Cell Class Reference

#include <Cell.h>

Collaboration diagram for Cell:

Classes
struct	MethodInfo

Public Member Functions
	Cell ()
string	getDescription () const
int	getImplicit () const
string	getMethod () const
Id	getSetup () const
unsigned int	getSolverClock () const
string	getSolverName () const
int	getVariableDt () const
void	processDummy (const Eref &e, ProcPtr p)
void	reinit (const Eref &e, ProcPtr p)
void	setMethod (string value)
void	setSolverClock (unsigned int value)
void	setSolverName (string value)
void	setupf (Id cell)

Static Public Member Functions
static void	addMethod (const string &name, const string &description, int isVariableDt, int isImplicit)
static const Cinfo *	initCinfo ()

Private Member Functions
void	setupSolver (Id cell, Id seed) const

Static Private Member Functions
static vector< Id >	children (Id obj)
static Id	findCompt (Id cell)

Private Attributes
string	method_
Shell *	shell_
unsigned int	solverClock_
string	solverName_

Static Private Attributes
static map< string, MethodInfo >	methodMap_

Detailed Description

Definition at line 13 of file Cell.h.

Constructor & Destructor Documentation

Cell::Cell

(

)

Definition at line 159 of file Cell.cpp.

References setMethod().

    :
    solverClock_( 2 ),
    solverName_( "_integ" ),
    shell_( reinterpret_cast< Shell* >( Id().eref().data() ) )
{
    setMethod( "hsolve" );
}

Here is the call graph for this function:

Member Function Documentation

void Cell::addMethod ( const string &  name, const string &  description, int  isVariableDt, int  isImplicit  )

static

Definition at line 168 of file Cell.cpp.

References methodMap_, and name.

Referenced by initCinfo().

{
    methodMap_[ name ] = MethodInfo( description, isVariableDt, isImplicit );
}

Here is the caller graph for this function:

vector< Id > Cell::children ( Id  obj )

staticprivate

Definition at line 237 of file Cell.cpp.

References Neutral::children(), and Id::eref().

Referenced by findCompt().

{
    //~ return Field< vector< Id > >::get( obj, "children" );
    //~ return Field< vector< Id > >::fastGet( obj.eref(), "children" );
    //~ return localGet< Neutral, vector< Id > >( obj.eref(), "children" );

    vector< Id > c;
    Neutral::children( obj.eref(), c );
    return c;
}

Here is the call graph for this function:

Here is the caller graph for this function:

Id Cell::findCompt ( Id  cell )

staticprivate

This function performs a depth-first search of the tree under the current cell. First compartment found is returned as the seed.

Definition at line 252 of file Cell.cpp.

References children(), compartmentCinfo, and Cinfo::find().

Referenced by reinit(), and setupf().

{
    /* 'curr' is the current element under consideration. 'cstack' is a list
     * of all elements (and their immediate siblings) found on the path from
     * the root element (the Cell) to the current element.
     */
    vector< vector< Id > > cstack;
    Id seed;

    const Cinfo* compartmentCinfo = Cinfo::find( "Compartment" );

    cstack.push_back( children( cell ) );
    while ( !cstack.empty() )
    {
        const vector< Id >& child = cstack.back();

        if ( child.empty() )
        {
            cstack.pop_back();
            if ( !cstack.empty() )
                cstack.back().pop_back();
        }
        else
        {
            dump("TODO", "TODO: Commented out code. ");
            Id curr = child.back();

#if  0     /* ----- #if 0 : If0Label_1 ----- */

            //~ string className = Field< string >::get( curr, "class" );
            if ( curr()->cinfo() == compartmentCinfo )
            {
                seed = curr;
                break;
            }
#endif     /* ----- #if 0 : If0Label_1 ----- */


            cstack.push_back( children( curr ) );
        }
    }

    return seed;
}

Here is the call graph for this function:

Here is the caller graph for this function:

string Cell::getDescription

(

)

const

Definition at line 368 of file Cell.cpp.

References method_, and methodMap_.

Referenced by initCinfo().

{
    return methodMap_[ method_ ].description;
}

Here is the caller graph for this function:

int Cell::getImplicit

(

)

const

Definition at line 363 of file Cell.cpp.

References method_, and methodMap_.

Referenced by initCinfo().

{
    return methodMap_[ method_ ].isImplicit;
}

Here is the caller graph for this function:

string Cell::getMethod

(

)

const

Definition at line 333 of file Cell.cpp.

References method_.

