer(dummy->GetBoundingBox()), anotherBoundingBox, "Setting bounds"); //Test needs to fail now dummy->SetBounds(aThirdBoundingBox->GetBounds()); MITK_ASSERT_NOT_EQUAL(BoundingBox::ConstPointer(dummy->GetBoundingBox()), anotherBoundingBox, "Setting unequal bounds"); //undo changes, new and changed object need to be the same! dummy->SetBounds(aBoundingBox->GetBounds()); DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy,newDummy, "Undo set bounds"); } void TestSetFloatBoundsDouble(){ double bounds[6] = {0,11,0,12,0,13}; DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetFloatBounds(bounds); MITK_ASSERT_EQUAL(BoundingBox::ConstPointer(dummy->GetBoundingBox()), anotherBoundingBox, "Float bounds"); //Test needs to fail now bounds[3]=7; dummy->SetFloatBounds(bounds); MITK_ASSERT_NOT_EQUAL(BoundingBox::ConstPointer(dummy->GetBoundingBox()), anotherBoundingBox, "Float bounds unequal"); //undo changes, new and changed object need to be the same! double originalBounds[6] = {0,1,0,1,0,1}; dummy->SetFloatBounds(originalBounds); DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy,newDummy, "Undo set float bounds"); } void TestSetFrameOfReferenceID() { DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetFrameOfReferenceID(5); CPPUNIT_ASSERT(dummy->GetFrameOfReferenceID()==5); //undo changes, new and changed object need to be the same! dummy->SetFrameOfReferenceID(0); DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy,newDummy, "Undo set frame of reference"); } void TestSetIndexToWorldTransform() { DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetIndexToWorldTransform(anotherTransform); MITK_ASSERT_EQUAL(anotherTransform,mitk::AffineTransform3D::Pointer(dummy->GetIndexToWorldTransform()),"Compare IndexToWorldTransform 1"); //Test needs to fail now dummy->SetIndexToWorldTransform(aThirdTransform); MITK_ASSERT_NOT_EQUAL(anotherTransform,mitk::AffineTransform3D::Pointer(dummy->GetIndexToWorldTransform()),"Compare IndexToWorldTransform 2"); //undo changes, new and changed object need to be the same! dummy->SetIndexToWorldTransform(aTransform); DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy,newDummy,"Compare IndexToWorldTransform 3"); } void TestSetIndexToWorldTransformWithoutChangingSpacing() { DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetIndexToWorldTransformWithoutChangingSpacing(anotherTransform); CPPUNIT_ASSERT(mitk::Equal(aSpacing,dummy->GetSpacing(),mitk::eps,true)); //calculate a new version of anotherTransform, so that the spacing should be the same as the original spacing of aTransform. mitk::AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; vnlmatrix = anotherTransform->GetMatrix().GetVnlMatrix(); mitk::VnlVector col; col = vnlmatrix.get_column(0); col.normalize(); col*=aSpacing[0]; vnlmatrix.set_column(0, col); col = vnlmatrix.get_column(1); col.normalize(); col*=aSpacing[1]; vnlmatrix.set_column(1, col); col = vnlmatrix.get_column(2); col.normalize(); col*=aSpacing[2]; vnlmatrix.set_column(2, col); mitk::Matrix3D matrix; matrix = vnlmatrix; anotherTransform->SetMatrix(matrix); CPPUNIT_ASSERT(mitk::Equal(anotherTransform,dummy->GetIndexToWorldTransform(),mitk::eps,true)); } void TestSetIndexToWorldTransform_WithPointerToSameTransform() { DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetOrigin(anotherPoint); dummy->SetIndexToWorldTransform(anotherTransform); dummy->SetSpacing(anotherSpacing); mitk::AffineTransform3D::Pointer testTransfrom = dummy->GetIndexToWorldTransform(); mitk::Vector3D modifiedPoint = anotherPoint.GetVectorFromOrigin() *2.; testTransfrom->SetOffset(modifiedPoint); dummy->SetIndexToWorldTransform(testTransfrom); CPPUNIT_ASSERT(mitk::Equal(modifiedPoint, dummy->GetOrigin().GetVectorFromOrigin())); } void TestSetIndexToWorldTransformByVtkMatrix() { vtkMatrix4x4* vtkmatrix; vtkmatrix = vtkMatrix4x4::New(); vtkmatrix->Identity(); vtkmatrix->SetElement(1,1,2); DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetIndexToWorldTransformByVtkMatrix(vtkmatrix); MITK_ASSERT_EQUAL(anotherTransform,mitk::AffineTransform3D::Pointer(dummy->GetIndexToWorldTransform()),"Compare IndexToWorldTransformByVtkMatrix 1"); //test needs to fail now vtkmatrix->SetElement(1,1,7); dummy->SetIndexToWorldTransformByVtkMatrix(vtkmatrix); MITK_ASSERT_NOT_EQUAL(anotherTransform,mitk::AffineTransform3D::Pointer(dummy->GetIndexToWorldTransform()),"Compare