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HSolveActiveSetup.cpp
6b27e69e' as 'moose-core'
Dilawar Singh authored
HSolveActiveSetup.cpp 19.92 KiB
/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
** copyright (C) 2003-2007 Upinder S. Bhalla, Niraj Dudani and NCBS
** It is made available under the terms of the
** GNU Lesser General Public License version 2.1
** See the file COPYING.LIB for the full notice.
**********************************************************************/
#include "HSolveActive.h"
//////////////////////////////////////////////////////////////////////
// Setup of data structures
//////////////////////////////////////////////////////////////////////
void HSolveActive::setup( Id seed, double dt )
{
//~ cout << ".. HA.setup()" << endl;
this->HSolvePassive::setup( seed, dt );
readHHChannels();
readGates();
readCalcium();
createLookupTables();
readSynapses(); // Reads SynChans, SpikeGens. Drops process msg for SpikeGens.
readExternalChannels();
manageOutgoingMessages(); // Manages messages going out from the cell's components.
//~ reinit();
cleanup();
//~ cout << "# of compartments: " << compartmentId_.size() << "." << endl;
//~ cout << "# of channels: " << channelId_.size() << "." << endl;
//~ cout << "# of gates: " << gateId_.size() << "." << endl;
//~ cout << "# of states: " << state_.size() << "." << endl;
//~ cout << "# of Ca pools: " << caConc_.size() << "." << endl;
//~ cout << "# of SynChans: " << synchan_.size() << "." << endl;
//~ cout << "# of SpikeGens: " << spikegen_.size() << "." << endl;
}
void HSolveActive::reinit( ProcPtr info )
{
externalCurrent_.assign( externalCurrent_.size(), 0.0 );
reinitSpikeGens( info );
reinitCompartments();
reinitCalcium();
reinitChannels();
sendValues( info );
}
void HSolveActive::reinitSpikeGens( ProcPtr info )
{
vector< SpikeGenStruct >::iterator ispike;
for ( ispike = spikegen_.begin(); ispike != spikegen_.end(); ++ispike )
ispike->reinit( info );
}
void HSolveActive::reinitCompartments()
{
for ( unsigned int ic = 0; ic < nCompt_; ++ic )
V_[ ic ] = tree_[ ic ].initVm;
}
void HSolveActive::reinitCalcium()
{
caActivation_.assign( caActivation_.size(), 0.0 );
for ( unsigned int i = 0; i < ca_.size(); ++i )
{
caConc_[ i ].c_ = 0.0;
ca_[ i ] = caConc_[ i ].CaBasal_;
}
}
void HSolveActive::reinitChannels()
{
vector< double >::iterator iv;
vector< double >::iterator istate = state_.begin();
vector< int >::iterator ichannelcount = channelCount_.begin();
vector< ChannelStruct >::iterator ichan = channel_.begin();
vector< ChannelStruct >::iterator chanBoundary;
vector< unsigned int >::iterator icacount = caCount_.begin();
vector< double >::iterator ica = ca_.begin();
vector< double >::iterator caBoundary;
vector< LookupColumn >::iterator icolumn = column_.begin();
vector< LookupRow >::iterator icarowcompt;
vector< LookupRow* >::iterator icarow = caRow_.begin();
LookupRow vRow;
double C1, C2;
for ( iv = V_.begin(); iv != V_.end(); ++iv )
{
vTable_.row( *iv, vRow );
icarowcompt = caRowCompt_.begin();
caBoundary = ica + *icacount;
for ( ; ica < caBoundary; ++ica )
{
caTable_.row( *ica, *icarowcompt );
++icarowcompt;
}
chanBoundary = ichan + *ichannelcount;
for ( ; ichan < chanBoundary; ++ichan )
{
if ( ichan->Xpower_ > 0.0 )
{
vTable_.lookup( *icolumn, vRow, C1, C2 );
*istate = C1 / C2;
++icolumn, ++istate;
}
if ( ichan->Ypower_ > 0.0 )
{
