#include <ReadCell.h>

Collaboration diagram for ReadCell:

Public Member Functions
Id	read (const string &filename, const string &cellname, Id parent)

	ReadCell ()

Static Public Member Functions
static void	addChannelMessage (Id chan)

Private Member Functions
bool	addCaConc (Id compt, Id chan, double value, double dia, double length)

bool	addCanonicalChannel (Id compt, Id chan, double value, double dia, double length)

Id	addChannel (Id compt, Id chan, double value, double dia, double length)

bool	addNernst (Id compt, Id chan, double value)

bool	addSpikeGen (Id compt, Id chan, double value, double dia, double length)

bool	buildChannels (Id compt, vector< string > &argv, double diameter, double length)

Id	buildCompartment (const string &name, const string &parent, double x0, double y0, double z0, double x, double y, double z, double d, double &length, vector< string > &argv)

void	countProtos ()

Id	findChannel (const string &name)

bool	innerRead (ifstream &fin)

bool	readData (const string &line)

bool	readScript (const string &line)

Id	startGraftCell (const string &cellPath)

Private Attributes
Id	cell_

map< string, Id >	chanProtos_

double	CM_

Id	currCell_

bool	doubleEndpointFlag_

double	ELEAK_

bool	eleakFlag_

double	EREST_ACT_

bool	erestFlag_

string	fileName_

bool	graftFlag_

Id	lastCompt_

unsigned int	lineNum_

unsigned int	numChannels_

unsigned int	numCompartments_

unsigned int	numOthers_

unsigned int	numProtoChans_

unsigned int	numProtoCompts_

unsigned int	numProtoOthers_

bool	polarFlag_

Id	protoCompt_

double	RA_

bool	relativeCoordsFlag_

double	RM_

Shell *	shell_

bool	symmetricFlag_

Detailed Description

The ReadCell class implements the old GENESIS cellreader functionality.

ReadCell is partially implemented but works for most common uses and will evolve to some further point.

One significant semantic difference from the GENESIS version is that in MOOSE ReadCell can accept values of globals defined in the script, but will NOT alter the script global values.

Definition at line 24 of file ReadCell.h.

Constructor & Destructor Documentation

ReadCell::ReadCell ( )

Definition at line 23 of file ReadCell.cpp.

References chanProtos_, id, name, and Id::path().

     :
     RM_( 10.0 ),
     CM_( 0.01 ),
     RA_( 1.0 ),
     EREST_ACT_( -0.065 ),
     ELEAK_( -0.065 ),
 
 #if 0
         // Unused privates. Causes error when -Werror is enabled. Uncomment them
         // appropriately when needed.
     dendrDiam( 0.0 ),
     aveLength( 0.0 ),
     spineSurf( 0.0 ),
     spineDens( 0.0 ),
     spineFreq( 0.0 ),
     membFactor( 0.0 ),
 #endif
 
     erestFlag_( 0 ),
     eleakFlag_( 0 ),
 
     cell_( Id() ),
     currCell_( Id() ),
 
     lastCompt_( Id() ),
     protoCompt_( Id() ),
 
     numCompartments_( 0 ),
     numChannels_( 0 ),
     numOthers_( 0 ),
 
     numProtoCompts_( 0 ),
     numProtoChans_( 0 ),
     numProtoOthers_( 0 ),
 
     graftFlag_( 0 ),
     polarFlag_( 0 ),
     relativeCoordsFlag_( 0 ),
     doubleEndpointFlag_( 0 ),
     symmetricFlag_( 0 ),
 
     shell_( reinterpret_cast< Shell* >( Id().eref().data() ) )
 {
     /*
     assert( globalParms.size() == 5 );
     if ( !isEqual( globalParms[0], 0.0 ) )
         CM_ = globalParms[0];
     if ( !isEqual( globalParms[1], 0.0 ) )
         RM_ = globalParms[1];
     if ( !isEqual( globalParms[2], 0.0 ) )
         RA_ = globalParms[2];
     if ( !isEqual( globalParms[3], 0.0 ) )
         EREST_ACT_ = globalParms[3];
     if ( !isEqual( globalParms[4], 0.0 ) )
         ELEAK_ = globalParms[4];
     else
         ELEAK_ = EREST_ACT_;
     */
 
     string libPath = "/library";
     Id libId( libPath );
 
     if ( libId.path() != libPath ) {
         cerr << "Warning: ReadCell: No library for channels.\n";
         return;
     }
 
     vector< Id > chanList =
         Field< vector< Id > >::get(
             ObjId( libId ), "children" );
 
     vector< Id >::iterator i;
     for ( i = chanList.begin(); i != chanList.end(); ++i ) {
         Id id = (*i);
         string name = id.element()->getName();
 
         chanProtos_[ name ] = id;
     }
 }

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Member Function Documentation

bool ReadCell::addCaConc	(	Id	compt,
		Id	chan,
		double	value,
		double	dia,
		double	length
	)

private

Definition at line 846 of file ReadCell.cpp.