IndexToWorldTransformByVtkMatrix 2"); //undo changes, new and changed object need to be the same! vtkmatrix->SetElement(1,1,1); dummy->SetIndexToWorldTransformByVtkMatrix(vtkmatrix); vtkmatrix->Delete(); DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy,newDummy,"Compare IndexToWorldTransformByVtkMatrix 3"); } void TestSetIdentity() { DummyTestClass::Pointer dummy = DummyTestClass::New(); //Change IndextoWorldTransform and Origin dummy->SetIndexToWorldTransform(anotherTransform); dummy->SetOrigin(anotherPoint); //Set Identity should reset ITWT and Origin dummy->SetIdentity(); MITK_ASSERT_EQUAL(aTransform,mitk::AffineTransform3D::Pointer(dummy->GetIndexToWorldTransform()),"Test set identity 1"); CPPUNIT_ASSERT(mitk::Equal(aPoint,dummy->GetOrigin())); CPPUNIT_ASSERT(mitk::Equal(aSpacing,dummy->GetSpacing())); //new and changed object need to be the same! DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy,newDummy,"Test set identity 2"); } void TestSetSpacing() { DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetSpacing(anotherSpacing); CPPUNIT_ASSERT(mitk::Equal(anotherSpacing,dummy->GetSpacing())); //undo changes, new and changed object need to be the same! dummy->SetSpacing(aSpacing); DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy,newDummy,"Dummy spacing"); } void TestTransferItkToVtkTransform() { DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetIndexToWorldTransform(anotherTransform); //calls TransferItkToVtkTransform mitk::AffineTransform3D::Pointer dummyTransform = dummy->GetIndexToWorldTransform(); CPPUNIT_ASSERT(mitk::MatrixEqualElementWise( anotherMatrix, dummyTransform->GetMatrix() )); } void TestConstructors() { //test standard constructor DummyTestClass::Pointer dummy1 = DummyTestClass::New(); bool test = dummy1->IsValid(); CPPUNIT_ASSERT(test == true); CPPUNIT_ASSERT(dummy1->GetFrameOfReferenceID() == 0); CPPUNIT_ASSERT(dummy1->GetIndexToWorldTransformLastModified() == 0); CPPUNIT_ASSERT(mitk::Equal(dummy1->GetSpacing(), aSpacing)); CPPUNIT_ASSERT(mitk::Equal(dummy1->GetOrigin(), aPoint)); CPPUNIT_ASSERT(dummy1->GetImageGeometry()==false); MITK_ASSERT_EQUAL(mitk::AffineTransform3D::Pointer(dummy1->GetIndexToWorldTransform()), aTransform,"Contructor test 1"); MITK_ASSERT_EQUAL(mitk::BaseGeometry::BoundingBoxType::ConstPointer(dummy1->GetBoundingBox()), aBoundingBox, "Constructor test 2"); DummyTestClass::Pointer dummy2 = DummyTestClass::New(); dummy2->SetOrigin(anotherPoint); float bounds[6] = {0,11,0,12,0,13}; dummy2->SetFloatBounds(bounds); dummy2->SetIndexToWorldTransform(anotherTransform); dummy2->SetSpacing(anotherSpacing); DummyTestClass::Pointer dummy3 = DummyTestClass::New(*dummy2); MITK_ASSERT_EQUAL(dummy3,dummy2,"Dummy contructor"); } //Equal Tests void Equal_CloneAndOriginal_ReturnsTrue() { MITK_ASSERT_EQUAL( aDummyGeometry, anotherDummyGeometry, "Clone test"); } void Equal_DifferentOrigin_ReturnsFalse() { anotherDummyGeometry->SetOrigin(anotherPoint); MITK_ASSERT_NOT_EQUAL(aDummyGeometry, anotherDummyGeometry, "Different origin test"); } void Equal_DifferentIndexToWorldTransform_ReturnsFalse() { anotherDummyGeometry->SetIndexToWorldTransform(anotherTransform); MITK_ASSERT_NOT_EQUAL( aDummyGeometry, anotherDummyGeometry, "Different index to world"); } void Equal_DifferentSpacing_ReturnsFalse() { anotherDummyGeometry->SetSpacing(anotherSpacing); MITK_ASSERT_NOT_EQUAL( aDummyGeometry, anotherDummyGeometry, "Different spacing"); } void Equal_InputIsNull_ReturnsFalse() { DummyTestClass::Pointer geometryNull = NULL; CPPUNIT_ASSERT_THROW( MITK_ASSERT_EQUAL(geometryNull,anotherDummyGeometry,"Input is null") , mitk::Exception ); } void Equal_DifferentBoundingBox_ReturnsFalse() { //create different bounds to make the comparison false mitk::ScalarType bounds[ ] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0}; anotherDummyGeometry->SetBounds(bounds); MITK_ASSERT_NOT_EQUAL( aDummyGeometry, anotherDummyGeometry , "Different bounding box"); } void TestComposeTransform(){ //Create Transformations to set and compare mitk::AffineTransform3D::Pointer transform1; transform1 = mitk::AffineTransform3D::New(); mitk::AffineTransform3D::MatrixType matrix1; matrix1.SetIdentity(); matrix1(1,1) = 2; transform1->SetMatrix( matrix1 ); //Spacing = 