diff --git a/Core/Code/DataManagement/mitkBaseGeometry.cpp b/Core/Code/DataManagement/mitkBaseGeometry.cpp index 8a9e1d3ce3..9b3693420b 100644 --- a/Core/Code/DataManagement/mitkBaseGeometry.cpp +++ b/Core/Code/DataManagement/mitkBaseGeometry.cpp @@ -1,365 +1,651 @@ /*=================================================================== 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 mitk::BaseGeometry::BaseGeometry(): Superclass(), mitk::OperationActor(), m_Valid(true), m_FrameOfReferenceID(0), m_IndexToWorldTransformLastModified(0) { FillVector3D(m_FloatSpacing, 1,1,1); m_VtkMatrix = vtkMatrix4x4::New(); m_VtkIndexToWorldTransform = vtkMatrixToLinearTransform::New(); m_VtkIndexToWorldTransform->SetInput(m_VtkMatrix); Initialize(); } mitk::BaseGeometry::BaseGeometry(const BaseGeometry& other): Superclass(), m_ParametricBoundingBox(other.m_ParametricBoundingBox), m_TimeBounds(other.m_TimeBounds), m_Valid(other.m_Valid), m_FrameOfReferenceID(other.m_FrameOfReferenceID), m_IndexToWorldTransformLastModified(other.m_IndexToWorldTransformLastModified), m_Origin(other.m_Origin) { // DEPRECATED(m_RotationQuaternion = other.m_RotationQuaternion); // AffineGeometryFrame SetBounds(other.GetBounds()); m_VtkMatrix = vtkMatrix4x4::New(); m_VtkMatrix->DeepCopy(other.m_VtkMatrix); if (other.m_ParametricBoundingBox.IsNotNull()) { m_ParametricBoundingBox = other.m_ParametricBoundingBox->DeepCopy(); } FillVector3D(m_FloatSpacing,other.m_FloatSpacing[0],other.m_FloatSpacing[1],other.m_FloatSpacing[2]); m_VtkIndexToWorldTransform = vtkMatrixToLinearTransform::New(); m_VtkIndexToWorldTransform->DeepCopy(other.m_VtkIndexToWorldTransform); m_VtkIndexToWorldTransform->SetInput(m_VtkMatrix); other.InitializeGeometry(this); } mitk::BaseGeometry::~BaseGeometry() { m_VtkMatrix->Delete(); m_VtkIndexToWorldTransform->Delete(); } const mitk::Point3D& mitk::BaseGeometry::GetOrigin() const { return m_Origin; } void mitk::BaseGeometry::SetOrigin(const Point3D & origin) { if(origin!=GetOrigin()) { m_Origin = origin; m_IndexToWorldTransform->SetOffset(m_Origin.GetVectorFromOrigin()); Modified(); TransferItkToVtkTransform(); } } void mitk::BaseGeometry::TransferItkToVtkTransform() { // copy m_IndexToWorldTransform into m_VtkIndexToWorldTransform TransferItkTransformToVtkMatrix(m_IndexToWorldTransform.GetPointer(), m_VtkMatrix); m_VtkIndexToWorldTransform->Modified(); } void mitk::BaseGeometry::CopySpacingFromTransform(mitk::AffineTransform3D* transform, mitk::Vector3D& spacing, float floatSpacing[3]) { mitk::AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; vnlmatrix = transform->GetMatrix().GetVnlMatrix(); spacing[0]=vnlmatrix.get_column(0).magnitude(); spacing[1]=vnlmatrix.get_column(1).magnitude(); spacing[2]=vnlmatrix.get_column(2).magnitude(); floatSpacing[0]=spacing[0]; floatSpacing[1]=spacing[1]; floatSpacing[2]=spacing[2]; } void mitk::BaseGeometry::Initialize() { float b[6] = {0,1,0,1,0,1}; SetFloatBounds(b); if(m_IndexToWorldTransform.IsNull()) m_IndexToWorldTransform = TransformType::New(); else m_IndexToWorldTransform->SetIdentity(); CopySpacingFromTransform(m_IndexToWorldTransform, m_Spacing, m_FloatSpacing); vtk2itk(m_IndexToWorldTransform->GetOffset(), m_Origin); m_VtkMatrix->Identity(); m_TimeBounds[0]=ScalarTypeNumericTraits::NonpositiveMin(); m_TimeBounds[1]=ScalarTypeNumericTraits::max(); m_FrameOfReferenceID = 0; } 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++; 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++; SetBounds(b); } /** Initialize the geometry */ void mitk::BaseGeometry::InitializeGeometry(BaseGeometry* newGeometry) const { newGeometry->SetBounds(m_BoundingBox->GetBounds()); // we have to create a new transform!! if(m_IndexToWorldTransform) { TransformType::Pointer indexToWorldTransform = TransformType::New(); indexToWorldTransform->SetCenter( m_IndexToWorldTransform->GetCenter() ); indexToWorldTransform->SetMatrix( m_IndexToWorldTransform->GetMatrix() ); indexToWorldTransform->SetOffset( m_IndexToWorldTransform->GetOffset() ); newGeometry->SetIndexToWorldTransform(indexToWorldTransform); } } /** Set the bounds */ void mitk::BaseGeometry::SetBounds(const BoundsArrayType& bounds) { m_BoundingBox = 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; iInsertElement(pointid, p); } m_BoundingBox->SetPoints(pointscontainer); m_BoundingBox->ComputeBoundingBox(); this->Modified(); } void mitk::BaseGeometry::SetIndexToWorldTransform(mitk::AffineTransform3D* transform) { if(m_IndexToWorldTransform.GetPointer() != transform) { m_IndexToWorldTransform = transform; CopySpacingFromTransform(m_IndexToWorldTransform, m_Spacing, m_FloatSpacing); vtk2itk(m_IndexToWorldTransform->GetOffset(), m_Origin); TransferItkToVtkTransform(); Modified(); } } const mitk::BaseGeometry::BoundsArrayType mitk::BaseGeometry::GetBounds() const { assert(m_BoundingBox.IsNotNull()); return m_BoundingBox->GetBounds(); } bool mitk::BaseGeometry::IsValid() const { return m_Valid; } const float* mitk::BaseGeometry::GetFloatSpacing() const { return m_FloatSpacing; } bool mitk::Equal(const BaseGeometry::TransformType *leftHandSide, const BaseGeometry::TransformType *rightHandSide, ScalarType eps, bool verbose ) { //Compare IndexToWorldTransform Matrix if( !mitk::MatrixEqualElementWise( leftHandSide->GetMatrix(), rightHandSide->GetMatrix() ) ) { if(verbose) { MITK_INFO << "[( BaseGeometry::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; } bool mitk::Equal( const mitk::BaseGeometry::BoundingBoxType *leftHandSide, const mitk::BaseGeometry::BoundingBoxType *rightHandSide, ScalarType eps, bool verbose ) { bool result = true; if( rightHandSide == NULL ) { if(verbose) MITK_INFO << "[( BaseGeometry::BoundingBoxType )] rightHandSide NULL."; return false; } if( leftHandSide == NULL ) { if(verbose) MITK_INFO << "[( BaseGeometry::BoundingBoxType )] leftHandSide NULL."; return false; } 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) { if(( !mitk::Equal( *itLeft, *itRight, eps )) ) { if(verbose) { MITK_INFO << "[( BaseGeometry::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) { bool result = true; if( rightHandSide == NULL ) { if(verbose) MITK_INFO << "[( BaseGeometry )] rightHandSide NULL."; return false; } if( leftHandSide == NULL) { if(verbose) MITK_INFO << "[( BaseGeometry )] leftHandSide NULL."; return false; } //Compare spacings if( !mitk::Equal( leftHandSide->GetSpacing(), rightHandSide->GetSpacing(), eps ) ) { if(verbose) { MITK_INFO << "[( BaseGeometry )] 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(verbose) { MITK_INFO << "[( BaseGeometry )] Origin differs."; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide->GetOrigin() << " : leftHandSide is " << leftHandSide->GetOrigin() << " and tolerance is " << eps; } result = false; } //Compare Axis and Extents -/* xxxxxxxxxxxxxxx Funktionen noch nciht umgezogen! for( unsigned int i=0; i<3; ++i) { if( !mitk::Equal( leftHandSide->GetAxisVector(i), rightHandSide->GetAxisVector(i), eps)) { if(verbose) { MITK_INFO << "[( BaseGeometry )] AxisVector #" << i << " differ"; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide->GetAxisVector(i) << " : leftHandSide is " << leftHandSide->GetAxisVector(i) << " and tolerance is " << eps; } result = false; } if( !mitk::Equal( leftHandSide->GetExtent(i), rightHandSide->GetExtent(i), eps) ) { if(verbose) { MITK_INFO << "[( BaseGeometry )] Extent #" << i << " differ"; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide->GetExtent(i) << " : leftHandSide is " << leftHandSide->GetExtent(i) << " and tolerance is " << eps; } result = false; } } -*/ - //Compare BoundingBoxes if( !mitk::Equal( leftHandSide->GetBoundingBox(), rightHandSide->GetBoundingBox(), eps, verbose) ) { result = false; } //Compare IndexToWorldTransform Matrix if( !mitk::Equal( leftHandSide->GetIndexToWorldTransform(), rightHandSide->GetIndexToWorldTransform(), eps, verbose) ) { result = false; } return result; } void mitk::BaseGeometry::SetSpacing(const mitk::Vector3D& aSpacing) { if(mitk::Equal(m_Spacing, aSpacing) == false) { assert(aSpacing[0]>0 && aSpacing[1]>0 && aSpacing[2]>0); m_Spacing = aSpacing; AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; vnlmatrix = m_IndexToWorldTransform->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); Matrix3D matrix; matrix = vnlmatrix; AffineTransform3D::Pointer transform = AffineTransform3D::New(); transform->SetMatrix(matrix); transform->SetOffset(m_IndexToWorldTransform->GetOffset()); SetIndexToWorldTransform(transform.GetPointer()); itk2vtk(m_Spacing, m_FloatSpacing); } } + +mitk::Vector3D