Neurons Neurons::operator & (const Circle<Micron> & circle)
{
CHECK_CONTAINER_MICROCIRCUIT_POINTER(*this);
Neurons result(_microcircuit.lock());
//! \todo Fix commented out code below. (TT)
//result._description = _description + " within a radius of " +
// boost::lexical_cast<const Word>(radius) + " from the center point ("
// +
// boost::lexical_cast<const Word>(circle.center().x()) + ", " +
// boost::lexical_cast<const Word>(circle.center().z()) + ")";
for (Neurons::iterator i = begin(); i != end(); ++i )
{
const Neuron & neuron = * i;
Micron distance =
std::sqrt((neuron.position().x() - circle.center().x()) *
(neuron.position().x() - circle.center().x()) +
(neuron.position().z() - circle.center().z()) *
(neuron.position().z() - circle.center().z()));
#ifndef NDEBUG
std::cout << "Distance:" << distance << std::endl;
#endif
if (distance <= circle.radius())
{
#ifndef NDEBUG
std::cout << "Neuron a" << neuron.gid() << " at position "
<< neuron.position() << " is within a radius of "
<< circle.radius() << std::endl;
#endif
result.insert(i.ptr());
}
#ifndef NDEBUG
else
{
std::cout << "Neuron a" << neuron.gid() << " at position "
<< neuron.position() << " is NOT within a radius of "
<< circle.radius() << std::endl;
}
#endif
}
return result;
}
int main(int argc, const char* argv[])
{
/*
* Build 48 Index with Links
*/
// Load Circuit
Experiment experiment;
experiment.open(blue_config_filename);
Microcircuit & microcircuit = experiment.microcircuit();
const Targets & targets = experiment.targets();
const Cell_Target target = targets.cell_target("Column");
microcircuit.load(target, NEURONS | MORPHOLOGIES);
//Make Neuron Rtrees
ISpatialIndex *neuronTrees[MORPHOLOGIES_COUNT];
string *morphologyLabels[MORPHOLOGIES_COUNT];
int cm=0;
Morphologies & myMorphologies = microcircuit.morphologies();
Morphologies::iterator myMorphologiesEnd = myMorphologies.end();
for (Morphologies::iterator i = myMorphologies.begin(); i != myMorphologiesEnd; ++i)
{
morphologyLabels[cm] = i->label();
neuronTrees[cm] = RTree::createNewRTree (createNewMemoryStorageManager(), 0.7, 127, 127, 3,RTree::RV_RSTAR,indexIdentifier);
cm++;
}
Neurons & myNeurons = microcircuit.neurons();
Neurons::iterator myNeuronsEnd = myNeurons.end();
for (Neurons::iterator i = myNeurons.begin(); i != myNeuronsEnd; ++i)
{
cm=0;
for (cm=0;cm<MORPHOLOGIES_COUNT;cm++)
if (strcmp(i->morphology().label(),morphologyLabels[cm])==0) break;
Transform_3D<Micron> trafo = i->global_transform();
Sections mySections = i->morphology().all_sections();
Sections::iterator mySectionsEnd = mySections.end();
for (Sections::iterator s = mySections.begin(); s != mySectionsEnd; ++s)
{
Segments segments = s->segments();
Segments::const_iterator segments_end = segments.end();
for (Segments::const_iterator j = segments.begin(); j != segments_end ; ++j)
{
vect plow, phigh;
get_segment_mbr (*j, trafo, &plow, &phigh);
SpatialIndex::Region mbr = SpatialIndex::Region(plow.data(),phigh.data(),3);
std::stringstream strStream;
strStream << i->gid() <<"-"<< s->id()<< "-" << j->id();
neuronTrees[cm]->insertData (strStream.str().length(), (byte*)(strStream.str().c_str()), mbr, segmentid);
}
}
}
// Make Morphology Rtrees
Morphologies & myMorphologies = microcircuit.morphologies();
Morphologies::iterator myMorphologiesEnd = myMorphologies.end();
for (Morphologies::iterator i = myMorphologies.begin(); i != myMorphologiesEnd; ++i)
{
cout << "Indexing Morphology: " << i->label();
string baseName = i->label();
IStorageManager* diskfile = StorageManager::createNewDiskStorageManager(baseName, 4096);
ISpatialIndex *tree = RTree::createNewRTree (*diskfile, 0.7, 127, 127, 3,RTree::RV_RSTAR,indexIdentifier);
indexIdentifier++; segmentid=0;
Sections mySections = i->all_sections();
Sections::iterator mySectionsEnd = mySections.end();
for (Sections::iterator s = mySections.begin(); s != mySectionsEnd; ++s)
{
Segments segments = s->segments();
