bool ReadSwc::build( Id parent,
double lambda, double RM, double RA, double CM )
{
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
vector< Id > compts( segs_.size() );
for ( unsigned int i = 0; i < branches_.size(); ++i ) {
SwcBranch& br = branches_[i];
for ( unsigned int j = 0; j < br.segs_.size(); ++j ) {
Id compt;
SwcSegment& seg = segs_[ br.segs_[j] -1 ];
unsigned int paIndex = seg.parent();
if ( paIndex == ~0U ) { // soma
compt = makeCompt( parent, seg, seg, RM, RA, CM, i, j );
} else {
SwcSegment& pa = segs_[ paIndex - 1 ];
compt = makeCompt( parent, seg, pa, RM, RA, CM, i, j );
assert( compt != Id() );
assert( compts[ paIndex -1 ] != Id() );
shell->doAddMsg( "Single",
compts[paIndex-1], "axial", compt, "raxial" );
}
assert( compt != Id() );
compts[ seg.myIndex() -1 ] = compt;
}
}
return true;
}
void testCellDiffn()
{
Id makeCompt( Id parentCompt, Id parentObj,
string name, double len, double dia, double theta );
Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
double len = 40e-6;
double dia = 10e-6;
double diffLength = 1e-6;
double dt = 1.0e-1;
double runtime = 100.0;
double diffConst = 1.0e-12;
Id model = s->doCreate( "Neutral", Id(), "model", 1 );
Id soma = makeCompt( Id(), model, "soma", dia, dia, 90 );
Id dend = makeCompt( soma, model, "dend", len, 3e-6, 0 );
Id branch1 = makeCompt( dend, model, "branch1", len, 2e-6, 45.0 );
Id branch2 = makeCompt( dend, model, "branch2", len, 2e-6, -45.0 );
Id twig1 = makeCompt( branch1, model, "twig1", len, 1.5e-6, 90.0 );
Id twig2 = makeCompt( branch1, model, "twig2", len, 1.5e-6, 0.0 );
Id nm = s->doCreate( "NeuroMesh", model, "neuromesh", 1 );
Field< double >::set( nm, "diffLength", diffLength );
Field< string >::set( nm, "geometryPolicy", "cylinder" );
Field< Id >::set( nm, "cell", model );
unsigned int ns = Field< unsigned int >::get( nm, "numSegments" );
assert( ns == 6 );
unsigned int ndc = Field< unsigned int >::get( nm, "numDiffCompts" );
assert( ndc == 210 );
Id pool1 = s->doCreate( "Pool", nm, "pool1", 1 );
Field< double >::set( pool1, "diffConst", diffConst );
Id pool2 = s->doCreate( "Pool", nm, "pool2", 1 );
Field< double >::set( pool2, "diffConst", diffConst );
Id dsolve = s->doCreate( "Dsolve", model, "dsolve", 1 );
Field< Id >::set( dsolve, "compartment", nm );
s->doUseClock( "/model/dsolve", "process", 1 );
s->doSetClock( 1, dt );
// Next: build by setting path
Field< string >::set( dsolve, "path", "/model/neuromesh/pool#" );
vector< double > nvec =
LookupField< unsigned int, vector< double > >::get(
dsolve, "nVec", 0);
assert( nvec.size() == ndc );
assert( pool1.element()->numData() == ndc );
Field< double >::set( ObjId( pool1, 0 ), "nInit", 1.0 );
Field< double >::set( ObjId( pool2, ndc - 1 ), "nInit", 2.0 );
s->doReinit();
s->doStart( runtime );
nvec = LookupField< unsigned int, vector< double > >::get(
dsolve, "nVec", 0);
vector< double > pool1Vec;
Field< double >::getVec( pool1, "n", pool1Vec );
assert( pool1Vec.size() == ndc );
vector< double > pool2Vec;
Field< double >::getVec( pool2, "n", pool2Vec );
assert( pool2Vec.size() == ndc );
double myTot1 = 0;
double myTot2 = 0;
for ( unsigned int i = 0; i < nvec.size(); ++i ) {
assert( doubleEq( pool1Vec[i], nvec[i] ) );
myTot1 += nvec[i];
myTot2 += pool2Vec[i];
}
assert( doubleEq( myTot1, 1.0 ) );
assert( doubleEq( myTot2, 2.0 ) );
/*
cout << endl;
cout << "Big cell: " << endl;
for ( unsigned int i = 0; i < nvec.size(); ++i )
cout << nvec[i] << ", " << pool2Vec[i] << endl;
cout << endl;
*/
s->doDelete( model );
cout << "." << flush;
}