References Element::cinfo(), Id::element(), Field< A >::get(), graftFlag_, M_PI, Cinfo::name(), numOthers_, Field< A >::set(), and value.

Referenced by addChannel().

 {
     double thickness = Field< double >::get( chan, "thick" );
     if ( thickness > dia / 2.0 )
         thickness = 0.0;
 
     string className = chan.element()->cinfo()->name();
     if ( className == "CaConc" ) {
         if ( value > 0.0 ) {
             double vol;
             if ( length > 0.0 ){
                 if ( thickness > 0.0 ) {
                     vol = M_PI * length * ( dia - thickness ) * thickness;
                 } else {
                     vol = dia * dia * M_PI * length / 4.0;
                 }
             } else { // spherical
                 if ( thickness > 0.0 ) {
                     double inner_dia = dia - 2 * thickness;
                     vol = M_PI * (
                         dia * dia * dia -
                         inner_dia * inner_dia * inner_dia
                     ) / 6.0;
                 } else {
                     vol = M_PI * dia * dia * dia / 6.0;
                 }
             }
             if ( vol > 0.0 ) // Scale by volume.
                 value /= vol;
         } else {
             value = - value;
         }
 
         if ( !graftFlag_ )
             ++numOthers_;
 
         return Field< double >::set( chan, "B", value );
     }
 
     return 0;
 }

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bool ReadCell::addCanonicalChannel	(	Id	compt,
		Id	chan,
		double	value,
		double	dia,
		double	length
	)

private

Adds a typical channel to a compartment:

Connects up the 'channel' message between chan and compt.
Sets the Gbar field on the channel.

Typical channels currently are: HHChannel, HHChannel2D and SynChan. All of these have the same "channel" interface, and have a "Gbar" field.

Definition at line 774 of file ReadCell.cpp.

References ObjId::bad(), calcSurf(), Element::cinfo(), Shell::doAddMsg(), Id::element(), graftFlag_, Cinfo::name(), numChannels_, Field< A >::set(), shell_, and value.

Referenced by addChannel().

 {
     string className = chan.element()->cinfo()->name();
     if (
         className == "HHChannel" ||
         className == "HHChannel2D" ||
         className == "SynChan" ||
         className == "NMDAChan"
     ) {
         ObjId mid = shell_->doAddMsg(
             "Single",
             compt,
             "channel",
             chan,
             "channel"
         );
         if ( mid.bad() )
             cout << "failed to connect message from compt " << compt <<
                     " to channel " << chan << endl;
 
         if ( value > 0 ) {
             value *= calcSurf( length, dia );
         } else {
             value = -value;
         }
 
         if ( !graftFlag_ )
             ++numChannels_;
 
         return Field< double >::set( chan, "Gbar", value );
     }
 
     return 0;
 }

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Id ReadCell::addChannel	(	Id	compt,
		Id	chan,
		double	value,
		double	dia,
		double	length
	)

private

Definition at line 738 of file ReadCell.cpp.

References addCaConc(), addCanonicalChannel(), addNernst(), addSpikeGen(), Shell::doCopy(), Id::element(), Element::getName(), and shell_.

Referenced by buildChannels().

 {
     Id copy = shell_->doCopy(
         proto,
         compt,
         "",     // newName: same as old name.
         1,      // n: number of copies
         false,  // toGlobal
         false   // copyExtMsgs
     );
         assert( copy.element()->getName() == proto.element()->getName() );
     assert( copy != Id() );
 
     if ( addCanonicalChannel( compt, copy, value, dia, length ) ) return copy;
     if ( addSpikeGen( compt, copy, value, dia, length ) ) return copy;
     if ( addCaConc( compt, copy, value, dia, length ) ) return copy;
     if ( addNernst( compt, copy, value ) ) return copy;
 
     return Id();
 }

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void ReadCell::addChannelMessage ( Id chan )

static

Definition at line 985 of file ReadCell.cpp.

References ObjId::bad(), Neutral::children(), Eref::data(), Id::eref(), Field< A >::get(), name, and moose::tokenize().

Referenced by buildChannels(), and doClassSpecificMessaging().