2 mitk::AffineTransform3D::Pointer transform2; transform2 = mitk::AffineTransform3D::New(); mitk::AffineTransform3D::MatrixType matrix2; matrix2.SetIdentity(); matrix2(1,1) = 2; transform2->SetMatrix( matrix2 ); //Spacing = 2 mitk::AffineTransform3D::Pointer transform3; transform3 = mitk::AffineTransform3D::New(); mitk::AffineTransform3D::MatrixType matrix3; matrix3.SetIdentity(); matrix3(1,1) = 4; transform3->SetMatrix( matrix3 ); //Spacing = 4 mitk::AffineTransform3D::Pointer transform4; transform4 = mitk::AffineTransform3D::New(); mitk::AffineTransform3D::MatrixType matrix4; matrix4.SetIdentity(); matrix4(1,1) = 0.25; transform4->SetMatrix( matrix4 ); //Spacing = 0.25 //Vector to compare spacing mitk::Vector3D expectedSpacing; expectedSpacing.Fill(1.0); expectedSpacing[1] = 4; DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetIndexToWorldTransform(transform1); //Spacing = 2 dummy->Compose(transform2); //Spacing = 4 CPPUNIT_ASSERT(mitk::Equal(dummy->GetSpacing(), expectedSpacing)); MITK_ASSERT_EQUAL(transform3,mitk::AffineTransform3D::Pointer(dummy->GetIndexToWorldTransform()),"Compose transform 2"); // 4=4 //undo changes, new and changed object need to be the same! dummy->Compose(transform4); //Spacing = 1 DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy,newDummy,"Compose transform 3"); // 1=1 } void TestComposeVtkMatrix(){ //Create Transformations to set and compare mitk::AffineTransform3D::Pointer transform1; transform1 = mitk::AffineTransform3D::New(); mitk::AffineTransform3D::MatrixType matrix1; matrix1.SetIdentity(); matrix1(1,1) = 2; transform1->SetMatrix( matrix1 ); //Spacing = 2 vtkMatrix4x4* vtkmatrix2; vtkmatrix2 = vtkMatrix4x4::New(); vtkmatrix2->Identity(); vtkmatrix2->SetElement(1,1,2); //Spacing = 2 mitk::AffineTransform3D::Pointer transform3; transform3 = mitk::AffineTransform3D::New(); mitk::AffineTransform3D::MatrixType matrix3; matrix3.SetIdentity(); matrix3(1,1) = 4; transform3->SetMatrix( matrix3 ); //Spacing = 4 vtkMatrix4x4* vtkmatrix4; vtkmatrix4 = vtkMatrix4x4::New(); vtkmatrix4->Identity(); vtkmatrix4->SetElement(1,1,0.25); //Spacing = 0.25 //Vector to compare spacing mitk::Vector3D expectedSpacing; expectedSpacing.Fill(1.0); expectedSpacing[1] = 4; DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetIndexToWorldTransform(transform1); //Spacing = 2 dummy->Compose(vtkmatrix2); //Spacing = 4 vtkmatrix2->Delete(); MITK_ASSERT_EQUAL(transform3, mitk::AffineTransform3D::Pointer(dummy->GetIndexToWorldTransform()),"Compose vtk matrix"); // 4=4 CPPUNIT_ASSERT(mitk::Equal(dummy->GetSpacing(), expectedSpacing)); //undo changes, new and changed object need to be the same! dummy->Compose(vtkmatrix4); //Spacing = 1 vtkmatrix4->Delete(); DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy,newDummy,"Compose vtk"); // 1=1 } void TestTranslate(){ DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetOrigin(anotherPoint); CPPUNIT_ASSERT(mitk::Equal(anotherPoint,dummy->GetOrigin())); //use some random values for translation mitk::Vector3D translationVector; translationVector.SetElement(0, 17.5f); translationVector.SetElement(1, -32.3f); translationVector.SetElement(2, 4.0f); //compute ground truth mitk::Point3D tmpResult = anotherPoint + translationVector; dummy->Translate(translationVector); CPPUNIT_ASSERT( mitk::Equal( dummy->GetOrigin(), tmpResult )); //undo changes translationVector*=-1; dummy->Translate(translationVector); CPPUNIT_ASSERT( mitk::Equal( dummy->GetOrigin(), anotherPoint )); //undo changes, new and changed object need to be the same! translationVector.SetElement(0, -1 * anotherPoint[0]); translationVector.SetElement(1, -1 * anotherPoint[1]); translationVector.SetElement(2, -1 * anotherPoint[2]); dummy->Translate(translationVector); DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy,newDummy,"Translate test"); } // a part of the test requires axis-parallel coordinates int testIndexAndWorldConsistency(DummyTestClass::Pointer dummyGeometry) { //Testing consistency of index and world coordinate systems mitk::Point3D origin = dummyGeometry->GetOrigin(); mitk::Point3D dummyPoint; //Testing index->world->index conversion consistency dummyGeometry->WorldToIndex(origin, dummyPoint); dummyGeometry->IndexToWorld(dummyPoint, dummyPoint); CPPUNIT_ASSERT(mitk::EqualArray(dummyPoint, origin, 