diff --git a/Modules/Core/include/mitkBaseGeometry.h b/Modules/Core/include/mitkBaseGeometry.h index 357c519236..8d2e4feb85 100644 --- a/Modules/Core/include/mitkBaseGeometry.h +++ b/Modules/Core/include/mitkBaseGeometry.h @@ -1,763 +1,763 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef BaseGeometry_H_HEADER_INCLUDED #define BaseGeometry_H_HEADER_INCLUDED #include "mitkOperationActor.h" #include #include #include "itkScalableAffineTransform.h" #include "mitkNumericTypes.h" #include #include #include #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 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: mitkClassMacroItkParent(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 override; 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 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 //## 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 = false); //##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 = false); //##Documentation //## @brief Translate the origin by a vector //## void Translate(const Vector3D &vector); //##Documentation //##@brief executes affine operations (translate, rotate, scale) void ExecuteOperation(Operation *operation) override; //##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) { index.Fill(0); dim = 3; } 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 { mitk::Point3D pt_units; pt_units.Fill(0); int i, dim = index.GetIndexDimension(); if (dim > 3) { dim = 3; } for (i = 0; i < dim; ++i) { pt_units[i] = index[i]; } IndexToWorld(pt_units, pt_mm); } //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em vector //## \a vec_units to world coordinates (in mm) //## @deprecated First parameter (Point3D) is not used. If possible, please use void IndexToWorld(const // mitk::Vector3D& vec_units, mitk::Vector3D& vec_mm) const. //## For further information about coordinates types, please see the Geometry documentation void IndexToWorld(const mitk::Point3D &atPt3d_units, const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em vector //## \a vec_mm to (continuous!) index coordinates. //## @deprecated First parameter (Point3D) is not used. If possible, please use void WorldToIndex(const // mitk::Vector3D& vec_mm, mitk::Vector3D& vec_units) const. //## For further information about coordinates types, please see the Geometry documentation void WorldToIndex(const mitk::Point3D &atPt3d_mm, const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const; //##Documentation //## @brief Deprecated for use with ITK version 3.10 or newer. //## Convert ITK physical coordinates of a \em point (in mm, //## but without a rotation) into MITK world coordinates (in mm) //## //## For more information, see WorldToItkPhysicalPoint. template 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); // 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; //##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(); Point3D pt_index; pt_index.Fill(0); 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); //##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; protected: // ********************************** Constructor ********************************** BaseGeometry(); BaseGeometry(const BaseGeometry &other); ~BaseGeometry() override; //##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 itk::LightObject::Pointer InternalClone() const override = 0; void PrintSelf(std::ostream &os, itk::Indent indent) const override; static const std::string GetTransformAsString(TransformType *transformType); itkGetConstMacro(NDimensions, unsigned int); bool IsBoundingBoxNull() const; bool IsIndexToWorldTransformNull() const; void SetVtkMatrixDeepCopy(vtkTransform *vtktransform); void _SetSpacing(const mitk::Vector3D &aSpacing, bool enforceSetSpacing = false); //##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*/){}; //##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: 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. * * @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 + * If you want to use different tolerance 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 coordinateEps Tolarence for comparison of all spatial aspects (spacing, origin and grid alignment). + * @param coordinateEps Tolerance for comparison of all spatial aspects (spacing, origin and grid alignment). * You can use mitk::eps in most cases. - * @param directionEps Tolarence for comparison of all directional aspects (axis). You can use mitk::eps in most cases. + * @param directionEps Tolerance for comparison of all directional aspects (axis). 