void
PlaneGeometry::InitializeStandardPlane(
mitk::ScalarType width, ScalarType height,
const VnlVector &rightVector, const VnlVector &downVector,
const Vector3D *spacing )
{
assert(width > 0);
assert(height > 0);
VnlVector rightDV = rightVector; rightDV.normalize();
VnlVector downDV = downVector; downDV.normalize();
VnlVector normal = vnl_cross_3d(rightVector, downVector);
normal.normalize();
if(spacing!=NULL)
{
rightDV *= (*spacing)[0];
downDV *= (*spacing)[1];
normal *= (*spacing)[2];
}
AffineTransform3D::Pointer transform = AffineTransform3D::New();
Matrix3D matrix;
matrix.GetVnlMatrix().set_column(0, rightDV);
matrix.GetVnlMatrix().set_column(1, downDV);
matrix.GetVnlMatrix().set_column(2, normal);
transform->SetMatrix(matrix);
transform->SetOffset(m_IndexToWorldTransform->GetOffset());
ScalarType bounds[6] = { 0, width, 0, height, 0, 1 };
this->SetBounds( bounds );
this->SetIndexToWorldTransform( transform );
}
void PlaneGeometry::EnsurePerpendicularNormal( mitk::AffineTransform3D *transform )
{
/** \brief ensure column(2) of indexToWorldTransform-matrix to be perpendicular to plane, keep length and handedness. */
VnlVector normal = vnl_cross_3d( transform->GetMatrix().GetVnlMatrix().get_column(0),
transform->GetMatrix().GetVnlMatrix().get_column(1) );
normal.normalize(); // Now normal is a righthand normal unit vector, perpendicular to the plane.
ScalarType len = transform->GetMatrix().GetVnlMatrix().get_column(2).two_norm();
if (len==0) { len = 1; }
normal *= len;
// Get the existing normal vector zed:
vnl_vector_fixed<double, 3> zed = transform->GetMatrix().GetVnlMatrix().get_column(2);
/** If det(matrix)<0, multiply normal vector by (-1) to keep geometry lefthanded. */
if( vnl_determinant( transform->GetMatrix().GetVnlMatrix()) < 0 )
{
MITK_DEBUG << "EnsurePerpendicularNormal(): Lefthanded geometry preserved, rh-normal: [ " << normal << " ],";
normal *= (-1.0);
MITK_DEBUG << "lh-normal: [ " << normal << " ], original vector zed is: [ " << zed << " ]";
}
// Now lets compare and only replace if necessary and only then warn the user:
// float epsilon is precise enough here, but we need to respect numerical condition:
// Higham, N., 2002, Accuracy and Stability of Numerical Algorithms,
// SIAM, page 37, 2nd edition:
double feps = std::numeric_limits<float>::epsilon();
double zedsMagnitude = zed.two_norm();
feps = feps * zedsMagnitude * 2;
/** Check if normal (3. column) was perpendicular: If not, replace with calculated normal vector: */
if( normal != zed )
{
vnl_vector_fixed<double, 3> parallel;
for ( unsigned int i = 0; i<3 ; ++i )
{
parallel[i] = normal[i] / zed[i]; // Remember linear algebra: checking for parallelity.
}
// Checking if really not paralell i.e. non-colinear vectors by comparing these floating point numbers:
if( (parallel[0]+feps < parallel[1] || feps+parallel[1] < parallel[0])
&& (parallel[0]+feps < parallel[2] || feps+parallel[2] < parallel[0]) )
{
MITK_WARN << "EnsurePerpendicularNormal(): Plane geometry was _/askew/_, so here it gets rectified by substituting"
<< " the 3rd column of the indexToWorldMatrix with an appropriate normal vector: [ " << normal
<< " ], original vector zed was: [ " << zed << " ].";
Matrix3D matrix = transform->GetMatrix();
matrix.GetVnlMatrix().set_column( 2, normal );
transform->SetMatrix( matrix );
}
}
else
{
// Nothing to do, 3rd column of indexToWorldTransformMatrix already was perfectly perpendicular.
