void ZombieFunction::setSolver( Id ksolve, Id dsolve )
{
if ( ksolve.element()->cinfo()->isA( "Ksolve" ) ||
ksolve.element()->cinfo()->isA( "Gsolve" ) ) {
Id sid = Field< Id >::get( ksolve, "stoich" );
_stoich = ObjId( sid, 0 ).data();
if ( _stoich == 0 )
cout << "Warning:ZombieFunction::setSolver: Empty Stoich on Ksolve" << ksolve.path() << endl;
} else if ( ksolve == Id() ) {
_stoich = 0;
} else {
cout << "Warning:ZombieFunction::setSolver: solver class " <<
ksolve.element()->cinfo()->name() <<
" not known.\nShould be Ksolve or Gsolve\n";
_stoich = 0;
}
/*
if ( dsolve.element()->cinfo()->isA( "Dsolve" ) ) {
dsolve_= ObjId( dsolve, 0 ).data();
} else if ( dsolve == Id() ) {
dsolve_ = 0;
} else {
cout << "Warning:ZombieFunction::vSetSolver: solver class " <<
dsolve.element()->cinfo()->name() <<
" not known.\nShould be Dsolve\n";
dsolve_ = 0;
}
*/
}
//////////////////////////////////////////////////////////////////
// The read functions.
//////////////////////////////////////////////////////////////////
Id makeStandardElements( Id pa, const string& modelname )
{
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
//cout << " kkit read " << pa << " " << modelname << " "<< MooseGlobal;
string modelPath = pa.path() + "/" + modelname;
if ( pa == Id() )
modelPath = "/" + modelname;
Id mgr( modelPath );
if ( mgr == Id() )
mgr = shell->doCreate( "Neutral", pa, modelname, 1, MooseGlobal );
Id kinetics( modelPath + "/kinetics" );
if ( kinetics == Id() ) {
kinetics =
shell->doCreate( "CubeMesh", mgr, "kinetics", 1, MooseGlobal );
SetGet2< double, unsigned int >::set( kinetics, "buildDefaultMesh", 1e-15, 1 );
}
assert( kinetics != Id() );
Id graphs = shell->doCreate( "Neutral", mgr, "graphs", 1, MooseGlobal);
assert( graphs != Id() );
Id moregraphs = shell->doCreate( "Neutral", mgr, "moregraphs", 1, MooseGlobal );
Id geometry = shell->doCreate( "Neutral", mgr, "geometry", 1, MooseGlobal );
assert( geometry != Id() );
Id groups =
shell->doCreate( "Neutral", mgr, "groups", 1, MooseGlobal );
assert( groups != Id() );
return mgr;
}
bool HHGate::checkOriginal( Id id, const string& field ) const
{
if ( id == originalGateId_ )
return 1;
cout << "Warning: HHGate: attempt to set field '" << field << "' on " <<
id.path() << "\nwhich is not the original Gate element. Ignored.\n";
return 0;
}
void HSolve::setSeed( Id seed )
{
if ( !seed()->cinfo()->isA( "Compartment" ) ) {
cerr << "Error: HSolve::setSeed(): Seed object '" << seed.path()
<< "' is not derived from type 'Compartment'." << endl;
return;
}
seed_ = seed;
}
void ZombieCaConc::vSetSolver( const Eref& e, Id hsolve )
{
if ( !hsolve.element()->cinfo()->isA( "HSolve" ) ) {
cout << "Error: ZombieCaConc::vSetSolver: Object: " <<
hsolve.path() << " is not an HSolve. Aborted\n";
hsolve_ = 0;
return;
}
hsolve_ = reinterpret_cast< HSolve* >( hsolve.eref().data() );
}
/**
* @brief Add a table to streamer.
*
* @param table Id of table.
*/
void Streamer::addTable( Id table )
{
// If this table is not already in the vector, add it.
for( size_t i = 0; i < tableIds_.size(); i++)
if( table.path() == tableIds_[i].path() )
return; /* Already added. */
Table* t = reinterpret_cast<Table*>(table.eref().data());
tableIds_.push_back( table );
tables_.push_back( t );
tableTick_.push_back( table.element()->getTick() );
// NOTE: If user can make sure that names are unique in table, using name is
// better than using the full path.
