bp::object Morphology_getSectionIDs( const MorphologyPtr& morphology,
bp::object types )
{
const SectionTypes typeVector = vectorFromPython< SectionType >(
types, "Cannot convert argument to SectionType list");
return toNumpy( morphology->getSectionIDs( typeVector ));
}
bp::object Section_getSamplesFromPositions( const SectionWrapper& section,
bp::object points )
{
const floats pointVector = vectorFromPython< float >(
points, "Cannot convert argument to float vector");
return toNumpy( section.getSamples( pointVector ));
}
bp::object CompartmentReportMapping_getIndex(
const CompartmentReportMappingProxy& mapping)
{
static_assert(sizeof(CompartmentReportMapping::IndexEntry) ==
sizeof(uint32_t) + sizeof(uint32_t),
"Bad alignment of IndexEntry");
return toNumpy(mapping.view->getMapping().getIndex(), mapping.view);
}
bp::object CompartmentReportMapping_getCompartmentCounts(
const CompartmentReportMappingProxy& mapping)
{
boost::python::list result;
auto& counts = mapping.view->getMapping().getCompartmentCounts();
for (auto& count : counts)
result.append(toNumpy(count, mapping.view));
return result;
}
static np::ndarray segmentBinaryGraph( const np::ndarray & DX, const np::ndarray & DY ) {
// Used to evaluate CPMC
Matrix<bool,Dynamic,Dynamic,RowMajor> dx = mapMatrixX<bool>(DX), dy = mapMatrixX<bool>(DY);
Matrix<short,Dynamic,Dynamic,RowMajor> r = -Matrix<short,Dynamic,Dynamic,RowMajor>::Ones(dx.rows(),dy.cols());
int id=0;
std::vector<Vector2i> q;
for( int j=0; j<r.rows(); j++ )
for( int i=0; i<r.cols(); i++ )
if( r(j,i) == -1 ){
r(j,i)=id;
q.clear();
q.push_back( Vector2i(i,j) );
while(!q.empty()) {
int x = q.back()[0], y=q.back()[1];
q.pop_back();
if( x && dx(y,x-1) && r(y,x-1)==-1 ) {
r(y,x-1) = id;
q.push_back( Vector2i(x-1,y) );
}
if( x+1<r.cols() && dx(y,x) && r(y,x+1)==-1 ) {
r(y,x+1) = id;
q.push_back( Vector2i(x+1,y) );
}
if( y && dy(y-1,x) && r(y-1,x)==-1 ) {
r(y-1,x) = id;
q.push_back( Vector2i(x,y-1) );
}
if( y+1<r.rows() && dy(y,x) && r(y+1,x)==-1 ) {
r(y+1,x) = id;
q.push_back( Vector2i(x,y+1) );
}
}
id++;
if( id > (1<<15) )
throw std::domain_error( "segmentBinaryGraph: Overflow (short)" );
}
return toNumpy(r);
}
bp::object Soma_getProfilePoints( const SomaWrapper& soma )
{
return toNumpy( soma.getProfilePoints( ));
}
bp::object Morphology_getTransformation( const MorphologyPtr& morphology )
{
return toNumpy( morphology->getTransformation( ));
}
bp::object Morphology_getSectionTypes( const MorphologyPtr& morphology )
{
return toNumpy( morphology->getSectionTypes( ), morphology );
}
bp::object CompartmentReportView_getGids(const CompartmentReportView& view)
{
return toNumpy(toVector(view.getGIDs()));
}
bp::object CompartmentReport_getGids(const CompartmentReport& report)
{
return toNumpy(toVector(report.getGIDs()));
}
bp::object Circuit_getRotations( const Circuit& circuit, bp::object gids )
{
return toNumpy( circuit.getRotations( gidsFromPython( gids )));
}