Referenced by initCinfo().

{
    return method_;
}

Here is the caller graph for this function:

Id Cell::getSetup

(

)

const

Definition at line 210 of file Cell.cpp.

Referenced by initCinfo().

{
    return Id();
}

Here is the caller graph for this function:

unsigned int Cell::getSolverClock

(

)

const

Definition at line 343 of file Cell.cpp.

References solverClock_.

Referenced by initCinfo().

{
    return solverClock_;
}

Here is the caller graph for this function:

string Cell::getSolverName

(

)

const

Definition at line 353 of file Cell.cpp.

References solverName_.

Referenced by initCinfo().

{
    return solverName_;
}

Here is the caller graph for this function:

int Cell::getVariableDt

(

)

const

Definition at line 358 of file Cell.cpp.

References method_, and methodMap_.

Referenced by initCinfo().

{
    return methodMap_[ method_ ].isVariableDt;
}

Here is the caller graph for this function:

const Cinfo * Cell::initCinfo ( )

static

Definition at line 23 of file Cell.cpp.

References addMethod(), cellCinfo, getDescription(), getImplicit(), getMethod(), getSetup(), getSolverClock(), getSolverName(), getVariableDt(), Neutral::initCinfo(), processDummy(), reinit(), setMethod(), setSolverClock(), setSolverName(), and setupf().

{
    static DestFinfo process(
        "process",
        "Cell does not process at simulation time--"
        "it only sets up the solver at reset.",
        new ProcOpFunc< Cell >( &Cell::processDummy )
    );

    static DestFinfo reinit(
        "reinit",
        "Handles 'reinit' call: This triggers setting up the solver.",
        new ProcOpFunc< Cell >( &Cell::reinit )
        //~ new EpFunc0< Cell >( &Cell::reinit )
    );

    static Finfo* processShared[] =
    {
        &process,
        &reinit
    };

    static SharedFinfo proc(
        "proc",
        "This shared message exists only to receive a 'reinit' call, which is "
        "taken as a trigger to create and set up HSolve.",
        processShared,
        sizeof( processShared ) / sizeof( Finfo* )
    );

    static DestFinfo setup1(
        "setup1",
        "Setup.",
        new OpFunc1< Cell, Id >( &Cell::setupf )
    );

    static ValueFinfo< Cell, Id > setup2(
        "setupv",
        "Setupv.",
        &Cell::setupf,
        &Cell::getSetup
    );

    static ValueFinfo< Cell, string > method(
        "method",
        "Specifies the integration method to be used for the neuron managed "
        "by this Cell object.",
        &Cell::setMethod,
        &Cell::getMethod
    );

    static ValueFinfo< Cell, unsigned int > solverClock(
        "solverClock",
        "Specifies which clock to use for the HSolve, if it is used.",
        &Cell::setSolverClock,
        &Cell::getSolverClock
    );

    static ValueFinfo< Cell, string > solverName(
        "solverName",
        "Specifies name for the solver object.",
        &Cell::setSolverName,
        &Cell::getSolverName
    );

    static ReadOnlyValueFinfo< Cell, int > variableDt(
        "variableDt",
        "Read-only field which tells if the current method is a variable "
        "time-step method.",
        &Cell::getVariableDt
    );

    static ReadOnlyValueFinfo< Cell, int > implicit(
        "implicit",
        "Read-only field which tells if the current method is an implicit "
        "method.",
        &Cell::getImplicit
    );

    static ReadOnlyValueFinfo< Cell, string > description(
        "description",
        "Read-only field giving a short description of the currently selected "
        "integration method.",
        &Cell::getDescription
    );

    static Finfo* cellFinfos[] =
    {
        &method,            // Value
        &solverClock,       // Value
        &solverName,        // Value
        &setup2,
        &variableDt,        // ReadOnlyValue
        &implicit,          // ReadOnlyValue
        &description,       // ReadOnlyValue
        &setup1,
        &proc,              // Shared
    };

    static string doc[] =
    {
        "Name",             "Cell",
        "Author",           "Niraj Dudani, 2012, NCBS",
        "Description",      "Container for a neuron's components. "
        "Also manages automatic solver setup. "
        "In case of solver setup, assumes that all the "
        "compartments under this Cell belong to a single "
        "neuron. If more than 1 group of axially "
        "connected compartments are present, then only "
        "one of them will be taken over by the solver.",
    };

    static Cinfo cellCinfo(
        "Cell",
        Neutral::initCinfo(),
        cellFinfos,
        sizeof( cellFinfos ) / sizeof( Finfo* ),
        new Dinfo< Cell >()
    );

    Cell::addMethod( "ee",
                     "Exponential Euler.",
                     0, 0 );
    Cell::addMethod( "hsolve",
                     "Hines' algorithm.",
                     0, 1 );

    return &cellCinfo;
}

Here is the call graph for this function:

void Cell::processDummy	(	const Eref &	e,
		ProcPtr	p
	)

Definition at line 181 of file Cell.cpp.