if( t->getColumnName().size() > 0 )
columns_.push_back( t->getColumnName( ) );
else
columns_.push_back( moose::moosePathToUserPath( table.path() ) );
}
void HHChannel2D::innerDestroyGate( const string& gateName,
HHGate2D** gatePtr, Id chanId )
{
if ( *gatePtr == 0 ) {
cout << "Warning: HHChannel2D::destroyGate: '" << gateName <<
"' on Element '" << chanId.path() << "' not present\n";
return;
}
delete (*gatePtr);
*gatePtr = 0;
}
void HHChannel2D::innerCreateGate( const string& gateName,
HHGate2D** gatePtr, Id chanId, Id gateId )
{
//Shell* shell = reinterpret_cast< Shell* >( ObjId( Id(), 0 ).data() );
if ( *gatePtr ) {
cout << "Warning: HHChannel2D::createGate: '" << gateName <<
"' on Element '" << chanId.path() << "' already present\n";
return;
}
*gatePtr = new HHGate2D( chanId, gateId );
}
void Cell::setupf( Id cell )
{
cout << "Cell::setup()" << endl;
cout << ".... cell path: " << cell.path() << endl;
//~ return;
// Delete existing solver
string solverPath = cell.path() + "/" + solverName_;
Id solver( solverPath );
if ( solver.path() == solverPath )
solver.destroy();
if ( method_ == "ee" )
return;
// Find any compartment that is a descendant of this cell
Id seed = findCompt( cell );
if ( seed == Id() ) // No compartment found.
return;
setupSolver( cell, seed );
}
void testHSolvePassiveSingleComp()
{
Shell * shell = reinterpret_cast< Shell* >( ObjId( Id(), 0 ).data() );
vector< int > dims( 1, 1 );
vector<Id> to_cleanup;
Id nid = create_testobject(to_cleanup, "Neuron", Id(), "n", dims );
Id comptId = create_testobject(to_cleanup, "Compartment", nid, "compt", dims );
Id hsolve = create_testobject(to_cleanup, "HSolve", nid, "solver", dims);
Field<string>::set(hsolve, "target", nid.path());
to_cleanup.push_back(nid);
clear_testobjects(to_cleanup);
cout << "." << flush;
}
void ZombieMMenz::setSolver( Id solver, Id orig )
{
static const DestFinfo* enz = dynamic_cast< const DestFinfo* >(
EnzBase::initCinfo()->findFinfo( "enzDest" ) );
static const SrcFinfo* sub = dynamic_cast< const SrcFinfo* >(
EnzBase::initCinfo()->findFinfo( "toSub" ) );
static const SrcFinfo* prd = dynamic_cast< const SrcFinfo* >(
EnzBase::initCinfo()->findFinfo( "toPrd" ) );
assert( enz );
assert( sub );
assert( prd );
stoich_ = reinterpret_cast< Stoich* >( solver.eref().data() );
/// Now set up the RateTerm
vector< Id > subvec;
vector< Id > prdvec;
unsigned int rateIndex = stoich_->convertIdToReacIndex( orig );
unsigned int num = orig.element()->getNeighbours( subvec, enz );
unsigned int enzIndex = stoich_->convertIdToPoolIndex( subvec[0] );
MMEnzymeBase* meb;
double numKm = 1.0; // Dummy default initial values, later to be reset
double kcat = 1.0;
/*
double numKm = base->zGetNumKm( orig.eref(), 0 );
double kcat = base->zGetKcat( orig.eref(), 0 );
*/
num = orig.element()->getNeighbours( subvec, sub );
if ( num == 1 ) {
unsigned int subIndex = stoich_->convertIdToPoolIndex( subvec[0] );
meb = new MMEnzyme1( numKm, kcat, enzIndex, subIndex );
} else if ( num > 1 ) {
vector< unsigned int > v;
for ( unsigned int i = 0; i < num; ++i )
v.push_back( stoich_->convertIdToPoolIndex( subvec[i] ) );
ZeroOrder* rateTerm = new NOrder( 1.0, v );
meb = new MMEnzyme( numKm, kcat, enzIndex, rateTerm );
} else {
cout << "Error: ZombieMMenz::zombify: No substrates for " <<
orig.path() << endl;
cout << "Will ignore and continue, but don't be surprised if "
"simulation fails.\n";
// assert( 0 );
return;
}
num = orig.element()->getNeighbours( prdvec, prd );
stoich_->installMMenz( meb, rateIndex, subvec, prdvec );
}
/**
* Identify parent Id from path that can optionally have the
* model name as the last part. Pass back the parent Id,
* and the model name.
* Returns true on success.
* Cases:
* First set: we want to fill in "model" as modelName
* "" where we want <cwe>/model
* "/" where we want /model.
* "/foo" where foo exists, so we want /foo/model
* "foo" where <cwe>/foo exists, and we want <cwe>/foo/model
* Second set: the last part of the path has the model name.