3, mitk::eps, true)); //Testing WorldToIndex(origin, mitk::Point3D)==(0,0,0) mitk::Point3D globalOrigin; mitk::FillVector3D(globalOrigin, 0,0,0); mitk::Point3D originContinuousIndex; dummyGeometry->WorldToIndex(origin, originContinuousIndex); CPPUNIT_ASSERT(mitk::EqualArray(originContinuousIndex, globalOrigin, 3, mitk::eps, true)); //Testing WorldToIndex(origin, itk::Index)==(0,0,0) itk::Index<3> itkindex; dummyGeometry->WorldToIndex(origin, itkindex); itk::Index<3> globalOriginIndex; mitk::vtk2itk(globalOrigin, globalOriginIndex); CPPUNIT_ASSERT(mitk::EqualArray(itkindex, globalOriginIndex, 3, mitk::eps, true)); //Testing WorldToIndex(origin-0.5*spacing, itk::Index)==(0,0,0) mitk::Vector3D halfSpacingStep = dummyGeometry->GetSpacing()*0.5; mitk::Matrix3D rotation; mitk::Point3D originOffCenter = origin-halfSpacingStep; dummyGeometry->WorldToIndex(originOffCenter, itkindex); CPPUNIT_ASSERT(mitk::EqualArray(itkindex, globalOriginIndex, 3, mitk::eps, true)); //Testing WorldToIndex(origin+0.5*spacing-eps, itk::Index)==(0,0,0) originOffCenter = origin+halfSpacingStep; originOffCenter -= 0.0001; dummyGeometry->WorldToIndex( originOffCenter, itkindex); CPPUNIT_ASSERT(mitk::EqualArray(itkindex, globalOriginIndex, 3, mitk::eps, true)); //Testing WorldToIndex(origin+0.5*spacing, itk::Index)==(1,1,1)"); originOffCenter = origin+halfSpacingStep; itk::Index<3> global111; mitk::FillVector3D(global111, 1,1,1); dummyGeometry->WorldToIndex( originOffCenter, itkindex); CPPUNIT_ASSERT(mitk::EqualArray(itkindex, global111, 3, mitk::eps, true)); //Testing WorldToIndex(GetCenter())==BoundingBox.GetCenter mitk::Point3D center = dummyGeometry->GetCenter(); mitk::Point3D centerContIndex; dummyGeometry->WorldToIndex(center, centerContIndex); mitk::BoundingBox::ConstPointer boundingBox = dummyGeometry->GetBoundingBox(); mitk::BoundingBox::PointType centerBounds = boundingBox->GetCenter(); CPPUNIT_ASSERT(mitk::Equal(centerContIndex,centerBounds)); //Testing GetCenter()==IndexToWorld(BoundingBox.GetCenter) center = dummyGeometry->GetCenter(); mitk::Point3D centerBoundsInWorldCoords; dummyGeometry->IndexToWorld(centerBounds, centerBoundsInWorldCoords); CPPUNIT_ASSERT(mitk::Equal(center,centerBoundsInWorldCoords)); //Test using random point, //Testing consistency of index and world coordinate systems mitk::Point3D point; mitk::FillVector3D(point,3.5,-2,4.6); //Testing index->world->index conversion consistency dummyGeometry->WorldToIndex(point, dummyPoint); dummyGeometry->IndexToWorld(dummyPoint, dummyPoint); CPPUNIT_ASSERT(mitk::EqualArray(dummyPoint, point, 3, mitk::eps, true)); return EXIT_SUCCESS; } int testIndexAndWorldConsistencyForVectors(DummyTestClass::Pointer dummyGeometry) { //Testing consistency of index and world coordinate systems for vectors mitk::Vector3D xAxisMM = dummyGeometry->GetAxisVector(0); mitk::Vector3D xAxisContinuousIndex; mitk::Point3D p, pIndex, origin; origin = dummyGeometry->GetOrigin(); p[0] = xAxisMM[0]+origin[0]; p[1] = xAxisMM[1]+origin[1]; p[2] = xAxisMM[2]+origin[2]; dummyGeometry->WorldToIndex(p,pIndex); dummyGeometry->WorldToIndex(xAxisMM,xAxisContinuousIndex); CPPUNIT_ASSERT(mitk::Equal(xAxisContinuousIndex[0], pIndex[0])); CPPUNIT_ASSERT(mitk::Equal(xAxisContinuousIndex[1], pIndex[1])); CPPUNIT_ASSERT(mitk::Equal(xAxisContinuousIndex[2], pIndex[2])); dummyGeometry->IndexToWorld(xAxisContinuousIndex,xAxisContinuousIndex); dummyGeometry->IndexToWorld(pIndex,p); CPPUNIT_ASSERT(xAxisContinuousIndex == xAxisMM); CPPUNIT_ASSERT(mitk::Equal(xAxisContinuousIndex[0], p[0]-origin[0])); CPPUNIT_ASSERT(mitk::Equal(xAxisContinuousIndex[1], p[1]-origin[1])); CPPUNIT_ASSERT(mitk::Equal(xAxisContinuousIndex[2], p[2]-origin[2])); //Test consictency for random vector mitk::Vector3D vector; mitk::FillVector3D(vector, 2.5,-3.2,8.1); mitk::Vector3D vectorContinuousIndex; p[0] = vector[0]+origin[0]; p[1] = vector[1]+origin[1]; p[2] = vector[2]+origin[2]; dummyGeometry->WorldToIndex(p,pIndex); dummyGeometry->WorldToIndex(vector,vectorContinuousIndex); CPPUNIT_ASSERT(mitk::Equal(vectorContinuousIndex[0], pIndex[0])); CPPUNIT_ASSERT(mitk::Equal(vectorContinuousIndex[1], pIndex[1])); CPPUNIT_ASSERT(mitk::Equal(vectorContinuousIndex[2], pIndex[2])); dummyGeometry->IndexToWorld(vectorContinuousIndex,vectorContinuousIndex); dummyGeometry->IndexToWorld(pIndex,p); CPPUNIT_ASSERT(vectorContinuousIndex == vector); CPPUNIT_ASSERT(mitk::Equal(vectorContinuousIndex[0], p[0]-origin[0])); CPPUNIT_ASSERT(mitk::Equal(vectorContinuousIndex[1], p[1]-origin[1])); CPPUNIT_ASSERT(mitk::Equal(vectorContinuousIndex[2], p[2]-origin[2])); return EXIT_SUCCESS; } int testIndexAndWorldConsistencyForIndex(DummyTestClass::Pointer dummyGeometry) { //Testing consistency of index and world coordinate systems // creating testing data itk::Index<4> itkIndex4, itkIndex4b; itk::Index<3> itkIndex3, itkIndex3b; itk::Index<2> itkIndex2, itkIndex2b; itk::Index<3> mitkIndex, mitkIndexb; itkIndex4[0] = itkIndex4[1] = itkIndex4[2] = itkIndex4[3] = 4; itkIndex3[0] = itkIndex3[1] = itkIndex3[2] = 6; itkIndex2[0] = itkIndex2[1] = 2; mitkIndex[0] = mitkIndex[1] = mitkIndex[2] = 13; // check for constistency mitk::Point3D point; dummyGeometry->IndexToWorld(itkIndex2,point); dummyGeometry->WorldToIndex(point,itkIndex2b); CPPUNIT_ASSERT( ((itkIndex2b[0] == itkIndex2[0]) && (itkIndex2b[1] == itkIndex2[1]))); //Testing itk::index<2> for IndexToWorld/WorldToIndex consistency dummyGeometry->IndexToWorld(itkIndex3,point); dummyGeometry->WorldToIndex(point,itkIndex3b); CPPUNIT_ASSERT( ((itkIndex3b[0] == itkIndex3[0]) && (itkIndex3b[1] == itkIndex3[1]) && (itkIndex3b[2] == itkIndex3[2]))); //Testing itk::index<3> for IndexToWorld/WorldToIndex consistency dummyGeometry->IndexToWorld(itkIndex4,point); dummyGeometry->WorldToIndex(point,itkIndex4b); CPPUNIT_ASSERT( ((itkIndex4b[0] == itkIndex4[0]) && (itkIndex4b[1] == itkIndex4[1]) && (itkIndex4b[2] == itkIndex4[2]) && (itkIndex4b[3] == 0))); //Testing itk::index<3> for IndexToWorld/WorldToIndex consistency dummyGeometry->IndexToWorld(mitkIndex,point); dummyGeometry->WorldToIndex(point,mitkIndexb); CPPUNIT_ASSERT( ((mitkIndexb[0] == mitkIndex[0]) && (mitkIndexb[1] == mitkIndex[1]) && (mitkIndexb[2] == mitkIndex[2]))); //Testing mitk::Index for IndexToWorld/WorldToIndex consistency return EXIT_SUCCESS; } void TestIndexToWorld(){ DummyTestClass::Pointer dummy = DummyTestClass::New(); testIndexAndWorldConsistency(dummy); testIndexAndWorldConsistencyForVectors(dummy); testIndexAndWorldConsistencyForIndex(dummy); //Geometry must not have changed DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy,newDummy,"Dummy index to world"); //Test with other geometries dummy->SetOrigin(anotherPoint); testIndexAndWorldConsistency(dummy); testIndexAndWorldConsistencyForVectors(dummy); testIndexAndWorldConsistencyForIndex(dummy); dummy->SetIndexToWorldTransform(anotherTransform); testIndexAndWorldConsistency(dummy); testIndexAndWorldConsistencyForVectors(dummy); testIndexAndWorldConsistencyForIndex(dummy); dummy->SetOrigin(anotherPoint); testIndexAndWorldConsistency(dummy); testIndexAndWorldConsistencyForVectors(dummy); testIndexAndWorldConsistencyForIndex(dummy); dummy->SetSpacing(anotherSpacing); testIndexAndWorldConsistency(dummy); testIndexAndWorldConsistencyForVectors(dummy); testIndexAndWorldConsistencyForIndex(dummy); } void TestExecuteOperation(){ DummyTestClass::Pointer dummy = DummyTestClass::New(); //Do same Operations with new Dummy and compare DummyTestClass::Pointer newDummy = DummyTestClass::New(); //Test operation Nothing mitk::Operation* opN = new mitk::Operation(mitk::OpNOTHING); dummy->ExecuteOperation(opN); MITK_ASSERT_EQUAL(dummy,newDummy,"Dummy execute operation 1"); //Test operation Move mitk::PointOperation* opP = new mitk::PointOperation(mitk::OpMOVE,anotherPoint); dummy->ExecuteOperation(opP); CPPUNIT_ASSERT(mitk::Equal(anotherPoint,dummy->GetOrigin())); newDummy->SetOrigin(anotherPoint); MITK_ASSERT_EQUAL(dummy,newDummy,"Dummy execute operation 2"); //Test operation Scale, Scale sets spacing to scale+1 mitk::Point3D spacing; spacing[0]=anotherSpacing[0]-1.; spacing[1]=anotherSpacing[1]-1.; spacing[2]=anotherSpacing[2]-1.; mitk::PointOperation* opS = new mitk::PointOperation(mitk::OpSCALE,spacing); dummy->ExecuteOperation(opS); CPPUNIT_ASSERT(mitk::Equal(anotherSpacing,dummy->GetSpacing())); newDummy->SetSpacing(anotherSpacing); MITK_ASSERT_EQUAL(dummy,newDummy,"Dummy execute operation 3"); //change Geometry to test more cases dummy->SetIndexToWorldTransform(anotherTransform); dummy->SetSpacing(anotherSpacing); //Testing a rotation of the geometry double angle = 35.0; mitk::Vector3D