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;
}
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
*/
}
/*!
\todo Clarify that spatio_temporal_average specifies milliseconds from
simulation start, not from simulation time window that is reported in
the file. also produce an error message if interval not in file. Should
actually probably go in the Stream_Playback_Control then.
*/
void spatiotemporal_average (URI blue_config_filename,
Filename volume_compartment_mapping_filename,
Filename output_filename_prefix,
Millisecond begin_time,
Millisecond end_time,
Millisecond average_time_window,
bool portable = false)
{
Count frames_per_second(10);
// experiment
Experiment experiment;
experiment.open(blue_config_filename);
Cell_Target circuit_target = experiment.cell_target("Column");
std::cout << "Microcircuit: loading target Column" << std::endl;
Count j = 0;
for (Cell_Target::const_iterator i = circuit_target.begin();
i != circuit_target.end(); ++i)
{
Neuron_Ptr new_neuron(new Neuron(experiment.microcircuit(), *i , j));
experiment.microcircuit().neurons().insert(new_neuron);
++j;
}
Volume_Temporal_Average<Millivolt, Micron, Millisecond>
temporal_average(Count (average_time_window * frames_per_second));
Filter_Data<Microcircuit> microcircuit(experiment.microcircuit_ptr());
// pipeline setup
Pipeline pipeline;
std::cout << "Loading compartment report..." << std::endl;
Reports_Specification::const_iterator result =
experiment.reports().find("allCompartments");
if (result == experiment.reports().end())
{
std::cerr << "No \"allCompartments\" report found" << std::endl;
exit(1);
}
Compartment_Report_Stream_Reader<Millivolt> binary_report_reader(* result, 2);
binary_report_reader.cell_target(circuit_target);
Compartment_Report_Printer<Millivolt> printer;
Compartment_Voltages_to_Microcircuit report_link;
Compartment_Voltage_Voxel_Average voltage_volume_average(volume_compartment_mapping_filename, false);
Volume_Voltage_to_Byte voltage_to_byte;
binary_report_reader.time_window(begin_time, end_time);
binary_report_reader.speed(1.0);
voltage_to_byte.dynamic_range(-65.0, -20.0);
std::cout << "Pipeline 1: Setup spatio-temporal average." << std::endl;
pipeline = binary_report_reader
+ printer
+ report_link
+ microcircuit
+ voltage_volume_average
+ temporal_average;
std::cout << "Pipeline 1: Started processing spatio-temporal average."
<< std::endl;
pipeline.start();
pipeline.wait_until_finished();
pipeline.stop();
std::cout << "Pipeline 1: Temporal average finished." << std::endl;
std::cout << "Pipeline 2: Setup NRRD volume file writer." << std::endl;
Pipeline pipeline2;
Filter_Reader<Volume<Millivolt, Micron, Millisecond> > volume_buffer_reader;
volume_buffer_reader.input_ptr(temporal_average.output_ptr());
Volume_NRRD_File_Stream_Writer nrrd_file_writer(output_filename_prefix);
pipeline2 = volume_buffer_reader
+ voltage_to_byte
+ nrrd_file_writer;
std::cout << "Pipeline 2: Started writing volumes to disk." << std::endl;
pipeline2.start();
pipeline2.wait_until_finished();
std::cout << "Pipeline 2: Written volumes to disk." << std::endl;
}