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 coordinateEps, ScalarType directionEps, - bool verbose); + bool verbose = false); /** * @brief Equal A function comparing two geometries for beeing identical. * * @ingroup MITKTestingAPI * - * @overload This is a overloaded version that uses one tolerance for spatial and directional aspects. For more details, - * see other function version. + * @overload This is an overloaded version that uses a single tolerance for spatial and directional aspects. For more details, + * see the other overloaded version. * @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); + ScalarType eps = mitk::eps, + bool verbose = false); /** * @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. * * @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); /** * @brief A function checks if a test geometry is a sub geometry of * a given reference geometry. * * Sub geometry means that both geometries have the same voxel grid (same spacing, same axes, * orgin is on voxel grid), but the bounding box of the checked geometry is contained or equal * to the bounding box of the reference geometry.\n * By this definition equal geometries are always sub geometries of each other. * * The function checks the spacing, origin, axis vectors, 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 comparison. + * The parameter eps is a tolerance value for all methods which are internally used for comparison. * @param testGeo Geometry that should be checked if it is a sub geometry of referenceGeo. * @param referenceGeo Geometry that should contain testedGeometry as sub geometry. - * @param coordinateEps Tolarence for comparison of all spatial aspects (spacing, origin and grid alignment). + * @param coordinateEps Tolerance for comparison of all spatial aspects (spacing, origin and grid alignment). * You can use mitk::eps in most cases. - * @param directionEps Tolarence for comparison of all directional aspects (axis). You can use mitk::eps in most cases. + * @param directionEps Tolerance for comparison of all directional aspects (axis). 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 otherwise. + * @return True, if all comparisons are true. False otherwise. */ MITKCORE_EXPORT bool IsSubGeometry(const mitk::BaseGeometry& testGeo, const mitk::BaseGeometry& referenceGeo, ScalarType coordinateEps, ScalarType directionEps, - bool verbose); + bool verbose = false); /** * @brief A function checks if a test geometry is a sub geometry of * a given reference geometry. * - * @overload This is a overloaded version that uses one tolerance for spatial and directional aspects. For more details, - * see other function version. + * @overload This is a overloaded version that uses a single tolerance for spatial and directional aspects. For more details, + * see the other overloaded version. * @param testGeo Geometry that should be checked if it is a sub geometry of referenceGeo. * @param referenceGeo Geometry that should contain testedGeometry as sub geometry. * @param eps Tolarence for comparison (both spatial and directional). 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 otherwise. */ MITKCORE_EXPORT bool IsSubGeometry(const mitk::BaseGeometry& testGeo, const mitk::BaseGeometry& referenceGeo, - ScalarType eps, - bool verbose); + ScalarType eps = mitk::eps, + bool verbose = false); } // namespace mitk #endif /* BaseGeometry_H_HEADER_INCLUDED */ diff --git a/Modules/Core/include/mitkNodePredicateGeometry.h b/Modules/Core/include/mitkNodePredicateGeometry.h index a0f6777ca6..42c8fd55c5 100644 --- a/Modules/Core/include/mitkNodePredicateGeometry.h +++ b/Modules/Core/include/mitkNodePredicateGeometry.h @@ -1,80 +1,80 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef MITKNODEPREDICATEGEOMETRY_H_HEADER_INCLUDED_ #define MITKNODEPREDICATEGEOMETRY_H_HEADER_INCLUDED_ #include "mitkNodePredicateBase.h" #include "mitkBaseGeometry.h" #include "mitkTimeGeometry.h" namespace mitk { class BaseData; /**Documentation @brief Predicate that evaluates if