mitk::BaseGeometry::GetAxisVector(unsigned int direction) const +{ + Vector3D frontToBack; + frontToBack.SetVnlVector(m_IndexToWorldTransform->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>=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]; +} + +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 m_IndexToWorldTransform->TransformPoint(m_BoundingBox->GetCenter()); +} + +double mitk::BaseGeometry::GetDiagonalLength2() const +{ + Vector3D diagonalvector = GetCornerPoint()-GetCornerPoint(false, false, false); + return diagonalvector.GetSquaredNorm(); +} + +//##Documentation +//## @brief Get the length of the diagonal of the bounding-box in mm +//## +double mitk::BaseGeometry::GetDiagonalLength() const +{ + return sqrt(GetDiagonalLength2()); +} + +mitk::Point3D mitk::BaseGeometry::GetCornerPoint(int id) const +{ + assert(id >= 0); + assert(m_BoundingBox.IsNotNull()); + + BoundingBox::BoundsArrayType bounds = m_BoundingBox->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; + default: + { + itkExceptionMacro(<<"A cube only has 8 corners. These are labeled 0-7."); + } + } + return m_IndexToWorldTransform->TransformPoint(cornerpoint); +} + +mitk::Point3D mitk::BaseGeometry::GetCornerPoint(bool xFront, bool yFront, bool zFront) const +{ + assert(m_BoundingBox.IsNotNull()); + BoundingBox::BoundsArrayType bounds = m_BoundingBox->GetBounds(); + + Point3D cornerpoint; + cornerpoint[0] = (xFront ? bounds[0] : bounds[1]); + cornerpoint[1] = (yFront ? bounds[2] : bounds[3]); + cornerpoint[2] = (zFront ? bounds[4] : bounds[5]); + + return m_IndexToWorldTransform->TransformPoint(cornerpoint); +} + +mitk::ScalarType mitk::BaseGeometry::GetExtentInMM(int direction) const +{ + return m_IndexToWorldTransform->GetMatrix().GetVnlMatrix().get_column(direction).magnitude()*GetExtent(direction); +} + +void mitk::BaseGeometry::SetExtentInMM(int direction, ScalarType extentInMM) +{ + ScalarType len = GetExtentInMM(direction); + if(fabs(len - extentInMM)>=mitk::eps) + { + AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; + vnlmatrix = m_IndexToWorldTransform->GetMatrix().GetVnlMatrix(); + if(len>extentInMM) + vnlmatrix.set_column(direction, vnlmatrix.get_column(direction)/len*extentInMM); + else + vnlmatrix.set_column(direction, vnlmatrix.get_column(direction)*extentInMM/len); + Matrix3D matrix; + matrix = vnlmatrix; + m_IndexToWorldTransform->SetMatrix(matrix); + Modified(); + } +} + +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) + inside = m_BoundingBox->IsInside(index); + + return inside; +} + +//##Documentation +//## @brief Convenience method for working with ITK indices +template +bool mitk::BaseGeometry::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); +} + +void mitk::BaseGeometry::WorldToIndex(const mitk::Point3D &pt_mm, mitk::Point3D &pt_units) const +{ + BackTransform(pt_mm, pt_units); +} + +void mitk::BaseGeometry::WorldToIndex( const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const +{ + BackTransform( vec_mm, vec_units); +} + +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 Geometry3D::WorldToIndex(point, vec, vec). Use Geometry3D::WorldToIndex(vec, vec) instead!"; + //BackTransform(atPt3d_mm, vec_mm, vec_units); + this->WorldToIndex(vec_mm, vec_units); +} + +void mitk::BaseGeometry::BackTransform(const mitk::Vector3D& in, mitk::Vector3D& out) const +{ + // Get WorldToIndex transform + if (m_IndexToWorldTransformLastModified != m_IndexToWorldTransform->GetMTime()) + { + m_InvertedTransform = TransformType::New(); + if (!m_IndexToWorldTransform->GetInverse( m_InvertedTransform.GetPointer() )) + { + itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed." ); + } + m_IndexToWorldTransformLastModified = m_IndexToWorldTransform->GetMTime(); + } + + // Check for valid matrix inversion + const TransformType::MatrixType& inverse = m_InvertedTransform->GetMatrix(); + if(inverse.GetVnlMatrix().has_nans()) + { + itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed. Matrix was: " << std::endl + << m_IndexToWorldTransform->GetMatrix() << "Suggested inverted matrix is:" << std::endl + << inverse ); + } + + // Transform vector + for (unsigned int i = 0; i < 3; i++) + { + out[i] = 0.0; + for (unsigned int j = 0; j < 3; j++) + { + out[i] += inverse[i][j]*in[j]; + } + } +} + +void mitk::BaseGeometry::BackTransform(const mitk::Point3D &in, mitk::Point3D& out) const +{ + ScalarType temp[3]; + unsigned int i, j; + const TransformType::OffsetType& offset = m_IndexToWorldTransform->GetOffset(); + + // Remove offset + for (j = 0; j < 3; j++) + { + temp[j] = in[j] - offset[j]; + } + + // Get WorldToIndex transform + if (m_IndexToWorldTransformLastModified != m_IndexToWorldTransform->GetMTime()) + { + m_InvertedTransform = TransformType::New(); + if (!m_IndexToWorldTransform->GetInverse( m_InvertedTransform.GetPointer() )) + { + itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed." ); + } + m_IndexToWorldTransformLastModified = m_IndexToWorldTransform->GetMTime(); + } + + // Check for valid matrix inversion + const TransformType::MatrixType& inverse = m_InvertedTransform->GetMatrix(); + if(inverse.GetVnlMatrix().has_nans()) + { + itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed. Matrix was: " << std::endl + << m_IndexToWorldTransform->GetMatrix() << "Suggested inverted matrix is:" << std::endl + << inverse ); + } + + // Transform point + for (i = 0; i < 3; i++) + { + out[i] = 0.0; + for (j = 0; j < 3; j++) + { + out[i] += inverse[i][j]*temp[j]; + } + } +} + +void mitk::BaseGeometry::BackTransform(const mitk::Point3D &/*at*/, const mitk::Vector3D &in, mitk::Vector3D& out) const +{ + MITK_INFO<<"Warning! Call of the deprecated function Geometry3D::BackTransform(point, vec, vec). Use Geometry3D::BackTransform(vec, vec) instead!"; + //// Get WorldToIndex transform + //if (m_IndexToWorldTransformLastModified != m_IndexToWorldTransform->GetMTime()) + //{ + // m_InvertedTransform = TransformType::New(); + // if (!m_IndexToWorldTransform->GetInverse( m_InvertedTransform.GetPointer() )) + // { + // itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed." ); + // } + // m_IndexToWorldTransformLastModified = m_IndexToWorldTransform->GetMTime(); + //} + + //// Check for valid matrix inversion + //const TransformType::MatrixType& inverse = m_InvertedTransform->GetMatrix(); + //if(inverse.GetVnlMatrix().has_nans()) + //{ + // itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed. Matrix was: " << std::endl + // << m_IndexToWorldTransform->GetMatrix() << "Suggested inverted matrix is:" << std::endl + // << inverse ); + //} + + //// Transform vector + //for (unsigned int i = 0; i < 3; i++) + //{ + // out[i] = 0.0; + // for (unsigned int j = 0; j < 3; j++) + // { + // out[i] += inverse[i][j]*in[j]; + // } + //} + this->BackTransform(in, out); +} diff --git a/Core/Code/DataManagement/mitkBaseGeometry.h b/Core/Code/DataManagement/mitkBaseGeometry.h index 5e7836c711..cdf041ea02 100644 --- a/Core/Code/DataManagement/mitkBaseGeometry.h +++ b/Core/Code/DataManagement/mitkBaseGeometry.h @@ -1,313 +1,424 @@ /*=================================================================== 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 "mitkvector.h" #include #include #include "itkScalableAffineTransform.h" #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; //##Documentation //## @brief BaseGeometry xxxxxxxxxxxxxx //## //## xxxxxxxxxxx //## //## Rule: everything is in mm (ms) if not stated otherwise. //## @ingroup Geometry class MITK_CORE_EXPORT BaseGeometry : public itk::Object, public OperationActor { public: mitkClassMacro(BaseGeometry, itk::Object); // ********************************** TypeDef ********************************** typedef itk::QuaternionRigidTransform< ScalarType > QuaternionTransformType; typedef QuaternionTransformType::VnlQuaternionType VnlQuaternionType; typedef itk::ScalableAffineTransform 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 //## - virtual void SetOrigin(const Point3D& origin); + void SetOrigin(const Point3D& origin); //##Documentation //## @brief Get the spacing (size of a pixel). //## itkGetConstReferenceMacro(Spacing, mitk::Vector3D); //##Documentation //## @brief Get the spacing as a float[3] array. const float* GetFloatSpacing() const; //##Documentation //## @brief Set the spacing (m_Spacing) virtual void SetSpacing(const mitk::Vector3D& aSpacing); // ********************************** 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); //##Documentation //## @brief