vTable_.lookup( *icolumn, vRow, C1, C2 );
*istate = C1 / C2;
++icolumn, ++istate;
}
if ( ichan->Zpower_ > 0.0 )
{
LookupRow* caRow = *icarow;
if ( caRow )
{
caTable_.lookup( *icolumn, *caRow, C1, C2 );
}
else
{
vTable_.lookup( *icolumn, vRow, C1, C2 );
}
*istate = C1 / C2;
++icolumn, ++istate, ++icarow; }
}
++ichannelcount, ++icacount;
}
}
void HSolveActive::readHHChannels()
{
vector< Id >::iterator icompt;
vector< Id >::iterator ichan;
int nChannel = 0;
double Gbar = 0.0, Ek = 0.0;
double X = 0.0, Y = 0.0, Z = 0.0;
double Xpower = 0.0, Ypower = 0.0, Zpower = 0.0;
int instant = 0;
for ( icompt = compartmentId_.begin(); icompt != compartmentId_.end(); ++icompt )
{
nChannel = HSolveUtils::hhchannels( *icompt, channelId_ );
// todo: discard channels with Gbar = 0.0
channelCount_.push_back( nChannel );
ichan = channelId_.end() - nChannel;
for ( ; ichan != channelId_.end(); ++ichan )
{
channel_.resize( channel_.size() + 1 );
ChannelStruct& channel = channel_.back();
current_.resize( current_.size() + 1 );
CurrentStruct& current = current_.back();
Gbar = Field< double >::get( *ichan, "Gbar" );
Ek = Field< double >::get( *ichan, "Ek" );
X = Field< double >::get( *ichan, "X" );
Y = Field< double >::get( *ichan, "Y" );
Z = Field< double >::get( *ichan, "Z" );
Xpower = Field< double >::get( *ichan, "Xpower" );
Ypower = Field< double >::get( *ichan, "Ypower" );
Zpower = Field< double >::get( *ichan, "Zpower" );
instant = Field< int >::get( *ichan, "instant" );
double modulation = Field< double >::get( *ichan, "modulation");
current.Ek = Ek;
channel.Gbar_ = Gbar;
channel.setPowers( Xpower, Ypower, Zpower );
channel.instant_ = instant;
channel.modulation_ = modulation;
/*
* Map channel index to state index. This is useful in the
* interface to find gate values.
*/
chan2state_.push_back( state_.size() );
if ( Xpower > 0.0 )
state_.push_back( X );
if ( Ypower > 0.0 )
state_.push_back( Y );
if ( Zpower > 0.0 )
state_.push_back( Z );
/*
* Map channel index to compartment index. This is useful in the
* interface to generate channel Ik values (since we then need the
* compartment Vm).
*/
chan2compt_.push_back( icompt - compartmentId_.begin() ); }
}
int nCumulative = 0;
currentBoundary_.resize( nCompt_ );
for ( unsigned int ic = 0; ic < nCompt_; ++ic )
{
nCumulative += channelCount_[ ic ];
currentBoundary_[ ic ] = current_.begin() + nCumulative;
}
}
void HSolveActive::readGates()
{
vector< Id >::iterator ichan;
unsigned int nGates = 0;
int useConcentration = 0;
for ( ichan = channelId_.begin(); ichan != channelId_.end(); ++ichan )
{
nGates = HSolveUtils::gates( *ichan, gateId_ );
gCaDepend_.insert( gCaDepend_.end(), nGates, 0 );
useConcentration = Field< int >::get( *ichan, "useConcentration" );
if ( useConcentration )
gCaDepend_.back() = 1;
}
}
void HSolveActive::readCalcium()
{
double Ca, CaBasal, tau, B, ceiling, floor;
vector< Id > caConcId;
vector< int > caTargetIndex;
map< Id, int > caConcIndex;
int nTarget, nDepend;
vector< Id >::iterator iconc;
caCount_.resize( nCompt_ );
unsigned int ichan = 0;
for ( unsigned int ic = 0; ic < nCompt_; ++ic )
{
unsigned int chanBoundary = ichan + channelCount_[ ic ];
unsigned int nCa = caConc_.size();
for ( ; ichan < chanBoundary; ++ichan )
{
caConcId.clear();
nTarget = HSolveUtils::caTarget( channelId_[ ichan ], caConcId );
if ( nTarget == 0 )
// No calcium pools fed by this channel.
