mitk::AffineTransform3D::Pointer mitk::NeedleProjectionFilter::NavigationDataToTransform(const mitk::NavigationData * nd)
{
mitk::AffineTransform3D::Pointer affineTransform = mitk::AffineTransform3D::New();
affineTransform->SetIdentity();
//calculate the transform from the quaternions
static itk::QuaternionRigidTransform<double>::Pointer quatTransform = itk::QuaternionRigidTransform<double>::New();
mitk::NavigationData::OrientationType orientation = nd->GetOrientation();
// convert mitk::ScalarType quaternion to double quaternion because of itk bug
vnl_quaternion<double> doubleQuaternion(orientation.x(), orientation.y(), orientation.z(), orientation.r());
quatTransform->SetIdentity();
quatTransform->SetRotation(doubleQuaternion);
quatTransform->Modified();
/* because of an itk bug, the transform can not be calculated with float data type.
To use it in the mitk geometry classes, it has to be transfered to mitk::ScalarType which is float */
static AffineTransform3D::MatrixType m;
mitk::TransferMatrix(quatTransform->GetMatrix(), m);
affineTransform->SetMatrix(m);
/*set the offset by convert from itkPoint to itkVector and setting offset of transform*/
mitk::Vector3D pos;
pos.SetVnlVector(nd->GetPosition().GetVnlVector());
affineTransform->SetOffset(pos);
affineTransform->Modified();
return affineTransform;
}
void mitk::NavigationDataObjectVisualizationFilter::GenerateData()
{
/*get each input, lookup the associated BaseData and transfer the data*/
DataObjectPointerArray inputs = this->GetInputs(); //get all inputs
for (unsigned int index=0; index < inputs.size(); index++)
{
//get the needed variables
const mitk::NavigationData* nd = this->GetInput(index);
assert(nd);
mitk::NavigationData* output = this->GetOutput(index);
assert(output);
//check if the data is valid
if (!nd->IsDataValid())
{
output->SetDataValid(false);
continue;
}
output->Graft(nd); // copy all information from input to output
const mitk::BaseData* data = this->GetRepresentationObject(index);
if (data == NULL)
{
MITK_WARN << "No BaseData associated with input " << index;
continue;
}
//get the transform from data
mitk::AffineTransform3D::Pointer affineTransform = data->GetGeometry()->GetIndexToWorldTransform();
if (affineTransform.IsNull())
{
MITK_WARN << "AffineTransform IndexToWorldTransform not initialized!";
continue;
}
//check for offset
mitk::AffineTransform3D::Pointer offset = this->GetOffset(index);
//store the current scaling to set it after transformation
mitk::Vector3D spacing = data->GetGeometry()->GetSpacing();
//clear spacing of data to be able to set it again afterwards
ScalarType scale[] = {1.0, 1.0, 1.0};
data->GetGeometry()->SetSpacing(scale);
/*now bring quaternion to affineTransform by using vnl_Quaternion*/
affineTransform->SetIdentity();
if (this->GetTransformOrientation(index) == true)
{
mitk::NavigationData::OrientationType orientation = nd->GetOrientation();
/* because of an itk bug, the transform can not be calculated with float data type.
To use it in the mitk geometry classes, it has to be transfered to mitk::ScalarType which is float */
static AffineTransform3D::MatrixType m;
//convert quaternion to rotation matrix depending on the rotation mode
if(m_RotationMode == RotationStandard)
{
//calculate the transform from the quaternions
static itk::QuaternionRigidTransform<double>::Pointer quatTransform = itk::QuaternionRigidTransform<double>::New();
// convert mitk::ScalarType quaternion to double quaternion because of itk bug
vnl_quaternion<double> doubleQuaternion(orientation.x(), orientation.y(), orientation.z(), orientation.r());
quatTransform->SetIdentity();
quatTransform->SetRotation(doubleQuaternion);
quatTransform->Modified();
mitk::TransferMatrix(quatTransform->GetMatrix(), m);
}
else if(m_RotationMode == RotationTransposed)
{
vnl_matrix_fixed<mitk::ScalarType,3,3> rot = orientation.rotation_matrix_transpose();
for(int i=0; i<3; i++) for (int j=0; j<3; j++) m[i][j] = rot[i][j];
}
affineTransform->SetMatrix(m);
}
if (this->GetTransformPosition(index) == true)
{
///*set the offset by convert from itkPoint to itkVector and setting offset of transform*/
mitk::Vector3D pos;
pos.SetVnlVector(nd->GetPosition().GetVnlVector());
affineTransform->SetOffset(pos);
}
affineTransform->Modified();
//set the transform to data
if(offset.IsNotNull()) //first use offset if there is one.
{
mitk::AffineTransform3D::Pointer overallTransform = mitk::AffineTransform3D::New();
overallTransform->SetIdentity();
overallTransform->Compose(offset);
overallTransform->Compose(affineTransform);
data->GetGeometry()->SetIndexToWorldTransform(overallTransform);
}
else
{
data->GetGeometry()->SetIndexToWorldTransform(affineTransform);
}
//set the original spacing to keep scaling of the geometrical object
data->GetGeometry()->SetSpacing(spacing);
data->GetGeometry()->Modified();
data->Modified();
output->SetDataValid(true); // operation was successful, therefore data of output is valid.
}
//m_Measurement->AddMeasurement(10);
}
