/**
* In this destructor we need to put messages back to process,
* and we need to replace the SolveFinfos on zombies with the
* original ThisFinfo. This should really just use the clearFunc.
*/
void HSolveHub::destroy( const Conn* c )
{
static Finfo* origCompartmentFinfo =
const_cast< Finfo* >(
initCompartmentCinfo()->getThisFinfo() );
static Finfo* origHHChannelFinfo =
const_cast< Finfo* >(
initHHChannelCinfo()->getThisFinfo() );
Element* hub = c->target().e;
unsigned int eIndex = c->target().i;
Conn* i = hub->targets( compartmentSolveFinfo->msg(), eIndex );
while ( i->good() ) {
i->target().e->setThisFinfo( origCompartmentFinfo );
i->increment();
}
delete i;
i = hub->targets( hhchannelSolveFinfo->msg(), eIndex );
while ( i->good() ) {
i->target().e->setThisFinfo( origHHChannelFinfo );
i->increment();
}
delete i;
Neutral::destroy( c );
}
Finfo* initCompartmentZombieFinfo()
{
static Finfo* compartmentFields[] =
{
new ValueFinfo( "Vm",
ValueFtype1< double >::global(),
GFCAST( &HSolveHub::getVm ),
RFCAST( &HSolveHub::setVm )
),
new ValueFinfo( "Im",
ValueFtype1< double >::global(),
GFCAST( &HSolveHub::getIm ),
&dummyFunc
),
new ValueFinfo( "inject",
ValueFtype1< double >::global(),
GFCAST( &HSolveHub::getInject ),
RFCAST( &HSolveHub::setInject )
),
};
static const ThisFinfo* tf = dynamic_cast< const ThisFinfo* >(
initCompartmentCinfo()->getThisFinfo() );
assert( tf != 0 );
static SolveFinfo compartmentZombieFinfo(
compartmentFields,
sizeof( compartmentFields ) / sizeof( Finfo* ),
tf,
"These fields will replace the original compartment fields so that the lookups refer to the solver rather "
"than the compartment."
);
return &compartmentZombieFinfo;
}
void SigNeur::makeCell2SigAdaptors()
{
static const Finfo* lookupChildFinfo =
initCompartmentCinfo()->findFinfo( "lookupChild" );
for ( map< string, string >::iterator i = calciumMap_.begin();
i != calciumMap_.end(); ++i ) {
for ( vector< TreeNode >::iterator j = tree_.begin();
j != tree_.end(); ++j ) {
Id caId;
bool ret = lookupGet< Id, string >( j->compt.eref(), lookupChildFinfo, caId, i->first );
if ( ret && caId.good() ) {
if ( j->category == SOMA ) {
adaptCa2Sig( *j, somaMap_, 0, calciumScale_,
caId, i->second );
} else if ( j->category == DEND ) {
adaptCa2Sig( *j, dendMap_, numSoma_, calciumScale_,
caId, i->second );
} else if ( j->category == SPINE ) {
adaptCa2Sig( *j, spineMap_, numDend_ + numSoma_,
calciumScale_,
caId, i->second );
}
}
}
}
}
void SigNeur::buildTree( Id soma, const vector< Id >& compts )
{
const Finfo* axialFinfo;
const Finfo* raxialFinfo;
if ( soma.eref().e->cinfo() == initSymCompartmentCinfo() ) {
axialFinfo = initSymCompartmentCinfo()->findFinfo( "raxial1" );
raxialFinfo = initSymCompartmentCinfo()->findFinfo( "raxial2" );
} else {
axialFinfo = initCompartmentCinfo()->findFinfo( "axial" );
raxialFinfo = initCompartmentCinfo()->findFinfo( "raxial" );
}
assert( axialFinfo != 0 );
assert( raxialFinfo != 0 );
// Soma may be in middle of messaging structure for cell, so we need
// to traverse both ways. But nothing below soma should
// change direction in the traversal.
innerBuildTree( 0, soma.eref(), soma.eref(),
axialFinfo->msg(), raxialFinfo->msg() );
// innerBuildTree( 0, soma.eref(), soma.eref(), raxialFinfo->msg() );
}
void HSolveHub::manageCompartments()
{
const vector< Id >& idlist = integ_->getCompartments();
vector< Element* > elist;
idlist2elist( idlist, elist );
const vector< vector< Id > >& externalChannelIds =
integ_->getExternalChannels();
vector< Element* > extChanList;
const Finfo* initFinfo = initCompartmentCinfo()->findFinfo( "init" );
vector< Element* >::const_iterator i;
for ( i = elist.begin(); i != elist.end(); i++ ) {
zombify( hub_, *i, compartmentSolveFinfo, compartmentZombieFinfo );
// Compartment receives 2 shared messages from Tick's "process"
Eref( *i ).dropAll( initFinfo->msg() );
redirectDynamicMessages( *i );
}
/*
* Redirecting dest/shared messages
*/
for ( unsigned int ic = 0; ic < elist.size(); ic++ ) {
// The 'retain' flag at the end is 1: we do not delete the original
// message to the compartment.
redirectDestMessages(
hub_, elist[ ic ],
hubCompartmentInjectFinfo, compartmentInjectFinfo,
ic, compartmentInjectMap_,
&elist, 0,
1 );
extChanList.clear();
idlist2elist( externalChannelIds[ ic ], extChanList );
redirectDestMessages(
hub_, elist[ ic ],
hubCompartmentChannelFinfo, compartmentChannelFinfo,
ic, compartmentChannelMap_,
&elist, &extChanList,
1 );
}
}
static const Finfo* hhchannelSolveFinfo = initHSolveHubCinfo()->findFinfo( "hhchannelSolve" ); static const Finfo* caconcSolveFinfo = initHSolveHubCinfo()->findFinfo( "caconcSolve" ); static const Finfo* hubCompartmentInjectFinfo = initHSolveHubCinfo()->findFinfo( "compartmentInjectMsg" ); static const Finfo* hubCompartmentChannelFinfo = initHSolveHubCinfo()->findFinfo( "compartmentChannel" ); /* * Finfos from biophysical objects. Needed so that 'set' operations are done * on the solver as well as the objects. Also needed for redirecting any dest * messages on these finfos to the solver (e.g.: to the inject field). */ static const Finfo* compartmentInjectFinfo = initCompartmentCinfo()->findFinfo( "injectMsg" ); static const Finfo* compartmentChannelFinfo = initCompartmentCinfo()->findFinfo( "channel" ); static const Finfo* compartmentVmFinfo = initCompartmentCinfo()->findFinfo( "Vm" ); static const Finfo* channelGbarFinfo = initHHChannelCinfo()->findFinfo( "Gbar" ); static const Finfo* channelEkFinfo = initHHChannelCinfo()->findFinfo( "Ek" ); static const Finfo* channelGkFinfo = initHHChannelCinfo()->findFinfo( "Gk" ); static const Finfo* channelXFinfo = initHHChannelCinfo()->findFinfo( "X" ); static const Finfo* channelYFinfo = initHHChannelCinfo()->findFinfo( "Y" ); static const Finfo* channelZFinfo =
