ReadSwc Class Reference

#include <ReadSwc.h>

Collaboration diagram for ReadSwc:

Public Member Functions
void	assignKids ()
bool	build (Id parent, double lambda, double RM, double RA, double CM)
void	cleanZeroLength ()
void	diagnostics () const
void	parseBranches ()
	ReadSwc (const string &fname)
void	traverseBranch (const SwcSegment &s, double &len, double &L, vector< int > &cable) const
bool	validate () const

Private Attributes
vector< SwcBranch >	branches_
vector< SwcSegment >	segs_

Detailed Description

This class is used to read in SWC files as found in NeuroMorph.org and other places. Note that these are only passive models at this stage.

Definition at line 18 of file ReadSwc.h.

Constructor & Destructor Documentation

ReadSwc::ReadSwc

(

const string &

fname

)

Each line is of the form n T x y z R P

Definition at line 24 of file ReadSwc.cpp.

References assignKids(), branches_, cleanZeroLength(), diagnostics(), SwcSegment::OK(), parseBranches(), segs_, and validate().

{
    ifstream fin( fname.c_str() );
    if ( !fin ) {
        cerr << "ReadSwc:: could not open file " << fname << endl;
        return;
    }

    string temp;
    int badSegs = 0;
    while( getline( fin, temp ) ) {
        if ( temp.length() == 0 )
            continue;
        string::size_type pos = temp.find_first_not_of( "\t " );
        if ( pos == string::npos )
            continue;
        if ( temp[pos] == '#' )
            continue;

        SwcSegment t( temp );
        if ( t.OK() )
            segs_.push_back( SwcSegment( temp ) );
        else
            badSegs++;
    }
    bool valid = validate();
    if ( valid ) {
        assignKids();
        cleanZeroLength();
        parseBranches();
    }
    cout << "ReadSwc: " << fname << "   : NumSegs = " << segs_.size() <<
            ", bad = " << badSegs <<
            ", Validated = " << valid <<
            ", numBranches = " << branches_.size() <<
            endl;
    diagnostics();
}

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Member Function Documentation

void ReadSwc::assignKids

(

)

Definition at line 98 of file ReadSwc.cpp.

References SwcSegment::myIndex(), SwcSegment::parent(), and segs_.

Referenced by ReadSwc().

{
    for ( unsigned int i = 0; i < segs_.size(); ++i ) {
        const SwcSegment& s = segs_[i];
        assert ( s.parent() != s.myIndex() );
        if ( s.parent() != ~0U ) {
            segs_[s.parent() - 1].addChild( i + 1 );
        }
    }
    for ( unsigned int i = 0; i < segs_.size(); ++i ) {
        segs_[i].figureOutType();
    }
}

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bool ReadSwc::build	(	Id	parent,
		double	lambda,
		double	RM,
		double	RA,
		double	CM
	)

Definition at line 256 of file ReadSwc.cpp.

References branches_, Eref::data(), Shell::doAddMsg(), Id::eref(), makeCompt(), SwcSegment::myIndex(), SwcSegment::parent(), segs_, and SwcBranch::segs_.

Referenced by Shell::doLoadModel().

{
    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
    vector< Id > compts( segs_.size() );
    for ( unsigned int i = 0; i < branches_.size(); ++i ) {
        SwcBranch& br = branches_[i];
        for ( unsigned int j = 0; j < br.segs_.size(); ++j ) {
            Id compt;
            SwcSegment& seg = segs_[ br.segs_[j] -1 ];
            unsigned int paIndex = seg.parent();
            if ( paIndex == ~0U ) { // soma
                compt = makeCompt( parent, seg, seg, RM, RA, CM, i, j );
            } else {
                SwcSegment& pa = segs_[ paIndex - 1 ];
                compt = makeCompt( parent, seg, pa, RM, RA, CM, i, j );
                assert( compt != Id() );
                assert( compts[ paIndex -1 ] != Id() );
                shell->doAddMsg( "Single",
                    compts[paIndex-1], "axial", compt, "raxial" );
            }
            assert( compt != Id() );
            compts[ seg.myIndex() -1 ] = compt;
        }
    }
    return true;
}

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void ReadSwc::cleanZeroLength

(

)

Definition at line 112 of file ReadSwc.cpp.

References SwcSegment::distance(), EPSILON, SwcSegment::kids(), SwcSegment::myIndex(), SwcSegment::parent(), SwcSegment::replaceKids(), segs_, SwcSegment::setBad(), and SwcSegment::setParent().

Referenced by ReadSwc().

{
    static double EPSILON = 1e-2; // Assume units in microns.
    for ( unsigned int i = 1; i < segs_.size(); ++i ) {
        SwcSegment& s = segs_[i];
        SwcSegment& pa = segs_[ s.parent() - 1 ];
        if ( s.distance( pa ) < EPSILON ) {
            // Remove the zero length child from pa.kids_
            vector< int > temp;
            for ( unsigned int j = 0; j < pa.kids().size(); ++j ) {
                if ( static_cast< unsigned int >( pa.kids()[j] ) != s.myIndex() )
                    temp.push_back( pa.kids()[j] );
            }
            // Go through all kids of s and reparent them.
            for ( unsigned int j = 0; j < s.kids().size(); ++j ) {
                SwcSegment& kid = segs_[ s.kids()[j] - 1 ];
                kid.setParent( pa.myIndex() );
                temp.push_back( kid.myIndex() );
            }
            pa.replaceKids( temp );
            s.setBad();
            cout << "ReadSwc:: Cleaned zero length " << s.myIndex() << endl;
        }
    }
}

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void ReadSwc::diagnostics

(

)

const

Definition at line 194 of file ReadSwc.cpp.