Segments::const_iterator segments_end = segments.end();
for (Segments::const_iterator j = segments.begin(); j != segments_end ; ++j)
{
Box<bbp::Micron> Mbr = AABBCylinder::calculateAABBForCylinder(j->begin().center(),
j->begin().radius(),j->end().center(),j->begin().radius());
vect plow, phigh;
plow[0] = Mbr.center().x() - Mbr.dimensions().x() / 2;
phigh[0] = Mbr.center().x() + Mbr.dimensions().x() / 2;
plow[1] = Mbr.center().y() - Mbr.dimensions().y() / 2;
phigh[1] = Mbr.center().y() + Mbr.dimensions().y() / 2;
plow[2] = Mbr.center().z() - Mbr.dimensions().z() / 2;
phigh[2] = Mbr.center().z() + Mbr.dimensions().z() / 2;
SpatialIndex::Region mbr = SpatialIndex::Region(plow.data(),phigh.data(),3);
std::stringstream strStream;
strStream << s->id()<< "-" << j->id();
tree->insertData (strStream.str().length(), (byte*)(strStream.str().c_str()), mbr, segmentid);
segmentid++;
}
}
cout << ".. Total Segments: " << segmentid << "\n";
tree->~ISpatialIndex();
diskfile->~IStorageManager();
}
// PRELOAD the Trees amd Neuron Morphology Mapping
ISpatialIndex *neurons[NEURONS_COUNT];
global_transformer *transforms[NEURONS_COUNT];
int cm=0;
int cn=0;
string baseName = "";
Morphologies & myMorphologies = microcircuit.morphologies();
Neurons & myNeurons = microcircuit.neurons();
cout << "PreLoading Mappings \n";
Morphologies::iterator myMorphologiesEnd = myMorphologies.end();
for (Morphologies::iterator m = myMorphologies.begin(); m != myMorphologiesEnd; ++m)
{
baseName = m->label();
m->
IStorageManager* diskfile = StorageManager::loadDiskStorageManager(baseName);
trees[cm] = RTree::loadRTree(*diskfile, 1);
std::cout << "Checking R-tree structure... ";
if (!trees[cm]->isIndexValid()) std::cerr << "R-tree internal checks failed!\n"; else std::cout << "OK\n";
IStatistics * tree_stats;
trees[cm]->getStatistics (&tree_stats);
cout << *tree_stats;
Neurons::iterator myNeuronsEnd = myNeurons.end();
for (Neurons::iterator n = myNeurons.begin(); n != myNeuronsEnd; ++n)
{
if (strcmp(n->morphology().label().c_str(),m->label().c_str())==0)
{
transforms[cn] = n->global_transform().inverse();
neurons[cn] = trees[cm];
}
cn++;
if (cn>=NEURONS_COUNT) break;
}
cn=0;cm++;
}
/*
* Query the Index
*/
}
int main(int argc, const char* argv[])
{
const URI blue_config_filename(argv[1]);
try {
// LOADING CURCUIT
Experiment experiment;
experiment.open(blue_config_filename);
Microcircuit & microcircuit = experiment.microcircuit();
const Targets & targets = experiment.targets();
const Cell_Target target = targets.cell_target("Column");
microcircuit.load(target, NEURONS | MORPHOLOGIES);
// PRELOAD the Trees amd Neuron Morphology Mapping
ISpatialIndex *trees[MORPHOLOGIES_COUNT];
ISpatialIndex *neurons[NEURONS_COUNT];
global_transformer *transforms[NEURONS_COUNT];
int cm=0;
int cn=0;
string baseName = "";
Morphologies & myMorphologies = microcircuit.morphologies();
Neurons & myNeurons = microcircuit.neurons();
cout << "PreLoading Mappings \n";
Morphologies::iterator myMorphologiesEnd = myMorphologies.end();
for (Morphologies::iterator m = myMorphologies.begin(); m != myMorphologiesEnd; ++m)
{
baseName = m->label();
IStorageManager* diskfile = StorageManager::loadDiskStorageManager(baseName);
trees[cm] = RTree::loadRTree(*diskfile, 1);
std::cout << "Checking R-tree structure... ";
if (!trees[cm]->isIndexValid()) std::cerr << "R-tree internal checks failed!\n"; else std::cout << "OK\n";
IStatistics * tree_stats;
trees[cm]->getStatistics (&tree_stats);
cout << *tree_stats;
Neurons::iterator myNeuronsEnd = myNeurons.end();
for (Neurons::iterator n = myNeurons.begin(); n != myNeuronsEnd; ++n)
{
if (strcmp(n->morphology().label().c_str(),m->label().c_str())==0)
{
transforms[cn] = n->global_transform().inverse();
neurons[cn] = trees[cm];
}
cn++;
if (cn>=NEURONS_COUNT) break;
}
cn=0;cm++;
}
/*
// SINGLE QUERY
cout << "Start Querying \n";
range_query_visitor visitor;
