cxBronchoscopyRegistration.cpp

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

Copyright (c) SINTEF Department of Medical Technology.
All rights reserved.

CustusX is released under a BSD 3-Clause license.

See Lisence.txt (https://github.com/SINTEFMedtek/CustusX/blob/master/License.txt) for details.
=========================================================================*/
#include "cxBronchoscopyRegistration.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

namespace cx
{


BronchoscopyRegistration::BronchoscopyRegistration():
        mCenterlineProcessed(false),
        mBranchListPtr(new BranchList)
{

}

M4Vector excludeClosePositions(M4Vector Tnavigation)
//              To avoid having too many tracking data samples in the registration,
//              we are only including tracking data with a distance to last included
//              tracking position of more than 1 mm.
{
        M4Vector TnavigationIncluded;
        if(Tnavigation.empty())
                return TnavigationIncluded;
        TnavigationIncluded.push_back(Tnavigation[0]); // first position is always included
        int numberOfIncluded = 0;
        size_t numberOfPos = Tnavigation.size();
        for ( size_t index = 1; index < numberOfPos; index++)
        {
                double xDistance = (TnavigationIncluded[numberOfIncluded](0,3) - Tnavigation[index](0,3) );
                                double xDistanceSquared = xDistance * xDistance;
                double yDistance = (TnavigationIncluded[numberOfIncluded](1,3) - Tnavigation[index](1,3) );
                                double yDistanceSquared = yDistance * yDistance;
                double zDistance = (TnavigationIncluded[numberOfIncluded](2,3) - Tnavigation[index](2,3) );
                                double zDistanceSquared = zDistance * zDistance;
                double distanceToLastIncluded = sqrt (xDistanceSquared + yDistanceSquared + zDistanceSquared);

                if (distanceToLastIncluded > 1) //condition of at least movement of 1 mm from last included sample
                {
                        numberOfIncluded ++;
                        TnavigationIncluded.push_back(Tnavigation[index]);
                }
        }

        return TnavigationIncluded;
}



Eigen::VectorXd sortVector(Eigen::VectorXd v)
{
        for (int i = 0; i < v.size() - 1; i++)  {
                for (int j = i + 1; j < v.size(); j++) {
                        if (v(i) > v(j)){
                                std::swap(v(i) , v(j));
                        }
                }
        }
        return v;
}


Eigen::VectorXd findMedian(Eigen::MatrixXd matrix)
{
        Eigen::VectorXd medianValues(matrix.rows());
        for (int i = 0; i < matrix.rows(); i++)  {
                Eigen::MatrixXd sortedMatrix = sortMatrix(i, matrix);
                if (sortedMatrix.cols()%2==1) {// odd number
                        medianValues(i) = (sortedMatrix(i,(sortedMatrix.cols()+1)/2) );
                }
                else { // even number
                        medianValues(i) = ( sortedMatrix(i,sortedMatrix.cols()/2) + sortedMatrix(i,sortedMatrix.cols()/2 - 1) ) / 2;
                }
        }
        return medianValues;
}


std::pair<Eigen::MatrixXd , Eigen::MatrixXd> findPositionsWithSmallesAngleDifference(int percentage , Eigen::VectorXd DAngle , Eigen::MatrixXd trackingPositions , Eigen::MatrixXd nearestCTPositions)
{
        Eigen::VectorXd DAngleSorted = sortVector(DAngle);
        int numberOfPositionsIncluded = floor((double)(DAngle.size() * percentage/100));
        Eigen::MatrixXd trackingPositionsIncluded(3 , numberOfPositionsIncluded );
        Eigen::MatrixXd nearestCTPositionsIncluded(3 , numberOfPositionsIncluded );
        float maxDAngle = DAngleSorted( numberOfPositionsIncluded );
        int counter = 0;
        for (int i = 0; i < DAngle.size(); i++)
        {
                if ((DAngle(i) <= maxDAngle) && (counter < numberOfPositionsIncluded))
                {
                        trackingPositionsIncluded.col(counter) = trackingPositions.col(i);
                        nearestCTPositionsIncluded.col(counter) = nearestCTPositions.col(i);
                        counter++;
                }
        }

        return std::make_pair(trackingPositionsIncluded , nearestCTPositionsIncluded);
}


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;
}

Eigen::Matrix4d performLandmarkRegistration(vtkPointsPtr source, vtkPointsPtr target /*, bool* ok */)
{
        //*ok = false;