* "bar" where we want <cwe>/bar
* "/bar" where we want /bar
* "/foo/bar" where we want /foo/bar
* "foo/bar" where we want <cwe>/foo/bar
*/
bool findModelParent( Id cwe, const string& path,
Id& parentId, string& modelName )
{
modelName = "model";
string fullPath = path;
if ( path.length() == 0 )
{
parentId = cwe;
return 1;
}
if ( path == "/" )
{
parentId = Id();
return 1;
}
if ( path[0] != '/' )
{
string temp = cwe.path();
if ( temp[temp.length() - 1] == '/' )
fullPath = temp + path;
else
fullPath = temp + "/" + path;
}
Id paId( fullPath );
if ( paId == Id() ) // Path includes new model name
{
string::size_type pos = fullPath.find_last_of( "/" );
assert( pos != string::npos );
string head = fullPath.substr( 0, pos );
Id ret( head );
// When head = "" it means paId should be root.
if ( ret == Id() && head != "" && head != "/root" )
return 0;
parentId = ret;
modelName = fullPath.substr( pos + 1 );
return 1;
}
else // Path is an existing element.
{
parentId = Neutral::parent( paId ).id;
modelName = paId.element()->getName();
return 1;
}
return 0;
}
void Gsolve::setDsolve( Id dsolve )
{
if ( dsolve == Id () ) {
dsolvePtr_ = 0;
dsolve_ = Id();
} else if ( dsolve.element()->cinfo()->isA( "Dsolve" ) ) {
dsolve_ = dsolve;
dsolvePtr_ = reinterpret_cast< ZombiePoolInterface* >(
dsolve.eref().data() );
} else {
cout << "Warning: Gsolve::setDsolve: Object '" << dsolve.path() <<
"' should be class Dsolve, is: " <<
dsolve.element()->cinfo()->name() << endl;
}
}
/**
* @brief Remove a table from Streamer.
*
* @param table. Id of table.
*/
void Streamer::removeTable( Id table )
{
int matchIndex = -1;
for (size_t i = 0; i < tableIds_.size(); i++)
if( table.path() == tableIds_[i].path() )
{
matchIndex = i;
break;
}
if( matchIndex > -1 )
{
tableIds_.erase( tableIds_.begin() + matchIndex );
tables_.erase( tables_.begin() + matchIndex );
columns_.erase( columns_.begin() + matchIndex );
}
}
/**
* The 'getOriginals' flag requests Id:s of the prototype gates from which
* copies were created, instead of Id:s of the copied gates. Default is true.
*/
int HSolveUtils::gates(
Id channel,
vector< Id >& ret,
bool getOriginals )
{
// dump("HSolveUtils::gates() is not tested with new hsolve api", "FIXME");
unsigned int oldSize = ret.size();
static string gateName[] = {
string( "gateX[0]" ),
string( "gateY[0]" ),
string( "gateZ[0]" )
};
static string powerField[] = {
string( "Xpower" ),
string( "Ypower" ),
string( "Zpower" )
};
unsigned int nGates = 3; // Number of possible gates
for ( unsigned int i = 0; i < nGates; i++ ) {
double power = Field< double >::get ( channel, powerField[i] );
if ( power > 0.0 ) {
// string gatePath = moose::joinPath(channel.path(), gateName[i]);
string gatePath = moose::fixPath( channel.path() ) +
"/" + gateName[i];
Id gate( gatePath );
string gPath = moose::fixPath(gate.path());
errorSS.str("");
errorSS << "Got " << gatePath << " expected " << gPath;
SIMPLE_ASSERT_MSG(gPath == gatePath, errorSS.str().c_str());
if ( getOriginals ) {
HHGate* g = reinterpret_cast< HHGate* >( gate.eref().data() );
gate = g->originalGateId();
}
ret.push_back( gate );
}
}
return ret.size() - oldSize;
}
void setMethod( Shell* s, Id mgr, double simdt, double plotdt,
const string& method )
{
Id compt( mgr.path() + "/kinetics" );
assert( compt != Id() );
string cpath = compt.path();
string simpath = cpath + "/##[]";
string simpath2 = cpath + "/##[ISA=StimulusTable]," +
cpath + "/##[ISA=PulseGen]";
string m = lower( method );
if ( m == "rk4" ) {
cout << "Warning, not yet implemented. Using rk5 instead\n";
m = "rk5";
}
if ( m == "ksolve" || m == "gsl" ||
m == "rk5" || m == "rkf" || m == "rk" ) {
Id ksolve = s->doCreate( "Ksolve", compt, "ksolve", 1 );
Id stoich = s->doCreate( "Stoich", compt, "stoich", 1 );
Field< Id >::set( stoich, "compartment", compt );
Field< Id >::set( stoich, "ksolve", ksolve );
Field< string >::set( stoich, "path", simpath );
simpath2 += "," + cpath + "/ksolve";
s->doUseClock( simpath2, "process", 4 );