rotationVector; mitk::FillVector3D( rotationVector, 1, 0, 0 ); mitk::Point3D center = dummy->GetCenter(); mitk::RotationOperation* opR = new mitk::RotationOperation( mitk::OpROTATE, center, rotationVector, angle ); dummy->ExecuteOperation(opR); mitk::Matrix3D rotation; mitk::GetRotation(dummy, rotation); mitk::Vector3D voxelStep=rotation*anotherSpacing; mitk::Vector3D voxelStepIndex; dummy->WorldToIndex(voxelStep, voxelStepIndex); mitk::Vector3D expectedVoxelStepIndex; expectedVoxelStepIndex.Fill(1); CPPUNIT_ASSERT(mitk::Equal(voxelStepIndex,expectedVoxelStepIndex)); delete opR; delete opN; delete opS; delete opP; } void TestCalculateBoundingBoxRelToTransform(){ DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetExtentInMM(0,15); dummy->SetExtentInMM(1,20); dummy->SetExtentInMM(2,8); mitk::BoundingBox::Pointer dummyBoundingBox = dummy->CalculateBoundingBoxRelativeToTransform(anotherTransform); mitk::BoundingBox::PointsContainer::Pointer pointscontainer=mitk::BoundingBox::PointsContainer::New(); mitk::BoundingBox::PointIdentifier pointid=0; unsigned char i; mitk::AffineTransform3D::Pointer inverse = mitk::AffineTransform3D::New(); anotherTransform->GetInverse(inverse); for(i=0; i<8; ++i) pointscontainer->InsertElement( pointid++, inverse->TransformPoint( dummy->GetCornerPoint(i) )); mitk::BoundingBox::Pointer result = mitk::BoundingBox::New(); result->SetPoints(pointscontainer); result->ComputeBoundingBox(); MITK_ASSERT_EQUAL(result,dummyBoundingBox,"BBox rel to transform"); //dummy still needs to be unchanged, except for extend DummyTestClass::Pointer newDummy = DummyTestClass::New(); newDummy->SetExtentInMM(0,15); newDummy->SetExtentInMM(1,20); newDummy->SetExtentInMM(2,8); MITK_ASSERT_EQUAL(dummy,newDummy,"Dummy BBox"); } //void TestSetTimeBounds(){ // mitk::TimeBounds timeBounds; // timeBounds[0] = 1; // timeBounds[1] = 9; // DummyTestClass::Pointer dummy = DummyTestClass::New(); // dummy->SetTimeBounds(timeBounds); // mitk::TimeBounds timeBounds2 = dummy->GetTimeBounds(); // CPPUNIT_ASSERT(timeBounds[0]==timeBounds2[0]); // CPPUNIT_ASSERT(timeBounds[1]==timeBounds2[1]); // //undo changes, new and changed object need to be the same! // timeBounds[0]=mitk::ScalarTypeNumericTraits::NonpositiveMin(); // timeBounds[1]=mitk::ScalarTypeNumericTraits::max(); // DummyTestClass::Pointer newDummy = DummyTestClass::New(); // CPPUNIT_ASSERT(mitk::Equal(dummy,newDummy,mitk::eps,true)); //} void TestIs2DConvertable(){ DummyTestClass::Pointer dummy = DummyTestClass::New(); //new initialized geometry is 2D convertable CPPUNIT_ASSERT(dummy->Is2DConvertable()); //Wrong Spacing needs to fail dummy->SetSpacing(anotherSpacing); CPPUNIT_ASSERT(dummy->Is2DConvertable()==false); //undo dummy->SetSpacing(aSpacing); CPPUNIT_ASSERT(dummy->Is2DConvertable()); //Wrong Origin needs to fail dummy->SetOrigin(anotherPoint); CPPUNIT_ASSERT(dummy->Is2DConvertable()==false); //undo dummy->SetOrigin(aPoint); CPPUNIT_ASSERT(dummy->Is2DConvertable()); //third dimension must not be transformed mitk::AffineTransform3D::Pointer dummyTransform = mitk::AffineTransform3D::New(); mitk::AffineTransform3D::MatrixType dummyMatrix; dummyMatrix.SetIdentity(); dummyTransform->SetMatrix( dummyMatrix ); dummy->SetIndexToWorldTransform(dummyTransform); //identity matrix is 2DConvertable CPPUNIT_ASSERT(dummy->Is2DConvertable()); dummyMatrix(0,2) = 3; dummyTransform->SetMatrix( dummyMatrix ); CPPUNIT_ASSERT(dummy->Is2DConvertable()==false); dummyMatrix.SetIdentity(); dummyMatrix(1,2) = 0.4; dummyTransform->SetMatrix( dummyMatrix ); CPPUNIT_ASSERT(dummy->Is2DConvertable()==false); dummyMatrix.SetIdentity(); dummyMatrix(2,2) = 3; dummyTransform->SetMatrix( dummyMatrix ); CPPUNIT_ASSERT(dummy->Is2DConvertable()==false); dummyMatrix.SetIdentity(); dummyMatrix(2,1) = 3; dummyTransform->SetMatrix( dummyMatrix ); CPPUNIT_ASSERT(dummy->Is2DConvertable()==false); dummyMatrix.SetIdentity(); dummyMatrix(2,0) = 3; dummyTransform->SetMatrix( dummyMatrix ); CPPUNIT_ASSERT(dummy->Is2DConvertable()==false); //undo changes, new and changed object need to be the same! dummyMatrix.SetIdentity(); dummyTransform->SetMatrix( dummyMatrix ); DummyTestClass::Pointer newDummy = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy,newDummy,"Is 2D convertable"); } void TestGetCornerPoint(){ DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetIndexToWorldTransform(anotherTransform); double bounds[6] = {0,11,0,12,0,13}; dummy->SetFloatBounds(bounds); mitk::Point3D corner, refCorner; //Corner 0 mitk::FillVector3D(refCorner,bounds[0],bounds[2],bounds[4]); refCorner = anotherTransform->TransformPoint(refCorner); corner=dummy->GetCornerPoint(0); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); corner=dummy->GetCornerPoint(true,true,true); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); //Corner 1 mitk::FillVector3D(refCorner,bounds[0],bounds[2],bounds[5]); refCorner = anotherTransform->TransformPoint(refCorner); corner=dummy->GetCornerPoint(1); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); corner=dummy->GetCornerPoint(true,true,false); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); //Corner 2 mitk::FillVector3D(refCorner,bounds[0],bounds[3],bounds[4]); refCorner = anotherTransform->TransformPoint(refCorner); corner=dummy->GetCornerPoint(2); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); corner=dummy->GetCornerPoint(true,false,true); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); //Corner 3 mitk::FillVector3D(refCorner,bounds[0],bounds[3],bounds[5]); refCorner = anotherTransform->TransformPoint(refCorner); corner=dummy->GetCornerPoint(3); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); corner=dummy->GetCornerPoint(true,false,false); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); //Corner 4 mitk::FillVector3D(refCorner,bounds[1],bounds[2],bounds[4]); refCorner = anotherTransform->TransformPoint(refCorner); corner=dummy->GetCornerPoint(4); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); corner=dummy->GetCornerPoint(false,true,true); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); //Corner 5 mitk::FillVector3D(refCorner,bounds[1],bounds[2],bounds[5]); refCorner = anotherTransform->TransformPoint(refCorner); corner=dummy->GetCornerPoint(5); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); corner=dummy->GetCornerPoint(false,true,false); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); //Corner 6 mitk::FillVector3D(refCorner,bounds[1],bounds[3],bounds[4]); refCorner = anotherTransform->TransformPoint(refCorner); corner=dummy->GetCornerPoint(6); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); corner=dummy->GetCornerPoint(false,false,true); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); //Corner 7 mitk::FillVector3D(refCorner,bounds[1],bounds[3],bounds[5]); refCorner = anotherTransform->TransformPoint(refCorner); corner=dummy->GetCornerPoint(7); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); corner=dummy->GetCornerPoint(false,false,false); CPPUNIT_ASSERT(mitk::Equal(refCorner,corner)); //Wrong Corner needs to fail CPPUNIT_ASSERT_THROW(dummy->GetCornerPoint(20),itk::ExceptionObject); //dummy geometry must not have changed! DummyTestClass::Pointer newDummy = DummyTestClass::New(); newDummy->SetIndexToWorldTransform(anotherTransform); newDummy->SetFloatBounds(bounds); MITK_ASSERT_EQUAL(dummy,newDummy,"Corner point"); } void TestExtentInMM() { DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetExtentInMM(0,50); CPPUNIT_ASSERT(mitk::Equal(50.,dummy->GetExtentInMM(0))); //Vnl Matrix has changed. The next line only works because the spacing is 1! CPPUNIT_ASSERT(mitk::Equal(50.,dummy->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(0).magnitude())); //Smaller extent than original dummy->SetExtentInMM(0,5); CPPUNIT_ASSERT(mitk::Equal(5.,dummy->GetExtentInMM(0))); CPPUNIT_ASSERT(mitk::Equal(5.,dummy->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(0).magnitude())); dummy->SetExtentInMM(1,4); CPPUNIT_ASSERT(mitk::Equal(4.,dummy->GetExtentInMM(1))); CPPUNIT_ASSERT(mitk::Equal(4.,dummy->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(1).magnitude())); dummy->SetExtentInMM(2,2.5); CPPUNIT_ASSERT(mitk::Equal(2.5,dummy->GetExtentInMM(2))); CPPUNIT_ASSERT(mitk::Equal(2.5,dummy->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(2).magnitude())); } void TestGetAxisVector(){ DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetIndexToWorldTransform(anotherTransform); double bounds[6] = {0,11,0,12,0,13}; dummy->SetFloatBounds(bounds); mitk::Vector3D