        // too few data samples: ignore
        if (source->GetNumberOfPoints() < 3)
        {
                std::cout << "Warning in performLandmarkRegistration: Need >3 positions, returning identity matrix." << std::endl;
                return Eigen::Matrix4d::Identity();
        }

        vtkLandmarkTransformPtr landmarktransform = vtkLandmarkTransformPtr::New();
        landmarktransform->SetSourceLandmarks(source);
        landmarktransform->SetTargetLandmarks(target);
        landmarktransform->SetModeToRigidBody();
        source->Modified();
        target->Modified();
        //landmarktransform->Update();

        vtkMatrix4x4* temp = landmarktransform->GetMatrix();
        Eigen::Matrix4d tar_M_src;
        for (int i = 0; i < 4; i++)
        {
                for (int j = 0; j < 4; j++)
                {
                        tar_M_src(i,j) = temp->GetElement(i,j);
                }
        }

        if ( boost::math::isnan(tar_M_src.sum()) )
        {
                std::cout << "Warning in performLandmarkRegistration: Returning identity matrix due to nan." << std::endl;
                return Eigen::Matrix4d::Identity();
        }

        return tar_M_src;
}




std::vector<Eigen::MatrixXd::Index> dsearch2n(Eigen::MatrixXd pos1, Eigen::MatrixXd pos2, Eigen::MatrixXd ori1, Eigen::MatrixXd ori2)
{
        Eigen::MatrixXd::Index index;
        std::vector<Eigen::MatrixXd::Index> indexVector;

        for (int i = 0; i < pos1.cols(); i++)
        {
                Eigen::VectorXd D(pos2.cols());
                Eigen::VectorXd P(pos2.cols());
                Eigen::VectorXd O(pos2.cols());
                Eigen::VectorXd R(pos2.cols());

                for (int j = 0; j < pos2.cols(); j++)
                {
                        float p0 = ( pos2(0,j) - pos1(0,i) );
                        float p1 = ( pos2(1,j) - pos1(1,i) );
                        float p2 = ( pos2(2,j) - pos1(2,i) );
                        float o0 = fmod( ori2(0,j) - ori1(0,i) , 2 );
                        float o1 = fmod( ori2(1,j) - ori1(1,i) , 2 );
                        float o2 = fmod( ori2(2,j) - ori1(2,i) , 2 );

                        P(j) = sqrt( p0*p0 + p1*p1 + p2*p2 );
                        O(j) = sqrt( o0*o0 + o1*o1 + o2*o2 );

                        if (boost::math::isnan( O(j) ))
                                O(j) = 4;

                        if ( (o0>2) || (o1>2) || (o2>2) )
                                std::cout << "Warning in bronchoscopyRegistration.cpp: Error on oriantation calculation in dsearch2n. Orientation > 2." << std::endl;

                        R(j) = P(j) / O(j);

                }
                float alpha = sqrt( R.mean() );
                if (boost::math::isnan( alpha ))
                        alpha = 0;

                D = P + alpha * O;
                D.minCoeff(&index);
                indexVector.push_back(index);
        }
        return indexVector;
}

std::pair<Eigen::MatrixXd , Eigen::MatrixXd> RemoveInvalidData(Eigen::MatrixXd positionData, Eigen::MatrixXd orientationData)
{
        std::vector<int> indicesToBeDeleted;

        for (int i = 0; i < fmin(positionData.cols(), orientationData.cols()); i++)
        {
                if ( boost::math::isinf( positionData.block(0 , i , 3 , 1).sum() ) || boost::math::isinf( orientationData.block(0 , i , 3 , 1).sum() ) )
                        indicesToBeDeleted.push_back(i);
                else if (boost::math::isnan( positionData.block(0 , i , 3 , 1).sum() ) || boost::math::isnan( orientationData.block(0 , i , 3 , 1).sum() ))
                        indicesToBeDeleted.push_back(i);
                else if ( (positionData.block(0 , i , 1 , 1).sum() == 0 && positionData.block(1 , i , 1 , 1).sum() == 0 && positionData.block(2 , i , 1 , 1).sum() == 0) ||
                                                        (orientationData.block(0 , i , 1 , 1).sum() == 0 && orientationData.block(1 , i , 1 , 1).sum() == 0 && orientationData.block(2 , i , 1 , 1).sum() == 0))
                        indicesToBeDeleted.push_back(i);
        }