 {
     /*
     * Get child objects of type Mstring, named addmsg1, 2, etc.
     * These define extra messages to be assembled at setup.
     * Similar to what was done with GENESIS.
     */
     vector< Id > kids;
     Neutral::children( chan.eref(), kids );
     Shell *shell = reinterpret_cast< Shell* >( Id().eref().data() );
     Id cwe = shell->getCwe();
     shell->setCwe( chan );
     for ( vector< Id >::iterator i = kids.begin(); i != kids.end(); ++i )
     {
         // Ignore kid if its name does not begin with "addmsg"..
         const string& name = i->element()->getName();
         if ( name.find( "addmsg", 0 ) != 0 )
             continue;
 
         string s = Field< string >::get( *i, "value" );
         vector< string > token;
                 moose::tokenize( s, "   ", token );
         assert( token.size() == 4 );
         ObjId src = shell->doFind( token[0] );
         ObjId dest = shell->doFind( token[2] );
 
         // I would like to assert, or warn here, but there are legitimate
         // cases where not all possible messages are actually available
         // to set up. So I just bail.
         if ( src.bad() || dest.bad()) {
 #ifndef NDEBUG
                 /*
             cout << "ReadCell::addChannelMessage( " << chan.path() <<
                 "): " << name << " " << s <<
                 ": Bad src " << src << " or dest " << dest << endl;
                 */
 #endif
             continue;
         }
         ObjId mid =
             shell->doAddMsg( "single", src, token[1], dest, token[3] );
         assert( !mid.bad());
     }
     shell->setCwe( cwe );
 }

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bool ReadCell::addNernst	(	Id	compt,
		Id	chan,
		double	value
	)

private

Definition at line 893 of file ReadCell.cpp.

References graftFlag_, and numOthers_.

Referenced by addChannel().

 {
     if ( !graftFlag_ )
         ++numOthers_;
     return 0;
 }

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bool ReadCell::addSpikeGen	(	Id	compt,
		Id	chan,
		double	value,
		double	dia,
		double	length
	)

private

Definition at line 814 of file ReadCell.cpp.

References Element::cinfo(), Shell::doAddMsg(), Id::element(), graftFlag_, Cinfo::name(), numOthers_, Field< A >::set(), and shell_.

Referenced by addChannel().

 {
     string className = chan.element()->cinfo()->name();
     if ( className == "SpikeGen" ) {
         shell_->doAddMsg(
             "Single",
             compt,
             "VmOut",
             chan,
             "Vm"
         );
 
         if ( !graftFlag_ )
             ++numOthers_;
 
         return Field< double >::set( chan, "threshold", value );
     }
 
     return 0;
 }

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bool ReadCell::buildChannels	(	Id	compt,
		vector< string > &	argv,
		double	diameter,
		double	length
	)

private

Definition at line 629 of file ReadCell.cpp.

References addChannel(), addChannelMessage(), calcSurf(), doubleEndpointFlag_, Id::element(), fileName_, findChannel(), Element::getName(), lineNum_, M_PI, Field< A >::set(), and value.

Referenced by readData().

 {
     bool isArgOK;
     int argStart;
     vector< Id > goodChannels;
 
     if ( doubleEndpointFlag_ ) {
         isArgOK = ( argv.size() % 2 ) == 1;
         argStart = 9;
     } else {
         isArgOK = ( argv.size() % 2 ) == 0;
         argStart = 6;
     }
 
     if ( !isArgOK ) {
         cerr << "Error: ReadCell: Bad number of arguments in channel list\n";
         cerr << "File: " << fileName_ << " Line: " << lineNum_ << endl;
         return 0;
     }
 
     for ( unsigned int j = argStart; j < argv.size(); j++ ) {
         // Here we explicitly set compt fields by scaling from the
         // specific value applied here.
         string chan = argv[ j ];
 