SpatialIndex::Region query;
micron_vector plow,phigh;
plow[0] = 0; plow[1] = 0; plow[2] = 0;
phigh[0]=90; phigh[1]=90; phigh[2]=90;
for (int i=0;i<NEURONS_COUNT;i++)
{
get_transformed_cube_mbr(plow,phigh,*transforms[i],&query);
neurons[i]->intersectsWithQuery(query,visitor);
visitor.inc_neuron();
}
visitor.print_stats();
*/
// PERFORMANCE EVALUATION RANDOM RANGE QUERIES
{
cout << "Start Range Query Analysis \n";
range_query_visitor visitor;
double plow[3],phigh[3];
plow[0] = 98.2538; plow[1] = 1005.14; plow[2] = 92.9046;
phigh[0] = 452.301; phigh[1] = 1385.56; phigh[2] = 456.743;
//plow[0] = -1698.38; plow[1] = -1065.03; plow[2] = -1724.75;
// phigh[0] = 2248.56; phigh[1]= 1894.28; phigh[2]= 2276.71;
SpatialIndex::Region query_region = SpatialIndex::Region(plow,phigh,3);
boost::mt11213b generator (42u);
const double x[3] = {0.0, 0.0, 0.0};
SpatialIndex::Point rnd_point1 (x, query_region.m_dimension);
SpatialIndex::Point rnd_point2 (x, query_region.m_dimension);
SpatialIndex::Region query;
for (int j=0;j<QUERIES_FOR_ANALYSIS;j++)
{
for (size_t i = 0; i < query_region.m_dimension; i++)
{
boost::uniform_real<> uni_dist (query_region.m_pLow[i],query_region.m_pHigh[i]);
boost::variate_generator<boost::mt11213b &,boost::uniform_real<> > uni(generator, uni_dist);
rnd_point1.m_pCoords[i] = uni();
boost::uniform_real<> uni_dist1 (rnd_point1.m_pCoords[i],query_region.m_pHigh[i]);
boost::variate_generator<boost::mt11213b &,boost::uniform_real<> > uni1(generator, uni_dist1);
rnd_point2.m_pCoords[i] = uni1();
}
visitor.new_query();
visitor.reset_neuron();
for (int i=0;i<NEURONS_COUNT;i++)
{
Vector_3D<Micron> low = Vector_3D<Micron>((Micron)rnd_point1.m_pCoords[0],(Micron)rnd_point1.m_pCoords[1],(Micron)rnd_point1.m_pCoords[2]);
Vector_3D<Micron> high = Vector_3D<Micron>((Micron)rnd_point2.m_pCoords[0],(Micron)rnd_point2.m_pCoords[1],(Micron)rnd_point2.m_pCoords[2]);
get_transformed_cube_mbr(low,high,*transforms[i],&query);
neurons[i]->intersectsWithQuery(query,visitor);
}
if (j%100==0) cout << "Queries Done: " << j << "\n";
}
visitor.print_stats();
}
/*
{
// PERFORMANCE EVALUATION RANDOM POINT QUERIES
cout << "Start Point Query Analysis \n";
range_query_visitor visitor;
double plow[3],phigh[3];
//plow[0] = 98.2538; plow[1] = 1005.14; plow[2] = 92.9046;
// phigh[0] = 452.301; phigh[1] = 1385.56; phigh[2] = 456.743;
plow[0] = -1698.38; plow[1] = -1065.03; plow[2] = -1724.75;
phigh[0] = 2248.56; phigh[1]= 1894.28; phigh[2]= 2276.71;
SpatialIndex::Region query_region = SpatialIndex::Region(plow,phigh,3);
boost::mt11213b generator (42u);
for (int j=0;j<QUERIES_FOR_ANALYSIS;j++)
{
const double x[3] = {0.0, 0.0, 0.0};
SpatialIndex::Point rnd_point (x, query_region.m_dimension);
SpatialIndex::Point tmp_point (x, query_region.m_dimension);
for (size_t i = 0; i < query_region.m_dimension; i++)
{
boost::uniform_real<> uni_dist (query_region.m_pLow[i],query_region.m_pHigh[i]);
boost::variate_generator<boost::mt11213b &,boost::uniform_real<> > uni(generator, uni_dist);
rnd_point.m_pCoords[i] = uni();
}
visitor.new_query();
visitor.reset_neuron();
//visitor.reset_stats();
for (int i=0;i<NEURONS_COUNT;i++)
{
// cout << "Point Query: (" << rnd_point.m_pCoords[0] << "," << rnd_point.m_pCoords[1] << "," << rnd_point.m_pCoords[2] << ") Transformed to: (";
Vector_3D<Micron> v = Vector_3D<Micron>((Micron)rnd_point.m_pCoords[0],(Micron)rnd_point.m_pCoords[1],(Micron)rnd_point.m_pCoords[2]);
v = *transforms[i]*v;
tmp_point.m_pCoords[0] = (double)v.x();
tmp_point.m_pCoords[1] = (double)v.y();
tmp_point.m_pCoords[2] = (double)v.z();
// cout << tmp_point.m_pCoords[0] << "," << tmp_point.m_pCoords[1] << "," << tmp_point.m_pCoords[2] << ")\n";
neurons[i]->pointLocationQuery(tmp_point,visitor);
}
}
visitor.print_stats();
}
*/
// PERFORMANCE EVALUATION RANDOM RANGE QUERIES
}
catch (Tools::Exception& e)
{
cout << e.what() << endl;
exit(0);
}
// delete tree_stats;
return 0;
}