Impl( EventSource& output, const URIHandler& params )
: _output( output )
, _report( params.getConfig().getReportSource( params.getReport( )),
brion::MODE_READ, params.getGIDs( ))
{
const brain::Circuit circuit( params.getConfig( ));
const auto morphologies = circuit.loadMorphologies(
params.getGIDs(), brain::Circuit::COORDINATES_GLOBAL );
helpers::addCompartmentEvents( morphologies, _report, output );
}
Impl( EventSource& output, const URIHandler& params )
: _output( output )
, _report( params.getConfig().getReportSource( params.getReport( )),
brion::MODE_READ, params.getGIDs( ))
{
const brain::Circuit circuit( params.getConfig( ));
const auto morphologies = circuit.loadMorphologies(
params.getGIDs(), brain::Circuit::Coordinates::global );
// add soma events only
helpers::addCompartmentEvents( morphologies, _report, output, true );
}
SpikeLoader::SpikeLoader( const URIHandler& params )
: EventSource( params )
, _impl( new Impl( *this, params ))
{
if( getDt() < 0.f )
setDt( params.getConfig().getTimestep( ));
}
Impl( EventSource& output, const URIHandler& params )
: _output( output )
, _circuit( params.getConfig( ))
, _gids( params.getGIDs( ))
, _voltageReport( params.getConfig().getReportSource( params.getReport( )),
brion::MODE_READ, _gids )
, _areaReport( URI( params.getAreas( )), brion::MODE_READ, _gids )
, _restingPotential( 0.f )
, _areaMultiplier( 0.f )
, _spikeFilter( false )
, _apThreshold( 0.f )
, _interpolate( false )
{
LBINFO << "Loading " << _gids.size() << " morphologies..." << std::endl;
const auto morphologies = _circuit.loadMorphologies(
_gids, brain::Circuit::Coordinates::global );
LBINFO << "Creating events..." << std::endl;
helpers::addCompartmentEvents( morphologies, _voltageReport, _output );
LBINFO << "Loading areas..." << std::endl;
_areas = _areaReport.loadFrame( 0.f );
}
Impl( EventSource& output, const URIHandler& params )
: _output( output )
{
const auto& gids = params.getGIDs();
LBINFO << "Loading synapses for " << gids.size() << " cells..."
<< std::endl;
boost::progress_display progress( gids.size( ));
const brion::Synapse synapses( params.getConfig().getSynapseSource().getPath() +
"/nrn_positions.h5" );
for( const uint32_t gid : gids )
{
const brion::SynapseMatrix& data =
synapses.read( gid, brion::SYNAPSE_PRESYNAPTIC_SURFACE_X |
brion::SYNAPSE_PRESYNAPTIC_SURFACE_Y |
brion::SYNAPSE_PRESYNAPTIC_SURFACE_Z );
for( size_t i = 0; i < data.shape()[0]; ++i )
_output.add( Event( Vector3f( data[i][0], data[i][1],
data[i][2] ), 1.f ));
++progress;
}
}
Impl( EventSource& output, const URIHandler& params )
: _output( output )
, _duration( params.getDuration( ))
, _spikesStart( 0.f )
, _spikesEnd( 0.f )
{
const brion::GIDSet& gids = params.getGIDs();
const brain::Circuit circuit( params.getConfig( ));
const brion::Vector3fs& positions = circuit.getPositions( gids );
size_t i = 0;
_gidIndex.resize( *gids.rbegin() + 1 );
for( const uint32_t gid: gids )
{
_output.add( Event( positions[ i ], VALUE_UNSET ));
_gidIndex[gid] = i++;
}
_spikesPerNeuron.resize( gids.size( ));
const std::string& spikePath = params.getSpikes();
_loadSpikes( spikePath.empty() ? params.getConfig().getSpikeSource() :
brion::URI( spikePath ));
}