         double value = atof( argv[ ++j ].c_str() );
         if ( chan == "RA" ) {
             double temp;
             if ( length == 0.0 ) // Spherical flag. Assume length = dia.
                 temp = 8.0 * value / ( diameter * M_PI );
             else
                 temp = 4.0 * value * length / ( diameter * diameter * M_PI );
             Field< double >::set( compt, "Ra", temp );
         } else if ( chan == "RM" ) {
             Field< double >::set( compt, "Rm", value * calcSurf( length, diameter ) );
         } else if ( chan == "CM" ) {
             Field< double >::set( compt, "Cm", value * calcSurf( length, diameter ) );
         } else if ( chan == "Rm" ) {
             Field< double >::set( compt, "Rm", value );
         } else if ( chan == "Ra" ) {
             Field< double >::set( compt, "Ra", value );
         } else if ( chan == "Cm" ) {
             Field< double >::set( compt, "Cm", value );
         } else if ( chan == "kinModel" ) {
             // Need 3 args here:
             // lambda, name of proto, method
             // We already have lambda from value. Note it is in microns
             if ( j + 2 < argv.size() ) {
                 string protoName = argv[ ++j ];
                 string method = argv[ ++j ];
                 //~ addKinModel( compt, value * 1.0e-6, protoName, method );
             } else {
                 cerr << "Error: ReadCell: kinModel needs 3 args\n";
                 cerr << "File: " << fileName_ << " Line: " << lineNum_ << endl;
                 break;
             }
         } else if ( chan == "m2c" ) {
             // Need 5 args here:
             // scale factor, mol, moloffset, chan, chanoffset
             // We already have scale factor from value.
             if ( j + 4 < argv.size() ) {
                 //~ addM2C( compt, value, argv.begin() + j + 1 );
                 j += 4;
             } else {
                 cerr << "Error: ReadCell: m2c adaptor needs 5 args\n";
                 cerr << "File: " << fileName_ << " Line: " << lineNum_ << endl;
                 break;
             }
         } else if ( chan == "c2m" ) {
             // Need another 5 args here:
             // scale factor, chan, chanoffset, mol, moloffset
             if ( j + 4 < argv.size() ) {
                 //~ addC2M( compt, value, argv.begin() + j + 1 );
                 j += 4;
             } else {
                 cerr << "Error: ReadCell: c2m adaptor needs 5 args\n";
                 cerr << "File: " << fileName_ << " Line: " << lineNum_ << endl;
                 break;
             }
         } else {
             Id chanId = findChannel( chan );
             if ( chanId == Id() ) {
                 cerr << "Error: ReadCell: Channel '" << chan <<
                         "' not found\n";
                 cerr << "File: " << fileName_ << " Line: " << lineNum_ << endl;
                 continue;
             }
 
             Id copy = addChannel( compt, chanId, value, diameter, length );
             if ( copy != Id() ) {
                 goodChannels.push_back( copy );
             } else {
                 cerr << "Error: ReadCell: Could not add " << chan
                                      << " in " << compt.element()->getName() << ".";
                 cerr << "File: " << fileName_ << " Line: " << lineNum_ << endl;
             }
         }
     }
 
     for ( unsigned int i = 0; i < goodChannels.size(); i++ )
         addChannelMessage( goodChannels[ i ] );
 
     return 1;
 }

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Id ReadCell::buildCompartment	(	const string &	name,
		const string &	parent,
		double	x0,
		double	y0,
		double	z0,
		double	x,
		double	y,
		double	z,
		double	d,
		double &	length,
		vector< string > &	argv
	)

private

Definition at line 378 of file ReadCell.cpp.

References ObjId::bad(), BADINDEX, calcSurf(), CM_, currCell_, Shell::doAddMsg(), Shell::doCopy(), Shell::doCreate(), doubleEndpointFlag_, ELEAK_, eleakFlag_, Id::element(), EREST_ACT_, erestFlag_, fileName_, Cinfo::findFinfo(), Field< A >::get(), Element::getNeighbors(), graftFlag_, SymCompartment::initCinfo(), lastCompt_, lineNum_, M_PI, MooseGlobal, numChannels_, numCompartments_, numOthers_, numProtoChans_, numProtoCompts_, numProtoOthers_, Id::path(), protoCompt_, RA_, relativeCoordsFlag_, RM_, Field< A >::set(), shell_, and symmetricFlag_.

Referenced by readData().

 {
     static const Finfo* raxial2OutFinfo =
             SymCompartment::initCinfo()->findFinfo( "distalOut" );
     /*
      * This section determines the parent compartment, to connect up with axial
      * messages. Here 'parent' refers to the biophysical relationship within
      * the neuron's tree, and not to the path hierarchy in the MOOSE element
      * tree.
      *
      * If the parent is specified as 'none', then the compartment is the root
      * of the cell's tree, and will not be connected axially to any compartments
      * except for its children, if any.
      */
     Id parentId;
     if ( parent == "." ) { // Shorthand: use the previous compartment.
         parentId = lastCompt_;
     } else if ( parent == "none" || parent == "nil" ) {
                 parentId = Id();
     } else {
         string parentPath = currCell_.path() + "/" + parent;
         ObjId parentObjId = ObjId( parentPath );
         if ( parentObjId.bad() ) {
             cerr << "Error: ReadCell: could not find parent compt '"
                 << parent
                 << "' for child '" << name << "'.\n";
             cerr << "File: " << fileName_ << " Line: " << lineNum_ << endl;
             return ObjId(0, BADINDEX);
         }
                 parentId = parentObjId;
     }
 