        for ( int i = indicesToBeDeleted.size() - 1; i >= 0; i-- )
        {
                std::cout << "Warning in bronchoscopyRegistration: Removed corrupted data: " << positionData.block(0 , indicesToBeDeleted[i] , 3 , 1) << " " << orientationData.block(0 , indicesToBeDeleted[i] , 3 , 1) << std::endl;
                positionData = eraseCol(indicesToBeDeleted[i],positionData);
                orientationData = eraseCol(indicesToBeDeleted[i],orientationData);
        }
        return std::make_pair(positionData , orientationData);
}

M4Vector RemoveInvalidData(M4Vector T_vector)
{
        Eigen::Vector3d position;
        Eigen::Vector3d orientation;
        std::vector<int> indicesToBeDeleted;

        for (int i = 0; i < T_vector.size(); i++)
        {
                position = T_vector[i].topRightCorner(3 , 1);
                orientation = T_vector[i].block(0 , 2 , 3 , 1);
                if ( boost::math::isinf( position.sum() ) || boost::math::isinf( orientation.sum() ) )
                        indicesToBeDeleted.push_back(i);
                else if (boost::math::isnan( position.sum() ) || boost::math::isnan( orientation.sum() ))
                        indicesToBeDeleted.push_back(i);
                else if ( (position[0] == 0 && position[1] == 0 && position[2] == 0) ||
                                                        (orientation[0] == 0 && orientation[1] == 0 && orientation[2] == 0) )
                        indicesToBeDeleted.push_back(i);
        }

        for ( int i = indicesToBeDeleted.size() - 1; i >= 0; i-- )
        {
                std::cout << "Warning in bronchoscopyRegistration: Removed corrupted data: " << T_vector[i].topRightCorner(3 , 1) << " " <<  T_vector[i].block(0 , 2 , 3 , 1) << std::endl;
                T_vector.erase(T_vector.begin() + indicesToBeDeleted[i]);
        }
        return T_vector;
}

Eigen::Matrix4d registrationAlgorithm(BranchListPtr branches, M4Vector Tnavigation, Transform3D old_rMpr)
{
        Eigen::Matrix4d registrationMatrix;
        Eigen::MatrixXd CTPositions;
        Eigen::MatrixXd CTOrientations;
        Eigen::MatrixXd trackingPositions(3 , Tnavigation.size());
        Eigen::MatrixXd trackingOrientations(3, Tnavigation.size());

        std::vector<BranchPtr> branchVector = branches->getBranches();
        CTPositions = branchVector[0]->getPositions();
        CTOrientations = branchVector[0]->getOrientations();

        if (trackingPositions.cols() < 10)
        {
                std::cout << "Warning: Too few positions in tracking data to perform registration." << std::endl;
                return Eigen::Matrix4d::Identity();
        }

        for (int i = 1; i < branchVector.size(); i++)
        {
                Eigen::MatrixXd CTPositionsNew(CTPositions.rows() , CTPositions.cols() + branchVector[i]->getPositions().cols());
                Eigen::MatrixXd CTOrientationsNew(CTOrientations.rows() , CTOrientations.cols() + branchVector[i]->getOrientations().cols());
                CTPositionsNew.leftCols(CTPositions.cols()) = CTPositions;
                CTPositionsNew.rightCols(branchVector[i]->getPositions().cols()) = branchVector[i]->getPositions();
                CTOrientationsNew.leftCols(CTOrientations.cols()) = CTOrientations;
                CTOrientationsNew.rightCols(branchVector[i]->getOrientations().cols()) = branchVector[i]->getOrientations();
                CTPositions.swap(CTPositionsNew);
                CTOrientations.swap(CTOrientationsNew);
        }

        if (CTPositions.cols() < 10)
        {
                std::cout << "Warning: Too few positions in centerline to perform registration." << std::endl;
                return Eigen::Matrix4d::Identity();
        }

        std::pair<Eigen::MatrixXd , Eigen::MatrixXd> qualityCheckedData = RemoveInvalidData(CTPositions, CTOrientations);
        CTPositions = qualityCheckedData.first;
        CTOrientations = qualityCheckedData.second;

        for (int i = 0; i < Tnavigation.size(); i++)
                Tnavigation[i] = old_rMpr * Tnavigation[i];

