cxBronchoscopePositionProjection.cpp

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#include "cxBronchoscopePositionProjection.h"
#include <vtkPolyData.h>
#include "cxDoubleProperty.h"
#include "cxBranchList.h"
#include "cxBranch.h"
#include <boost/math/special_functions/fpclassify.hpp> // isnan
#include "cxLogger.h"


namespace cx
{

BronchoscopePositionProjection::BronchoscopePositionProjection():
        isPreviousProjectedPointSet(false),
        mBranchListPtr(new BranchList),
        mProjectedIndex(0),
        mUseAdvancedCenterlineProjection(false)
{
}

BronchoscopePositionProjection::BronchoscopePositionProjection(vtkPolyDataPtr centerline, Transform3D prMd):
        isPreviousProjectedPointSet(false),
        mProjectedIndex(0),
        mUseAdvancedCenterlineProjection(false)
{
    mCLpoints = this->getCenterlinePositions(centerline, prMd);
}

BronchoscopePositionProjection::~BronchoscopePositionProjection()
{
}

void BronchoscopePositionProjection::setRunFromWidget(bool runFromWidget)
{
        mRunFromWidget = runFromWidget;
}

void BronchoscopePositionProjection::setAdvancedCenterlineOption(bool useAdvancedCenterlineProjection)
{
        mUseAdvancedCenterlineProjection = useAdvancedCenterlineProjection;
}

void BronchoscopePositionProjection::createMaxDistanceToCenterlineOption(QDomElement root)
{
    mMaxDistanceToCenterline = DoubleProperty::initialize("Max distance to centerline (mm)", "",
        "Set max distance to centerline in mm", 30, DoubleRange(1, 100, 1), 0,
                                        root);
    mMaxDistanceToCenterline->setGuiRepresentation(DoubleProperty::grSLIDER);
}

DoublePropertyPtr BronchoscopePositionProjection::getMaxDistanceToCenterlineOption()
{
        return mMaxDistanceToCenterline;
}

double BronchoscopePositionProjection::getMaxDistanceToCenterlineValue()
{
        if (mRunFromWidget && mMaxDistanceToCenterline->getValue())
                mMaxDistanceToCenterlineValue = mMaxDistanceToCenterline->getValue();

        return mMaxDistanceToCenterlineValue;
}

void BronchoscopePositionProjection::createMaxSearchDistanceOption(QDomElement root)
{
    mMaxSearchDistance = DoubleProperty::initialize("Max search distance along centerline (mm)", "",
    "Set max search distance along centerline in mm", 20, DoubleRange(1, 100, 1), 0,
                    root);
    mMaxSearchDistance->setGuiRepresentation(DoubleProperty::grSLIDER);
}

DoublePropertyPtr BronchoscopePositionProjection::getMaxSearchDistanceOption()
{
        return mMaxSearchDistance;
}

double BronchoscopePositionProjection::getMaxSearchDistanceValue()
{
        if (mRunFromWidget && mMaxSearchDistance->getValue())
                mMaxSearchDistanceValue = mMaxSearchDistance->getValue();

        return mMaxSearchDistanceValue;
}

void BronchoscopePositionProjection::createAlphaOption(QDomElement root)
{
    mAlpha = DoubleProperty::initialize("Alpha ", "",
    "Weighting of position and orientation in projection (high alpha is giving orientations high weight).", 1.0, DoubleRange(0, 10, 0.1), 1, root);
    mAlpha->setGuiRepresentation(DoubleProperty::grSLIDER);
}

DoublePropertyPtr BronchoscopePositionProjection::getAlphaOption()
{
        return mAlpha;
}

double BronchoscopePositionProjection::getAlphaValue()
{
        if (mRunFromWidget && mAlpha->getValue())
                mAlphaValue = mAlpha->getValue();

        return mAlphaValue;
}

Eigen::MatrixXd BronchoscopePositionProjection::getCenterlinePositions(vtkPolyDataPtr centerline, Transform3D rMd)
{

        int N = centerline->GetNumberOfPoints();
        Eigen::MatrixXd CLpoints(3,N);
        for(vtkIdType i = 0; i < N; i++)
                {
                double p[3];
                centerline->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;
}

void BronchoscopePositionProjection::processCenterline(vtkPolyDataPtr centerline, Transform3D rMd, Transform3D rMpr)
{
        m_rMpr = rMpr;
        if (mBranchListPtr)
                mBranchListPtr->deleteAllBranches();

        mCLpoints = getCenterlinePositions(centerline, rMd);

        mBranchListPtr->findBranchesInCenterline(mCLpoints);
        //mBranchListPtr->interpolateBranchPositions(10);
    //mBranchListPtr->smoothBranchPositions();
        mBranchListPtr->smoothOrientations();