     //~ Id childId;
     //~ bool ret = lookupGet< Id, string >(
         //~ currCell_, "lookupChild", childId, name );
     //~ assert( ret );
     //~ if ( !childId.bad() ) {
         //~ if ( name[ name.length() - 1 ] == ']' ) {
             //~ string::size_type pos = name.rfind( '[' );
             //~ if ( pos == string::npos ) {
                 //~ cerr << "Error: ReadCell: bad child name:" << name << endl;
                 //~ cerr << "File: " << fileName_ << " Line: " << lineNum_ << endl;
                 //~ return 0;
             //~ }
             //~ unsigned int index =
                 //~ atoi( name.substr( pos + 1, name.length() - pos ).c_str() );
             //~ if ( childId.index() == index ) {
                 //~ cerr << "Error: ReadCell: duplicate child on parent compt '" <<
                         //~ parent << "' for child '" << name << "'\n";
                 //~ cerr << "File: " << fileName_ << " Line: " << lineNum_ << endl;
                 //~ return 0;
             //~ }
         //~ } else {
             //~ cerr << "Error: ReadCell: duplicate child on parent compt '" <<
                     //~ parent << "' for child '" << name << "'\n";
             //~ cerr << "File: " << fileName_ << " Line: " << lineNum_ << endl;
             //~ return 0;
         //~ }
     //~ }
 
     unsigned int size = 1;
     Id compt;
     if ( graftFlag_ && ( parent == "none" || parent == "nil" ) ) {
         compt = currCell_;
     } else {
             if ( protoCompt_ != Id() ) {
                         compt = shell_->doCopy(
                                 protoCompt_,
                 currCell_,
                 name,
                 1,        // n: number of copies
                 false,    // toGlobal
                 false     // copyExtMsgs
             );
             numCompartments_ += numProtoCompts_;
             numChannels_ += numProtoChans_;
             numOthers_ += numProtoOthers_;
         } else {
             string comptType = ( symmetricFlag_ ) ?
                 "SymCompartment" : "Compartment";
             compt = shell_->doCreate(
                             comptType, currCell_, name, size, MooseGlobal );
             if ( !graftFlag_ )
                 ++numCompartments_;
         }
     }
     lastCompt_ = compt;
 
     if ( parentId != Id()){
         double px, py, pz;
         double dx, dy, dz;
 
         px = Field< double >::get( parentId, "x" );
         py = Field< double >::get( parentId, "y" );
         pz = Field< double >::get( parentId, "z" );
 
         if ( !doubleEndpointFlag_ ) {
             x0 = px;
             y0 = py;
             z0 = pz;
         }
 
         if ( relativeCoordsFlag_ == 1 ) {
             x += px;
             y += py;
             z += pz;
             if ( doubleEndpointFlag_ ) {
                 x0 += px;
                 y0 += py;
                 z0 += pz;
             }
         }
         dx = x - x0;
         dy = y - y0;
         dz = z - z0;
 
         length = sqrt( dx * dx + dy * dy + dz * dz );
         if ( symmetricFlag_ ) {
             // Now find all sibling compartments on the same parent.
             // They must be connected up using 'sibling'.
             vector< Id > sibs;
             parentId.element()->getNeighbors( sibs, raxial2OutFinfo );
             // Later put in the soma as a sphere, with its special msgs.
             shell_->doAddMsg( "Single",
                 parentId, "distal", compt, "proximal" );
             for ( vector< Id >::iterator i = sibs.begin();
                 i != sibs.end(); ++i ) {
                 shell_->doAddMsg( "Single",
                     compt, "sibling", *i, "sibling" );
             }
 
         } else {
             shell_->doAddMsg( "Single",
                 parentId, "axial", compt, "raxial" );
         }
     } else {
         length = sqrt( x * x + y * y + z * z );
         // or it could be a sphere.
     }
 
     double Cm, Rm, Ra;
 
     Cm = CM_ * calcSurf( length, d );
     Rm = RM_ / calcSurf( length, d );
 
     if ( length > 0 ) {
         Ra = RA_ * length * 4.0 / ( d * d * M_PI );
     } else {
         Ra = RA_ * 8.0 / ( d * M_PI );
     }
 
     // Set each of these to the other only if the only one set was other
     double eleak = ( erestFlag_ && !eleakFlag_ ) ? EREST_ACT_ : ELEAK_;
     double erest = ( !erestFlag_ && eleakFlag_ ) ? ELEAK_ : EREST_ACT_;
 
     Field< double >::set( compt, "x0", x0 );
     Field< double >::set( compt, "y0", y0 );
     Field< double >::set( compt, "z0", z0 );
     Field< double >::set( compt, "x", x );
     Field< double >::set( compt, "y", y );
     Field< double >::set( compt, "z", z );
     Field< double >::set( compt, "diameter", d );
     Field< double >::set( compt, "length", length );
     Field< double >::set( compt, "Rm", Rm );
     Field< double >::set( compt, "Ra", Ra );
     Field< double >::set( compt, "Cm", Cm );
     Field< double >::set( compt, "initVm", erest );
     Field< double >::set( compt, "Em", eleak );
     Field< double >::set( compt, "Vm", erest );
 
     return compt;
 }

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void ReadCell::countProtos ( )

private

Count elements under a tree.