Is this Geometry3D in a state that is valid? virtual bool IsValid() const; // ********************************** Initialize ********************************** //##Documentation //## @brief Initialize the Geometry3D virtual void Initialize(); virtual void InitializeGeometry(Self * newGeometry) const; static void CopySpacingFromTransform(mitk::AffineTransform3D* transform, mitk::Vector3D& spacing, float floatSpacing[3]); // ********************************** Transformations Set/Get ********************************** // a bit of a misuse, but we want only doxygen to see the following: #ifdef DOXYGEN_SKIP //##Documentation //## @brief Get the transformation used to convert from index //## to world coordinates itkGetObjectMacro(IndexToWorldTransform, AffineTransform3D); #endif //## @brief Set the transformation used to convert from index //## to world coordinates virtual void SetIndexToWorldTransform(mitk::AffineTransform3D* transform); /** Set/Get the IndexToWorldTransform */ itkGetConstObjectMacro(IndexToWorldTransform, AffineTransform3D); itkGetObjectMacro(IndexToWorldTransform, AffineTransform3D); // ********************************** Transformations ********************************** //##Documentation //## @brief Copy the ITK transform //## (m_IndexToWorldTransform) to the VTK transform //## \sa SetIndexToWorldTransform - virtual void TransferItkToVtkTransform(); + void TransferItkToVtkTransform(); + + //##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 + virtual 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 + virtual 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( pt_units[i] ); + } + } + + //##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 + virtual void WorldToIndex(const mitk::Point3D& atPt3d_mm, const mitk::Vector3D& vec_mm, mitk::Vector3D& vec_units) const; // ********************************** BoundingBox ********************************** //##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. - // xx This was not vitrual! - //virtual const BoundingBox::BoundsArrayType& GetParametricBounds() const = 0 ; //ToDo /** Get the bounding box */ itkGetConstObjectMacro(BoundingBox, BoundingBoxType); //##Documentation //## @brief Get the time bounds (in ms) itkGetConstReferenceMacro(TimeBounds, TimeBounds); - const BoundsArrayType GetBounds() const; - // 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. virtual void SetBounds(const BoundsArrayType& bounds); //##Documentation //## @brief Set the bounding box (in index/unit coordinates) via a float array - virtual void SetFloatBounds(const float bounds[6]); + void SetFloatBounds(const float bounds[6]); //##Documentation //## @brief Set the bounding box (in index/unit coordinates) via a double array - virtual void SetFloatBounds(const double bounds[6]); - - //##Documentation - //## @brief Set the time bounds (in ms) - //virtual void SetTimeBounds(const TimeBounds& timebounds) = 0 ; //ToDo + void SetFloatBounds(const double bounds[6]); // ********************************** 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. + virtual 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. + virtual 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! + virtual 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 + virtual bool IsIndexInside(const mitk::Point3D& index) const; + + //##Documentation + //## @brief Convenience method for working with ITK indices + template + bool IsIndexInside(const itk::Index &index) const; + protected: // ********************************** Constructor ********************************** BaseGeometry(); BaseGeometry(const BaseGeometry& other); virtual ~BaseGeometry(); //itkGetConstMacro(IndexToWorldTransformLastModified, unsigned long); + virtual void BackTransform(const mitk::Point3D& in, mitk::Point3D& out) const; + + //Without redundant parameter Point3D + virtual void BackTransform(const mitk::Vector3D& in, mitk::Vector3D& out) const; + + //##Documentation + //## @brief Deprecated + virtual void BackTransform(const mitk::Point3D& at, const mitk::Vector3D& in, mitk::Vector3D& out) const; + // ********************************** Variables ********************************** AffineTransform3D::Pointer m_IndexToWorldTransform; vtkMatrixToLinearTransform* m_VtkIndexToWorldTransform; vtkMatrix4x4* m_VtkMatrix; bool m_Valid; unsigned int m_FrameOfReferenceID; mutable mitk::BoundingBox::Pointer m_ParametricBoundingBox; mutable mitk::TimeBounds m_TimeBounds; mutable BoundingBoxPointer m_BoundingBox; //##Documentation //## @brief Origin, i.e. upper-left corner of the plane //## Point3D m_Origin; //##Documentation //## @brief Spacing of the data. Only significant if the geometry describes //## an Image (m_ImageGeometry==true). mitk::Vector3D m_Spacing; static const unsigned int NDimensions = 3; mutable TransformType::Pointer m_InvertedTransform; //this was private mutable unsigned long m_IndexToWorldTransformLastModified; //this was private float m_FloatSpacing[3]; //this was private // DEPRECATED(VnlQuaternionType m_RotationQuaternion); //this was private }; // ********************************** Equal Functions ********************************** // // Static compare functions mainly for testing // /** * @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. */ MITK_CORE_EXPORT bool Equal( const mitk::BaseGeometry::BoundingBoxType *leftHandSide, const mitk::BaseGeometry::BoundingBoxType *rightHandSide, mitk::ScalarType eps, bool verbose); //ToDo // // 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 * 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. */ MITK_CORE_EXPORT bool Equal(const mitk::BaseGeometry* leftHandSide, const mitk::BaseGeometry* rightHandSide, mitk::ScalarType eps, bool verbose); //ToDo /** * @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. */ MITK_CORE_EXPORT bool Equal(const mitk::BaseGeometry::TransformType *leftHandSide, const mitk::BaseGeometry::TransformType *rightHandSide, mitk::ScalarType eps, bool verbose); //ToDo } // namespace mitk #endif /* BaseGeometry_H_HEADER_INCLUDED */ diff --git a/Core/Code/DataManagement/mitkGeometry3D.cpp b/Core/Code/DataManagement/mitkGeometry3D.cpp index 25f60b1b29..0fa762470c 100644 --- a/Core/Code/DataManagement/mitkGeometry3D.cpp +++ b/Core/Code/DataManagement/mitkGeometry3D.cpp @@ -1,729 +1,681 @@ /*=================================================================== 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 "mitkGeometry3D.h" #include "mitkRotationOperation.h" #include "mitkRestorePlanePositionOperation.h" #include "mitkApplyTransformMatrixOperation.h" #include "mitkPointOperation.h" #include "mitkInteractionConst.h" #include #include #include "mitkMatrixConvert.h" // Standard constructor for the New() macro. Sets the geometry to 3 dimensions mitk::Geometry3D::Geometry3D() : m_ImageGeometry(false) { } mitk::Geometry3D::Geometry3D(const Geometry3D& other) : BaseGeometry(other), m_ImageGeometry(other.m_ImageGeometry) { } mitk::Geometry3D::~Geometry3D() { } void mitk::Geometry3D::TransferVtkToItkTransform() { TransferVtkMatrixToItkTransform(m_VtkMatrix, m_IndexToWorldTransform.GetPointer()); CopySpacingFromTransform(m_IndexToWorldTransform, m_Spacing, m_FloatSpacing); vtk2itk(m_IndexToWorldTransform->GetOffset(), m_Origin); } void mitk::Geometry3D::SetIndexToWorldTransformByVtkMatrix(vtkMatrix4x4* vtkmatrix) { m_VtkMatrix->DeepCopy(vtkmatrix); TransferVtkToItkTransform(); } void mitk::Geometry3D::SetTimeBounds(const TimeBounds& timebounds) { if(m_TimeBounds != timebounds) { m_TimeBounds = timebounds; Modified(); } } void mitk::Geometry3D::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) { unsigned int i; for(i=0; iInsertElement(pointid, p); } m_ParametricBoundingBox->SetPoints(pointscontainer); m_ParametricBoundingBox->ComputeBoundingBox(); this->Modified(); } void mitk::Geometry3D::WorldToIndex(const mitk::Point3D &pt_mm, mitk::Point3D &pt_units) const { BackTransform(pt_mm, pt_units); } void mitk::Geometry3D::IndexToWorld(const mitk::Point3D &pt_units, mitk::Point3D &pt_mm) const { pt_mm = m_IndexToWorldTransform->TransformPoint(pt_units); } void mitk::Geometry3D::WorldToIndex(const mitk::Point3D & /*atPt3d_mm*/, const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const { MITK_WARN<<"Warning! Call of the deprecated function Geometry3D::WorldToIndex(point, vec, vec). Use Geometry3D::WorldToIndex(vec, vec) instead!"; //BackTransform(atPt3d_mm, vec_mm, vec_units); this->WorldToIndex(vec_mm, vec_units); } void mitk::Geometry3D::WorldToIndex( const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const { BackTransform( vec_mm, vec_units); } void mitk::Geometry3D::IndexToWorld(const mitk::Point3D &/*atPt3d_units*/, const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const { MITK_WARN<<"Warning! Call of the deprecated function Geometry3D::IndexToWorld(point, vec, vec). Use Geometry3D::IndexToWorld(vec, vec) instead!"; //vec_mm = m_IndexToWorldTransform->TransformVector(vec_units); this->IndexToWorld(vec_units, vec_mm); } void mitk::Geometry3D::IndexToWorld(const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const { vec_mm = m_IndexToWorldTransform->TransformVector(vec_units); } itk::LightObject::Pointer mitk::Geometry3D::InternalClone() const { Self::Pointer newGeometry = new Self(*this); newGeometry->UnRegister(); return newGeometry.GetPointer(); } -/* + void mitk::Geometry3D::InitializeGeometry(Geometry3D * newGeometry) const { -Superclass::InitializeGeometry(newGeometry); + Superclass::InitializeGeometry(newGeometry); -newGeometry->SetTimeBounds(m_TimeBounds); + newGeometry->SetTimeBounds(m_TimeBounds); -//newGeometry->GetVtkTransform()->SetMatrix(m_VtkIndexToWorldTransform->GetMatrix()); IW -//newGeometry->TransferVtkToItkTransform(); //MH + //newGeometry->GetVtkTransform()->SetMatrix(m_VtkIndexToWorldTransform->GetMatrix()); IW + //newGeometry->TransferVtkToItkTransform(); //MH -newGeometry->SetFrameOfReferenceID(GetFrameOfReferenceID()); -newGeometry->m_ImageGeometry = m_ImageGeometry; -} -*/ -void mitk::Geometry3D::SetExtentInMM(int direction, ScalarType extentInMM) -{ - ScalarType len = GetExtentInMM(direction); - if(fabs(len - extentInMM)>=mitk::eps) - { - AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; - vnlmatrix = m_IndexToWorldTransform->GetMatrix().GetVnlMatrix(); - if(len>extentInMM) - vnlmatrix.set_column(direction, vnlmatrix.get_column(direction)/len*extentInMM); - else - vnlmatrix.set_column(direction, vnlmatrix.get_column(direction)*extentInMM/len); - Matrix3D matrix; - matrix = vnlmatrix; - m_IndexToWorldTransform->SetMatrix(matrix); - Modified(); - } + newGeometry->SetFrameOfReferenceID(GetFrameOfReferenceID()); + newGeometry->m_ImageGeometry = m_ImageGeometry; } mitk::BoundingBox::Pointer mitk::Geometry3D::CalculateBoundingBoxRelativeToTransform(const mitk::AffineTransform3D* transform) const { mitk::BoundingBox::PointsContainer::Pointer pointscontainer=mitk::BoundingBox::PointsContainer::New(); mitk::BoundingBox::PointIdentifier pointid=0; unsigned char i; 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) )); } else { 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; } #include void mitk::Geometry3D::ExecuteOperation(Operation* operation) { vtkTransform *vtktransform = vtkTransform::New(); vtktransform->SetMatrix(m_VtkMatrix); switch (operation->GetOperationType()) { case OpNOTHING: break; case OpMOVE: { 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; } case OpSCALE: { 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; } case OpROTATE: { 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; } case OpRESTOREPLANEPOSITION: { //Copy necessary to avoid vtk warning vtkMatrix4x4* matrix = vtkMatrix4x4::New(); TransferItkTransformToVtkMatrix(dynamic_cast(operation)->GetTransform().GetPointer(), matrix); vtktransform->SetMatrix(matrix); break; } case OpAPPLYTRANSFORMMATRIX: { ApplyTransformMatrixOperation *applyMatrixOp = dynamic_cast< ApplyTransformMatrixOperation* >( operation ); vtktransform->SetMatrix(applyMatrixOp->GetMatrix()); break; } default: vtktransform->Delete(); return; } m_VtkMatrix->DeepCopy(vtktransform->GetMatrix()); TransferVtkToItkTransform(); Modified(); vtktransform->Delete(); } void mitk::Geometry3D::BackTransform(const mitk::Point3D &in, mitk::Point3D& out) const { ScalarType temp[3]; unsigned int i, j; const TransformType::OffsetType& offset = m_IndexToWorldTransform->GetOffset(); // Remove offset for (j = 0; j < 3; j++) { temp[j] = in[j] - offset[j]; } // Get WorldToIndex transform if (m_IndexToWorldTransformLastModified != m_IndexToWorldTransform->GetMTime()) { m_InvertedTransform = TransformType::New(); if (!m_IndexToWorldTransform->GetInverse( m_InvertedTransform.GetPointer() )) { itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed." ); } m_IndexToWorldTransformLastModified = m_IndexToWorldTransform->GetMTime(); } // Check for valid matrix inversion const TransformType::MatrixType& inverse = m_InvertedTransform->GetMatrix(); if(inverse.GetVnlMatrix().has_nans()) { itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed. Matrix was: " << std::endl << m_IndexToWorldTransform->GetMatrix() << "Suggested inverted matrix is:" << std::endl << inverse ); } // Transform point for (i = 0; i < 3; i++) { out[i] = 0.0; for (j = 0; j < 3; j++) { out[i] += inverse[i][j]*temp[j]; } } } void mitk::Geometry3D::BackTransform(const mitk::Point3D &/*at*/, const mitk::Vector3D &in, mitk::Vector3D& out) const { MITK_INFO<<"Warning! Call of the deprecated function Geometry3D::BackTransform(point, vec, vec). Use Geometry3D::BackTransform(vec, vec) instead!"; //// Get WorldToIndex transform //if (m_IndexToWorldTransformLastModified != m_IndexToWorldTransform->GetMTime()) //{ // m_InvertedTransform = TransformType::New(); // if (!m_IndexToWorldTransform->GetInverse( m_InvertedTransform.GetPointer() )) // { // itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed." ); // } // m_IndexToWorldTransformLastModified = m_IndexToWorldTransform->GetMTime(); //} //// Check for valid matrix inversion //const TransformType::MatrixType& inverse = m_InvertedTransform->GetMatrix(); //if(inverse.GetVnlMatrix().has_nans()) //{ // itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed. Matrix was: " << std::endl // << m_IndexToWorldTransform->GetMatrix() << "Suggested inverted matrix is:" << std::endl // << inverse ); //} //// Transform vector //for (unsigned int i = 0; i < 3; i++) //{ // out[i] = 0.0; // for (unsigned int j = 0; j < 3; j++) // { // out[i] += inverse[i][j]*in[j]; // } //} this->BackTransform(in, out); } void mitk::Geometry3D::BackTransform(const mitk::Vector3D& in, mitk::Vector3D& out) const { // Get WorldToIndex transform if (m_IndexToWorldTransformLastModified != m_IndexToWorldTransform->GetMTime()) { m_InvertedTransform = TransformType::New(); if (!m_IndexToWorldTransform->GetInverse( m_InvertedTransform.GetPointer() )) { itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed." ); } m_IndexToWorldTransformLastModified = m_IndexToWorldTransform->GetMTime(); } // Check for valid matrix inversion const TransformType::MatrixType& inverse = m_InvertedTransform->GetMatrix(); if(inverse.GetVnlMatrix().has_nans()) { itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed. Matrix was: " << std::endl << m_IndexToWorldTransform->GetMatrix() << "Suggested inverted matrix is:" << std::endl << inverse ); } // Transform vector for (unsigned int i = 0; i < 3; i++) { out[i] = 0.0; for (unsigned int j = 0; j < 3; j++) { out[i] += inverse[i][j]*in[j]; } } } void mitk::Geometry3D::Translate(const Vector3D & vector) { if((vector[0] != 0) || (vector[1] != 0) || (vector[2] != 0)) { this->SetOrigin(m_Origin + vector); // m_IndexToWorldTransform->SetOffset(m_IndexToWorldTransform->GetOffset()+vector); // TransferItkToVtkTransform(); // Modified(); } } void mitk::Geometry3D::SetIdentity() { m_IndexToWorldTransform->SetIdentity(); m_Origin.Fill(0); Modified(); TransferItkToVtkTransform(); } void mitk::Geometry3D::Compose( const mitk::Geometry3D::TransformType * other, bool pre ) { m_IndexToWorldTransform->Compose(other, pre); CopySpacingFromTransform(m_IndexToWorldTransform, m_Spacing, m_FloatSpacing); vtk2itk(m_IndexToWorldTransform->GetOffset(), m_Origin); Modified(); TransferItkToVtkTransform(); } void mitk::Geometry3D::Compose( const vtkMatrix4x4 * vtkmatrix, bool pre ) { mitk::Geometry3D::TransformType::Pointer itkTransform = mitk::Geometry3D::TransformType::New(); TransferVtkMatrixToItkTransform(vtkmatrix, itkTransform.GetPointer()); Compose(itkTransform, pre); } const std::string mitk::Geometry3D::GetTransformAsString( TransformType* transformType ) { std::ostringstream out; out << '['; for( int i=0; i<3; ++i ) { out << '['; for( int j=0; j<3; ++j ) out << transformType->GetMatrix().GetVnlMatrix().get(i, j) << ' '; out << ']'; } out << "]["; for( int i=0; i<3; ++i ) out << transformType->GetOffset()[i] << ' '; out << "]\0"; return out.str(); } void mitk::Geometry3D::PrintSelf(std::ostream& os, itk::Indent indent) const { os << indent << " IndexToWorldTransform: "; if(m_IndexToWorldTransform.IsNull()) 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 << m_IndexToWorldTransform->GetMatrix()[i][j] << " "; } os << std::endl; } os << indent << "Offset: " << m_IndexToWorldTransform->GetOffset() << std::endl; os << indent << "Center: " << m_IndexToWorldTransform->GetCenter() << std::endl; os << indent << "Translation: " << m_IndexToWorldTransform->GetTranslation() << std::endl; os << indent << "Inverse: " << std::endl; for (i = 0; i < 3; i++) { os << indent.GetNextIndent(); for (j = 0; j < 3; j++) { os << m_IndexToWorldTransform->GetInverseMatrix()[i][j] << " "; } os << std::endl; } // from itk::ScalableAffineTransform os << indent << "Scale : "; for (i = 0; i < 3; i++) { os << m_IndexToWorldTransform->GetScale()[i] << " "; } os << std::endl; } os << indent << " BoundingBox: "; if(m_BoundingBox.IsNull()) os << "NULL" << std::endl; else { os << indent << "( "; for (unsigned int i=0; i<3; i++) { os << m_BoundingBox->GetBounds()[2*i] << "," << m_BoundingBox->GetBounds()[2*i+1] << " "; } os << " )" << std::endl; } os << indent << " Origin: " << m_Origin << std::endl; os << indent << " ImageGeometry: " << m_ImageGeometry << std::endl; os << indent << " Spacing: " << m_Spacing << std::endl; os << indent << " TimeBounds: " << m_TimeBounds << std::endl; } mitk::Point3D mitk::Geometry3D::GetCornerPoint(int id) const { assert(id >= 0); assert(m_BoundingBox.IsNotNull()); BoundingBox::BoundsArrayType bounds = m_BoundingBox->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; default: { itkExceptionMacro(<<"A cube only has 8 corners. These are labeled 0-7."); } } 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); } return m_IndexToWorldTransform->TransformPoint(cornerpoint); } mitk::Point3D mitk::Geometry3D::GetCornerPoint(bool xFront, bool yFront, bool zFront) const { assert(m_BoundingBox.IsNotNull()); BoundingBox::BoundsArrayType bounds = m_BoundingBox->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) { // 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); } return m_IndexToWorldTransform->TransformPoint(cornerpoint); } void mitk::Geometry3D::ResetSubTransforms() { } void mitk::Geometry3D::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) return; const BoundingBox::BoundsArrayType& boundsarray = this->GetBoundingBox()->GetBounds(); Point3D originIndex; FillVector3D(originIndex, boundsarray[0], boundsarray[2], boundsarray[4]); if(isAnImageGeometry == true) FillVector3D( originIndex, originIndex[0] + 0.5, originIndex[1] + 0.5, originIndex[2] + 0.5 ); else FillVector3D( originIndex, originIndex[0] - 0.5, originIndex[1] - 0.5, originIndex[2] - 0.5 ); Point3D originWorld; originWorld = GetIndexToWorldTransform() ->TransformPoint( originIndex ); // instead could as well call IndexToWorld(originIndex,originWorld); SetOrigin(originWorld); this->SetImageGeometry(isAnImageGeometry); } -bool mitk::Geometry3D::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; -} - bool mitk::Equal(const mitk::Geometry3D *leftHandSide, const mitk::Geometry3D *rightHandSide, ScalarType eps, bool verbose) { bool result = true; if( rightHandSide == NULL ) { if(verbose) MITK_INFO << "[( Geometry3D )] rightHandSide NULL."; return false; } if( leftHandSide == NULL) { if(verbose) MITK_INFO << "[( Geometry3D )] leftHandSide NULL."; return false; } //Compare spacings if( !mitk::Equal( leftHandSide->GetSpacing(), rightHandSide->GetSpacing(), eps ) ) { 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(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) { if( !mitk::Equal( leftHandSide->GetAxisVector(i), rightHandSide->GetAxisVector(i), eps)) { 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; } if( !mitk::Equal( leftHandSide->GetExtent(i), rightHandSide->GetExtent(i), eps) ) { 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(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) ) { result = false; } //Compare IndexToWorldTransform Matrix if( !mitk::Equal( leftHandSide->GetIndexToWorldTransform(), rightHandSide->GetIndexToWorldTransform(), eps, verbose) ) { result = false; } return result; } diff --git a/Core/Code/DataManagement/mitkGeometry3D.h b/Core/Code/DataManagement/mitkGeometry3D.h index 5a38fef39d..b308d614d2 100644 --- a/Core/Code/DataManagement/mitkGeometry3D.h +++ b/Core/Code/DataManagement/mitkGeometry3D.h @@ -1,590 +1,513 @@ /*=================================================================== 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 "itkScalableAffineTransform.h" #include #include "mitkBaseGeometry.h" class vtkLinearTransform; namespace mitk { //##Documentation //## @brief Standard typedef for time-bounds typedef itk::FixedArray TimeBounds; typedef itk::FixedArray FixedArrayType; //##Documentation //## @brief Standard 3D-BoundingBox typedef //## //## Standard 3D-BoundingBox typedef to get rid of template arguments (3D, type). typedef itk::BoundingBox BoundingBox; //##Documentation //## @brief Describes the geometry of a data object //## //## At least, it can return the bounding box of the 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 a life span, i.e. a bounding box in time in ms (with //## start and end time), to be accessed by GetTimeBounds(). //## The default is minus infinity to plus infinity. //## //## Geometry3D 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. //## //## Geometry3D instances referring to an Image need a slightly //## different definition of corners, see SetImageGeometry. This //## is usualy automatically called by Image. //## //## Geometry3D 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(). //## //## Rule: everything is in mm (ms) if not stated otherwise. //## @ingroup Geometry class MITK_CORE_EXPORT Geometry3D : public BaseGeometry { public: mitkClassMacro(Geometry3D, mitk::BaseGeometry); typedef itk::QuaternionRigidTransform< ScalarType > QuaternionTransformType; typedef QuaternionTransformType::VnlQuaternionType VnlQuaternionType; /** Method for creation through the object factory. */ itkNewMacro(Self); //##Documentation //## @brief Convenience method for setting the ITK transform //## (m_IndexToWorldTransform) via an vtkMatrix4x4 //## \sa SetIndexToWorldTransform virtual void SetIndexToWorldTransformByVtkMatrix(vtkMatrix4x4* vtkmatrix); //##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 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 Set the time bounds (in ms) virtual void SetTimeBounds(const TimeBounds& timebounds); //##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 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 - { - Vector3D frontToBack; - frontToBack.SetVnlVector(m_IndexToWorldTransform->GetMatrix().GetVnlMatrix().get_column(direction)); - frontToBack *= GetExtent(direction); - return frontToBack; - } - - //##Documentation - //## @brief Get the center of the bounding-box in mm - //## - Point3D GetCenter() const - { - assert(m_BoundingBox.IsNotNull()); - return m_IndexToWorldTransform->TransformPoint(m_BoundingBox->GetCenter()); - } - - //##Documentation - //## @brief Get the squared length of the diagonal of the bounding-box in mm - //## - double GetDiagonalLength2() const - { - Vector3D diagonalvector = GetCornerPoint()-GetCornerPoint(false, false, false); - return diagonalvector.GetSquaredNorm(); - } - - //##Documentation - //## @brief Get the length of the diagonal of the bounding-box in mm - //## - double GetDiagonalLength() const - { - return sqrt(GetDiagonalLength2()); - } + virtual void InitializeGeometry(Self * newGeometry) const; //##Documentation //## @brief Get a VnlVector along bounding-box in the specified //## @a direction, length is spacing //## //## \sa GetAxisVector VnlVector GetMatrixColumn(unsigned int direction) const { return m_IndexToWorldTransform->GetMatrix().GetVnlMatrix().get_column(direction); } -#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 - - //##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 - { - return m_IndexToWorldTransform->GetMatrix().GetVnlMatrix().get_column(direction).magnitude()*GetExtent(direction); - } - - //##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! - virtual void SetExtentInMM(int direction, ScalarType extentInMM); - //##Documentation //## @brief Get the m_IndexToWorldTransform as a vtkLinearTransform vtkLinearTransform* GetVtkTransform() const { return (vtkLinearTransform*)m_VtkIndexToWorldTransform; } //##Documentation //## @brief Translate the origin by a vector //## virtual void Translate(const Vector3D& vector); //##Documentation //## @brief Set the