}
}
void
PlaneGeometry::SetMatrixByVectors( const VnlVector &rightVector,
const VnlVector &downVector, ScalarType thickness )
{
VnlVector normal = vnl_cross_3d(rightVector, downVector);
normal.normalize();
normal *= thickness;
AffineTransform3D::Pointer transform = AffineTransform3D::New();
Matrix3D matrix;
matrix.GetVnlMatrix().set_column(0, rightVector);
matrix.GetVnlMatrix().set_column(1, downVector);
matrix.GetVnlMatrix().set_column(2, normal);
transform->SetMatrix(matrix);
transform->SetOffset(m_IndexToWorldTransform->GetOffset());
SetIndexToWorldTransform(transform);
}
void
PlaneGeometry::SetMatrixByVectors( const VnlVector &rightVector,
const VnlVector &downVector, ScalarType thickness /* = 1.0 */ )
{
VnlVector normal = vnl_cross_3d(rightVector, downVector);
normal.normalize();
normal *= thickness;
// Crossproduct vnl_cross_3d is always righthanded, but that is okay here
// because in this method we create a new IndexToWorldTransform and
// a negative thickness could still make it lefthanded.
AffineTransform3D::Pointer transform = AffineTransform3D::New();
Matrix3D matrix;
matrix.GetVnlMatrix().set_column(0, rightVector);
matrix.GetVnlMatrix().set_column(1, downVector);
matrix.GetVnlMatrix().set_column(2, normal);
transform->SetMatrix(matrix);
transform->SetOffset(this->GetIndexToWorldTransform()->GetOffset());
SetIndexToWorldTransform(transform);
}
unsigned int mitk::PlanePositionManagerService::AddNewPlanePosition ( const Geometry2D* plane, unsigned int sliceIndex )
{
for (unsigned int i = 0; i < m_PositionList.size(); ++i)
{
if (m_PositionList[i] != 0)
{
bool isSameMatrix(true);
bool isSameOffset(true);
isSameOffset = mitk::Equal(m_PositionList[i]->GetTransform()->GetOffset(), plane->GetIndexToWorldTransform()->GetOffset());
if(!isSameOffset || sliceIndex != m_PositionList[i]->GetPos())
continue;
isSameMatrix = mitk::MatrixEqualElementWise(m_PositionList[i]->GetTransform()->GetMatrix(), plane->GetIndexToWorldTransform()->GetMatrix());
if(isSameMatrix)
return i;
}
}
AffineTransform3D::Pointer transform = AffineTransform3D::New();
Matrix3D matrix;
matrix.GetVnlMatrix().set_column(0, plane->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(0));
matrix.GetVnlMatrix().set_column(1, plane->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(1));
matrix.GetVnlMatrix().set_column(2, plane->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(2));
transform->SetMatrix(matrix);
transform->SetOffset(plane->GetIndexToWorldTransform()->GetOffset());
mitk::Vector3D direction;
direction[0] = plane->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(2)[0];
direction[1] = plane->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(2)[1];
direction[2] = plane->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(2)[2];
direction.Normalize();
mitk::RestorePlanePositionOperation* newOp = new mitk::RestorePlanePositionOperation (OpRESTOREPLANEPOSITION, plane->GetExtent(0),
plane->GetExtent(1), plane->GetSpacing(), sliceIndex, direction, transform);
m_PositionList.push_back( newOp );
return GetNumberOfPlanePositions()-1;
}
void
PlaneGeometry::InitializeStandardPlane( mitk::ScalarType width, ScalarType height,
const VnlVector &rightVector, const VnlVector &downVector,
const Vector3D *spacing )
{
assert(width > 0);
assert(height > 0);
VnlVector rightDV = rightVector; rightDV.normalize();
VnlVector downDV = downVector; downDV.normalize();
VnlVector normal = vnl_cross_3d(rightVector, downVector);
normal.normalize();
// Crossproduct vnl_cross_3d is always righthanded, but that is okay here
// because in this method we create a new IndexToWorldTransform and
// spacing with 1 or 3 negative components could still make it lefthanded.
