cxBranchList.cpp

Go to the documentation of this file.

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

Copyright (c) 2008-2014, SINTEF Department of Medical Technology
All rights reserved.

Redistribution and use in source and binary forms, with or without 
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, 
   this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, 
   this list of conditions and the following disclaimer in the documentation 
   and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors 
   may be used to endorse or promote products derived from this software 
   without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=========================================================================*/
#include "cxBranchList.h"
#include "cxBranch.h"
#include "cxMesh.h"
#include "cxVector3D.h"
#include <vtkPolyData.h>
#include "vtkCardinalSpline.h"

typedef vtkSmartPointer<class vtkCardinalSpline> vtkCardinalSplinePtr;

namespace cx
{

BranchList::BranchList()
{

}


BranchList::~BranchList()
{
//      for (int i = 0; i < mBranches.size(); i++)
//              mBranches[i]->~Branch();
}

void BranchList::addBranch(BranchPtr b)
{
        mBranches.push_back(b);
}

void BranchList::deleteBranch(BranchPtr b)
{
        for( int i = 0; i < mBranches.size(); i++ )
        {
                if (b == mBranches[i])
                {
                        mBranches.erase(mBranches.begin() + i);
                        return;
                }
        }
}

void BranchList::deleteAllBranches()
{
        mBranches.clear();
}

std::vector<BranchPtr> BranchList::getBranches()
{
        return mBranches;
}

void BranchList::selectGenerations(int maxGeneration)
{
        std::vector<int> branchNumbersToBeDeleted;
        for( int i = 0; i < mBranches.size(); i++ )
        {
                int generationCounter = 1;
                BranchPtr currentBranch = mBranches[i];
                while (currentBranch->getParentBranch()){
                        generationCounter++;
                        currentBranch = currentBranch->getParentBranch();
                        if (generationCounter > maxGeneration)
                        {
                                branchNumbersToBeDeleted.push_back(i);
                                break;
                        }
                }

        }

        for ( int i = branchNumbersToBeDeleted.size() - 1; i >= 0; i-- )
                deleteBranch(mBranches[branchNumbersToBeDeleted[i]]);
}


void BranchList::calculateOrientations()
{
        for (int i = 0; i < mBranches.size(); i++)
        {
                Eigen::MatrixXd positions = mBranches[i]->getPositions();
                Eigen::MatrixXd diff = positions.rightCols(positions.cols() - 1) - positions.leftCols(positions.cols() - 1);
                Eigen::MatrixXd orientations(positions.rows(),positions.cols());
                orientations.leftCols(orientations.cols() - 1) = diff / diff.norm();
                orientations.rightCols(1) = orientations.col(orientations.cols() - 1);
                mBranches[i]->setOrientations(orientations);
        }
}

void BranchList::smoothOrientations()
{
        for (int i = 0; i < mBranches.size(); i++)
        {
                Eigen::MatrixXd orientations = mBranches[i]->getOrientations();
                Eigen::MatrixXd newOrientations(orientations.rows(),orientations.cols());
                int numberOfColumns = orientations.cols();
                for (int j = 0; j < numberOfColumns; j++)
                {
                        newOrientations.col(j) = orientations.block(0,std::max(j-2,0),orientations.rows(),std::min(5,numberOfColumns-j)).rowwise().mean(); //smoothing
                        newOrientations.col(j) = newOrientations.col(j) / newOrientations.col(j).norm(); // normalizing
                }
                mBranches[i]->setOrientations(newOrientations);
        }
}

void BranchList::interpolateBranchPositions(int interpolationFactor){

        for (int i = 0; i < mBranches.size(); i++)
        {
                Eigen::MatrixXd positions = mBranches[i]->getPositions();
                std::vector<Eigen::Vector3d> interpolatedPositions;
                for (int j = 0; j < positions.cols()-1; j++)
                {
                        for (int k = 0; k < interpolationFactor; k++){
                                Eigen::Vector3d interpolationPoint;
                                interpolationPoint[0] = (positions(0,j)*(interpolationFactor-k) + positions(0,j+1)*(k) ) / interpolationFactor;
                                interpolationPoint[1] = (positions(1,j)*(interpolationFactor-k) + positions(1,j+1)*(k) ) / interpolationFactor;
                                interpolationPoint[2] = (positions(2,j)*(interpolationFactor-k) + positions(2,j+1)*(k) ) / interpolationFactor;
                                interpolatedPositions.push_back(interpolationPoint);
                        }
                }
                Eigen::MatrixXd interpolationResult(3 , interpolatedPositions.size());
                for (int j = 0; j < interpolatedPositions.size(); j++)
                {
                        interpolationResult(0,j) = interpolatedPositions[j](0);
                        interpolationResult(1,j) = interpolatedPositions[j](1);
                        interpolationResult(2,j) = interpolatedPositions[j](2);
                }
                mBranches[i]->setPositions(interpolationResult);
        }

}

void BranchList::smoothBranchPositions()
{
        for (int i = 0; i < mBranches.size(); i++)
        {
                Eigen::MatrixXd positions = mBranches[i]->getPositions();
                int numberOfInputPoints = positions.cols();
        int controlPointFactor = 10;
                int numberOfControlPoints = numberOfInputPoints / controlPointFactor;

