cxCenterlineRegistration.cpp

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/*=========================================================================
This file is part of CustusX, an Image Guided Therapy Application.

Copyright (c) 2008-2014, SINTEF Department of Medical Technology
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#include "cxCenterlineRegistration.h"
#include <vtkPointData.h>
#include <vtkPolyData.h>
#include <vtkPolyDataWriter.h>
#include <vtkCellArray.h>
#include <vtkMatrix4x4.h>
#include <vtkLinearTransform.h>
#include <vtkLandmarkTransform.h>
#include "cxTransform3D.h"
#include "cxVector3D.h"
#include "cxLogger.h"
#include <boost/math/special_functions/fpclassify.hpp> // isnan
#include "vtkCardinalSpline.h"

typedef vtkSmartPointer<class vtkCardinalSpline> vtkCardinalSplinePtr;

namespace cx
{


CenterlineRegistration::CenterlineRegistration()
{
    mFixedPointSet = PointSetType::New();
    mMovingPointSet = PointSetType::New();
    mRegistration = RegistrationType::New();
    mTransform = TransformType::New();
    MetricType::Pointer         metric = MetricType::New();
    mOptimizer = OptimizerType::New();
    mOptimizer->SetUseCostFunctionGradient(false);
    OptimizerType::ScalesType   scales(mTransform->GetNumberOfParameters());

    unsigned long   numberOfIterations = 2000;
    double          gradientTolerance = 1e-4;
    double          valueTolerance = 1e-4;
    double          epsilonFunction = 1e-5;

    UpdateScales(true,true,true,true,true,true);
    mOptimizer->SetNumberOfIterations(numberOfIterations);
    mOptimizer->SetValueTolerance(valueTolerance);
    mOptimizer->SetGradientTolerance(gradientTolerance);
    mOptimizer->SetEpsilonFunction(epsilonFunction);

    // Initialize transform
    mTransform->SetIdentity();
    mRegistration->SetInitialTransformParameters(mTransform->GetParameters());

    // Setup framework
    mRegistration->SetMetric(metric);
    mRegistration->SetOptimizer(mOptimizer);
    mRegistration->SetTransform(mTransform);

}



vtkPointsPtr convertTovtkPoints(Eigen::MatrixXd positions)
{
  vtkPointsPtr retval = vtkPointsPtr::New();

  for (unsigned i=0; i<positions.cols(); ++i)
  {
    retval->InsertNextPoint(positions(0,i), positions(1,i), positions(2,i));
  }
  return retval;
}

void CenterlineRegistration::UpdateScales(bool xRot, bool yRot, bool zRot, bool xTrans, bool yTrans, bool zTrans)
{

    OptimizerType::ScalesType   scales(mTransform->GetNumberOfParameters());
    const double translationScale = 40.0;    // dynamic range of translations
    const double rotationScale = 0.3;    // dynamic range of rotations

    if (xRot)
        scales[0] = 1.0 / rotationScale;
    else
        scales[0] = 1e50;
    if (yRot)
        scales[1] = 1.0 / rotationScale;
    else
        scales[1] = 1e50;
    if (zRot)
        scales[2] = 1.0 / rotationScale;
    else
        scales[2] = 1e50;
    if (xTrans)
        scales[3] = 1.0 / translationScale;
    else
        scales[3] = 1e50;
    if (yTrans)
        scales[4] = 1.0 / translationScale;
    else
        scales[4] = 1e50;
    if (zTrans)
        scales[5] = 1.0 / translationScale;
    else
        scales[5] = 1e50;

    mOptimizer->SetScales(scales);
    mRegistration->SetOptimizer(mOptimizer);

    std::cout << "Update scales: "
              << mRegistration->GetOptimizer()->GetScales()
              << scales
              << std::endl;