Definition at line 1034 of file ReadCell.cpp.

Referenced by readScript().

 {
     //~ if ( protoCompt_ == 0 )
         //~ return;
     //~
     //~ numProtoCompts_ = 1; // protoCompt_ itself
     //~ numProtoChans_ = 0;
     //~ numProtoOthers_ = 0;
 //~
     //~ vector< vector< Id > > cstack;
     //~ cstack.push_back( Neutral::getChildList( protoCompt_ ) );
     //~ while ( !cstack.empty() ) {
         //~ vector< Id >& child = cstack.back();
         //~
         //~ if ( child.empty() ) {
             //~ cstack.pop_back();
             //~ if ( !cstack.empty() )
                 //~ cstack.back().pop_back();
         //~ } else {
             //~ const Id& curr = child.back();
             //~ const Cinfo* currCinfo = curr()->cinfo();
             //~
             //~ if ( currCinfo->isA( comptCinfo ) )
                 //~ ++numProtoCompts_;
             //~ else if ( currCinfo->isA( chanCinfo ) ||
                       //~ currCinfo->isA( synchanCinfo ) )
                 //~ ++numProtoChans_;
             //~ else if ( currCinfo->isA( spikegenCinfo ) ||
                       //~ currCinfo->isA( caconcCinfo ) ||
                       //~ currCinfo->isA( nernstCinfo ) )
                 //~ ++numProtoOthers_;
             //~
             //~ cstack.push_back( Neutral::getChildList( curr() ) );
         //~ }
     //~ }
 }

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Id ReadCell::findChannel ( const string & name )

private

Definition at line 603 of file ReadCell.cpp.

References chanProtos_.

Referenced by buildChannels().

 {
     //~ vector< Id >::iterator i;
     //~ for ( i = chanProtos_.begin(); i != chanProtos_.end(); i++ )
         //~ if ( i->name() == name )
             //~ return *i;
     //~ return Id();
 
     map< string, Id >::iterator pos = chanProtos_.find( name );
     if ( pos != chanProtos_.end() )
         return pos->second;
     else
         return Id();
 }

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bool ReadCell::innerRead ( ifstream & fin )

private

Definition at line 155 of file ReadCell.cpp.

References COMMENT, DATA, lineNum_, numChannels_, numCompartments_, numOthers_, readData(), readScript(), SCRIPT, and moose::trim().

Referenced by read().

 {
     string line;
     lineNum_ = 0;
 
     ParseStage parseMode = DATA;
     string::size_type pos;
 
     while ( getline( fin, line ) ) {
         line = moose::trim( line );
         lineNum_++;
 
         if ( line.length() == 0 )
             continue;
 
         pos = line.find_first_not_of( "\t " );
         if ( pos == string::npos )
             continue;
         else
             line = line.substr( pos );
 
         if ( line.substr( 0, 2 ) == "//" )
             continue;
 
         if ( ( pos = line.find( "//" ) ) != string::npos )
             line = line.substr( 0, pos );
 
         if ( line.substr( 0, 2 ) == "/*" ) {
             parseMode = COMMENT;
         } else if ( line.find( "*/" ) != string::npos ) {
             parseMode = DATA;
             continue;
         } else if ( line[ 0 ] == '*' ) {
             parseMode = SCRIPT;
         }
 
         if ( parseMode == COMMENT ) {
             pos = line.find( "*/" );
             if ( pos != string::npos ) {
                 parseMode = DATA;
                 if ( line.length() > pos + 2 )
                     line = line.substr( pos + 2 );
             }
         }
 
         if ( parseMode == DATA ) {
             // For now not keeping it strict. Ignoring return status, and
             // continuing even if there was error in processing this line.
             readData( line );
         } else if ( parseMode == SCRIPT ) {
             // For now not keeping it strict. Ignoring return status, and
             // continuing even if there was error in processing this line.
             readScript( line );
             parseMode = DATA;
         }
     }
 
     cout <<
         "ReadCell: " <<
         numCompartments_ << " compartments, " <<
         numChannels_ << " channels, " <<
         numOthers_ << " others\n";
 
     return 1;
 }

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Id ReadCell::read	(	const string &	filename,
		const string &	cellname,
		Id	parent
	)

The readcell function implements the old GENESIS cellreader functionality.

Definition at line 108 of file ReadCell.cpp.

References cell_, Element::cinfo(), currCell_, Shell::doCreate(), Id::element(), fileName_, innerRead(), Cinfo::isA(), MooseGlobal, and shell_.

Referenced by Shell::doLoadModel().