transform to identity and origin to 0 //## virtual void SetIdentity(); //##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. virtual void Compose( const Geometry3D::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. virtual void Compose( const vtkMatrix4x4 * vtkmatrix, bool pre = 0 ); //##Documentation //## @brief Get the origin as VnlVector //## //## \sa GetOrigin VnlVector GetOriginVnl() const { return const_cast(this)->m_Origin.GetVnlVector(); } //##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 (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 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( pt_units[i] ); } } //##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 Geometry3D 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); } //##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 Is this an ImageGeometry? //## //## For more information, see SetImageGeometry itkGetConstMacro(ImageGeometry, bool); //##Documentation //## @brief Define that this Geometry3D 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 Geometry3D is referring to an Image. itkSetMacro(ImageGeometry, bool); itkBooleanMacro(ImageGeometry); //##Documentation //## @brief Test whether the point \a p (world coordinates in mm) is //## inside the bounding box bool IsInside(const mitk::Point3D& p) const { mitk::Point3D index; WorldToIndex(p, index); return IsIndexInside(index); } //##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 { 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] ); inside = m_BoundingBox->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 = m_BoundingBox->GetBounds(); if((discretIndex[0] == bounds[1]) || (discretIndex[1] == bounds[3]) || (discretIndex[2] == bounds[5])) inside = false; } } else inside = m_BoundingBox->IsInside(index); return inside; } //##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); } //##Documentation //## @brief Copy the VTK transform //## to the ITK transform (m_IndexToWorldTransform) //## \sa SetIndexToWorldTransform void TransferVtkToItkTransform(); //##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 { assert(m_ParametricBoundingBox.IsNotNull()); return m_ParametricBoundingBox->GetBounds(); } //##Documentation //## @brief Get the parametric extent //## //## See AbstractTransformGeometry for an example usage of this. mitk::ScalarType GetParametricExtent(int direction) const { 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]; } //##Documentation //## @brief Get the parametric extent in mm //## //## See AbstractTransformGeometry for an example usage of this. virtual mitk::ScalarType GetParametricExtentInMM(int direction) const { return GetExtentInMM(direction); } //##Documentation //## @brief Get the parametric transform //## //## See AbstractTransformGeometry for an example usage of this. virtual const Transform3D* GetParametricTransform() const { return m_IndexToWorldTransform; } //##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 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; //##Documentation //##@brief executes affine operations (translate, rotate, scale) virtual void ExecuteOperation(Operation* operation); - /** Get the extent of the bounding box */ - ScalarType GetExtent(unsigned int direction) const - { - assert(m_BoundingBox.IsNotNull()); - if (direction>=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]; - } protected: Geometry3D(); Geometry3D(const Geometry3D& other); static const std::string GetTransformAsString( TransformType* transformType ); virtual ~Geometry3D(); virtual void PrintSelf(std::ostream& os, itk::Indent indent) const; virtual void BackTransform(const mitk::Point3D& in, mitk::Point3D& out) const; //##Documentation //## @brief Deprecated virtual void BackTransform(const mitk::Point3D& at, const mitk::Vector3D& in, mitk::Vector3D& out) const; //Without redundant parameter Point3D virtual void BackTransform(const mitk::Vector3D& in, mitk::Vector3D& out) const; //##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); /** Resets sub-transforms that compose m_IndexToWorldTransform, by using * the current value of m_IndexToWorldTransform and setting the rotation * component to zero. */ virtual void ResetSubTransforms(); bool m_ImageGeometry; static const std::string INDEX_TO_OBJECT_TRANSFORM; static const std::string OBJECT_TO_NODE_TRANSFORM; static const std::string INDEX_TO_NODE_TRANSFORM; static const std::string INDEX_TO_WORLD_TRANSFORM; }; // // 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 * 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. */ MITK_CORE_EXPORT bool Equal(const mitk::Geometry3D* leftHandSide, const mitk::Geometry3D* rightHandSide, ScalarType eps, bool verbose); } // namespace mitk #endif /* GEOMETRY3D_H_HEADER_INCLUDED_C1EBD0AD */ diff --git a/Core/Code/DataManagement/mitkSlicedGeometry3D.cpp b/Core/Code/DataManagement/mitkSlicedGeometry3D.cpp index e63b6ea31a..4da37ac5b0 100644 --- a/Core/Code/DataManagement/mitkSlicedGeometry3D.cpp +++ b/Core/Code/DataManagement/mitkSlicedGeometry3D.cpp @@ -1,1055 +1,1035 @@ /*=================================================================== 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" const mitk::ScalarType PI = 3.14159265359; mitk::SlicedGeometry3D::SlicedGeometry3D() -: m_EvenlySpaced( true ), + : m_EvenlySpaced( true ), m_Slices( 0 ), m_ReferenceGeometry( NULL ), m_SliceNavigationController( NULL ) { - m_DirectionVector.Fill(0); + m_DirectionVector.Fill(0); this->InitializeSlicedGeometry( m_Slices ); } mitk::SlicedGeometry3D::SlicedGeometry3D(const SlicedGeometry3D& other) -: Superclass(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); + m_DirectionVector.Fill(0); SetSpacing( other.GetSpacing() ); SetDirectionVector( other.GetDirectionVector() ); if ( m_EvenlySpaced ) { Geometry2D::Pointer geometry = other.m_Geometry2Ds[0]->Clone(); Geometry2D* geometry2D = dynamic_cast(geometry.GetPointer()); assert(geometry2D!=NULL); SetGeometry2D(geometry2D, 0); } else { unsigned int s; for ( s = 0; s < other.m_Slices; ++s ) { if ( other.m_Geometry2Ds[s].IsNull() ) { assert(other.m_EvenlySpaced); m_Geometry2Ds[s] = NULL; } else { Geometry2D* geometry2D = other.m_Geometry2Ds[s]->Clone(); assert(geometry2D!=NULL); SetGeometry2D(geometry2D, s); } } } } mitk::SlicedGeometry3D::~SlicedGeometry3D() { } - mitk::Geometry2D * -mitk::SlicedGeometry3D::GetGeometry2D( int s ) const + mitk::SlicedGeometry3D::GetGeometry2D( int s ) const { mitk::Geometry2D::Pointer geometry2D = NULL; if ( this->IsValidSlice(s) ) { geometry2D = m_Geometry2Ds[s]; // If (a) m_EvenlySpaced==true, (b) we don't have a Geometry2D 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 = dynamic_cast< PlaneGeometry * > ( m_Geometry2Ds[0].GetPointer() ); if ( firstSlice != 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 * m_Spacing[2]; mitk::PlaneGeometry::Pointer requestedslice; requestedslice = static_cast< mitk::PlaneGeometry * >( firstSlice->Clone().GetPointer() ); requestedslice->SetOrigin( requestedslice->GetOrigin() + direction * s ); geometry2D = requestedslice; m_Geometry2Ds[s] = geometry2D; } } return geometry2D; } else { return NULL; } } const mitk::BoundingBox * -mitk::SlicedGeometry3D::GetBoundingBox() const + mitk::SlicedGeometry3D::GetBoundingBox() const { assert(m_BoundingBox.IsNotNull()); return m_BoundingBox.GetPointer(); } - bool -mitk::SlicedGeometry3D::SetGeometry2D( mitk::Geometry2D *geometry2D, int s ) + mitk::SlicedGeometry3D::SetGeometry2D( mitk::Geometry2D *geometry2D, int s ) { if ( this->IsValidSlice(s) ) { m_Geometry2Ds[s] = geometry2D; m_Geometry2Ds[s]->SetReferenceGeometry( m_ReferenceGeometry ); return true; } return false; } - void -mitk::SlicedGeometry3D::InitializeSlicedGeometry( unsigned int slices ) + mitk::SlicedGeometry3D::InitializeSlicedGeometry( unsigned int slices ) { Superclass::Initialize(); m_Slices = slices; Geometry2D::Pointer gnull = NULL; m_Geometry2Ds.assign( m_Slices, gnull ); Vector3D spacing; spacing.Fill( 1.0 ); this->SetSpacing( spacing ); m_DirectionVector.Fill( 0 ); } - void -mitk::SlicedGeometry3D::InitializeEvenlySpaced( + mitk::SlicedGeometry3D::InitializeEvenlySpaced( mitk::Geometry2D* 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::SlicedGeometry3D::InitializeEvenlySpaced( mitk::Geometry2D* 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 Geometry2D::Pointer gnull = NULL; m_Geometry2Ds.