References segs_, SwcSegment::type(), and SwcSegment::typeName.

Referenced by ReadSwc().

{
    vector< int > diag( 14 );
    for ( unsigned int i = 0; i < segs_.size(); ++i ) {
        const SwcSegment& s = segs_[i];
        if ( s.type() < 14 )
            diag[s.type()]++;
    }
    for ( int i = 0; i < 14; ++i )
        cout << "ReadSwc::diagnostics: " << SwcSegment::typeName[i] << " :  " << diag[i] << endl;

    /*
    for ( unsigned int i = 0; i < branches_.size(); ++i )
        branches_[i].printDiagnostics();
        */
}

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void ReadSwc::parseBranches

(

)

Definition at line 162 of file ReadSwc.cpp.

References branches_, SwcSegment::kids(), SwcSegment::OK(), segs_, and traverseBranch().

Referenced by ReadSwc().

{
    // Fill vector of all branches.
    for ( unsigned int i = 0; i < segs_.size(); ++i ) {
        const SwcSegment& s = segs_[i];
        if ( s.OK() && s.kids().size() != 1 ) { // Either use a fork or an end.
            vector< int > cable;
            // int branchIndex = branches_.
            // branches_.push_back( i + 1 );
            double len = 0;
            double L = 0;
            traverseBranch( s, len, L, cable );
            // branchGeomLength_.push_back( len );
            // branchElectroLength_.push_back( L );
            SwcBranch br( branches_.size(), s, len, L, cable );
            branches_.push_back( br );
        }
    }
    // Assign the parent of each branch. This is known because the
    // parent of the first segment in the branch is the last segment
    // in the parent branch. I construct a reverse lookup table to find
    // the branch # from its last segment number.
    vector< int > reverseSeg ( segs_.size() + 1, 0 );
    for ( unsigned int i = 0; i < branches_.size(); ++i )
        reverseSeg[ branches_[i].segs_.back() ] = i;
    for ( unsigned int i = 0; i < branches_.size(); ++i ) {
        int parentSeg = segs_[ branches_[i].segs_[0] - 1 ].parent();
        assert( parentSeg != 0 ); // Note that segment indices start from 1
        branches_[i].setParent( reverseSeg[ parentSeg ] );
    }
}

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void ReadSwc::traverseBranch	(	const SwcSegment &	s,
		double &	len,
		double &	L,
		vector< int > &	cable
	)		const

Definition at line 138 of file ReadSwc.cpp.

References SwcSegment::distance(), SwcSegment::kids(), SwcSegment::L(), SwcSegment::myIndex(), SwcSegment::parent(), SwcSegment::radius(), and segs_.

Referenced by parseBranches().

{
    const SwcSegment* prev = &s;
    cable.resize( 1, s.myIndex() ); // Always include the starting seg.
    // Note that the cable is filled up with entries in reverse order.

    if ( s.parent() == ~0U ) {
        len = s.radius();
        L = sqrt( len );
        return ;
    }

    do {
        // Beware the indexing!
        const SwcSegment& pa = segs_[prev->parent() - 1];
        len += pa.distance( *prev );
        L += pa.L( );
        cable.push_back( pa.myIndex() );
        prev = &pa;
    } while ( (prev->parent() != ~0U) && (prev->kids().size() == 1) );
    cable.pop_back(); // Get rid of the last entry, it is on the parent.
}

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bool ReadSwc::validate

(

)

const

Definition at line 63 of file ReadSwc.cpp.

References branches_, MinRadius, SwcSegment::myIndex(), SwcSegment::parent(), SwcSegment::radius(), and segs_.

Referenced by ReadSwc().

{
    int numStart = 0;
    int numOrphans = 0;
    int badIndex = 0;
    int badRadius = 0;
    for ( unsigned int i = 0; i < segs_.size(); ++i ) {
        const SwcSegment& s = segs_[i];
        if ( s.myIndex() != i + 1 )
            badIndex++;
        if ( s.parent() == ~0U ) {
            numStart++;
        } else {
            if ( s.parent() > i ) {
                numOrphans++;
            }
        }
        if ( s.radius() < MinRadius ) {
            badRadius++;
        }
    }
    bool valid = ( numStart == 1 && numOrphans == 0 && badRadius == 0 );
    if ( !valid ) {
        cout << "ReadSwc::validate() failed: \nNumSegs = " <<
                segs_.size() <<
                ", numStart = " << numStart <<
                ", orphans = " << numOrphans <<
                ", badIndex = " << badIndex <<
                ", badRadius = " << badRadius <<
                ", numBranches = " << branches_.size() <<
                endl;
    }
    return valid;
}

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Member Data Documentation

vector< SwcBranch > ReadSwc::branches_

private

branches holds the NeuroMorpho index of the end segment of each branch. Note that NeuroMorph index starts from 1. To traverse the branch, go to the end segment, and traverse through all parents till you get to a fork.

Definition at line 45 of file ReadSwc.h.

Referenced by build(), parseBranches(), ReadSwc(), and validate().

vector< SwcSegment > ReadSwc::segs_

private

Definition at line 37 of file ReadSwc.h.

Referenced by assignKids(), build(), cleanZeroLength(), diagnostics(), parseBranches(), ReadSwc(), traverseBranch(), and validate().

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

• moose-core/biophysics/ReadSwc.h
• moose-core/biophysics/ReadSwc.cpp