        Tnavigation = RemoveInvalidData(Tnavigation);

        for (int i = 0; i < Tnavigation.size(); i++)
        {
                trackingPositions.block(0 , i , 3 , 1) = Tnavigation[i].topRightCorner(3 , 1);
                trackingOrientations.block(0 , i , 3 , 1) = Tnavigation[i].block(0 , 2 , 3 , 1);
        }

        //Adjusting points to initially match top positoins in CT and tracking data
        Eigen::MatrixXd::Index maxIndex;
        trackingPositions.row(2).maxCoeff( &maxIndex );
        Eigen::Vector3d translation = CTPositions.col(0) - trackingPositions.col(maxIndex);
        //Eigen::Vector3d translation = findMedian(CTPositions) - findMedian(trackingPositions);
        //trackingPositions = trackingPositions.colwise() + translation;


        registrationMatrix << 1, 0, 0, translation(0),
                        0, 1, 0, translation(1),
                        0, 0, 1, translation(2),
                        0, 0, 0, 1;

        for (int i = 0; i < Tnavigation.size(); i++)
        {
                Tnavigation[i] = registrationMatrix * Tnavigation[i];
        }

        int iterationNumber = 0;
        int maxIterations = 50;
        while ( translation.array().abs().sum() > 1 && iterationNumber < maxIterations)
        {
                for (int i = 0; i < Tnavigation.size(); i++)
                {
                        trackingPositions.block(0 , i , 3 , 1) = Tnavigation[i].topRightCorner(3 , 1);
                        trackingOrientations.block(0 , i , 3 , 1) = Tnavigation[i].block(0 , 2 , 3 , 1);
                }


                iterationNumber++;
                std::vector<Eigen::MatrixXd::Index> indexVector = dsearch2n( trackingPositions, CTPositions, trackingOrientations, CTOrientations );
                Eigen::MatrixXd nearestCTPositions(3,indexVector.size());
                Eigen::MatrixXd nearestCTOrientations(3,indexVector.size());
                Eigen::VectorXd DAngle(indexVector.size());
                for (int i = 0; i < indexVector.size(); i++)
                {
                        nearestCTPositions.col(i) = CTPositions.col(indexVector[i]);
                        nearestCTOrientations.col(i) = CTOrientations.col(indexVector[i]);
                        float o0 = fmod( trackingOrientations(0,i) - nearestCTOrientations(0,i) , 2 );
                        float o1 = fmod( trackingOrientations(1,i) - nearestCTOrientations(1,i) , 2 );
                        float o2 = fmod( trackingOrientations(2,i) - nearestCTOrientations(2,i) , 2 );
                        DAngle(i) = sqrt(o0*o0+o1*o1+o2*o2);
                }

                std::pair<Eigen::MatrixXd , Eigen::MatrixXd> result = findPositionsWithSmallesAngleDifference(70 , DAngle , trackingPositions , nearestCTPositions);
                vtkPointsPtr trackingPositions_vtk = convertTovtkPoints(result.first);
                vtkPointsPtr CTPositions_vtk = convertTovtkPoints(result.second);

                Eigen::Matrix4d tempMatrix = performLandmarkRegistration(trackingPositions_vtk, CTPositions_vtk);

                registrationMatrix = tempMatrix * registrationMatrix;

                for (int i = 0; i < Tnavigation.size(); i++)
                {
                        Tnavigation[i] = tempMatrix * Tnavigation[i];
                }

                translation << tempMatrix(0,3), tempMatrix(1,3), tempMatrix(2,3);

                std::cout << "Iteration nr " << iterationNumber << " translation: " << translation.array().abs().sum() << std::endl;
        }

        if (translation.array().abs().sum() > 1)
                std::cout << "Warning: Registration did not converge within " << maxIterations <<" iterations, which is max number of iterations." << std::endl;

        return registrationMatrix;
}

Eigen::Matrix4d registrationAlgorithmImage2Image(BranchListPtr branchesFixed, BranchListPtr branchesMoving)
{
        Eigen::Matrix4d registrationMatrix;
        Eigen::MatrixXd CTPositionsFixed;
        Eigen::MatrixXd CTOrientationsFixed;
        Eigen::MatrixXd CTPositionsMoving;
        Eigen::MatrixXd CTOrientationsMoving;