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); m_IndexToWorldTransform = const_cast< AffineTransform3D * >( geometry2D->GetIndexToWorldTransform() ); } else { directionVector *= -1.0; m_IndexToWorldTransform = AffineTransform3D::New(); m_IndexToWorldTransform->SetMatrix( geometry2D->GetIndexToWorldTransform()->GetMatrix() ); AffineTransform3D::OutputVectorType scaleVector; FillVector3D(scaleVector, 1.0, 1.0, -1.0); m_IndexToWorldTransform->Scale(scaleVector, true); m_IndexToWorldTransform->SetOffset( geometry2D->GetIndexToWorldTransform()->GetOffset() ); } mitk::Vector3D spacing; FillVector3D( spacing, geometry2D->GetExtentInMM(0) / bounds[1], geometry2D->GetExtentInMM(1) / bounds[3], zSpacing ); // Ensure that spacing differs from m_Spacing to make SetSpacing change the // matrix. m_Spacing[2] = zSpacing - 1; this->SetDirectionVector( directionVector ); this->SetBounds( bounds ); this->SetGeometry2D( geometry2D, 0 ); this->SetSpacing( spacing ); this->SetEvenlySpaced(); this->SetTimeBounds( geometry2D->GetTimeBounds() ); assert(m_IndexToWorldTransform.GetPointer() - != geometry2D->GetIndexToWorldTransform()); // (**) see above. + != geometry2D->GetIndexToWorldTransform()); // (**) see above. this->SetFrameOfReferenceID( geometry2D->GetFrameOfReferenceID() ); this->SetImageGeometry( geometry2D->GetImageGeometry() ); geometry2D->UnRegister(); } - void -mitk::SlicedGeometry3D::InitializePlanes( + mitk::SlicedGeometry3D::InitializePlanes( const mitk::Geometry3D *geometry3D, mitk::PlaneGeometry::PlaneOrientation planeorientation, bool top, bool frontside, bool rotated ) { m_ReferenceGeometry = const_cast< Geometry3D * >( 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"); + 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( 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 ) + 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 = dynamic_cast< PlaneGeometry * >( m_Geometry2Ds[0].GetPointer() ); // If plane stack is empty, exit if ( firstPlane == NULL ) { 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( 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_Geometry2Ds.assign( m_Slices, Geometry2D::Pointer( NULL ) ); if ( m_Slices > 0 ) { m_Geometry2Ds[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 + 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 ); + // 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 + 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 ) + mitk::SlicedGeometry3D::SetImageGeometry( const bool isAnImageGeometry ) { Superclass::SetImageGeometry( isAnImageGeometry ); mitk::Geometry3D* geometry; unsigned int s; for ( s = 0; s < m_Slices; ++s ) { geometry = m_Geometry2Ds[s]; if ( geometry!=NULL ) { geometry->SetImageGeometry( isAnImageGeometry ); } } } void -mitk::SlicedGeometry3D::ChangeImageGeometryConsideringOriginOffset( const bool isAnImageGeometry ) + mitk::SlicedGeometry3D::ChangeImageGeometryConsideringOriginOffset( const bool isAnImageGeometry ) { mitk::Geometry3D* geometry; unsigned int s; for ( s = 0; s < m_Slices; ++s ) { geometry = m_Geometry2Ds[s]; if ( geometry!=NULL ) { geometry->ChangeImageGeometryConsideringOriginOffset( isAnImageGeometry ); } } Superclass::ChangeImageGeometryConsideringOriginOffset( isAnImageGeometry ); } - bool -mitk::SlicedGeometry3D::IsValidSlice( int s ) const + mitk::SlicedGeometry3D::IsValidSlice( int s ) const { return ((s >= 0) && (s < (int)m_Slices)); } void -mitk::SlicedGeometry3D::SetReferenceGeometry( Geometry3D *referenceGeometry ) + mitk::SlicedGeometry3D::SetReferenceGeometry( Geometry3D *referenceGeometry ) { m_ReferenceGeometry = referenceGeometry; std::vector::iterator it; for ( it = m_Geometry2Ds.begin(); it != m_Geometry2Ds.end(); ++it ) { (*it)->SetReferenceGeometry( referenceGeometry ); } } void -mitk::SlicedGeometry3D::SetSpacing( const mitk::Vector3D &aSpacing ) + mitk::SlicedGeometry3D::SetSpacing( const mitk::Vector3D &aSpacing ) { bool hasEvenlySpacedPlaneGeometry = false; mitk::Point3D origin; mitk::Vector3D rightDV, bottomDV; BoundingBox::BoundsArrayType bounds; assert(aSpacing[0]>0 && aSpacing[1]>0 && aSpacing[2]>0); // In case of evenly-spaced data: re-initialize instances of Geometry2D, // since the spacing influences them if ((m_EvenlySpaced) && (m_Geometry2Ds.size() > 0)) { mitk::Geometry2D::ConstPointer firstGeometry = m_Geometry2Ds[0].GetPointer(); const PlaneGeometry *planeGeometry = dynamic_cast< const PlaneGeometry * >( firstGeometry.GetPointer() ); if (planeGeometry != NULL ) { this->WorldToIndex( planeGeometry->GetOrigin(), origin ); this->WorldToIndex( planeGeometry->GetAxisVector(0), rightDV ); this->WorldToIndex( planeGeometry->GetAxisVector(1), bottomDV ); bounds = planeGeometry->GetBounds(); hasEvenlySpacedPlaneGeometry = true; } } Superclass::SetSpacing(aSpacing); mitk::Geometry2D::Pointer firstGeometry; // In case of evenly-spaced data: re-initialize instances of Geometry2D, // 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 ); planeGeometry->InitializeStandardPlane( rightDV.GetVnlVector(), bottomDV.GetVnlVector(), &m_Spacing ); planeGeometry->SetOrigin(origin); planeGeometry->SetBounds(bounds); firstGeometry = planeGeometry; } else if ( (m_EvenlySpaced) && (m_Geometry2Ds.size() > 0) ) { firstGeometry = m_Geometry2Ds[0].GetPointer(); } //clear and reserve Geometry2D::Pointer gnull=NULL; m_Geometry2Ds.assign(m_Slices, gnull); if ( m_Slices > 0 ) { m_Geometry2Ds[0] = firstGeometry; } this->Modified(); } - void -mitk::SlicedGeometry3D -::SetSliceNavigationController( SliceNavigationController *snc ) + mitk::SlicedGeometry3D + ::SetSliceNavigationController( SliceNavigationController *snc ) { m_SliceNavigationController = snc; } - mitk::SliceNavigationController * -mitk::SlicedGeometry3D::GetSliceNavigationController() + mitk::SlicedGeometry3D::GetSliceNavigationController() { return m_SliceNavigationController; } void -mitk::SlicedGeometry3D::SetEvenlySpaced(bool on) + mitk::SlicedGeometry3D::SetEvenlySpaced(bool on) { if(m_EvenlySpaced!=on) { m_EvenlySpaced=on; this->Modified(); } } - void -mitk::SlicedGeometry3D -::SetDirectionVector( const mitk::Vector3D& directionVector ) + mitk::SlicedGeometry3D + ::SetDirectionVector( const mitk::Vector3D& directionVector ) { - Vector3D newDir = directionVector; - newDir.Normalize(); - if ( newDir != m_DirectionVector ) + Vector3D newDir = directionVector; + newDir.Normalize(); + if ( newDir != m_DirectionVector ) { - m_DirectionVector = newDir; + m_DirectionVector = newDir; this->Modified(); } } - void -mitk::SlicedGeometry3D::SetTimeBounds( const mitk::TimeBounds& timebounds ) + 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 + 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 + 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 << " GetGeometry2D(0): "; if ( this->GetGeometry2D(0) == NULL ) { os << "NULL" << std::endl; } else { this->GetGeometry2D(0)->Print(os, indent); } } void -mitk::SlicedGeometry3D::ExecuteOperation(Operation* operation) + 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 Geometry2D::Pointer geometry2D = m_Geometry2Ds[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(); } Geometry3D::ExecuteOperation( ¢eredRotation ); } else { // we also have to consider the case, that there is no reference geometry available. if ( m_Geometry2Ds.size() > 0 ) { - // Reach through to all slices in my container - for (std::vector::iterator iter = m_Geometry2Ds.begin(); - iter != m_Geometry2Ds.end(); - ++iter) - { - // Test for empty slices, which can happen if evenly spaced geometry - if ((*iter).IsNotNull()) - { - (*iter)->ExecuteOperation(operation); - } - } + // Reach through to all slices in my container + for (std::vector::iterator iter = m_Geometry2Ds.begin(); + iter != m_Geometry2Ds.