}


vtkPointsPtr CenterlineRegistration::smoothPositions(vtkPointsPtr centerline)
{
    int numberOfInputPoints = centerline->GetNumberOfPoints();
    int controlPointFactor = 10;
    int numberOfControlPoints = numberOfInputPoints / controlPointFactor;
    if (numberOfControlPoints < 10)
        numberOfControlPoints = std::min(numberOfInputPoints,10);

    int numberOfOutputPoints = std::max(numberOfInputPoints, 100); //interpolate to at least 100 output points
    vtkPointsPtr newCenterline = vtkPointsPtr::New();;

    vtkCardinalSplinePtr splineX = vtkSmartPointer<vtkCardinalSpline>::New();
    vtkCardinalSplinePtr splineY = vtkSmartPointer<vtkCardinalSpline>::New();
    vtkCardinalSplinePtr splineZ = vtkSmartPointer<vtkCardinalSpline>::New();

    if (numberOfControlPoints >= 2)
    {
        //add control points to spline
        for(int i=0; i<numberOfControlPoints; i++)
        {
            int indexP = (i*numberOfInputPoints)/numberOfControlPoints;
            double p[3];
            centerline->GetPoint(indexP,p);
            int indexSpline = (i*numberOfOutputPoints)/numberOfControlPoints;
            splineX->AddPoint( indexSpline, p[0] );
            splineY->AddPoint( indexSpline, p[1] );
            splineZ->AddPoint( indexSpline, p[2] );
            //std::cout << "spline point: " << "(" << indexSpline << ") " << p[0] << " " << p[1]  << " " << p[2] << std::endl;
        }

        //Always add the last point to complete spline
        double p[3];
        centerline->GetPoint( numberOfInputPoints-1, p );
        splineX->AddPoint( numberOfOutputPoints-1, p[0] );
        splineY->AddPoint( numberOfOutputPoints-1, p[1] );
        splineZ->AddPoint( numberOfOutputPoints-1, p[2] );
        //std::cout << "spline point: " << "(" << numberOfOutputPoints-1 << ") " << p[0] << " " << p[1]  << " " << p[2] << std::endl;

        //evaluate spline - get smoothed positions
        for(int i=0; i<numberOfOutputPoints; i++)
        {
            double splineParameter = i;
            newCenterline->InsertNextPoint(splineX->Evaluate(splineParameter),
                                           splineY->Evaluate(splineParameter),
                                           splineZ->Evaluate(splineParameter));
        }
    }
    else
        return centerline;

    return newCenterline;
}

vtkPointsPtr CenterlineRegistration::processCenterline(vtkPolyDataPtr centerline, Transform3D rMd)
{

    vtkPointsPtr processedPositions = vtkPointsPtr::New();
        int N = centerline->GetNumberOfPoints();
        Eigen::MatrixXd CLpoints(3,N);
        for(vtkIdType i = 0; i < N; i++)
                {
        double p[3];
        centerline->GetPoint(i,p);
        Vector3D pos;
        pos(0) = p[0]; pos(1) = p[1]; pos(2) = p[2];
        pos = rMd.coord(pos);
        processedPositions->InsertNextPoint(pos[0],pos[1],pos[2]);
        }

    //sort positions?
    processedPositions = smoothPositions(processedPositions);

    return processedPositions;
}

vtkPointsPtr CenterlineRegistration::ConvertTrackingDataToVTK(TimedTransformMap trackingData_prMt, Transform3D rMpr)
{
    vtkPointsPtr loggedPositions = vtkPointsPtr::New();

    for(TimedTransformMap::iterator iter=trackingData_prMt.begin();
                iter!=trackingData_prMt.end();++iter)
            {
                Transform3D prMt = iter->second;
                Vector3D pos = prMt.matrix().block<3,1> (0, 3);
                pos = rMpr.coord(pos);
                loggedPositions->InsertNextPoint(pos[0],pos[1],pos[2]);
            }

    return loggedPositions;
}

void   CenterlineRegistration::SetFixedPoints(vtkPointsPtr vtkPoints)
{
    mFixedPointSet->Initialize();           // Clear previous pointset
//    PointsContainerPtr  itkPoints = mFixedPointSet->GetPoints();
    PointsContainerPtr  itkPoints = PointsContainer::New();
    PointType   point;

