Quaternionfs getRotations( const GIDSet& gids ) const final
{
const float deg2rad = float( M_PI ) / 180.f;
const brion::NeuronMatrix& data =
_circuit.get( gids, brion::NEURON_ROTATION );
Quaternionfs rotations( gids.size( ));
#pragma omp parallel for
for( size_t i = 0; i < gids.size(); ++i )
{
try
{
// transform rotation Y angle in degree into rotation quaternion
const float angle = lexical_cast<float>( data[i][0] ) * deg2rad;
rotations[i] = Quaternionf( angle, Vector3f( 0, 1, 0 ));
}
catch( const boost::bad_lexical_cast& )
{
GIDSet::const_iterator gid = gids.begin();
std::advance( gid, i );
LBWARN << "Error parsing circuit orientation for gid "
<< *gid << std::endl;
}
}
return rotations;
}
Vector3fs getPositions( const GIDSet& gids ) const final
{
const brion::NeuronMatrix& data = _circuit.get( gids,
brion::NEURON_POSITION_X | brion::NEURON_POSITION_Y |
brion::NEURON_POSITION_Z );
Vector3fs positions( gids.size( ));
#pragma omp parallel for
for( size_t i = 0; i < gids.size(); ++i )
{
try
{
positions[i] =
brion::Vector3f( lexical_cast< float >( data[i][0] ),
lexical_cast< float >( data[i][1] ),
lexical_cast< float >( data[i][2] ));
}
catch( const boost::bad_lexical_cast& )
{
GIDSet::const_iterator gid = gids.begin();
std::advance( gid, i );
LBWARN << "Error parsing circuit position for gid "
<< *gid << std::endl;
}
}
return positions;
}
Strings getMorphologyNames( const GIDSet& gids ) const final
{
Strings results( gids.size( ));
const ::MVD3::Range& range = getRange( gids );
const Strings& morphos = _circuit.getMorphologies( range );
assign( range, gids, morphos, results, toString );
return results;
}
Quaternionfs getRotations( const GIDSet& gids ) const final
{
Quaternionfs results( gids.size( ));
const ::MVD3::Range& range = getRange( gids );
const ::MVD3::Rotations& rotations = _circuit.getRotations( range );
assign( range, gids, rotations, results, toQuaternion );
return results;
}
Vector3fs getPositions( const GIDSet& gids ) const final
{
Vector3fs results( gids.size( ));
const ::MVD3::Range& range = getRange( gids );
const ::MVD3::Positions& positions = _circuit.getPositions( range );
assign( range, gids, positions, results, toVector3f );
return results;
}
std::vector<uint32_t> CompartmentReportCommon::_computeSubsetIndices(
const GIDSet& source, const GIDSet& target)
{
GIDSet::iterator i = source.begin();
std::vector<uint32_t> indices;
indices.reserve(target.size());
uint32_t sourceIndex = 0;
for (const auto gid : target)
{
assert(i != source.end());
while (*i != gid)
{
++i;
++sourceIndex;
}
indices.push_back(sourceIndex);
}
return indices;
}
neuron::Morphologies Circuit::loadMorphologies( const GIDSet& gids,
const Coordinates coords ) const
{
const URIs& uris = getMorphologyURIs( gids );
const auto circuitPath =
// cache outside of loop, canonical does stat() which is slow on GPFS
fs::canonical( _impl->getCircuitSource().getPath( )).generic_string();
// < GID, hash >
Strings gidHashes;
gidHashes.reserve( uris.size( ));
std::set< std::string > hashes;
GIDSet::const_iterator gid = gids.begin();
for( size_t i = 0; i < uris.size(); ++i, ++gid )
{
auto hash = uris[i].getPath();
if( hash[0] != '/' ) // opt: don't stat abs file path (see above)
hash = fs::canonical( hash ).generic_string();
if( coords == Coordinates::global )
// store circuit + GID for transformed morphology
hash += circuitPath + boost::lexical_cast< std::string >( *gid );
hash = servus::make_uint128( hash ).getString();
gidHashes.push_back( hash );
hashes.insert( hash );
}
CachedMorphologies cached = _impl->loadMorphologiesFromCache( hashes );
// resolve missing morphologies and put them in GID-order into result
neuron::Morphologies result;
result.reserve( uris.size( ));
const Matrix4fs transforms =
coords == Coordinates::global ? getTransforms( gids ) : Matrix4fs();
for( size_t i = 0; i < uris.size(); ++i )
{
const URI& uri = uris[i];
const std::string& hash = gidHashes[i];
CachedMorphologies::const_iterator it = cached.find( hash );
if( it == cached.end( ))
{
neuron::MorphologyPtr morphology;
const brion::Morphology raw( uri.getPath( ));
if( coords == Coordinates::global )
morphology.reset( new neuron::Morphology( raw, transforms[i] ));
else
morphology.reset( new neuron::Morphology( raw ));
cached.insert( std::make_pair( hash, morphology ));
_impl->saveMorphologiesToCache( uri.getPath(), hash, morphology );
result.push_back( morphology );
}
else
result.push_back( it->second );
}
return result;
}
GIDSet CompartmentReportCommon::_computeIntersection(const GIDSet& all,
const GIDSet& subset)
{
GIDSet intersection;
std::set_intersection(subset.begin(), subset.end(), all.begin(), all.end(),
std::inserter(intersection, intersection.begin()));
if (intersection != subset || intersection.empty())
{
LBWARN << "Requested " << subset.size() << " GIDs [" << *subset.begin()
<< ":" << *subset.rbegin() << "] are not a subset of the "
<< all.size() << " GIDs in the report [" << *all.begin() << ":"
<< *all.rbegin();
if (intersection.empty())
LBWARN << " with no GIDs in common" << std::endl;
else
LBWARN << "], using intersection size " << intersection.size()
<< " [" << *intersection.begin() << ":"
<< *intersection.rbegin() << "]" << std::endl;
}
return intersection;
}