void mitk::NavigationDataLandmarkTransformFilter::GenerateData()
{
this->CreateOutputsForAllInputs(); // make sure that we have the same number of outputs as inputs
TransformInitializerType::LandmarkPointType lPointIn, lPointOut;
/* update outputs with tracking data from tools */
for (unsigned int i = 0; i < this->GetNumberOfOutputs() ; ++i)
{
mitk::NavigationData* output = this->GetOutput(i);
assert(output);
const mitk::NavigationData* input = this->GetInput(i);
assert(input);
if (input->IsDataValid() == false)
{
output->SetDataValid(false);
continue;
}
output->Graft(input); // First, copy all information from input to output
if (this->IsInitialized() == false) // as long as there is no valid transformation matrix, only graft the outputs
continue;
mitk::NavigationData::PositionType tempCoordinate;
tempCoordinate = input->GetPosition();
lPointIn[0] = tempCoordinate[0]; // convert navigation data position to transform point
lPointIn[1] = tempCoordinate[1];
lPointIn[2] = tempCoordinate[2];
/* transform position */
lPointOut = m_LandmarkTransform->TransformPoint(lPointIn); // transform position
tempCoordinate[0] = lPointOut[0]; // convert back into navigation data position
tempCoordinate[1] = lPointOut[1];
tempCoordinate[2] = lPointOut[2];
output->SetPosition(tempCoordinate); // update output navigation data with new position
/* transform orientation */
NavigationData::OrientationType quatIn = input->GetOrientation();
vnl_quaternion<double> const vnlQuatIn(quatIn.x(), quatIn.y(), quatIn.z(), quatIn.r()); // convert orientation into vnl quaternion
m_QuatTransform->SetRotation(vnlQuatIn); // convert orientation into transform
m_QuatLandmarkTransform->SetMatrix(m_LandmarkTransform->GetMatrix());
m_QuatLandmarkTransform->Compose(m_QuatTransform, true); // compose navigation data transform and landmark transform
vnl_quaternion<double> vnlQuatOut = m_QuatLandmarkTransform->GetRotation(); // convert composed transform back into a quaternion
NavigationData::OrientationType quatOut(vnlQuatOut[0], vnlQuatOut[1], vnlQuatOut[2], vnlQuatOut[3]); // convert back into navigation data orientation
output->SetOrientation(quatOut); // update output navigation data with new orientation
output->SetDataValid(true); // operation was successful, therefore data of output is valid.
}
}
void mitk::NavigationDataTransformFilter::GenerateData()
{
// only update data if m_Transform was set
if(m_Transform.IsNull())
{
itkExceptionMacro("Invalid parameter: Transform was not set! Use SetRigid3DTransform() before updating the filter.");
return;
}
else
{
this->CreateOutputsForAllInputs(); // make sure that we have the same number of outputs as inputs
/* update outputs with tracking data from tools */
for (unsigned int i = 0; i < this->GetNumberOfOutputs() ; ++i)
{
mitk::NavigationData* output = this->GetOutput(i);
assert(output);
const mitk::NavigationData* input = this->GetInput(i);
assert(input);
if (input->IsDataValid() == false)
{
output->SetDataValid(false);
continue;
}
mitk::NavigationData::PositionType tempCoordinateIn, tempCoordinateOut;
tempCoordinateIn = input->GetPosition();
itk::Point<float,3> itkPointIn, itkPointOut;
itkPointIn[0] = tempCoordinateIn[0];
itkPointIn[1] = tempCoordinateIn[1];
itkPointIn[2] = tempCoordinateIn[2];
//do the transform
itkPointOut = m_Transform->TransformPoint( itkPointIn );
tempCoordinateOut[0] = itkPointOut[0];
tempCoordinateOut[1] = itkPointOut[1];
tempCoordinateOut[2] = itkPointOut[2];
output->Graft(input); // First, copy all information from input to output
output->SetPosition(tempCoordinateOut);// Then change the member(s): add new position of navigation data after tranformation
output->SetDataValid(true); // operation was successful, therefore data of output is valid.