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

//Can be used instead of processCenterline(...) if you have a preprosessed branchList to be used in the registration process.
void BronchoscopePositionProjection::setBranchList(BranchListPtr branchList, Transform3D rMpr)
{
        if (!branchList)
                return;

        m_rMpr = rMpr;
        mBranchListPtr = branchList;
}

//Used when run without widget
void BronchoscopePositionProjection::setMaxDistanceToCenterline(double maxDistance)
{
        mMaxDistanceToCenterlineValue = maxDistance;
}

//Used when run without widget
void BronchoscopePositionProjection::setMaxSearchDistance(double maxDistance)
{
        mMaxSearchDistanceValue = maxDistance;
}

//Used when run without widget
void BronchoscopePositionProjection::setAlpha(double alpha)
{
        mAlphaValue = alpha;
}

Transform3D BronchoscopePositionProjection::findClosestPoint(Transform3D prMt, double maxDistance)
{
        Transform3D rMt = m_rMpr * prMt;
        Eigen::VectorXd toolPos  = rMt.matrix().topRightCorner(3 , 1);
        Eigen::MatrixXd::Index index;
        Transform3D new_rMt = rMt;

                Eigen::VectorXd P(mCLpoints.cols());
                for (int i = 0; i < mCLpoints.cols(); i++)
                {
                        double p0 = ( mCLpoints(0,i) - toolPos(0) );
                        double p1 = ( mCLpoints(1,i) - toolPos(1) );
                        double p2 = ( mCLpoints(2,i) - toolPos(2) );

                        P(i) = sqrt( p0*p0 + p1*p1 + p2*p2 );
                }

                P.minCoeff(&index);
                if (P.minCoeff() < maxDistance)
                {
                        new_rMt.matrix().topRightCorner(3 , 1) = mCLpoints.col(index);
                }

        Transform3D new_prMt = m_rMpr.inverse() * new_rMt;
        return new_prMt;
}

Transform3D BronchoscopePositionProjection::findClosestPointInBranches(Transform3D prMt, double maxDistance)
{
        Transform3D rMt = m_rMpr * prMt;
    Eigen::VectorXd toolPos  = rMt.matrix().topRightCorner(3 , 1);
        Transform3D new_rMt = rMt;

        double minDistance = 100000;
        int minDistancePositionIndex;
        BranchPtr minDistanceBranch;
        std::vector<BranchPtr> branches = mBranchListPtr->getBranches();
        for (int i = 0; i < branches.size(); i++)
        {
                Eigen::MatrixXd positions = branches[i]->getPositions();
                for (int j = 0; j < positions.cols(); j++)
                {
            double D = findDistance(positions.col(j), toolPos);
                        if (D < minDistance)
                        {
                                minDistance = D;
                                minDistanceBranch = branches[i];
                                minDistancePositionIndex = j;
                        }
                }
        }

                if (minDistance < maxDistance)
                {
                        Eigen::MatrixXd positions = minDistanceBranch->getPositions();
                        new_rMt.matrix().topRightCorner(3 , 1) = positions.col(minDistancePositionIndex);
                        mProjectedBranchPtr = minDistanceBranch;
                        mProjectedIndex = minDistancePositionIndex;
                        isPreviousProjectedPointSet = true;
            //new_rMt = updateProjectedCameraOrientation(new_rMt, mProjectedBranchPtr, mProjectedIndex);
                }
                else
                {
                        isPreviousProjectedPointSet = false;
                }