                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 j=0; j<numberOfControlPoints; j++)
                        {
                                int indexP = (j*numberOfInputPoints)/numberOfControlPoints;

                                splineX->AddPoint(indexP,positions(0,indexP));
                                splineY->AddPoint(indexP,positions(1,indexP));
                                splineZ->AddPoint(indexP,positions(2,indexP));
                        }
                        //Always add the last point to complete spline
                        splineX->AddPoint(numberOfInputPoints-1,positions(0,numberOfInputPoints-1));
                        splineY->AddPoint(numberOfInputPoints-1,positions(1,numberOfInputPoints-1));
                        splineZ->AddPoint(numberOfInputPoints-1,positions(2,numberOfInputPoints-1));

                        //evaluate spline - get smoothed positions
                        Eigen::MatrixXd smoothingResult(3 , numberOfInputPoints);
                        for(int j=0; j<numberOfInputPoints; j++)
                        {
                                double splineParameter = j;
                                smoothingResult(0,j) = splineX->Evaluate(splineParameter);
                                smoothingResult(1,j) = splineY->Evaluate(splineParameter);
                                smoothingResult(2,j) = splineZ->Evaluate(splineParameter);
                        }
                        mBranches[i]->setPositions(smoothingResult);
                }
        }
}

void BranchList::findBranchesInCenterline(Eigen::MatrixXd positions)
{
        positions = sortMatrix(2,positions);
        Eigen::MatrixXd positionsNotUsed = positions;

//      int minIndex;
        int index;
        int splitIndex;
        Eigen::MatrixXd::Index startIndex;
        BranchPtr branchToSplit;
    while (positionsNotUsed.cols() > 0)
        {
                if (!mBranches.empty())
                {
                        double minDistance = 1000;
                        for (int i = 0; i < mBranches.size(); i++)
                        {
                                std::pair<std::vector<Eigen::MatrixXd::Index>, Eigen::VectorXd> distances;
                                distances = dsearchn(positionsNotUsed, mBranches[i]->getPositions());
                                double d = distances.second.minCoeff(&index);
                                if (d < minDistance)
                                {
                                        minDistance = d;
                                        branchToSplit = mBranches[i];
                                        startIndex = index;
                                        if (minDistance < 2)
                                                break;
                                }
                        }
                        std::pair<Eigen::MatrixXd::Index, double> dsearchResult = dsearch(positionsNotUsed.col(startIndex) , branchToSplit->getPositions());
                        splitIndex = dsearchResult.first;
                }
                else //if this is the first branch. Select the top position (Trachea).
                        startIndex = positionsNotUsed.cols() - 1;

                std::pair<Eigen::MatrixXd,Eigen::MatrixXd > connectedPointsResult = findConnectedPointsInCT(startIndex , positionsNotUsed);
                Eigen::MatrixXd branchPositions = connectedPointsResult.first;
                positionsNotUsed = connectedPointsResult.second;

                if (branchPositions.cols() >= 5) //only include brances of length >= 5 points
                {
                        BranchPtr newBranch = BranchPtr(new Branch());
                        newBranch->setPositions(branchPositions);
                        mBranches.push_back(newBranch);

                        if (mBranches.size() > 1) // do not try to split another branch when the first branch is processed
                        {
                                if ((splitIndex + 1 >= 5) && (branchToSplit->getPositions().cols() - splitIndex - 1 >= 5))
                                        //do not split branch if the new branch is close to the edge of the branch
                                        //if the new branch is not close to one of the edges of the
                                        //connected existing branch: Split the existing branch
                                {
                                        BranchPtr newBranchFromSplit = BranchPtr(new Branch());
                                        Eigen::MatrixXd branchToSplitPositions = branchToSplit->getPositions();
                                        newBranchFromSplit->setPositions(branchToSplitPositions.rightCols(branchToSplitPositions.cols() - splitIndex - 1));
                                        branchToSplit->setPositions(branchToSplitPositions.leftCols(splitIndex + 1));
                                        mBranches.push_back(newBranchFromSplit);
                                        newBranchFromSplit->setParentBranch(branchToSplit);
                                        newBranch->setParentBranch(branchToSplit);
                                        newBranchFromSplit->setChildBranches(branchToSplit->getChildBranches());
                                        branchVector branchToSplitChildren = branchToSplit->getChildBranches();
                                        for (int i = 0; i < branchToSplitChildren.size(); i++)
                                                branchToSplitChildren[i]->setParentBranch(newBranchFromSplit);
                                        branchToSplit->deleteChildBranches();
                                        branchToSplit->addChildBranch(newBranchFromSplit);
                                        branchToSplit->addChildBranch(newBranch);
                                }
                                else if (splitIndex + 1 < 5)
                                         // If the new branch is close to the start of the existing
                                         // branch: Connect it to the same position start as the
                                         // existing branch
                                {
                                        newBranch->setParentBranch(branchToSplit->getParentBranch());
                                        if(branchToSplit->getParentBranch())
                                                branchToSplit->getParentBranch()->addChildBranch(newBranch);
                                }
                                else if (branchToSplit->getPositions().cols() - splitIndex - 1 < 5)
                                        // If the new branch is close to the end of the existing
                                        // branch: Connect it to the end of the existing branch
                                {
                                        newBranch->setParentBranch(branchToSplit);
                                        branchToSplit->addChildBranch(newBranch);
                                }