caTargetIndex.push_back( -1 );
nDepend = HSolveUtils::caDepend( channelId_[ ichan ], caConcId );
if ( nDepend == 0 )
// Channel does not depend on calcium.
caDependIndex_.push_back( -1 );
for ( iconc = caConcId.begin(); iconc != caConcId.end(); ++iconc )
if ( caConcIndex.find( *iconc ) == caConcIndex.end() )
{
caConcIndex[ *iconc ] = caCount_[ ic ];
++caCount_[ ic ];
Ca = Field< double >::get( *iconc, "Ca" );
CaBasal = Field< double >::get( *iconc, "CaBasal" );
tau = Field< double >::get( *iconc, "tau" );
B = Field< double >::get( *iconc, "B" );
ceiling = Field< double >::get( *iconc, "ceiling" );
floor = Field< double >::get( *iconc, "floor" );
caConc_.push_back(
CaConcStruct(
Ca, CaBasal,
tau, B,
ceiling, floor,
dt_
)
);
caConcId_.push_back( *iconc );
}
if ( nTarget != 0 )
caTargetIndex.push_back( caConcIndex[ caConcId.front() ] + nCa );
if ( nDepend != 0 )
caDependIndex_.push_back( caConcIndex[ caConcId.back() ] );
}
}
caTarget_.resize( channel_.size() );
ca_.resize( caConc_.size() );
caActivation_.resize( caConc_.size() );
for ( unsigned int ichan = 0; ichan < channel_.size(); ++ichan )
{
if ( caTargetIndex[ ichan ] == -1 )
caTarget_[ ichan ] = 0;
else
caTarget_[ ichan ] = &caActivation_[ caTargetIndex[ ichan ] ];
}
}
void HSolveActive::createLookupTables()
{
std::set< Id > caSet;
std::set< Id > vSet;
vector< Id > caGate;
vector< Id > vGate;
map< Id, unsigned int > gateSpecies;
for ( unsigned int ig = 0; ig < gateId_.size(); ++ig )
if ( gCaDepend_[ ig ] )
caSet.insert( gateId_[ ig ] );
else
vSet.insert( gateId_[ ig ] );
caGate.insert( caGate.end(), caSet.begin(), caSet.end() );
vGate.insert( vGate.end(), vSet.begin(), vSet.end() );
for ( unsigned int ig = 0; ig < caGate.size(); ++ig )
gateSpecies[ caGate[ ig ] ] = ig;
for ( unsigned int ig = 0; ig < vGate.size(); ++ig )
gateSpecies[ vGate[ ig ] ] = ig;
/*
* Finding the smallest xmin and largest xmax across all gates' lookup
* tables.
*
* # of divs is determined by finding the smallest dx (highest density).
*/
vMin_ = numeric_limits< double >::max();
vMax_ = numeric_limits< double >::min();
double vDx = numeric_limits< double >::max();
caMin_ = numeric_limits< double >::max();
caMax_ = numeric_limits< double >::min();
double caDx = numeric_limits< double >::max();
double min;
double max;
unsigned int divs;
double dx;
for ( unsigned int ig = 0; ig < caGate.size(); ++ig )
{
min = Field< double >::get( caGate[ ig ], "min" );
max = Field< double >::get( caGate[ ig ], "max" );
divs = Field< unsigned int >::get( caGate[ ig ], "divs" );
dx = ( max - min ) / divs;
if ( min < caMin_ )
caMin_ = min;
if ( max > caMax_ )
caMax_ = max;
if ( dx < caDx )
caDx = dx;
}
double caDiv = ( caMax_ - caMin_ ) / caDx;
caDiv_ = static_cast< int >( caDiv + 0.5 ); // Round-off to nearest int.
for ( unsigned int ig = 0; ig < vGate.size(); ++ig )
{
min = Field< double >::get( vGate[ ig ], "min" );
max = Field< double >::get( vGate[ ig ], "max" );
divs = Field< unsigned int >::get( vGate[ ig ], "divs" );
dx = ( max - min ) / divs;
if ( min < vMin_ )
vMin_ = min;
if ( max > vMax_ )
vMax_ = max;
if ( dx < vDx )
vDx = dx;
}
double vDiv = ( vMax_ - vMin_ ) / vDx;
vDiv_ = static_cast< int >( vDiv + 0.5 ); // Round-off to nearest int.