    for(vtkIdType n=0;n<vtkPoints->GetNumberOfPoints();n++)
    {
        double temp_Point[3];
        vtkPoints->GetPoint(n, temp_Point);
        point[0] = temp_Point[0];
        point[1] = temp_Point[1];
        point[2] = temp_Point[2];
        Vector3D vPoint(temp_Point[0], temp_Point[1], temp_Point[2]);
        itkPoints->InsertElement(n,point);
    }
    mFixedPointSet->SetPoints(itkPoints);
}

void CenterlineRegistration::SetMovingPoints(vtkPointsPtr vtkPoints)
{
    mMovingPointSet->Initialize();
    PointsContainerPtr  itkPoints = PointsContainer::New();
    PointType   point;

    for(vtkIdType n=0;n<vtkPoints->GetNumberOfPoints();n++)
    {
        double temp_Point[3];
        vtkPoints->GetPoint(n, temp_Point);
        Vector3D vPoint(temp_Point[0], temp_Point[1], temp_Point[2]);
        point[0] = temp_Point[0];
        point[1] = temp_Point[1];
        point[2] = temp_Point[2];
        itkPoints->InsertElement(n,point);
    }
    mMovingPointSet->SetPoints(itkPoints);
}

Transform3D CenterlineRegistration::FullRegisterMoving(Transform3D init_transform)
{
    mRegistration->SetFixedPointSet(mFixedPointSet);
    mRegistration->SetMovingPointSet(mMovingPointSet);

    typedef itk::Matrix<double,3,3>     MatrixType;
    typedef TransformType::OffsetType   TranslateVector;
    MatrixType                          initMatrix;
    TranslateVector                     initTranslation;

    // Set initial rotation
    for(int i=0; i<3; i++)
        for(int j=0;j<3;j++) {
            double element = init_transform(i,j);
            initMatrix(i,j) = element;
        }

    // Set initial translation
    initTranslation[0] = init_transform(0,3);
    initTranslation[1] = init_transform(1,3);
    initTranslation[2] = init_transform(2,3);

    mTransform->SetMatrix(initMatrix, 1e-5);
    mTransform->SetTranslation(initTranslation);

    mRegistration->SetInitialTransformParameters(mTransform->GetParameters());

    try
    {
        mRegistration->Update();
    }
    catch (itk::ExceptionObject &exp)
    {
        std::cout << "CenterlineRegMethod - Exception caught ! " << std::endl;
        std::cout << exp << std::endl;
    }

    RegistrationType::ParametersType finalParameters =
            mRegistration->GetLastTransformParameters();

    TransformType::MatrixType regMatrix = mTransform->GetMatrix();

    for(int i=0; i<3; i++)
        for(int j=0;j<3;j++) {
            double element = regMatrix(i,j);
            mResultTransform(i,j) = element;
        }

    mResultTransform(0,3) = finalParameters(3);
    mResultTransform(1,3) = finalParameters(4);
    mResultTransform(2,3) = finalParameters(5);

    mRegistrationUpdated = true;

    return Transform3D(mResultTransform);
}


Transform3D CenterlineRegistration::runCenterlineRegistration(vtkPolyDataPtr centerline, Transform3D rMd, TimedTransformMap trackingData_prMt, Transform3D old_rMpr)
{

    vtkPointsPtr centerlinePoints = processCenterline(centerline, rMd);

    SetFixedPoints( centerlinePoints );
    SetMovingPoints( ConvertTrackingDataToVTK(trackingData_prMt, old_rMpr) );

    Transform3D rMpr = FullRegisterMoving(Transform3D::Identity());

    std::cout << "rMpr : " << std::endl;
    std::cout << rMpr << std::endl;

    return rMpr;
}

CenterlineRegistration::~CenterlineRegistration()
{

}



}//namespace cx