the given DataNode's data object has the same geometry (in terms of spacing, origin, orientation) like the reference geometry. One can either check the whole time geometry of the date node by defining a referenc time geometry or check against one given reference base geometry. If the predicate should check against a base geometry, you can specify the timepoint of the data's time geometry that should be checked. If no timepoint is defined the predicate will evaluate the data geometry in the first timestep. Evaluates to "false" for unsupported or undefined data objects/geometries. - On can specify the tolerance/precesion of the check via SetCheckPrecision(). + One can specify the tolerance/precision of the check via SetCheckPrecision(). @remark The default tolerance is 1e-6 and therefore not as strict as mitk::eps. The reason is, - that, for the typicale usage of the node predicate, mitk::eps would be to pedantic. We + that, for the typical use of the node predicate, mitk::eps would be to pedantic. We often encounter floating point differences and practically it makes no difference e.g. - if two images differ something like 0.000001 mm in size or spacing + if two images differ something like 0.000001 mm in size or spacing. @ingroup DataStorage */ class MITKCORE_EXPORT NodePredicateGeometry : public NodePredicateBase { public: mitkClassMacro(NodePredicateGeometry, NodePredicateBase); mitkNewMacro1Param(NodePredicateGeometry, const TimeGeometry*); mitkNewMacro1Param(NodePredicateGeometry, const BaseGeometry*); mitkNewMacro2Param(NodePredicateGeometry, const BaseGeometry*, TimePointType); itkSetMacro(CheckPrecision, mitk::ScalarType); itkGetMacro(CheckPrecision, mitk::ScalarType); ~NodePredicateGeometry() override; bool CheckNode(const mitk::DataNode *node) const override; protected: /**Constructor that is used configures the predicate to check the reference geometry against the first data timepoint.*/ NodePredicateGeometry(const BaseGeometry* refGeometry); /**Constructor allows to define the timepoint that should be evaluated against the reference.*/ NodePredicateGeometry(const BaseGeometry* refGeometry, TimePointType relevantTimePoint); /**Constructor that is used configures the predicate to check against the whole time geometry.*/ NodePredicateGeometry(const TimeGeometry* refGeometry); BaseGeometry::ConstPointer m_RefGeometry; TimeGeometry::ConstPointer m_RefTimeGeometry; TimePointType m_TimePoint; /**Indicates if m_TimePoint should be regarded or always the first timestep should be used.*/ bool m_UseTimePoint; /**Precision that should be used for the equal checks.*/ mitk::ScalarType m_CheckPrecision; }; constexpr double NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_PRECISION = 1e-6; } // namespace mitk #endif /* MITKNodePredicateGeometry_H_HEADER_INCLUDED_ */ diff --git a/Modules/Core/include/mitkNodePredicateSubGeometry.h b/Modules/Core/include/mitkNodePredicateSubGeometry.h index fb8f19fd63..b777a64099 100644 --- a/Modules/Core/include/mitkNodePredicateSubGeometry.h +++ b/Modules/Core/include/mitkNodePredicateSubGeometry.h @@ -1,74 +1,74 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef MITKNODEPREDICATESUBGEOMETRY_H_HEADER_INCLUDED_ #define MITKNODEPREDICATESUBGEOMETRY_H_HEADER_INCLUDED_ #include "mitkNodePredicateBase.h" #include "mitkBaseGeometry.h" #include "mitkTimeGeometry.h" namespace mitk { class BaseData; /**Documentation @brief Predicate that evaluates if the given DataNode's data object has a geometry that is a sub geomety of the reference geometry. Sub geometry means that both geometries have the same voxel grid (same spacing, same axes, orgin is on voxel grid), but the bounding box of the checked geometry is contained or equal to the bounding box of the reference geometry.