caTable_ = LookupTable( caMin_, caMax_, caDiv_, caGate.size() );
vTable_ = LookupTable( vMin_, vMax_, vDiv_, vGate.size() );
vector< double > A, B;
vector< double >::iterator ia, ib;
// double a, b;
//~ int AMode, BMode;
//~ bool interpolate;
// Calcium-dependent lookup tables
HSolveUtils::Grid caGrid( caMin_, caMax_, caDiv_ );
//~ if ( !caGate.empty() ) {
//~ grid.resize( 1 + caDiv_ );
//~ double dca = ( caMax_ - caMin_ ) / caDiv_;
//~ for ( int igrid = 0; igrid <= caDiv_; ++igrid )
//~ grid[ igrid ] = caMin_ + igrid * dca;
//~ }
for ( unsigned int ig = 0; ig < caGate.size(); ++ig )
{
HSolveUtils::rates( caGate[ ig ], caGrid, A, B );
//~ HSolveUtils::modes( caGate[ ig ], AMode, BMode );
//~ interpolate = ( AMode == 1 ) || ( BMode == 1 );
ia = A.begin();
ib = B.begin();
for ( unsigned int igrid = 0; igrid < caGrid.size(); ++igrid )
{
// Use one of the optimized forms below, instead of A and B
// directly. Also updated reinit() accordingly (for gate state).
// a = *ia;
// b = *ib;
// *ia = ( 2.0 - dt_ * b ) / ( 2.0 + dt_ * b );
// *ib = dt_ * a / ( 1.0 + dt_ * b / 2.0 ); // *ia = dt_ * a;
// *ib = 1.0 + dt_ * b / 2.0;
++ia, ++ib;
}
//~ caTable_.addColumns( ig, A, B, interpolate );
caTable_.addColumns( ig, A, B );
}
// Voltage-dependent lookup tables
HSolveUtils::Grid vGrid( vMin_, vMax_, vDiv_ );
//~ if ( !vGate.empty() ) {
//~ grid.resize( 1 + vDiv_ );
//~ double dv = ( vMax_ - vMin_ ) / vDiv_;
//~ for ( int igrid = 0; igrid <= vDiv_; ++igrid )
//~ grid[ igrid ] = vMin_ + igrid * dv;
//~ }
for ( unsigned int ig = 0; ig < vGate.size(); ++ig )
{
//~ interpolate = HSolveUtils::get< HHGate, bool >( vGate[ ig ], "useInterpolation" );
HSolveUtils::rates( vGate[ ig ], vGrid, A, B );
//~ HSolveUtils::modes( vGate[ ig ], AMode, BMode );
//~ interpolate = ( AMode == 1 ) || ( BMode == 1 );
ia = A.begin();
ib = B.begin();
for ( unsigned int igrid = 0; igrid < vGrid.size(); ++igrid )
{
// Use one of the optimized forms below, instead of A and B
// directly. Also updated reinit() accordingly (for gate state).
// a = *ia;
// b = *ib;
// *ia = ( 2.0 - dt_ * b ) / ( 2.0 + dt_ * b );
// *ib = dt_ * a / ( 1.0 + dt_ * b / 2.0 );
// *ia = dt_ * a;
// *ib = 1.0 + dt_ * b / 2.0;
++ia, ++ib;
}
//~ vTable_.addColumns( ig, A, B, interpolate );
vTable_.addColumns( ig, A, B );
}
column_.reserve( gateId_.size() );
for ( unsigned int ig = 0; ig < gateId_.size(); ++ig )
{
unsigned int species = gateSpecies[ gateId_[ ig ] ];
LookupColumn column;
if ( gCaDepend_[ ig ] )
caTable_.column( species, column );
else
vTable_.column( species, column );
column_.push_back( column );
}
///////////////////!!!!!!!!!!
unsigned int maxN = *( max_element( caCount_.begin(), caCount_.end() ) );
caRowCompt_.resize( maxN );
for ( unsigned int ichan = 0; ichan < channel_.size(); ++ichan )
{
if ( channel_[ ichan ].Zpower_ > 0.0 )
{
int index = caDependIndex_[ ichan ];
if ( index == -1 )
caRow_.push_back( 0 );
else caRow_.push_back( &caRowCompt_[ index ] );
}
}
}
/**
* Reads in SynChans and SpikeGens.