vector; mitk::FillVector3D(vector,bounds[1],0,0); dummy->IndexToWorld(vector,vector); CPPUNIT_ASSERT(mitk::Equal(dummy->GetAxisVector(0),vector)); mitk::FillVector3D(vector,0,bounds[3],0); dummy->IndexToWorld(vector,vector); CPPUNIT_ASSERT(mitk::Equal(dummy->GetAxisVector(1),vector)); mitk::FillVector3D(vector,0,0,bounds[5]); dummy->IndexToWorld(vector,vector); CPPUNIT_ASSERT(mitk::Equal(dummy->GetAxisVector(2),vector)); } void TestGetCenter(){ DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetIndexToWorldTransform(anotherTransform); double bounds[6] = {0,11,2,12,1,13}; dummy->SetFloatBounds(bounds); mitk::Point3D refCenter; for( int i=0;i<3;i++) refCenter.SetElement(i,( bounds[2 * i] + bounds[2 * i + 1] ) / 2.0); dummy->IndexToWorld(refCenter,refCenter); CPPUNIT_ASSERT(mitk::Equal(dummy->GetCenter(),refCenter)); } void TestGetDiagonalLength(){ DummyTestClass::Pointer dummy = DummyTestClass::New(); double bounds[6] = {1,3,5,8,7.5,11.5}; dummy->SetFloatBounds(bounds); //3-1=2, 8-5=3, 11.5-7.5=4; 2^2+3^2+4^2 = 29 double expectedLength = sqrt(29.); CPPUNIT_ASSERT(mitk::Equal(expectedLength, dummy->GetDiagonalLength(), mitk::eps, true)); CPPUNIT_ASSERT(mitk::Equal(29., dummy->GetDiagonalLength2(), mitk::eps, true)); //dummy must not have changed DummyTestClass::Pointer newDummy = DummyTestClass::New(); newDummy->SetFloatBounds(bounds); MITK_ASSERT_EQUAL(dummy,newDummy,"Diagonal length"); } void TestGetExtent(){ DummyTestClass::Pointer dummy = DummyTestClass::New(); double bounds[6] = {1,3,5,8,7.5,11.5}; dummy->SetFloatBounds(bounds); CPPUNIT_ASSERT(mitk::Equal(2.,dummy->GetExtent(0))); CPPUNIT_ASSERT(mitk::Equal(3.,dummy->GetExtent(1))); CPPUNIT_ASSERT(mitk::Equal(4.,dummy->GetExtent(2))); //dummy must not have changed DummyTestClass::Pointer newDummy = DummyTestClass::New(); newDummy->SetFloatBounds(bounds); MITK_ASSERT_EQUAL(dummy,newDummy,"Extend"); } void TestIsInside(){ DummyTestClass::Pointer dummy = DummyTestClass::New(); double bounds[6] = {1,3,5,8,7.5,11.5}; dummy->SetFloatBounds(bounds); mitk::Point3D insidePoint; mitk::Point3D outsidePoint; mitk::FillVector3D(insidePoint,2,6,7.6); mitk::FillVector3D(outsidePoint,0,9,8.2); CPPUNIT_ASSERT(dummy->IsIndexInside(insidePoint)); CPPUNIT_ASSERT(false==dummy->IsIndexInside(outsidePoint)); dummy->IndexToWorld(insidePoint,insidePoint); dummy->IndexToWorld(outsidePoint,outsidePoint); CPPUNIT_ASSERT(dummy->IsInside(insidePoint)); CPPUNIT_ASSERT(false==dummy->IsInside(outsidePoint)); //dummy must not have changed DummyTestClass::Pointer newDummy = DummyTestClass::New(); newDummy->SetFloatBounds(bounds); MITK_ASSERT_EQUAL(dummy,newDummy,"Is inside"); } void TestInitialize() { //test standard constructor DummyTestClass::Pointer dummy1 = DummyTestClass::New(); DummyTestClass::Pointer dummy2 = DummyTestClass::New(); dummy2->SetOrigin(anotherPoint); dummy2->SetBounds(anotherBoundingBox->GetBounds()); //mitk::TimeBounds timeBounds; //timeBounds[0] = 1; //timeBounds[1] = 9; //dummy2->SetTimeBounds(timeBounds); dummy2->SetIndexToWorldTransform(anotherTransform); dummy2->SetSpacing(anotherSpacing); dummy1->InitializeGeometry(dummy2); MITK_ASSERT_EQUAL(dummy1,dummy2,"Initialize 1"); dummy1->Initialize(); DummyTestClass::Pointer dummy3 = DummyTestClass::New(); MITK_ASSERT_EQUAL(dummy3,dummy1,"Initialize 2"); } void TestGetMatrixColumn(){ DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetIndexToWorldTransform(anotherTransform); mitk::Vector3D testVector,refVector; testVector.SetVnlVector(dummy->GetMatrixColumn(0)); mitk::FillVector3D(refVector,1,0,0); CPPUNIT_ASSERT(testVector==refVector); testVector.SetVnlVector(dummy->GetMatrixColumn(1)); mitk::FillVector3D(refVector,0,2,0); CPPUNIT_ASSERT(testVector==refVector); testVector.SetVnlVector(dummy->GetMatrixColumn(2)); mitk::FillVector3D(refVector,0,0,1); CPPUNIT_ASSERT(testVector==refVector); //dummy must not have changed DummyTestClass::Pointer newDummy = DummyTestClass::New(); newDummy->SetIndexToWorldTransform(anotherTransform); MITK_ASSERT_EQUAL(dummy,newDummy,"GetMatrixColumn"); } /* void (){ DummyTestClass::Pointer dummy = DummyTestClass::New(); CPPUNIT_ASSERT(); //undo changes, new and changed object need to be the same! DummyTestClass::Pointer newDummy = DummyTestClass::New(); CPPUNIT_ASSERT(mitk::Equal(dummy,newDummy,mitk::eps,true)); } */ };//end class mitkBaseGeometryTestSuite MITK_TEST_SUITE_REGISTRATION(mitkBaseGeometry)