void mitk::PointSetToCurvedGeometryFilter::GenerateOutputInformation()
{
mitk::PointSet::ConstPointer input = this->GetInput();
mitk::Geometry2DData::Pointer output = dynamic_cast<mitk::Geometry2DData*> ( this->GetOutput() );
if ( input.IsNull() )
itkGenericExceptionMacro ( "Input point set is NULL!" );
if ( input->GetTimeGeometry()->CountTimeSteps() != 1 )
itkWarningMacro ( "More than one time step is not yet supported!" );
if ( output.IsNull() )
itkGenericExceptionMacro ( "Output is NULL!" );
if ( m_ImageToBeMapped.IsNull() )
itkGenericExceptionMacro ( "Image to be mapped is NULL!" );
bool update = false;
if ( output->GetGeometry() == NULL || output->GetGeometry2D() == NULL || output->GetTimeGeometry() == NULL )
update = true;
if ( ( ! update ) && ( output->GetTimeGeometry()->CountTimeSteps() != input->GetTimeGeometry()->CountTimeSteps() ) )
update = true;
if ( update )
{
mitk::ThinPlateSplineCurvedGeometry::Pointer curvedGeometry = mitk::ThinPlateSplineCurvedGeometry::New();
output->SetGeometry(curvedGeometry);
}
}
void mitk::PointSetToCurvedGeometryFilter::GenerateOutputInformation()
{
mitk::PointSet::ConstPointer input = this->GetInput();
mitk::Geometry2DData::Pointer output = dynamic_cast<mitk::Geometry2DData*> ( this->GetOutput() );
if ( input.IsNull() )
itkGenericExceptionMacro ( "Input point set is NULL!" );
if ( input->GetTimeSlicedGeometry()->GetTimeSteps() != 1 )
itkWarningMacro ( "More than one time step is not yet supported!" );
if ( output.IsNull() )
itkGenericExceptionMacro ( "Output is NULL!" );
if ( m_ImageToBeMapped.IsNull() )
itkGenericExceptionMacro ( "Image to be mapped is NULL!" );
bool update = false;
if ( output->GetGeometry() == NULL || output->GetGeometry2D() == NULL || output->GetTimeSlicedGeometry() == NULL )
update = true;
if ( ( ! update ) && ( output->GetTimeSlicedGeometry()->GetTimeSteps() != input->GetTimeSlicedGeometry()->GetTimeSteps() ) )
update = true;
if ( update )
{
mitk::ThinPlateSplineCurvedGeometry::Pointer curvedGeometry = mitk::ThinPlateSplineCurvedGeometry::New();
output->SetGeometry(curvedGeometry);
/*
mitk::TimeSlicedGeometry::Pointer timeGeometry = mitk::TimeSlicedGeometry::New();
mitk::ThinPlateSplineCurvedGeometry::Pointer curvedGeometry = mitk::ThinPlateSplineCurvedGeometry::New();
timeGeometry->InitializeEvenlyTimed ( curvedGeometry, input->GetPointSetSeriesSize() );
for ( unsigned int t = 1; t < input->GetPointSetSeriesSize(); ++t )
{
mitk::ThinPlateSplineCurvedGeometry::Pointer tmpCurvedGeometry = mitk::ThinPlateSplineCurvedGeometry::New();
timeGeometry->SetGeometry3D ( tmpCurvedGeometry.GetPointer(), t );
}
output->SetGeometry ( timeGeometry );
output->SetGeometry2D ( curvedGeometry ); // @FIXME SetGeometry2D of mitk::Geometry2DData reinitializes the TimeSlicedGeometry to 1 time step
*/
}
}
mitk::Image::Pointer LoadImage( std::string filename )
{
mitk::ItkImageFileReader::Pointer reader = mitk::ItkImageFileReader::New();
reader->SetFileName ( filename.c_str() );
reader->Update();
if ( reader->GetOutput() == NULL )
itkGenericExceptionMacro("File "<<filename <<" could not be read!");
mitk::Image::Pointer image = reader->GetOutput();
return image;
}
mitk::ModelBase::ModelResultType mitk::InterpolateSignalToNewTimeGrid(const ModelBase::ModelResultType& inputSignal, const ModelBase::TimeGridType& inputGrid, const ModelBase::TimeGridType& outputGrid)
{
mitk::ModelBase::ModelResultType result(outputGrid.GetSize());
if (! inputSignal.GetSize())
{
return result;
}
if (inputSignal.GetSize() != inputGrid.GetSize())
{
itkGenericExceptionMacro("Input signal and input time grid have not the same size.");
}
mitk::ModelBase::ModelResultType::ValueType lastValue = inputSignal[0];
mitk::ModelBase::TimeGridType::ValueType lastTime = itk::NumericTraits<mitk::ModelBase::TimeGridType::ValueType>::NonpositiveMin();
mitk::ModelBase::TimeGridType::const_iterator posITime = inputGrid.begin();
mitk::ModelBase::ModelResultType::const_iterator posValue = inputSignal.begin();
mitk::ModelBase::ModelResultType::iterator posResult = result.begin();
for(mitk::ModelBase::TimeGridType::const_iterator posOTime = outputGrid.begin(); posOTime != outputGrid.end(); ++posResult, ++posOTime)
{
while(posITime!=inputGrid.end() && *posOTime > *posITime)
{ //forward in the input grid until the current output point
//is between last and the current input point.