*
* Unlike Compartments, HHChannels, etc., neither of these are zombified.
* In other words, their fields are not managed by HSolve, and their "process"
* functions are invoked to do their calculations. For SynChans, the process
* calls are made by their respective clocks, and hence the process message is
* not dropped. On the other hand, we drop the SpikeGen process messages here,
* and explicitly call the SpikeGen process() from the HSolve via a pointer.
*/
void HSolveActive::readSynapses()
{
vector< Id > spikeId;
vector< Id > synId;
vector< Id >::iterator syn;
vector< Id >::iterator spike;
SynChanStruct synchan;
for ( unsigned int ic = 0; ic < nCompt_; ++ic )
{
synId.clear();
HSolveUtils::synchans( compartmentId_[ ic ], synId );
for ( syn = synId.begin(); syn != synId.end(); ++syn )
{
synchan.compt_ = ic;
synchan.elm_ = *syn;
synchan_.push_back( synchan );
}
static const Finfo* procDest = SpikeGen::initCinfo()->findFinfo( "process");
assert( procDest );
const DestFinfo* df = dynamic_cast< const DestFinfo* >( procDest );
assert( df );
spikeId.clear();
HSolveUtils::spikegens( compartmentId_[ ic ], spikeId );
// Very unlikely that there will be >1 spikegens in a compartment,
// but lets take care of it anyway.
for ( spike = spikeId.begin(); spike != spikeId.end(); ++spike )
{
spikegen_.push_back(
SpikeGenStruct( &V_[ ic ], spike->eref() )
);
ObjId mid = spike->element()->findCaller( df->getFid() );
if ( ! mid.bad() )
Msg::deleteMsg( mid );
}
}
}
void HSolveActive::readExternalChannels()
{
vector< string > filter;
filter.push_back( "HHChannel" );
//~ filter.push_back( "SynChan" );
//~ externalChannelId_.resize( compartmentId_.size() );
externalCurrent_.resize( 2 * compartmentId_.size(), 0.0 );
//~ for ( unsigned int ic = 0; ic < compartmentId_.size(); ++ic )
//~ HSolveUtils::targets(
//~ compartmentId_[ ic ],
//~ "channel",
//~ externalChannelId_[ ic ], //~ filter,
//~ false // include = false. That is, use filter to exclude.
//~ );
}
void HSolveActive::manageOutgoingMessages()
{
vector< Id > targets;
vector< string > filter;
/*
* Going through all comparments, and finding out which ones have external
* targets through the VmOut msg. External refers to objects that do not
* belong the cell being managed by this HSolve. We find these by excluding
* any HHChannels and SpikeGens from the VmOut targets. These will then
* be used in HSolveActive::sendValues() to send out the messages behalf of
* the original objects.
*/
filter.push_back( "HHChannel" );
filter.push_back( "SpikeGen" );
for ( unsigned int ic = 0; ic < compartmentId_.size(); ++ic )
{
targets.clear();
int nTargets = HSolveUtils::targets(
compartmentId_[ ic ],
"VmOut",
targets,
filter,
false // include = false. That is, use filter to exclude.
);
if ( nTargets )
outVm_.push_back( ic );
}
/*
* As before, going through all CaConcs, and finding any which have external
* targets.
*/
filter.clear();
filter.push_back( "HHChannel" );
for ( unsigned int ica = 0; ica < caConcId_.size(); ++ica )
{
targets.clear();
int nTargets = HSolveUtils::targets(
caConcId_[ ica ],
"concOut",
targets,
filter,
false // include = false. That is, use filter to exclude.
);
if ( nTargets )
outCa_.push_back( ica );
}
}
void HSolveActive::cleanup()
{
// compartmentId_.clear();
gCaDepend_.clear();
caDependIndex_.clear();
}