s->doSetClock( 4, plotdt );
} else if ( m == "gssa" || m == "gsolve" ||
m == "gillespie" || m == "stochastic" ) {
Id gsolve = s->doCreate( "Gsolve", compt, "gsolve", 1 );
Id stoich = s->doCreate( "Stoich", compt, "stoich", 1 );
Field< Id >::set( stoich, "compartment", compt );
Field< Id >::set( stoich, "ksolve", gsolve );
Field< string >::set( stoich, "path", simpath );
simpath2 += "," + cpath + "/gsolve";
s->doUseClock( simpath2, "process", 4 );
s->doSetClock( 4, plotdt );
} else if ( m == "ee" || m == "neutral" ) {
s->doUseClock( simpath, "process", 4 );
s->doSetClock( 4, simdt );
} else {
cout << "ReadKkit::setMethod: option " << method <<
" not known, using Exponential Euler (ee)\n";
s->doUseClock( simpath, "process", 4 );
s->doSetClock( 4, simdt );
}
}
/**
* The readcell function implements the old GENESIS cellreader
* functionality. Although it is really a parser operation, I
* put it here in Kinetics because the cell format is independent
* of parser and is likely to remain a legacy for a while.
*/
Id ReadKkit::read(
const string& filename,
const string& modelname,
Id pa, const string& methodArg )
{
string method = methodArg;
ifstream fin( filename.c_str() );
if (!fin){
cerr << "ReadKkit::read: could not open file " << filename << endl;
return Id();
}
if ( method.substr(0, 4) == "old_" ) {
moveOntoCompartment_ = false;
method = method.substr( 4 );
}
Shell* s = reinterpret_cast< Shell* >( ObjId().data() );
Id mgr = makeStandardElements( pa, modelname );
assert( mgr != Id() );
baseId_ = mgr;
basePath_ = mgr.path();
enzCplxMols_.resize( 0 );
innerRead( fin );
assignPoolCompartments();
assignReacCompartments();
assignEnzCompartments();
assignMMenzCompartments();
convertParametersToConcUnits();
s->doSetClock( 8, plotdt_ );
string plotpath = basePath_ + "/graphs/##[TYPE=Table]," +
basePath_ + "/moregraphs/##[TYPE=Table]";
s->doUseClock( plotpath, "process", 8 );
setMethod( s, mgr, simdt_, plotdt_, method );
s->doReinit();
return mgr;
}
/**
* The 'getOriginals' flag requests Id:s of the prototype gates from which
* copies were created, instead of Id:s of the copied gates. Default is true.
*/
int HSolveUtils::gates(
Id channel,
vector< Id >& ret,
bool getOriginals )
{
unsigned int oldSize = ret.size();
static string gateName[] = {
string( "gateX[0]" ),
string( "gateY[0]" ),
string( "gateZ[0]" )
};
static string powerField[] = {
string( "Xpower" ),
string( "Ypower" ),
string( "Zpower" )
};
unsigned int nGates = 3; // Number of possible gates
for ( unsigned int i = 0; i < nGates; i++ ) {
double power = HSolveUtils::get< HHChannel, double >(
channel, powerField[ i ] );
if ( power > 0.0 ) {
string gatePath = channel.path() + "/" + gateName[ i ];
Id gate( gatePath );
assert( gate.path() == gatePath );
if ( getOriginals ) {
HHGate* g = reinterpret_cast< HHGate* >( gate.eref().data() );
gate = g->originalGateId();
}
ret.push_back( gate );
}
}
return ret.size() - oldSize;
}
void SbmlReader ::findModelParent( Id cwe, const string& path, Id& parentId, string& modelName ) {
//Taken from LoadModels.cpp
//If path exist example /model when come from GUI it creates model under /model/filename
// i.e. because by default we creat genesis,sbml models under '/model', which is created before and path exist
// at the time it comes to SbmlReader.cpp
//When run directly (command line readSBML() )it ignores the path and creates under '/' and filename takes as "SBMLtoMoose"
//modelName = "test";
cout << "here " << path;
string fullPath = path;
if ( path.length() == 0 )
parentId = cwe;
if ( path == "/" )
parentId = Id();
if ( path[0] != '/' ) {
string temp = cwe.path();
if ( temp[temp.length() - 1] == '/' )
fullPath = temp + path;
else
fullPath = temp + "/" + path;
}
Id paId( fullPath );
if ( paId == Id() ) { // Path includes new model name
string::size_type pos = fullPath.find_last_of( "/" );
assert( pos != string::npos );
string head = fullPath.substr( 0, pos );
Id ret( head );
// When head = "" it means paId should be root.