 {
     fileName_ = fileName;
 
     ifstream fin( fileName.c_str() );
     if ( !fin ) {
         cerr << "ReadCell::read -- could not open file " << fileName << ".\n";
         return Id();
     }
 
     /*
     // Search for file in list of paths.
     PathUtility pathUtil( Property::getProperty( Property::SIMPATH ) );
     ifstream fin( filename.c_str() );
     for (unsigned int i = 0; i < pathUtil.size() && !fin; ++i )
     {
         string path = pathUtil.makeFilePath(filename, i);
         fin.clear( );
         fin.open( path.c_str() );
     }
     if ( !fin ) {
         cerr << "ReadCell::read -- could not open file " << filename << endl;
         return Id();
     }
     */
 
     unsigned int size =  1;
     if ( parent.element()->cinfo()->isA( "Neuron" ) ) {
         cell_ = parent;
         currCell_ = cell_;
     } else {
         cell_ = shell_->doCreate( "Neuron", parent,
                         cellName, size, MooseGlobal );
         currCell_ = cell_;
     }
 
     if ( innerRead( fin ) ) {
         return cell_;
     } else {
         cerr << "Readcell failed.\n";
         return Id();
     }
 }

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bool ReadCell::readData ( const string & line )

private

Definition at line 309 of file ReadCell.cpp.

References buildChannels(), buildCompartment(), doubleEndpointFlag_, fileName_, lineNum_, M_PI, name, polarFlag_, and moose::tokenize().

Referenced by innerRead().

 {
     vector< string > argv;
     string delimiters( "\t " );
         moose::tokenize( line, delimiters, argv );
 
     if ( argv.size() < 6 ) {
         cerr << "Error: ReadCell: Too few arguments in line: " << argv.size() <<
                 ", should be > 6.\n";
         cerr << "File: " << fileName_ << " Line: " << lineNum_ << endl;
         return 0;
     }
 
     double x0 = 0.0;
     double y0 = 0.0;
     double z0 = 0.0;
     double x, y, z;
     double d;
     int argOffset = 0;
 
     string name = argv[ 0 ];
     string parent = argv[ 1 ];
 
     if ( doubleEndpointFlag_ ) {
         argOffset = 3;
 
         x0 = 1.0e-6 * atof( argv[ 2 ].c_str() );
         y0 = atof( argv[ 3 ].c_str() );
         z0 = atof( argv[ 4 ].c_str() );
         if ( polarFlag_ ) {
             double r = x0;
             double theta = y0 * M_PI / 180.0;
             double phi = z0 * M_PI / 180.0;
             x0 = r * sin( phi ) * cos ( theta );
             y0 = r * sin( phi ) * sin ( theta );
             z0 = r * cos( phi );
         } else {
             y0 *= 1.0e-6;
             z0 *= 1.0e-6;
         }
     }
 
     x = 1.0e-6 * atof( argv[ argOffset + 2 ].c_str() );
     y = atof( argv[ argOffset + 3 ].c_str() );
     z = atof( argv[ argOffset + 4 ].c_str() );
     if ( polarFlag_ ) {
         double r = x;
         double theta = y * M_PI / 180.0;
         double phi = z * M_PI / 180.0;
         x = r * sin( phi ) * cos ( theta );
         y = r * sin( phi ) * sin ( theta );
         z = r * cos( phi );
     } else {
         y *= 1.0e-6;
         z *= 1.0e-6;
     }
 
     d = 1.0e-6 * atof( argv[ argOffset + 5 ].c_str() );
 
     double length;
     Id compt =
         buildCompartment( name, parent, x0, y0, z0, x, y, z, d, length, argv );
 
     if ( compt == Id() )
         return 0;
 
     return buildChannels( compt, argv, d, length );
 }

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bool ReadCell::readScript ( const string & line )

private

Definition at line 221 of file ReadCell.cpp.

References cell_, CM_, countProtos(), currCell_, doubleEndpointFlag_, ELEAK_, eleakFlag_, EREST_ACT_, erestFlag_, fileName_, graftFlag_, lineNum_, Id::path(), polarFlag_, protoCompt_, RA_, relativeCoordsFlag_, RM_, startGraftCell(), symmetricFlag_, and moose::tokenize().

Referenced by innerRead().

