CubeMesh.cpp File Reference

#include "header.h"
#include "SparseMatrix.h"
#include "ElementValueFinfo.h"
#include "Boundary.h"
#include "MeshEntry.h"
#include "VoxelJunction.h"
#include "ChemCompt.h"
#include "MeshCompt.h"
#include "CubeMesh.h"
#include "EndoMesh.h"

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Typedefs
typedef pair< unsigned int, unsigned int >	PII

Functions
void	checkAbut (const vector< PII > &intersect, unsigned int ix, unsigned int iy, unsigned int iz, unsigned int nx, unsigned int ny, unsigned int nz, unsigned int meshIndex, vector< VoxelJunction > &ret)
void	setAbut (PII &voxel, unsigned int meshIndex, unsigned int axis)
void	setIntersectVoxel (vector< PII > &intersect, unsigned int ix, unsigned int iy, unsigned int iz, unsigned int nx, unsigned int ny, unsigned int nz, unsigned int meshIndex)
void	swapIfBackward (double &x0, double &x1)

Variables
static const Cinfo *	cubeMeshCinfo = CubeMesh::initCinfo()

Typedef Documentation

typedef pair< unsigned int, unsigned int > PII

Definition at line 29 of file CubeMesh.cpp.

Function Documentation

void checkAbut	(	const vector< PII > &	intersect,
		unsigned int	ix,
		unsigned int	iy,
		unsigned int	iz,
		unsigned int	nx,
		unsigned int	ny,
		unsigned int	nz,
		unsigned int	meshIndex,
		vector< VoxelJunction > &	ret
	)

checkAbut checks the intersect vector for the current position ix, iy, iz, to determine how many diffusion terms to extract. It then puts each of the extracted terms into the ret vector. There is a minor efficiency for one and two diffusion terms as they are encoded within the intersect vector. Higher-order surface alignments require an in-line scan of neighboring voxels. In all casesl the function inserts a flag indicating surface direction into the diffScale field of the VoxelJunction. 0 = x; 1 = y; 2 = z.

Definition at line 1348 of file CubeMesh.cpp.

References CubeMesh::ABUTX, CubeMesh::ABUTY, CubeMesh::ABUTZ, CubeMesh::EMPTY, CubeMesh::MULTI, and CubeMesh::SURFACE.

Referenced by CubeMesh::matchCubeMeshEntries(), and testIntersectVoxel().

{
    unsigned int index = ( iz * ny + iy ) * nx + ix;
    unsigned int localFlag = intersect[index].second;

    if ( localFlag == CubeMesh::EMPTY || localFlag == CubeMesh::SURFACE )
            return; // Nothing to put into the ret vector
    if ( localFlag == CubeMesh::ABUTX ) {
        ret.push_back(
                VoxelJunction( intersect[index].first, meshIndex, 0 ));
    } else if ( localFlag == CubeMesh::ABUTY ) {
        ret.push_back(
                VoxelJunction( intersect[index].first, meshIndex, 1 ));
    } else if ( localFlag == CubeMesh::ABUTZ ) {
        ret.push_back(
                VoxelJunction( intersect[index].first, meshIndex, 2 ));
    } else if ( localFlag == CubeMesh::MULTI ) { // go through all 6 cases.
        if ( ix > 0 ) {
            index = ( iz * ny + iy ) * nx + ix - 1;
            if ( intersect[index].second == CubeMesh::SURFACE )
                ret.push_back(
                    VoxelJunction( intersect[index].first, meshIndex, 0 ));
        }
        if ( ix + 1 < nx ) {
            index = ( iz * ny + iy ) * nx + ix + 1;
            if ( intersect[index].second == CubeMesh::SURFACE )
                ret.push_back(
                    VoxelJunction( intersect[index].first, meshIndex, 0 ));
        }
        if ( iy > 0 ) {
            index = ( iz * ny + iy -1 ) * nx + ix;
            if ( intersect[index].second == CubeMesh::SURFACE )
                ret.push_back(
                    VoxelJunction( intersect[index].first, meshIndex, 1 ));
        }
        if ( iy + 1 < ny ) {
            index = ( iz * ny + iy + 1 ) * nx + ix;
            if ( intersect[index].second == CubeMesh::SURFACE )
                ret.push_back(
                    VoxelJunction( intersect[index].first, meshIndex, 1 ));
        }
        if ( iz > 0 ) {
            index = ( (iz-1) * ny + iy ) * nx + ix;
            if ( intersect[index].second == CubeMesh::SURFACE )
                ret.push_back(
                    VoxelJunction( intersect[index].first, meshIndex, 2 ));
        }
        if ( iz + 1 < nz ) {
            index = ( (iz+1) * ny + iy ) * nx + ix;
            if ( intersect[index].second == CubeMesh::SURFACE )
                ret.push_back(
                    VoxelJunction( intersect[index].first, meshIndex, 2 ));
        }
    }
}