        Transform3D new_prMt = m_rMpr.inverse() * new_rMt;
        return new_prMt;
}

Transform3D BronchoscopePositionProjection::findClosestPointInSearchPositions(Transform3D prMt, double maxDistance)
{
        Transform3D rMt = m_rMpr * prMt;
        Eigen::VectorXd toolPos  = rMt.matrix().topRightCorner(3 , 1);
    Eigen::VectorXd toolOrientation  = rMt.matrix().block(0 , 2 , 3 , 1);
        Transform3D new_rMt = rMt;

        double minDistance = 100000;
        int minDistancePositionIndex;
        BranchPtr minDistanceBranch;
        for (int i = 0; i < mSearchBranchPtrVector.size(); i++)
        {
                Eigen::MatrixXd positions = mSearchBranchPtrVector[i]->getPositions();
                Eigen::MatrixXd orientations = mSearchBranchPtrVector[i]->getOrientations();

                //double D = findDistance(positions.col(mSearchIndexVector[i]), toolPos);
                double alpha = getAlphaValue();
                double D = findDistanceWithOrientation(positions.col(mSearchIndexVector[i]), toolPos, orientations.col(mSearchIndexVector[i]), toolOrientation, alpha);
                if (D < minDistance)
                {
                        minDistance = D;
                        minDistanceBranch = mSearchBranchPtrVector[i];
                        minDistancePositionIndex = mSearchIndexVector[i];
                }
        }
        if (minDistance < maxDistance)
        {
                Eigen::MatrixXd positions = minDistanceBranch->getPositions();
                new_rMt.matrix().topRightCorner(3 , 1) = positions.col(minDistancePositionIndex);
                mProjectedBranchPtr = minDistanceBranch;
                mProjectedIndex = minDistancePositionIndex;
                isPreviousProjectedPointSet = true;
        //new_rMt = updateProjectedCameraOrientation(new_rMt, mProjectedBranchPtr, mProjectedIndex);
        }
        else
        {
                isPreviousProjectedPointSet = false;
        }

        Transform3D new_prMt = m_rMpr.inverse() * new_rMt;
        return new_prMt;

}

void BronchoscopePositionProjection::findSearchPositions(double maxSearchDistance)
{
        mSearchBranchPtrVector.clear();
        mSearchIndexVector.clear();
        mSearchBranchPtrVector.push_back(mProjectedBranchPtr);
        mSearchIndexVector.push_back(mProjectedIndex);
        double currentSearchDistance = 0;

        Eigen::MatrixXd positions = mProjectedBranchPtr->getPositions();
        if (mProjectedIndex < positions.cols() - 1)
        {
        currentSearchDistance = findDistance( positions.col(mProjectedIndex), positions.col(mProjectedIndex+1) );
                searchBranchDown(mProjectedBranchPtr, mProjectedIndex + 1, currentSearchDistance, maxSearchDistance);
        }
        if (mProjectedIndex > 0)
        {
        currentSearchDistance = findDistance( positions.col(mProjectedIndex), positions.col(mProjectedIndex-1) );
                searchBranchUp(mProjectedBranchPtr, mProjectedIndex - 1, currentSearchDistance, maxSearchDistance);
        }

}

void BronchoscopePositionProjection::searchBranchUp(BranchPtr searchBranchPtr, int startIndex, double currentSearchDistance, double maxSearchDistance)
{
        Eigen::MatrixXd positions = searchBranchPtr->getPositions();
        mSearchBranchPtrVector.push_back(searchBranchPtr);
        mSearchIndexVector.push_back(startIndex);
        for (int i = startIndex-1; i>=0; i--)
        {
        currentSearchDistance = currentSearchDistance + findDistance( positions.col(i+1), positions.col(i) );
                if (currentSearchDistance < maxSearchDistance)
                {
                        mSearchBranchPtrVector.push_back(searchBranchPtr);
                        mSearchIndexVector.push_back(i);
                }
                else
                        return;
        }
        BranchPtr parentBranchPtr = searchBranchPtr->getParentBranch();

    if (parentBranchPtr)
    {
        std::vector<BranchPtr> childBranches = parentBranchPtr->getChildBranches();
        searchBranchUp(parentBranchPtr, parentBranchPtr->getPositions().cols()-1, currentSearchDistance, maxSearchDistance);
        for (int i = 0; i < childBranches.size(); i++)
            if (childBranches[i] != searchBranchPtr)
                searchBranchDown(childBranches[i], 0, currentSearchDistance, maxSearchDistance);
    }
}