                        }

                }
        }
}


BranchListPtr BranchList::removePositionsForLocalRegistration(Eigen::MatrixXd trackingPositions, double maxDistance)
{
        BranchListPtr retval = BranchListPtr(new BranchList());
        BranchPtr b;
        for (int i = 0; i < mBranches.size(); i++)
        {
                b = BranchPtr(new Branch());
                b->setPositions(mBranches[i]->getPositions());
                b->setOrientations(mBranches[i]->getOrientations());
                retval->addBranch(b);
        }

        std::vector<BranchPtr> branches = retval->getBranches();
        Eigen::MatrixXd positions;
        Eigen::MatrixXd orientations;
        for (int i = 0; i < branches.size(); i++)
        {
                positions = branches[i]->getPositions();
                orientations = branches[i]->getOrientations();
                std::pair<std::vector<Eigen::MatrixXd::Index>, Eigen::VectorXd> distanceData;
                distanceData = dsearchn(positions, trackingPositions);
                Eigen::VectorXd distance = distanceData.second;
        for (int j = positions.cols() - 1; j >= 0; j--)
                {
                        if (distance(j) > maxDistance)
                        {
                                positions = eraseCol(j, positions);
                                orientations = eraseCol(j, orientations);
                        }
                }
                branches[i]->setPositions(positions);
                branches[i]->setOrientations(orientations);
        }
        return retval;
}

Eigen::MatrixXd sortMatrix(int rowNumber, Eigen::MatrixXd matrix)
{
        for (int i = 0; i < matrix.cols() - 1; i++)  {
           for (int j = i + 1; j < matrix.cols(); j++) {
                  if (matrix(rowNumber,i) > matrix(rowNumber,j)){
                          matrix.col(i).swap(matrix.col(j));
                  }
           }
        }
return matrix;
}



Eigen::MatrixXd eraseCol(int removeIndex, Eigen::MatrixXd positions)
{
        positions.block(0 , removeIndex , positions.rows() , positions.cols() - removeIndex - 1) = positions.rightCols(positions.cols() - removeIndex - 1);
    positions.conservativeResize(Eigen::NoChange, positions.cols() - 1);
        return positions;
}

std::pair<Eigen::MatrixXd::Index, double> dsearch(Eigen::Vector3d p, Eigen::MatrixXd positions)
{
        Eigen::MatrixXd::Index index;
        // find nearest neighbour
        (positions.colwise() - p).colwise().squaredNorm().minCoeff(&index);
        double d = (positions.col(index) - p).norm();

        return std::make_pair(index , d);
}

std::pair<std::vector<Eigen::MatrixXd::Index>, Eigen::VectorXd > dsearchn(Eigen::MatrixXd p1, Eigen::MatrixXd p2)
{
        Eigen::MatrixXd::Index index;
        std::vector<Eigen::MatrixXd::Index> indexVector;
        Eigen::VectorXd D(p1.cols());
        for (int i = 0; i < p1.cols(); i++)
        {
                // find nearest neighbour
                (p2.colwise() - p1.col(i)).colwise().squaredNorm().minCoeff(&index);
                D(i) = (p2.col(index) - p1.col(i)).norm();
                indexVector.push_back(index);
        }
        return std::make_pair(indexVector , D);
}

std::pair<Eigen::MatrixXd,Eigen::MatrixXd > findConnectedPointsInCT(int startIndex , Eigen::MatrixXd positionsNotUsed)
{
    //Eigen::MatrixXd branchPositions(positionsNotUsed.rows(), positionsNotUsed.cols());
        Eigen::MatrixXd thisPosition(3,1);
    std::vector<Eigen::MatrixXd> branchPositionsVector;
        thisPosition = positionsNotUsed.col(startIndex);
    branchPositionsVector.push_back(thisPosition); //add first position to branch
        positionsNotUsed = eraseCol(startIndex,positionsNotUsed);; //remove first position from list of remaining points

    while (positionsNotUsed.cols() > 0)
        {
                std::pair<Eigen::MatrixXd::Index, double > minDistance = dsearch(thisPosition, positionsNotUsed);
                Eigen::MatrixXd::Index index = minDistance.first;
        double d = minDistance.second;
                if (d > 3) // more than 3 mm distance to closest point --> branch is compledted
                        break;

                thisPosition = positionsNotUsed.col(index);
                positionsNotUsed = eraseCol(index,positionsNotUsed);
                //add position to branch
        branchPositionsVector.push_back(thisPosition);

        }

    Eigen::MatrixXd branchPositions(3,branchPositionsVector.size());

    for (int j = 0; j < branchPositionsVector.size(); j++)
    {
        branchPositions.block(0,j,3,1) = branchPositionsVector[j];
    }

    return std::make_pair(branchPositions, positionsNotUsed);
}


}//namespace cx