        std::vector<BranchPtr> branchVectorFixed = branchesFixed->getBranches();
        CTPositionsFixed = branchVectorFixed[0]->getPositions();
        CTOrientationsFixed = branchVectorFixed[0]->getOrientations();

        std::vector<BranchPtr> branchVectorMoving = branchesMoving->getBranches();
        CTPositionsMoving = branchVectorMoving[0]->getPositions();
        CTOrientationsMoving = branchVectorMoving[0]->getOrientations();

        for (int i = 1; i < branchVectorFixed.size(); i++)
        {
                Eigen::MatrixXd CTPositionsFixedNew(CTPositionsFixed.rows() , CTPositionsFixed.cols() + branchVectorFixed[i]->getPositions().cols());
                Eigen::MatrixXd CTOrientationsFixedNew(CTOrientationsFixed.rows() , CTOrientationsFixed.cols() + branchVectorFixed[i]->getOrientations().cols());
                CTPositionsFixedNew.leftCols(CTPositionsFixed.cols()) = CTPositionsFixed;
                CTPositionsFixedNew.rightCols(branchVectorFixed[i]->getPositions().cols()) = branchVectorFixed[i]->getPositions();
                CTOrientationsFixedNew.leftCols(CTOrientationsFixed.cols()) = CTOrientationsFixed;
                CTOrientationsFixedNew.rightCols(branchVectorFixed[i]->getOrientations().cols()) = branchVectorFixed[i]->getOrientations();
                CTPositionsFixed.swap(CTPositionsFixedNew);
                CTOrientationsFixed.swap(CTOrientationsFixedNew);
        }

        for (int i = 1; i < branchVectorMoving.size(); i++)
        {
                Eigen::MatrixXd CTPositionsMovingNew(CTPositionsMoving.rows() , CTPositionsMoving.cols() + branchVectorMoving[i]->getPositions().cols());
                Eigen::MatrixXd CTOrientationsMovingNew(CTOrientationsMoving.rows() , CTOrientationsMoving.cols() + branchVectorMoving[i]->getOrientations().cols());
                CTPositionsMovingNew.leftCols(CTPositionsMoving.cols()) = CTPositionsMoving;
                CTPositionsMovingNew.rightCols(branchVectorMoving[i]->getPositions().cols()) = branchVectorMoving[i]->getPositions();
                CTOrientationsMovingNew.leftCols(CTOrientationsMoving.cols()) = CTOrientationsMoving;
                CTOrientationsMovingNew.rightCols(branchVectorMoving[i]->getOrientations().cols()) = branchVectorMoving[i]->getOrientations();
                CTPositionsMoving.swap(CTPositionsMovingNew);
                CTOrientationsMoving.swap(CTOrientationsMovingNew);
        }

        if (CTPositionsFixed.cols() < 10 || CTPositionsMoving.cols() < 10)
        {
                CX_LOG_WARNING() << "Too few positions in centerline to perform registration.";
                return Eigen::Matrix4d::Identity();
        }

        std::pair<Eigen::MatrixXd , Eigen::MatrixXd> qualityCheckedDataFixed = RemoveInvalidData(CTPositionsFixed, CTOrientationsFixed);
        CTPositionsFixed = qualityCheckedDataFixed.first;
        CTOrientationsFixed = qualityCheckedDataFixed.second;

        std::pair<Eigen::MatrixXd , Eigen::MatrixXd> qualityCheckedDataMoving = RemoveInvalidData(CTPositionsMoving, CTOrientationsMoving);
        CTPositionsMoving = qualityCheckedDataMoving.first;
        CTOrientationsMoving = qualityCheckedDataMoving.second;

        //Adjusting points for centeroids
        Eigen::Vector3d translation = findMedian(CTPositionsFixed) - findMedian(CTPositionsMoving);

        registrationMatrix << 1, 0, 0, translation(0),
                        0, 1, 0, translation(1),
                        0, 0, 1, translation(2),
                        0, 0, 0, 1;

        for (int i = 0; i < CTPositionsMoving.cols(); i++)
        {
                CTPositionsMoving.col(i) = CTPositionsMoving.col(i) + translation;
        }

        int iterationNumber = 0;
        int maxIterations = 200;
        while ( translation.array().abs().sum() > 0.5 && iterationNumber < maxIterations)
        {