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 ); Geometry3D::ExecuteOperation( rotOp); } - } } else { // Reach through to all slices for (std::vector::iterator iter = m_Geometry2Ds.begin(); - iter != m_Geometry2Ds.end(); - ++iter) + iter != m_Geometry2Ds.end(); + ++iter) { (*iter)->ExecuteOperation(operation); } } break; case OpORIENT: if ( m_EvenlySpaced ) { - // get operation data + // get operation data PlaneOperation *planeOp = dynamic_cast< PlaneOperation * >( operation ); // Get first slice Geometry2D::Pointer geometry2D = m_Geometry2Ds[0]; PlaneGeometry *planeGeometry = dynamic_cast< PlaneGeometry * >( geometry2D.GetPointer() ); // 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 || !planeOp ) { - break; + 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()); + // 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(); + // 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 ); + // 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 - ); + mitk::OpROTATE, + center, + rotationAxis, + rotationAngle + ); // Rotate first slice geometry2D->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(); - } + // 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) Geometry3D::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 = geometry2D->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); - geometry2D->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) - Geometry3D::ExecuteOperation( &op ); + mitk::Vector3D vecAxixNew = planeOp->GetAxisVec0(); + vecAxixNew.Normalize(); + mitk::Vector3D VecAxisCurr = geometry2D->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); + geometry2D->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) + Geometry3D::ExecuteOperation( &op ); } } else { // Reach through to all slices for (std::vector::iterator iter = m_Geometry2Ds.begin(); - iter != m_Geometry2Ds.end(); - ++iter) + iter != m_Geometry2Ds.end(); + ++iter) { (*iter)->ExecuteOperation(operation); } } break; case OpRESTOREPLANEPOSITION: if ( m_EvenlySpaced ) { // Save first slice Geometry2D::Pointer geometry2D = m_Geometry2Ds[0]; PlaneGeometry* planeGeometry = dynamic_cast< PlaneGeometry * >( geometry2D.GetPointer() ); 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 && restorePlaneOp ) { // Clear all generated geometries and then rotate only the first slice. // The other slices will be re-generated on demand // Rotate first slice geometry2D->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_Geometry2Ds.assign( m_Slices, Geometry2D::Pointer( NULL ) ); + m_Geometry2Ds.assign( m_Slices, Geometry2D::Pointer( NULL ) ); - if ( m_Slices > 0 ) - { - m_Geometry2Ds[0] = geometry2D; - } + if ( m_Slices > 0 ) + { + m_Geometry2Ds[0] = geometry2D; + } m_SliceNavigationController->GetSlice()->SetSteps( m_Slices ); this->Modified(); //End Reinitialization if ( m_SliceNavigationController ) { m_SliceNavigationController->GetSlice()->SetPos( restorePlaneOp->GetPos() ); m_SliceNavigationController->AdjustSliceStepperRange(); } Geometry3D::ExecuteOperation(restorePlaneOp); } } else { // Reach through to all slices for (std::vector::iterator iter = m_Geometry2Ds.begin(); - iter != m_Geometry2Ds.end(); - ++iter) + iter != m_Geometry2Ds.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 Geometry2D::Pointer geometry2D = m_Geometry2Ds[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() ); Geometry3D::ExecuteOperation( applyMatrixOp ); break; } this->Modified(); } - diff --git a/Core/Code/Testing/mitkBaseGeometryTest.cpp b/Core/Code/Testing/mitkBaseGeometryTest.cpp index c9c67b5b57..0abd724ebc 100644 --- a/Core/Code/Testing/mitkBaseGeometryTest.cpp +++ b/Core/Code/Testing/mitkBaseGeometryTest.cpp @@ -1,236 +1,278 @@ /*=================================================================== 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 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); itkGetConstMacro(IndexToWorldTransformLastModified, unsigned long); itkGetConstMacro(VtkMatrix, vtkMatrix4x4*); void DummyTestClass::ExecuteOperation(mitk::Operation* operation){}; }; class mitkBaseGeometryTestSuite : public mitk::TestFixture { // List of Tests CPPUNIT_TEST_SUITE(mitkBaseGeometryTestSuite); MITK_TEST(TestConstructors); MITK_TEST(TestSetOrigin); MITK_TEST(TestSetBounds); MITK_TEST(TestSetFloatBounds); MITK_TEST(TestSetFloatBoundsDouble); + MITK_TEST(TestSetFrameOfReferenceID); + MITK_TEST(TestSetIndexToWorldTransform); + MITK_TEST(TestSetSpacing); + MITK_TEST(TestTransferItkToVtkTransform); 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; mitk::AffineTransform3D::Pointer anotherTransform; + mitk::AffineTransform3D::MatrixType anotherMatrix; 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(); anotherTransform = mitk::AffineTransform3D::New(); - mitk::AffineTransform3D::MatrixType differentMatrix; - differentMatrix.SetIdentity(); - differentMatrix(1,1) = 2; - anotherTransform->SetMatrix( differentMatrix ); + + aMatrix.SetIdentity(); + + anotherMatrix.SetIdentity(); + anotherMatrix(1,1) = 2; + anotherTransform->SetMatrix( anotherMatrix ); //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(); mitk::FillVector3D(anotherPoint, 2,3,4); mitk::FillVector3D(anotherSpacing, 5,6,7); } // Test functions void TestSetOrigin() { - DummyTestClass::Pointer dummy; - dummy = new DummyTestClass(); + DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetOrigin(anotherPoint); CPPUNIT_ASSERT(anotherPoint==dummy->GetOrigin()); //undo changes, new and changed object need to be the same! dummy->SetOrigin(aPoint); - DummyTestClass::Pointer newDummy; - newDummy = new DummyTestClass(); + DummyTestClass::Pointer newDummy = DummyTestClass::New(); CPPUNIT_ASSERT(mitk::Equal(dummy,newDummy,mitk::eps,true)); } void TestSetFloatBounds(){ float bounds[6] = {0,11,0,12,0,13}; - DummyTestClass::Pointer dummy; - dummy = new DummyTestClass(); + DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetFloatBounds(bounds); CPPUNIT_ASSERT(mitk::Equal( dummy->GetBoundingBox(), anotherBoundingBox, mitk::eps, true)); //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; - newDummy = new DummyTestClass(); + DummyTestClass::Pointer newDummy = DummyTestClass::New(); CPPUNIT_ASSERT(mitk::Equal(dummy,newDummy,mitk::eps,true)); } void TestSetBounds(){ - DummyTestClass::Pointer dummy; - dummy = new DummyTestClass(); + DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetBounds(anotherBoundingBox->GetBounds()); CPPUNIT_ASSERT(mitk::Equal( dummy->GetBoundingBox(), anotherBoundingBox, mitk::eps, true)); //undo changes, new and changed object need to be the same! dummy->SetBounds(aBoundingBox->GetBounds()); - DummyTestClass::Pointer newDummy; - newDummy = new DummyTestClass(); + DummyTestClass::Pointer newDummy = DummyTestClass::New(); CPPUNIT_ASSERT(mitk::Equal(dummy,newDummy,mitk::eps,true)); } void TestSetFloatBoundsDouble(){ double bounds[6] = {0,11,0,12,0,13}; - DummyTestClass::Pointer dummy; - dummy = new DummyTestClass(); + DummyTestClass::Pointer dummy = DummyTestClass::New(); dummy->SetFloatBounds(bounds); CPPUNIT_ASSERT(mitk::Equal( dummy->GetBoundingBox(), anotherBoundingBox, mitk::eps, true)); //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; - newDummy = new DummyTestClass(); + DummyTestClass::Pointer newDummy = DummyTestClass::New(); + CPPUNIT_ASSERT(mitk::Equal(dummy,newDummy,mitk::eps,true)); + } + + 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(); CPPUNIT_ASSERT(mitk::Equal(dummy,newDummy,mitk::eps,true)); } + void TestSetIndexToWorldTransform() + { + DummyTestClass::Pointer dummy = DummyTestClass::New(); + dummy->SetIndexToWorldTransform(anotherTransform); + CPPUNIT_ASSERT(mitk::Equal(anotherTransform,dummy->GetIndexToWorldTransform(),mitk::eps,true)); + + //undo changes, new and changed object need to be the same! + dummy->SetIndexToWorldTransform(aTransform); + DummyTestClass::Pointer newDummy = DummyTestClass::New(); + CPPUNIT_ASSERT(mitk::Equal(dummy,newDummy,mitk::eps,true)); + } + + void TestSetSpacing() + { + DummyTestClass::Pointer dummy = DummyTestClass::New(); + dummy->SetSpacing(anotherSpacing); + CPPUNIT_ASSERT(anotherSpacing==dummy->GetSpacing()); + + //undo changes, new and changed object need to be the same! + dummy->SetSpacing(aSpacing); + DummyTestClass::Pointer newDummy = DummyTestClass::New(); + CPPUNIT_ASSERT(mitk::Equal(dummy,newDummy,mitk::eps,true)); + } + + 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; - dummy1 = new DummyTestClass(); + DummyTestClass::Pointer dummy1 = DummyTestClass::New(); bool test = dummy1->IsValid(); CPPUNIT_ASSERT(test == true); CPPUNIT_ASSERT(dummy1->GetFrameOfReferenceID() == 0); CPPUNIT_ASSERT(dummy1->GetIndexToWorldTransformLastModified() == 0); const float *dummy1FloatSpacing = dummy1->GetFloatSpacing(); CPPUNIT_ASSERT(dummy1FloatSpacing[0]==aFloatSpacing[0]); CPPUNIT_ASSERT(dummy1FloatSpacing[1]==aFloatSpacing[1]); CPPUNIT_ASSERT(dummy1FloatSpacing[2]==aFloatSpacing[2]); CPPUNIT_ASSERT(dummy1->GetSpacing() == aSpacing); CPPUNIT_ASSERT(dummy1->GetOrigin()==aPoint); CPPUNIT_ASSERT(mitk::Equal( dummy1->GetIndexToWorldTransform(), aTransform, mitk::eps, true)); CPPUNIT_ASSERT(mitk::Equal( dummy1->GetBoundingBox(), aBoundingBox, mitk::eps, true)); - DummyTestClass::Pointer dummy2; - dummy2 = new DummyTestClass(); + 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; dummy3 = new DummyTestClass(*dummy2); CPPUNIT_ASSERT(mitk::Equal(dummy3,dummy2,mitk::eps,true)); } }; MITK_TEST_SUITE_REGISTRATION(mitkBaseGeometry)