InputMatrix::InputMatrix(std::istream& input)
{
START_COLLECT_TIME(readingInput, Counters::ReadingInput);
input >> _rowsCount;
input >> _qColsCount;
_qMatrix = new int[_rowsCount * _qColsCount];
_qMinimum = new int[_qColsCount];
_qMaximum = new int[_qColsCount];
for(auto j=0; j<_qColsCount; ++j) {
_qMinimum[j] = DASH;
_qMaximum[j] = DASH;
}
for(auto i=0; i<_rowsCount; ++i) {
for(auto j=0; j<_qColsCount; ++j) {
auto value = parseValue(input);
setFeature(i, j, value);
if (value != DASH) {
if (_qMinimum[j] == DASH || value < _qMinimum[j])
_qMinimum[j] = value;
if (_qMaximum[j] == DASH || _qMaximum[j] < value)
_qMaximum[j] = value;
}
}
}
input >> _rColsCount;
_rMatrix = new int[_rowsCount * _rColsCount];
for(auto i=0; i<_rowsCount; ++i) {
for(auto j=0; j<_rColsCount; ++j) {
setImage(i, j, parseValue(input));
}
}
_r2Matrix = new int[_rowsCount];
STOP_COLLECT_TIME(readingInput);
START_COLLECT_TIME(preparingInput, Counters::PreparingInput);
calcR2Matrix();
sortMatrix();
calcR2Indexes();
STOP_COLLECT_TIME(preparingInput);
}
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());
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);
}
}
}
}
}