//---transform orientation
NavigationData::OrientationType quatIn = input->GetOrientation();
vnl_quaternion<double> const vnlQuatIn(quatIn.x(), quatIn.y(), quatIn.z(), quatIn.r());
itk::Matrix<float,3,3> rotMatrix = m_Transform->GetMatrix();
itk::Matrix<double,3,3> rotMatrixD;
mitk::TransferMatrix(rotMatrix,rotMatrixD);
m_QuatOrgRigidTransform->SetRotationMatrix(rotMatrixD);
m_QuatTmpTransform->SetRotation(vnlQuatIn);
m_QuatTmpTransform->Compose(m_QuatOrgRigidTransform,false);
vnl_quaternion<double> vnlQuatOut = m_QuatTmpTransform->GetRotation();
NavigationData::OrientationType quatOut(vnlQuatOut[0], vnlQuatOut[1], vnlQuatOut[2], vnlQuatOut[3]);
output->SetOrientation(quatOut);
}
}
}
void mitk::NavigationDataReferenceTransformFilter::GenerateData()
{
LandmarkPointContainer newSourcePoints; // for the quaternion transformed reference landmarks
if(m_OneSourceRegistration) // check if less than 3 reference inputs
{
NavigationData::ConstPointer nd = this->GetInput(m_ReferenceInputIndexes.at(0));
if (nd->IsDataValid() == false)
{
for (unsigned int i = 0; i < this->GetNumberOfOutputs() ; ++i)
{
mitk::NavigationData::Pointer output = this->GetOutput(i);
assert(output);
output->SetDataValid(false);
}
return;
}
QuaternionTransformType::Pointer referenceTransform = QuaternionTransformType::New();
QuaternionTransformType::VnlQuaternionType doubleOrientation(nd->GetOrientation().x(), nd->GetOrientation().y(), nd->GetOrientation().z(), nd->GetOrientation().r()); // convert to double quaternion as workaround for ITK 3.10 bug
referenceTransform->SetRotation(doubleOrientation);
referenceTransform->SetOffset(nd->GetPosition().GetVectorFromOrigin());
referenceTransform->Modified();
for (NavigationDataReferenceTransformFilter::LandmarkPointContainer::const_iterator it = m_ReferencePoints.begin(); it != m_ReferencePoints.end(); ++it)
{
TransformInitializerType::LandmarkPointType rLPoint; // reference landmark point
rLPoint = referenceTransform->TransformPoint(*it);
newSourcePoints.push_back(rLPoint);
}
this->UpdateLandmarkTransform(newSourcePoints, m_TargetPoints);
m_SourcePoints = newSourcePoints;
}
if(this->IsInitialized() && !m_OneSourceRegistration && m_ReferenceRegistration)
this->GenerateSourceLandmarks(); // generates landmarks from the moving points
this->CreateOutputsForAllInputs();
TransformInitializerType::LandmarkPointType lPointIn, lPointOut;
for(unsigned int i = 0; i < this->GetNumberOfOutputs(); i++)
{
mitk::NavigationData::Pointer output = this->GetOutput(i);
assert(output);
mitk::NavigationData::ConstPointer input = this->GetInput(i);
assert(input);
if(input->IsDataValid() == false)
{
output->SetDataValid(false);
continue;
}
output->Graft(input); // First, copy all information from input to output
if(this->IsInitialized() == false)
continue;
mitk::NavigationData::PositionType tempCoordinate;
tempCoordinate = input->GetPosition();
lPointIn[0] = tempCoordinate[0];
lPointIn[1] = tempCoordinate[1];
lPointIn[2] = tempCoordinate[2];
/* transform position */
lPointOut = m_LandmarkTransform->TransformPoint(lPointIn);
tempCoordinate[0] = lPointOut[0];
tempCoordinate[1] = lPointOut[1];
tempCoordinate[2] = lPointOut[2];
output->SetPosition(tempCoordinate); // update output navigation data with new position
/* transform orientation */
NavigationData::OrientationType quatIn = input->GetOrientation();
vnl_quaternion<double> const vnlQuatIn(quatIn.x(), quatIn.y(), quatIn.z(), quatIn.r());
m_QuaternionTransform->SetRotation(vnlQuatIn);
m_QuaternionLandmarkTransform->SetMatrix(m_LandmarkTransform->GetRotationMatrix());
m_QuaternionLandmarkTransform->Compose(m_QuaternionTransform, true);
vnl_quaternion<double> vnlQuatOut = m_QuaternionLandmarkTransform->GetRotation();
NavigationData::OrientationType quatOut( vnlQuatOut[0], vnlQuatOut[1], vnlQuatOut[2], vnlQuatOut[3]);
output->SetOrientation(quatOut);
output->SetDataValid(true);
}
}
