CylBase.cpp File Reference

#include "header.h"
#include "SparseMatrix.h"
#include "Boundary.h"
#include "MeshEntry.h"
#include "VoxelJunction.h"
#include "ChemCompt.h"
#include "MeshCompt.h"
#include "CubeMesh.h"
#include "CylBase.h"
#include "../utility/Vec.h"

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Functions
static void	fillPointsOnCircle (const Vec &u, const Vec &v, const Vec &q, double h, double r, vector< double > &area, const CubeMesh *other)
static void	fillPointsOnDisc (const Vec &u, const Vec &v, const Vec &q, double h, double r, vector< double > &area, const CubeMesh *other)

Variables
const double	PI

Function Documentation

static void fillPointsOnCircle ( const Vec &  u, const Vec &  v, const Vec &  q, double  h, double  r, vector< double > &  area, const CubeMesh *  other  )

static

Definition at line 263 of file CylBase.cpp.

References Vec::a0(), Vec::a1(), Vec::a2(), CubeMesh::EMPTY, PI, and CubeMesh::spaceToIndex().

Referenced by CylBase::matchCubeMeshEntries().

{
    // fine-tune the h spacing so it is integral around circle.
    // This will cause small errors in area estimate but they will
    // be anisotropic. The alternative will have large errors toward
    // 360 degrees, but not elsewhere.
    unsigned int numAngle = floor( 2.0 * PI * r / h + 0.5 );
    assert( numAngle > 0 );
    double dtheta = 2.0 * PI / numAngle;
    double dArea = h * dtheta * r;
    // March along points on surface of circle centred at q.
    for ( unsigned int j = 0; j < numAngle; ++j ) {
        double theta = j * dtheta;
        double c = cos( theta );
        double s = sin( theta );
        double p0 = q.a0() + r * ( u.a0() * c + v.a0() * s );
        double p1 = q.a1() + r * ( u.a1() * c + v.a1() * s );
        double p2 = q.a2() + r * ( u.a2() * c + v.a2() * s );
        unsigned int index = other->spaceToIndex( p0, p1, p2 );
        if ( index != CubeMesh::EMPTY )
            area[index] += dArea;
    }
}

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static void fillPointsOnDisc ( const Vec &  u, const Vec &  v, const Vec &  q, double  h, double  r, vector< double > &  area, const CubeMesh *  other  )

static

Definition at line 291 of file CylBase.cpp.

References Vec::a0(), Vec::a1(), Vec::a2(), CubeMesh::EMPTY, PI, and CubeMesh::spaceToIndex().

Referenced by CylBase::matchCubeMeshEntries().

{
    unsigned int numRadial = floor( r / h + 0.5 );
    double dRadial = r / numRadial;
    for ( unsigned int i = 0; i < numRadial; ++i ) {
        double a = ( i + 0.5 ) * dRadial;
        unsigned int numAngle = floor( 2.0 * PI * a / h + 0.5 );
        if ( i == 0 )
            numAngle = 1;
        double dtheta = 2.0 * PI / numAngle;
        double dArea = dRadial * dtheta * a;
        for ( unsigned int j = 0; j < numAngle; ++j ) {
            double theta = j * dtheta;
            double c = cos( theta );
            double s = sin( theta );
            double p0 = q.a0() + a * ( u.a0() * c + v.a0() * s );
            double p1 = q.a1() + a * ( u.a1() * c + v.a1() * s );
            double p2 = q.a2() + a * ( u.a2() * c + v.a2() * s );
            unsigned int index = other->spaceToIndex( p0, p1, p2 );
            if ( index != CubeMesh::EMPTY )
                area[index] += dArea;
        }
    }
}

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Variable Documentation

const double PI

Definition at line 12 of file consts.cpp.

Referenced by assignParam(), assignSingleCompartmentParams(), CylMesh::buildStencil(), fillPointsOnCircle(), fillPointsOnDisc(), CylBase::getDiffusionArea(), CylMesh::getDiffusionArea(), Spine::getHeadVolume(), CylBase::getMiddleArea(), Spine::getPsdArea(), CylMesh::getVoxelArea(), CylMesh::innerBuildDefaultMesh(), makeCompt(), makeReacTest(), CylMesh::matchCylMeshEntries(), EndoMesh::matchMeshEntries(), SpineEntry::rootArea(), Neuron::scaleHeadDiffusion(), Neuron::scaleShaftDiffusion(), Spine::setHeadVolume(), PsdMesh::setMeshEntryVolume(), Spine::setPsdArea(), testCalcJunction(), testCylDiffn(), testCylDiffnWithStoich(), testPoolVolumeScaling(), testRunGsolve(), testStats(), CaConcBase::updateDimensions(), CylBase::volume(), and CylBase::voxelVolume().