SwcSegment.cpp

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2003-2015 Upinder S. Bhalla. 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 <string>
#include <vector>
#include <iostream>
#include <sstream>
#include <cstdlib>
#include <math.h>
using namespace std;
#include "../utility/Vec.h"
#include "SwcSegment.h"

const short SwcSegment::UNDEF = 0;
const short SwcSegment::SOMA = 1;
const short SwcSegment::AXON = 2;
const short SwcSegment::DEND = 3;
const short SwcSegment::APICAL = 4;
const short SwcSegment::FORK = 5; // Assumed to be on regular dend
const short SwcSegment::END = 6; // Assumed to be on regular dend
const short SwcSegment::CUSTOM = 7;
        // Here are a few more
const short SwcSegment::BadSegment = 8;
const short SwcSegment::AXON_FORK = 10;
const short SwcSegment::AXON_END = 11;
const short SwcSegment::APICAL_FORK = 12;
const short SwcSegment::APICAL_END = 13;

const string SwcSegment::typeName[] = {
    "undef", "soma", "axon", "dend", "apical", "dend_f", "dend_e",
    "custom", "bad", "undef",
    "axon_f", "axon_e", "apical_f", "apical_e" };

SwcSegment::SwcSegment( const string& line )
        :
            geometricalDistanceFromSoma_( 0.0 ),
            electrotonicDistanceFromSoma_( 0.0 )
{
    vector< string > args;
    stringstream ss( line );
    string temp;
    while (ss >> temp ) {
        args.push_back( temp );
    }
    if ( args.size() == 7 ) {
        myIndex_ = atoi( args[0].c_str() );
        type_ = atoi( args[1].c_str() );
        double x = atof( args[2].c_str() );
        double y = atof( args[3].c_str() );
        double z = atof( args[4].c_str() );
        v_ = Vec( x, y, z );
        radius_ = atof( args[5].c_str() );
        int pa = atoi( args[6].c_str() );
        if ( pa > 0 )
            parent_ = pa;
        else
            parent_ = ~0U;
    } else {
        type_ = BadSegment;
    }
}

SwcSegment::SwcSegment( int i,  short type,
                double x, double y, double z,
                double r, int parent )
                :
                        myIndex_( i ),
                        type_( type ),
                        v_( x, y, z ),
                        radius_( r ),
                        length_( 0.0 ),
                        L_( 0.0 ),
                        geometricalDistanceFromSoma_( 0.0 ),
                        electrotonicDistanceFromSoma_( 0.0 )
{
    if ( parent >= 0 )
        parent_ = parent;
    else
        parent_ = ~0U;
}

void SwcSegment::figureOutType()
{
    if ( type_ == SOMA ) // already defined as soma
        return;
    if ( type_ == DEND ) {
        if ( kids_.size() > 1 )
            type_ = FORK; // Dend fork point
        else if ( kids_.size() == 0 )
            type_ = END; // end point
    } else if ( type_ == APICAL ) {
        if ( kids_.size() > 1 )
            type_ = APICAL_FORK; // apical Dend fork point
        else if ( kids_.size() == 0 )
            type_ = APICAL_END; // apical end point
    } else if ( type_ == AXON ) {
        if ( kids_.size() > 1 )
            type_ = AXON_FORK; // apical Dend fork point
        else if ( kids_.size() == 0 )
            type_ = AXON_END; // apical end point
    }
}


SwcBranch::SwcBranch( int i,  const SwcSegment& start, double len, double L,
                const vector< int >& cable )
                : SwcSegment( start ),
                r0( start.radius() ),
                r1( start.radius() ),
                geomLength( len ),
                electroLength( L )
{
    myIndex_ = i;
    parent_ = 0;
    kids_.resize( 0 );
    segs_.resize( cable.size() );
    // Put the contents of cable into segs, in reverse order.
    vector< int >::const_reverse_iterator j = cable.rbegin();
    vector< int >::iterator k = segs_.begin();
    for ( k = segs_.begin(); k != segs_.end(); ++k )
        *k = *j++;
}

void SwcBranch::printDiagnostics() const
{
    cout << myIndex() << ":  " << segs_[0] << " -> " << segs_.back() <<
            " = " << segs_.size() <<
            " : pa = " << parent() << " ,   length=( " <<
            geomLength << ", " << electroLength << " )\n";
}