lastValue = *posValue;
lastTime = *posITime;
++posValue;
++posITime;
}
double weightLast = 1 - (*posOTime - lastTime)/(*posITime - lastTime);
double weightNext = 1 - (*posITime - *posOTime)/(*posITime - lastTime);
*posResult = weightLast * lastValue + weightNext * (*posValue);
}
return result;
};
void mitk::PointSetToCurvedGeometryFilter::GenerateData()
{
mitk::PointSet::ConstPointer input = this->GetInput();
mitk::GeometryData::Pointer output = this->GetOutput();
//
// check preconditions
//
if ( input.IsNull() )
itkGenericExceptionMacro ( "Input point set is NULL!" );
if ( output.IsNull() )
itkGenericExceptionMacro ( "output geometry data is NULL!" );
if ( output->GetTimeGeometry() == NULL )
itkGenericExceptionMacro ( "Output time sliced geometry is NULL!" );
if ( output->GetTimeGeometry()->GetGeometryForTimeStep ( 0 ).IsNull() )
itkGenericExceptionMacro ( "Output geometry3d is NULL!" );
mitk::ThinPlateSplineCurvedGeometry::Pointer curvedGeometry = dynamic_cast<mitk::ThinPlateSplineCurvedGeometry*> ( output->GetTimeGeometry()->GetGeometryForTimeStep( 0 ).GetPointer() );
if ( curvedGeometry.IsNull() )
itkGenericExceptionMacro ( "Output geometry3d is not an instance of mitk::ThinPlateSPlineCurvedGeometry!" );
if ( m_ImageToBeMapped.IsNull() )
itkGenericExceptionMacro ( "Image to be mapped is NULL!" );
//
// initialize members if needed
//
if ( m_XYPlane.IsNull() || m_XZPlane.IsNull() || m_YZPlane.IsNull() )
{
m_ImageToBeMapped->UpdateOutputInformation();
const mitk::Geometry3D* imageGeometry = m_ImageToBeMapped->GetUpdatedGeometry();
imageGeometry = m_ImageToBeMapped->GetUpdatedGeometry();
m_XYPlane = mitk::PlaneGeometry::New();
m_XZPlane = mitk::PlaneGeometry::New();
m_YZPlane = mitk::PlaneGeometry::New();
m_XYPlane->InitializeStandardPlane ( imageGeometry, mitk::PlaneGeometry::Axial );
m_YZPlane->InitializeStandardPlane ( imageGeometry, mitk::PlaneGeometry::Sagittal );
m_XZPlane->InitializeStandardPlane ( imageGeometry, mitk::PlaneGeometry::Frontal );
}
if ( m_PlaneLandmarkProjector.IsNull() )
{
m_PlaneLandmarkProjector = mitk::PlaneLandmarkProjector::New();
m_SphereLandmarkProjector = mitk::SphereLandmarkProjector::New();
}
//
// set up geometry according to the current settings
//
if ( m_ProjectionMode == Sphere )
{
curvedGeometry->SetLandmarkProjector ( m_SphereLandmarkProjector );
}
else
{
if ( m_ProjectionMode == XYPlane )
m_PlaneLandmarkProjector->SetProjectionPlane ( m_XYPlane );
else if ( m_ProjectionMode == XZPlane )
m_PlaneLandmarkProjector->SetProjectionPlane ( m_XZPlane );
else if ( m_ProjectionMode == YZPlane )
m_PlaneLandmarkProjector->SetProjectionPlane ( m_YZPlane );
else if ( m_ProjectionMode == PCAPlane )
{
itkExceptionMacro ( "PCAPlane not yet implemented!" );
m_PCAPlaneCalculator->SetInput ( input );
m_PCAPlaneCalculator->Update();
m_PlaneLandmarkProjector->SetProjectionPlane ( dynamic_cast<mitk::PlaneGeometry*> ( m_PCAPlaneCalculator->GetOutput() ) );
}
else
itkExceptionMacro ( "Unknown projection mode" );
curvedGeometry->SetLandmarkProjector ( m_PlaneLandmarkProjector );
}
//curvedGeometry->SetReferenceGeometry( m_ImageToBeMapped->GetGeometry() );
curvedGeometry->SetTargetLandmarks ( input->GetPointSet ( 0 )->GetPoints() );
curvedGeometry->SetSigma ( m_Sigma );
curvedGeometry->ComputeGeometry();
curvedGeometry->SetOversampling ( 1.0 );
}