Referenced by initCinfo().

{
    ;
}

Here is the caller graph for this function:

void Cell::reinit	(	const Eref &	e,
		ProcPtr	p
	)

Definition at line 186 of file Cell.cpp.

References findCompt(), Eref::id(), method_, and setupSolver().

Referenced by initCinfo().

{
    cout << ".. Cell::reinit()" << endl;
    //~ if ( q->protectedAddToStructuralQ() )
    //~ return;

    // Delete existing solver
    //~ string solverPath = cell.id().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.id() );
    if ( seed == Id() ) // No compartment found.
        return;

    setupSolver( cell.id(), seed );
}

Here is the call graph for this function:

Here is the caller graph for this function:

void Cell::setMethod

(

string

value

)

Definition at line 316 of file Cell.cpp.

References method_, methodMap_, and value.

Referenced by Cell(), and initCinfo().

{
    map< string, MethodInfo >::iterator i = methodMap_.find( value );

    if ( i != methodMap_.end() )
    {
        method_ = value;
    }
    else
    {
        method_ = "hsolve";
        cerr << "Warning: Cell::setMethod(): method '" << value
             << "' not known. Using '" << method_ << "'.\n";
        setMethod( method_ );
    }
}

Here is the caller graph for this function:

void Cell::setSolverClock

(

unsigned int

value

)

Definition at line 338 of file Cell.cpp.

References solverClock_, and value.

Referenced by initCinfo().

{
    solverClock_ = value;
}

Here is the caller graph for this function:

void Cell::setSolverName

(

string

value

)

Definition at line 348 of file Cell.cpp.

References solverName_, and value.

Referenced by initCinfo().

{
    solverName_ = value;
}

Here is the caller graph for this function:

void Cell::setupf

(

Id

cell

)

Definition at line 214 of file Cell.cpp.

References Id::destroy(), findCompt(), method_, Id::path(), setupSolver(), and solverName_.

Referenced by initCinfo().

{
    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 );
}

Here is the call graph for this function:

Here is the caller graph for this function:

void Cell::setupSolver ( Id  cell, Id  seed  ) const

private

Definition at line 297 of file Cell.cpp.

References Eref::data(), Id::eref(), Shell::innerCreate(), MooseBlockBalance, Id::nextId(), HSolve::setSeed(), shell_, and solverName_.

Referenced by reinit(), and setupf().

{
    Id solver = Id::nextId();
    dump("FIXME"
         , "Using 0 for parentMsgIndex in function call Shell::innerCreate"
         "0 in first and third argument to NodeBalance. "
         "I am not sure if I should be doing this here in this function."
         " -- Dilawar"
        );
    NodeBalance nb(0, MooseBlockBalance, 0);
    shell_->innerCreate("HSolve", cell, solver, solverName_, nb, 0);
    HSolve* data = reinterpret_cast< HSolve* >( solver.eref().data() );
    data->setSeed( seed );
}

Here is the call graph for this function:

Here is the caller graph for this function:

Member Data Documentation

string Cell::method_

private

Definition at line 71 of file Cell.h.

Referenced by getDescription(), getImplicit(), getMethod(), getVariableDt(), reinit(), setMethod(), and setupf().

map< string, Cell::MethodInfo > Cell::methodMap_

staticprivate

Definition at line 79 of file Cell.h.

Referenced by addMethod(), getDescription(), getImplicit(), getVariableDt(), and setMethod().

Shell* Cell::shell_

private

Definition at line 74 of file Cell.h.

Referenced by setupSolver().

unsigned int Cell::solverClock_

private

Definition at line 72 of file Cell.h.

Referenced by getSolverClock(), and setSolverClock().

string Cell::solverName_

private

Definition at line 73 of file Cell.h.

Referenced by getSolverName(), setSolverName(), setupf(), and setupSolver().

---

The documentation for this class was generated from the following files:

• moose-core/hsolve/Cell.h
• moose-core/hsolve/Cell.cpp