void BronchoscopePositionProjection::searchBranchDown(BranchPtr searchBranchPtr, int startIndex, double currentSearchDistance, double maxSearchDistance)
{
        Eigen::MatrixXd positions = searchBranchPtr->getPositions();
        mSearchBranchPtrVector.push_back(searchBranchPtr);
        mSearchIndexVector.push_back(startIndex);
        for (int i = startIndex+1; i<positions.cols(); i++)
        {
        currentSearchDistance = currentSearchDistance + findDistance( positions.col(i), positions.col(i-1) );
                if (currentSearchDistance < maxSearchDistance)
                {
                        mSearchBranchPtrVector.push_back(searchBranchPtr);
                        mSearchIndexVector.push_back(i);
                }
                else
                        return;
        }
        std::vector<BranchPtr> childBranches = searchBranchPtr->getChildBranches();
        for (int i = 0; i < childBranches.size(); i++)
                searchBranchDown(childBranches[i], 0,currentSearchDistance,maxSearchDistance);
}

Transform3D BronchoscopePositionProjection::findProjectedPoint(Transform3D prMt, double maxDistance, double maxSearchDistance)
{
    //double maxSearchDistance = 25; //mm
    Transform3D new_prMt;
        if (isPreviousProjectedPointSet)
        {
                findSearchPositions(maxSearchDistance);
        new_prMt = findClosestPointInSearchPositions(prMt, maxDistance);
        }
        else
        new_prMt = findClosestPointInBranches(prMt, maxDistance);

        return new_prMt;
}

bool BronchoscopePositionProjection::isAdvancedCenterlineProjectionSelected()
{
        return mUseAdvancedCenterlineProjection;
}

double findDistance(Eigen::MatrixXd p1, Eigen::MatrixXd p2)
{
        double d0 = p1(0) - p2(0);
        double d1 = p1(1) - p2(1);
        double d2 = p1(2) - p2(2);

        double D = sqrt( d0*d0 + d1*d1 + d2*d2 );

        return D;
}

double findDistanceWithOrientation(Eigen::VectorXd position1, Eigen::VectorXd position2, Eigen::VectorXd orientation1, Eigen::VectorXd orientation2, double alpha)
{
    double d0 = position1(0) - position2(0);
    double d1 = position1(1) - position2(1);
    double d2 = position1(2) - position2(2);
    double o0 = fmod( orientation2(0) - orientation1(0) , 2 );
    double o1 = fmod( orientation2(1) - orientation1(1) , 2 );
    double o2 = fmod( orientation2(2) - orientation1(2) , 2 );

    double P = sqrt( d0*d0 + d1*d1 + d2*d2 );
    double O = sqrt( o0*o0 + o1*o1 + o2*o2 );

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

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

    double D = P + alpha * O;

    return D;
}

Transform3D BronchoscopePositionProjection::updateProjectedCameraOrientation(Transform3D prMt, BranchPtr branch, int index)
{
        Eigen::MatrixXd branchPositions = branch->getPositions();
        int numberOfPositions = branchPositions.cols();
        int lookBackIndex; // = std::max(0 , index-20);
        Vector3D lookBackPosition;
//      if (index >=20){
//              lookBackIndex = index-20;
//              lookBackPosition = branchPositions.col(lookBackIndex);
//      }
//      else if (branch->getParentBranch())
//      {
//              Eigen::MatrixXd parentBranchPositions = branch->getParentBranch()->getPositions();
//              lookBackIndex = parentBranchPositions.cols() - 1 - index - 20;
//              lookBackIndex = std::max(0 , index-20);
//      }
//      else
//      {
//              lookBackIndex = 0;
//              lookBackPosition = branchPositions.col(lookBackIndex);
//      }

    lookBackIndex = std::max(0 , index-20);
    lookBackPosition = branchPositions.col(lookBackIndex);
    int lookForwardIndex = std::min(numberOfPositions-1 , index+20);
        Vector3D lookForwardPosition = branchPositions.col(lookForwardIndex);

        Vector3D viewDirection = (lookForwardPosition - lookBackPosition).normalized();

    prMt.matrix().col(2).head(3) = viewDirection;

        return prMt;
}

} /* namespace cx */