 {
     vector< string > argv;
     string delimiters( "\t " );
         moose::tokenize( line, delimiters, argv );
 
     if ( argv[ 0 ] == "*cartesian" ) {
         polarFlag_ = 0;
     } else if ( argv[ 0 ] == "*polar" ) {
         polarFlag_ = 1;
     } else if ( argv[ 0 ] == "*relative" ) {
         relativeCoordsFlag_ = 1;
     } else if ( argv[ 0 ] == "*absolute" ) {
         relativeCoordsFlag_ = 0;
     } else if ( argv[ 0 ] == "*symmetric" ) {
         symmetricFlag_ = 1;
     } else if ( argv[ 0 ] == "*asymmetric" ) {
         symmetricFlag_ = 0;
     } else if ( argv[ 0 ] == "*set_global" || argv[ 0 ] == "*set_compt_param" ) {
         if ( argv.size() != 3 ) {
             cerr << "Error: ReadCell: Bad line: " <<
                 "File: " << fileName_ <<
                 "Line: " << lineNum_ << "\n";
             return 0;
         }
 
         if ( argv[ 1 ] == "RM" )
             RM_ = atof( argv[ 2 ].c_str() );
         if ( argv[ 1 ] == "RA" )
             RA_ = atof( argv[ 2 ].c_str() );
         if ( argv[ 1 ] == "CM" )
             CM_ = atof( argv[ 2 ].c_str() );
         if ( argv[ 1 ] == "EREST_ACT" ) {
             EREST_ACT_ = atof( argv[ 2 ].c_str() );
             erestFlag_ = 1;
         } if (argv[ 1 ] == "ELEAK" ) {
             ELEAK_ = atof( argv[ 2 ].c_str() );
             eleakFlag_ = 1;
         }
     } else if ( argv[ 0 ] == "*start_cell" ) {
         if ( argv.size() == 1 ) {
             graftFlag_ = 0;
             currCell_ = cell_;
         } else if ( argv.size() == 2 ) {
             graftFlag_ = 1;
             currCell_ = startGraftCell( argv[ 1 ] );
             if ( currCell_ == Id() )
                 return 0;
         } else {
             cerr << "Error: ReadCell: Bad line: " <<
                 "File: " << fileName_ <<
                 "Line: " << lineNum_ << "\n";
             return 0;
         }
     } else if ( argv[ 0 ] == "*compt" ) {
         if ( argv.size() != 2 ) {
             cerr << "Error: ReadCell: Bad line: " <<
                 "File: " << fileName_ <<
                 "Line: " << lineNum_ << "\n";
             return 0;
         }
 
         Id protoId( argv[ 1 ] );
         if ( protoId.path() != argv[ 1 ] ) {
             cerr << "Error: ReadCell: Bad path: " << argv[ 1 ] << " " <<
                 "File: " << fileName_ <<
                 "Line: " << lineNum_ << "\n";
             return 0;
         }
 
         protoCompt_ = protoId;
         countProtos();
     } else if ( argv[ 0 ] == "*double_endpoint" ) {
         doubleEndpointFlag_ = 1;
     } else if ( argv[ 0 ] == "*double_endpoint_off" ) {
         doubleEndpointFlag_ = 0;
     } else if ( argv[ 0 ] == "*makeproto" ) {
         ; // Nothing to be done.
     } else {
         cerr << "Warning: ReadCell: Command " <<
             argv[ 0 ] << " not recognized. Ignoring. " <<
             "File: " << fileName_ <<
             "Line: " << lineNum_ << "\n";
     }
 
     return 1;
 }

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Id ReadCell::startGraftCell ( const string & cellPath )

private

Definition at line 558 of file ReadCell.cpp.

References ObjId::bad(), Shell::doCreate(), fileName_, lineNum_, MooseGlobal, Id::path(), and shell_.

Referenced by readScript().

 {
     /*
      * If path exists, return with error. This will also catch the case where
      * cellPath is "/", and we will not have to check for this separately
      * later.
      */
     Id cellId( cellPath );
     if ( cellId.path() == cellPath ) {
         cerr << "Warning: ReadCell: cell '" << cellPath << "' already exists.\n";
         cerr << "File: " << fileName_ << " Line: " << lineNum_ << endl;
         return Id();
     }
 
         ObjId parentObjId;
     string cellName;
     string::size_type pos_1 = cellPath.find_first_of( "/" );
     string::size_type pos_2 = cellPath.find_last_of( "/" );
 
     if ( pos_1 != 0 ) {
         cerr << "Error: ReadCell: *start_cell should be given absolute path.\n";
         cerr << "File: " << fileName_ << " Line: " << lineNum_ << endl;
         return Id();
     }
 
     if ( pos_2 == 0 ) {
             parentObjId = ObjId("/");
         cellName = cellPath.substr( 1 );
     } else {
         string parentPath = cellPath.substr( 0, pos_2  );
         parentObjId = ObjId( parentPath );
         if ( parentObjId.bad() ) {
             cerr << "Error: ReadCell: cell path '" << cellPath
                 << "' not found.\n";
             cerr << "File: " << fileName_ << " Line: " << lineNum_ << endl;
             return Id();
         }
 
         cellName = cellPath.substr( pos_2 + 1 );
     }
 
     unsigned int size = 1;
     return shell_->doCreate( "Compartment", parentObjId, cellName, size, MooseGlobal );
 }