                iterationNumber++;
                std::vector<Eigen::MatrixXd::Index> indexVector = dsearch2n( CTPositionsMoving, CTPositionsFixed, CTOrientationsMoving, CTOrientationsFixed );
                Eigen::MatrixXd nearestCTPositions(3,indexVector.size());
                Eigen::MatrixXd nearestCTOrientations(3,indexVector.size());
                Eigen::VectorXd DAngle(indexVector.size());
                for (int i = 0; i < indexVector.size(); i++)
                {
                        nearestCTPositions.col(i) = CTPositionsFixed.col(indexVector[i]);
                        nearestCTOrientations.col(i) = CTOrientationsFixed.col(indexVector[i]);
                        float o0 = fmod( CTOrientationsMoving(0,i) - nearestCTOrientations(0,i) , 2 );
                        float o1 = fmod( CTOrientationsMoving(1,i) - nearestCTOrientations(1,i) , 2 );
                        float o2 = fmod( CTOrientationsMoving(2,i) - nearestCTOrientations(2,i) , 2 );
                        DAngle(i) = sqrt(o0*o0+o1*o1+o2*o2);
                }

                std::pair<Eigen::MatrixXd , Eigen::MatrixXd> result = findPositionsWithSmallesAngleDifference(70 , DAngle , CTPositionsMoving , nearestCTPositions);
                vtkPointsPtr CTPositionsMoving_vtk = convertTovtkPoints(result.first);
                vtkPointsPtr CTPositionsFixed_vtk = convertTovtkPoints(result.second);

                Eigen::Matrix4d tempMatrix = performLandmarkRegistration(CTPositionsMoving_vtk, CTPositionsFixed_vtk);

                registrationMatrix = tempMatrix * registrationMatrix;

                for (int i = 0; i < CTPositionsMoving.cols(); i++)
                {
                        CTPositionsMoving.col(i) = tempMatrix.topLeftCorner(3,3) * CTPositionsMoving.col(i) + tempMatrix.topRightCorner(3,1);
                }

                translation << tempMatrix(0,3), tempMatrix(1,3), tempMatrix(2,3);

        }

        if (translation.array().abs().sum() > 1)
                CX_LOG_WARNING() << "Registration did not converge within " << maxIterations <<" iterations, which is max number of iterations.";

        return registrationMatrix;
}

vtkPolyDataPtr BronchoscopyRegistration::processCenterline(vtkPolyDataPtr centerline, Transform3D rMd, int numberOfGenerations)
{
        if (mBranchListPtr)
                mBranchListPtr->deleteAllBranches();

        Eigen::MatrixXd CLpoints = makeTransformedMatrix(centerline, rMd);
        mBranchListPtr->findBranchesInCenterline(CLpoints);
        if (numberOfGenerations != 0)
        {
                mBranchListPtr->selectGenerations(numberOfGenerations);
        }

        mBranchListPtr->smoothBranchPositions(10);
        mBranchListPtr->smoothOrientations();

        double minPointDistance = 0.5; //mm
        mBranchListPtr->excludeClosePositionsInCTCenterline(minPointDistance); // to increase speed in registration

        vtkPolyDataPtr retval = mBranchListPtr->createVtkPolyDataFromBranches();

        std::cout << "Number of branches in CT centerline: " << mBranchListPtr->getBranches().size() << std::endl;

        mCenterlineProcessed = true;

        return retval;
}

//Can be used instead of processCenterline(...) if you have a preprosessed branchList to be used in the registration process.
void BronchoscopyRegistration::setBranchList(BranchListPtr branchList, int numberOfGenerations)
{
        if (!branchList)
                return;

        mBranchListPtr = branchList;

        if (numberOfGenerations != 0)
        {
                mBranchListPtr->selectGenerations(numberOfGenerations);
        }

        mCenterlineProcessed = true;
}

BranchListPtr BronchoscopyRegistration::getBranchList()
{
        return mBranchListPtr;
}