\n One can either check the whole time geometry of the data node by defining a referenc time geometry or check against one given2 reference base geometry. If the predicate should check against a base geometry, you can specify the timepoint of the data's time geometry that should be checked. If no timepoint is defined the predicate will evaluate the data geometry in the first timestep. Evaluates to "false" for unsupported or undefined data objects/geometries. - On can specify the tolerance/precesion of the check via SetCheckPrecision(). - @remark The default tolerance is the same like for NodePredicateGeometry and therefore not as strict as mitk::eps. The reason is, - that, for the typicale usage of the node predicate, mitk::eps would be to pedantic. We + On can specify the tolerance/precision of the check via SetCheckPrecision(). + @remark The default tolerance is the same as for NodePredicateGeometry and therefore not as strict as mitk::eps. The reason is, + that, for the typical use of the node predicate, mitk::eps would be to pedantic. We often encounter floating point differences and practically it makes no difference e.g. - if two images differ something like 0.000001 mm in size or spacing + if two images differ something like 0.000001 mm in size or spacing. @ingroup DataStorage */ class MITKCORE_EXPORT NodePredicateSubGeometry : public NodePredicateBase { public: mitkClassMacro(NodePredicateSubGeometry, NodePredicateBase); mitkNewMacro1Param(NodePredicateSubGeometry, const BaseGeometry*); mitkNewMacro2Param(NodePredicateSubGeometry, const BaseGeometry*, TimePointType); itkSetMacro(CheckPrecision, mitk::ScalarType); itkGetMacro(CheckPrecision, mitk::ScalarType); ~NodePredicateSubGeometry() override; bool CheckNode(const mitk::DataNode *node) const override; protected: /**Constructor that is used configures the predicate to check the reference geometry against the first data timepoint.*/ NodePredicateSubGeometry(const BaseGeometry* refGeometry); /**Constructor allows to define the timepoint that should be evaluated against the reference.*/ NodePredicateSubGeometry(const BaseGeometry* refGeometry, TimePointType relevantTimePoint); BaseGeometry::ConstPointer m_RefGeometry; TimePointType m_TimePoint; /**Indicates if m_TimePoint should be regarded or always the first timestep should be used.*/ bool m_UseTimePoint; /**Precision that should be used for the equal checks.*/ mitk::ScalarType m_CheckPrecision; }; } // namespace mitk #endif diff --git a/Modules/Core/src/DataManagement/mitkNodePredicateSubGeometry.cpp b/Modules/Core/src/DataManagement/mitkNodePredicateSubGeometry.cpp index 0826e927ac..264744e492 100644 --- a/Modules/Core/src/DataManagement/mitkNodePredicateSubGeometry.cpp +++ b/Modules/Core/src/DataManagement/mitkNodePredicateSubGeometry.cpp @@ -1,58 +1,58 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkNodePredicateSubGeometry.h" #include "mitkDataNode.h" #include "mitkImage.h" #include "mitkNodePredicateGeometry.h" mitk::NodePredicateSubGeometry::NodePredicateSubGeometry(const BaseGeometry* refGeometry, TimePointType relevantTimePoint) - : m_RefGeometry(refGeometry), m_TimePoint(relevantTimePoint), m_UseTimePoint(true), m_CheckPrecision(mitk::NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_PRECISION) + : m_RefGeometry(refGeometry), m_TimePoint(relevantTimePoint), m_UseTimePoint(true), m_CheckPrecision(NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_PRECISION) { if (m_RefGeometry.IsNull()) mitkThrow() << "Invalid constructor initialization. Reference base geometry instance is nullptr pointer."; } mitk::NodePredicateSubGeometry::NodePredicateSubGeometry(const BaseGeometry* refGeometry) - : m_RefGeometry(refGeometry), m_TimePoint(0), m_UseTimePoint(false), m_CheckPrecision(mitk::NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_PRECISION) + : m_RefGeometry(refGeometry), m_TimePoint(0), m_UseTimePoint(false), m_CheckPrecision(NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_PRECISION) { if (m_RefGeometry.IsNull()) mitkThrow() << "Invalid constructor initialization. Reference base geometry instance is nullptr pointer."; } mitk::NodePredicateSubGeometry::~NodePredicateSubGeometry() { } bool mitk::NodePredicateSubGeometry::CheckNode(const mitk::DataNode *node) const { if (node == nullptr) mitkThrow() << "NodePredicateSubGeometry: invalid node"; const auto *data = node->GetData(); if (data) { if (nullptr != data && m_RefGeometry.IsNotNull()) { //check only one time point. mitk::BaseGeometry::Pointer testGeometry = data->GetGeometry(); if (this->m_UseTimePoint) { testGeometry = data->GetTimeGeometry()->GetGeometryForTimePoint(m_TimePoint); } if (testGeometry.IsNotNull()) { return IsSubGeometry(*testGeometry, *m_RefGeometry, this->m_CheckPrecision, false); } } } return false; }