if ( ret == Id() && head != "" && head != "/root" )
;//return 0;
parentId = ret;
modelName = fullPath.substr( pos + 1 );
}
else { // Path is an existing element.
parentId = paId;
}
}
/**
* This takes the baseclass for an MMEnzyme and builds the
* MMenz into the Stoich.
*/
void GslStoich::installMMenz( Id enzId, Id enzMolId,
const vector< Id >& subs, const vector< Id >& prds )
{
MMEnzymeBase* meb;
unsigned int enzIndex = coreStoich()->convertIdToPoolIndex( enzMolId );
unsigned int enzSiteIndex = coreStoich()->convertIdToReacIndex( enzId );
if ( subs.size() == 1 ) {
unsigned int subIndex = coreStoich()->convertIdToPoolIndex( subs[0] );
meb = new MMEnzyme1( 1, 1, enzIndex, subIndex );
} else if ( subs.size() > 1 ) {
vector< unsigned int > v;
for ( unsigned int i = 0; i < subs.size(); ++i )
v.push_back( coreStoich()->convertIdToPoolIndex( subs[i] ) );
ZeroOrder* rateTerm = new NOrder( 1.0, v );
meb = new MMEnzyme( 1, 1, enzIndex, rateTerm );
} else {
cout << "Error: GslStoich::installEnzyme: No substrates for " <<
enzId.path() << endl;
return;
}
coreStoich_.installMMenz( meb, enzSiteIndex, subs, prds );
}
Id SigNeur::findSoma( const vector< Id >& compts )
{
double maxDia = 0;
Id maxCompt;
vector< Id > somaCompts; // Theoretically possible to have an array.
for ( vector< Id >::const_iterator i = compts.begin();
i != compts.end(); ++i )
{
string className = i->eref()->className();
if ( className == "Compartment" || className == "SymCompartment" ) {
string name = i->eref().e->name();
if ( name == "soma" || name == "Soma" || name == "SOMA" )
somaCompts.push_back( *i );
double dia;
get< double >( i->eref(), "diameter", dia );
if ( dia > maxDia )
maxCompt = *i;
}
}
if ( somaCompts.size() == 1 ) // First, go by name.
return somaCompts[0];
if ( somaCompts.size() == 0 & maxCompt.good() ) //if no name, use maxdia
return maxCompt;
if ( somaCompts.size() > 1 ) { // Messy but unlikely cases.
if ( maxCompt.good() ) {
if ( find( somaCompts.begin(), somaCompts.end(), maxCompt ) != somaCompts.end() )
return maxCompt;
else
cout << "Error, soma '" << somaCompts.front().path() <<
"' != biggest compartment '" << maxCompt.path() <<
"'\n";
}
return somaCompts[0]; // Should never happen, but an OK response.
}
cout << "Error: SigNeur::findSoma failed to find soma\n";
return Id();
}
// static func to convert id into a string.
string Id::id2str( Id id )
{
return id.path();
}
string SigNeur::__get_cellProto() const
{
Id cellProto;
get < Id > (id_(), "cellProto", cellProto);
return cellProto.path();
}
string SigNeur::__get_dend() const
{
Id dend;
get < Id > (id_(), "dend",dend);
return dend.path();
}
string SigNeur::__get_dendProto() const
{
Id dendProto;
get < Id > (id_(), "dendProto", dendProto);
return dendProto.path();
}
string SigNeur::__get_somaProto() const
{
Id somaProto;
get < Id > (id_(), "somaProto",somaProto);
return somaProto.path();
}
string SigNeur::__get_cell() const
{
Id cell;
get < Id > (id_(), "cell",cell);
return cell.path();
}
string SigNeur::__get_spine() const
{
Id spine;
get < Id > (id_(), "spine",spine);
return spine.path();
}
string SigNeur::__get_spineProto() const
{
Id spineProto;
get < Id > (id_(), "spineProto",spineProto);
return spineProto.path();
}
string SigNeur::__get_soma() const
{
Id soma;
get < Id > (id_(), "soma",soma);
return soma.path();
}