BranchListPtr BronchoscopyRegistration::processCenterlineImage2Image(vtkPolyDataPtr centerline, int numberOfGenerations)
{
        BranchListPtr branchListPtr;
        branchListPtr = BranchListPtr(new BranchList());
        Eigen::MatrixXd CLpoints = makeTransformedMatrix(centerline);

        branchListPtr->findBranchesInCenterline(CLpoints);

        if (numberOfGenerations != 0)
        {
                branchListPtr->selectGenerations(numberOfGenerations);
        }

        branchListPtr->smoothBranchPositions(10);
        branchListPtr->smoothOrientations();

        return branchListPtr;
}

Eigen::Matrix4d BronchoscopyRegistration::runBronchoscopyRegistration(TimedTransformMap trackingData_prMt, Transform3D old_rMpr, double maxDistanceForLocalRegistration)
{
        if(trackingData_prMt.empty())
                reportError("BronchoscopyRegistration::runBronchoscopyRegistration(): No tracking data");

        M4Vector Tnavigation;
        for(TimedTransformMap::iterator iter=trackingData_prMt.begin(); iter!=trackingData_prMt.end(); ++iter)
        {
                Tnavigation.push_back(iter->second.     matrix());
        }

        Tnavigation = excludeClosePositions(Tnavigation);

        Eigen::Matrix4d regMatrix;
        if (maxDistanceForLocalRegistration != 0)
        {
                Eigen::MatrixXd trackingPositions_temp(3 , Tnavigation.size());
                M4Vector Tnavigation_temp = Tnavigation;
                for (int i = 0; i < Tnavigation.size(); i++)
                {
                        Tnavigation_temp[i] = old_rMpr * Tnavigation[i];
                        trackingPositions_temp.block(0 , i , 3 , 1) = Tnavigation_temp[i].topRightCorner(3 , 1);
                }
                BranchListPtr tempPtr = mBranchListPtr->removePositionsForLocalRegistration(trackingPositions_temp, maxDistanceForLocalRegistration);
                regMatrix = registrationAlgorithm(tempPtr, Tnavigation, old_rMpr);
        }
        else
                regMatrix = registrationAlgorithm(mBranchListPtr, Tnavigation, old_rMpr);


        if ( boost::math::isnan(regMatrix.sum()) )
        {
                std::cout << "Warning: Registration matrix contains 'nan' number, using identity matrix." << std::endl;
                return Eigen::Matrix4d::Identity();
        }

        if ( boost::math::isinf(regMatrix.sum()) )
        {
                std::cout << "Warning: Registration matrix contains 'inf' number, using identity matrix." << std::endl;
                return Eigen::Matrix4d::Identity();
        }

        std::cout << "prMt from bronchoscopyRegistration: " << std::endl;
        for (int i = 0; i < 4; i++)
                std::cout << regMatrix.row(i) << std::endl;

        return regMatrix;
}

Eigen::Matrix4d BronchoscopyRegistration::runBronchoscopyRegistrationImage2Image(vtkPolyDataPtr centerlineFixed, vtkPolyDataPtr centerlineMoving)
{

        int numberOfGenerations = 4;
        Eigen::Matrix4d regMatrix;

        BranchListPtr branchesFixed;
        BranchListPtr branchesMoving;
        branchesFixed = processCenterlineImage2Image(centerlineFixed, numberOfGenerations);
        branchesMoving = processCenterlineImage2Image(centerlineMoving, numberOfGenerations);

        regMatrix = registrationAlgorithmImage2Image(branchesFixed, branchesMoving);


        if ( boost::math::isnan(regMatrix.sum()) )
        {
                CX_LOG_WARNING() << "Registration matrix contains 'nan' number, using identity matrix.";
                return Eigen::Matrix4d::Identity();
        }

        if ( boost::math::isinf(regMatrix.sum()) )
        {
                CX_LOG_WARNING() << "Registration matrix contains 'inf' number, using identity matrix.";
                return Eigen::Matrix4d::Identity();
        }

        return regMatrix;
}

bool BronchoscopyRegistration::isCenterlineProcessed()
{
        return mCenterlineProcessed;
}


BronchoscopyRegistration::~BronchoscopyRegistration()
{

}

Eigen::MatrixXd makeTransformedMatrix(vtkPolyDataPtr linesPolyData, Transform3D rMd)
{
        vtkIdType N = linesPolyData->GetNumberOfPoints();
        Eigen::MatrixXd CLpoints(3,N);

        for(vtkIdType i = 0; i < N; i++)
        {
                double p[3];
                linesPolyData->GetPoint(i,p);
                Eigen::Vector3d position;
                position(0) = p[0]; position(1) = p[1]; position(2) = p[2];
                CLpoints.block(0 , i , 3 , 1) = rMd.coord(position);
        }

        return CLpoints;
}



}//namespace cx