if(spacing!=nullptr)
{
rightDV *= (*spacing)[0];
downDV *= (*spacing)[1];
normal *= (*spacing)[2];
}
AffineTransform3D::Pointer transform = AffineTransform3D::New();
Matrix3D matrix;
matrix.GetVnlMatrix().set_column(0, rightDV);
matrix.GetVnlMatrix().set_column(1, downDV);
matrix.GetVnlMatrix().set_column(2, normal);
transform->SetMatrix(matrix);
transform->SetOffset(this->GetIndexToWorldTransform()->GetOffset());
ScalarType bounds[6] = { 0, width, 0, height, 0, 1 };
this->SetBounds( bounds );
this->SetIndexToWorldTransform( transform );
}
void
PlaneGeometry::EnsurePerpendicularNormal(mitk::AffineTransform3D *transform)
{
//ensure row(2) of transform to be perpendicular to plane, keep length.
VnlVector normal = vnl_cross_3d(
transform->GetMatrix().GetVnlMatrix().get_column(0),
transform->GetMatrix().GetVnlMatrix().get_column(1) );
normal.normalize();
ScalarType len = transform->GetMatrix()
.GetVnlMatrix().get_column(2).two_norm();
if (len==0) len = 1;
normal*=len;
Matrix3D matrix = transform->GetMatrix();
matrix.GetVnlMatrix().set_column(2, normal);
transform->SetMatrix(matrix);
}
void
PlaneGeometry::ExecuteOperation( Operation *operation )
{
vtkTransform *transform = vtkTransform::New();
transform->SetMatrix( m_VtkMatrix );
switch ( operation->GetOperationType() )
{
case OpORIENT:
{
mitk::PlaneOperation *planeOp = dynamic_cast< mitk::PlaneOperation * >( operation );
if ( planeOp == NULL )
{
return;
}
Point3D center = planeOp->GetPoint();
Vector3D orientationVector = planeOp->GetNormal();
Vector3D defaultVector;
FillVector3D( defaultVector, 0.0, 0.0, 1.0 );
Vector3D rotationAxis = itk::CrossProduct( orientationVector, defaultVector );
//vtkFloatingPointType rotationAngle = acos( orientationVector[2] / orientationVector.GetNorm() );
vtkFloatingPointType rotationAngle = atan2( (double) rotationAxis.GetNorm(), (double) (orientationVector * defaultVector) );
rotationAngle *= 180.0 / vnl_math::pi;
transform->PostMultiply();
transform->Identity();
transform->Translate( center[0], center[1], center[2] );
transform->RotateWXYZ( rotationAngle, rotationAxis[0], rotationAxis[1], rotationAxis[2] );
transform->Translate( -center[0], -center[1], -center[2] );
break;
}
case OpRESTOREPLANEPOSITION:
{
RestorePlanePositionOperation *op = dynamic_cast< mitk::RestorePlanePositionOperation* >(operation);
if(op == NULL)
{
return;
}
AffineTransform3D::Pointer transform2 = AffineTransform3D::New();
Matrix3D matrix;
matrix.GetVnlMatrix().set_column(0, op->GetTransform()->GetMatrix().GetVnlMatrix().get_column(0));
matrix.GetVnlMatrix().set_column(1, op->GetTransform()->GetMatrix().GetVnlMatrix().get_column(1));
matrix.GetVnlMatrix().set_column(2, op->GetTransform()->GetMatrix().GetVnlMatrix().get_column(2));
transform2->SetMatrix(matrix);
Vector3D offset = op->GetTransform()->GetOffset();
transform2->SetOffset(offset);
this->SetIndexToWorldTransform(transform2);
ScalarType bounds[6] = {0, op->GetWidth(), 0, op->GetHeight(), 0 ,1 };
this->SetBounds(bounds);
TransferItkToVtkTransform();
this->Modified();
transform->Delete();
return;
}
default:
Superclass::ExecuteOperation( operation );
transform->Delete();
return;
}
m_VtkMatrix->DeepCopy(transform->GetMatrix());
this->TransferVtkToItkTransform();
this->Modified();
transform->Delete();
}