int main (int argc, char** argv)
{
pcl::PointCloud<pcl::PointXYZ>::Ptr model (new pcl::PointCloud<pcl::PointXYZ>);
pcl::PointCloud<pcl::PointXYZ>::Ptr scene (new pcl::PointCloud<pcl::PointXYZ>);
pcl::PointCloud<pcl::PointXYZ>::Ptr output (new pcl::PointCloud<pcl::PointXYZ>);
// Fill in the CloudIn data
pcl::io::loadPCDFile<pcl::PointXYZ> ("../models/arm_segment_last.pcd", *model);
std::cout << "Model " << model->points.size () << " points." << std::endl;
pcl::io::loadPCDFile<pcl::PointXYZ> ("../queries/arm_segment_last_query1.pcd", *scene);
std::cout << "Query " << scene->points.size () << " points." << std::endl;
Eigen::Matrix4f final_transform;
pairAlign (model, scene, output, final_transform);
}
void FastPairwiseAlign::pairwiseAlign(Alignment *alignPtr, DistMatrix *distMat, int iStart,
int iEnd, int jStart, int jEnd)
{
try
{
if(distMat->getSize() != alignPtr->getNumSeqs() + 1)
{
cerr << "The distance matrix is not the right size!\n"
<< "Need to terminate program.\n";
exit(1);
}
if((iStart < 0) || (iEnd < iStart) || (jStart < 0) || (jEnd < jStart))
{
cout << "The range for pairwise Alignment is incorrect.\n"
<< "Need to terminate program.\n";
exit(1);
}
int i, j, dsr;
double calcScore;
bool _DNAFlag = userParameters->getDNAFlag();
_maxAlnLength = alignPtr->getMaxAlnLength();
int num = (2 * _maxAlnLength) + 1;
accum.ResizeRect(5, num);
displ.resize(num);
slopes.resize(num);
diagIndex.resize(num);
zza.resize(_maxAlnLength + 1);
zzb.resize(_maxAlnLength + 1);
zzc.resize(_maxAlnLength + 1);
zzd.resize(_maxAlnLength + 1);
if (_DNAFlag)
{
userParameters->setDNAParams();
}
else
{
userParameters->setProtParams();
}
cout << "\n\n";
for (i = iStart + 1; i <= iEnd; ++i)
{
const vector<int>* _seqIPtr = alignPtr->getSequence(i);
int _seqILength = alignPtr->getSeqLength(i);
if (_DNAFlag)
{
makeNPtrs(zza, zzc, _seqIPtr, _seqILength);
}
else
{
makePPtrs(zza, zzc, _seqIPtr, _seqILength);
}
double _score;
for (j = jStart + 2 > i+1 ? jStart + 2 : i+1; j <= jEnd; ++j)
{
const vector<int>* _seqJPtr = alignPtr->getSequence(j);
int _seqJLength = alignPtr->getSeqLength(j);
if (_DNAFlag)
{
makeNPtrs(zzb, zzd, _seqJPtr, _seqJLength);
}
else
{
makePPtrs(zzb, zzd, _seqJPtr, _seqJLength);
}
pairAlign(_seqIPtr, _seqILength, _seqJLength);
if (!maxSoFar)
{
calcScore = 0.0;
}
else
{
calcScore = (double)accum[0][maxSoFar];
if (userParameters->getPercent())
{
dsr = (_seqILength < _seqJLength) ? _seqILength
: _seqJLength;
calcScore = (calcScore / (double)dsr) *100.0;
}
}
_score = (100.0 - calcScore) / 100.0;
distMat->SetAt(i, j, _score);
//distMat->SetAt(j, i, _score); /* distMat symmetric, FS, 2009-04-06 */
if(userParameters->getDisplayInfo())
{
if (calcScore > 0.1)
{
utilityObject->info("Sequences (%d:%d) Aligned. Score: %lg",
i, j, calcScore);
}
else
{
utilityObject->info("Sequences (%d:%d) Not Aligned", i, j);
}
}
}
}
accum.clearArray();
displ.clear();
slopes.clear();
diagIndex.clear();
zza.clear();
zzb.clear();
zzc.clear();
zzd.clear();
}
catch(const exception& e)
{
cerr << "An exception has occured in the FastPairwiseAlign class.\n"
<< e.what() << "\n";
exit(1);
}
}
