ReadSwc.cpp File Reference

#include "header.h"
#include "../shell/Shell.h"
#include "../utility/Vec.h"
#include "SwcSegment.h"
#include "ReadSwc.h"
#include "CompartmentBase.h"
#include "Compartment.h"
#include "SymCompartment.h"
#include <fstream>

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Functions
static Id	makeCompt (Id parent, const SwcSegment &seg, const SwcSegment &pa, double RM, double RA, double CM, unsigned int i, unsigned int j)

Variables
static const double	MinRadius = 0.04

Function Documentation

static Id makeCompt ( Id  parent, const SwcSegment &  seg, const SwcSegment &  pa, double  RM, double  RA, double  CM, unsigned int  i, unsigned int  j  )

static

Definition at line 211 of file ReadSwc.cpp.

References Vec::a0(), Vec::a1(), Vec::a2(), Eref::data(), SwcSegment::distance(), Shell::doCreate(), Id::eref(), name, SwcSegment::parent(), PI, SwcSegment::radius(), moose::CompartmentBase::setCm(), moose::CompartmentBase::setDiameter(), moose::CompartmentBase::setLength(), moose::CompartmentBase::setRa(), moose::CompartmentBase::setRm(), moose::CompartmentBase::setX(), moose::CompartmentBase::setX0(), moose::CompartmentBase::setY(), moose::CompartmentBase::setY0(), moose::CompartmentBase::setZ(), moose::CompartmentBase::setZ0(), SwcSegment::type(), SwcSegment::typeName, and SwcSegment::vec().

Referenced by ReadSwc::build().

{
    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
    double len = seg.radius() * 2.0;
    string name = "soma";
    Id compt;
    double x0, y0, z0;
    if ( seg.parent() != ~0U ) {
        len = seg.distance( pa );
        stringstream ss;
        ss << SwcSegment::typeName[ seg.type() ] << "_" << i << "_" << j;
        name = ss.str();
        x0 = pa.vec().a0();
        y0 = pa.vec().a1();
        z0 = pa.vec().a2();
    } else {
        x0 = seg.vec().a0() - len;
        y0 = seg.vec().a1();
        z0 = seg.vec().a2();
    }
    assert( len > 0.0 );
    compt = shell->doCreate( "Compartment", parent, name, 1 );
    Eref er = compt.eref();
    moose::CompartmentBase *cptr = reinterpret_cast< moose::CompartmentBase* >(
                    compt.eref().data() );
    double xa = seg.radius() * seg.radius() * PI * 1e-12;
    len *= 1e-6;
    double dia = seg.radius() * 2.0e-6;
    cptr->setRm( er, RM / ( len * dia * PI ) );
    cptr->setRa( er, RA * len / xa );
    cptr->setCm( er, CM * ( len * dia * PI ) );
    cptr->setDiameter( dia );
    cptr->setLength( len );
    cptr->setX0( x0 * 1e-6 );
    cptr->setY0( y0 * 1e-6 );
    cptr->setZ0( z0 * 1e-6 );
    cptr->setX( seg.vec().a0() * 1e-6 );
    cptr->setY( seg.vec().a1() * 1e-6 );
    cptr->setZ( seg.vec().a2() * 1e-6 );
    return compt;
}

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Variable Documentation

const double MinRadius = 0.04

static

Definition at line 22 of file ReadSwc.cpp.

Referenced by ReadSwc::validate().