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void setAbut	(	PII &	voxel,
		unsigned int	meshIndex,
		unsigned int	axis
	)

The intersect pairs are always meshIndex in first, and a flag in the second. The flag can be: EMPTY: empty SURFACE: on the surface ABUT[X,Y,Z]: One place removed from the surface, only one entry MULTI: Multiple surface voxels are only one place removed from here. a number: Special case where 2 surface voxels abut. The number is the meshIndex of the second surface voxel. setAbut assigns the voxel flags based on what was already there

Definition at line 1294 of file CubeMesh.cpp.

References CubeMesh::EMPTY, CubeMesh::MULTI, and CubeMesh::SURFACE.

Referenced by setIntersectVoxel().

{
    if ( voxel.second == CubeMesh::SURFACE ) // Don't touch surface voxels.
        return;
    if ( voxel.second == CubeMesh::EMPTY )
            voxel = PII( meshIndex, axis );
    else // 1 or more indices are already here.
            voxel.second = CubeMesh::MULTI;
}

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void setIntersectVoxel	(	vector< PII > &	intersect,
		unsigned int	ix,
		unsigned int	iy,
		unsigned int	iz,
		unsigned int	nx,
		unsigned int	ny,
		unsigned int	nz,
		unsigned int	meshIndex
	)

Definition at line 1304 of file CubeMesh.cpp.

References CubeMesh::ABUTX, CubeMesh::ABUTY, CubeMesh::ABUTZ, setAbut(), and CubeMesh::SURFACE.

Referenced by CubeMesh::assignVoxels(), and testIntersectVoxel().

{
    assert( ix < nx && iy < ny && iz < nz );
    unsigned int index = ( iz * ny + iy ) * nx + ix;
    assert( index < intersect.size() );
    intersect[index] = PII( meshIndex, CubeMesh::SURFACE );
    if ( ix > 0 )
        setAbut( intersect[ (iz*ny + iy) * nx + ix-1 ], meshIndex,
                        CubeMesh::ABUTX );
    if ( ix + 1 < nx )
        setAbut( intersect[ (iz*ny + iy) * nx + ix+1 ], meshIndex,
                        CubeMesh::ABUTX );

    if ( iy > 0 )
        setAbut( intersect[ ( iz*ny + iy-1 ) * nx + ix ], meshIndex,
                        CubeMesh::ABUTY);
    if ( iy + 1 < ny )
        setAbut( intersect[ ( iz*ny + iy+1 ) * nx + ix ], meshIndex,
                        CubeMesh::ABUTY);

    if ( iz > 0 )
        setAbut( intersect[ ( (iz-1)*ny + iy ) * nx + ix ], meshIndex,
                        CubeMesh::ABUTZ);
    if ( iz + 1 < nz )
        setAbut( intersect[ ( (iz+1)*ny + iy ) * nx + ix ], meshIndex,
                        CubeMesh::ABUTZ);
}

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void swapIfBackward	(	double &	x0,
		double &	x1
	)

Definition at line 294 of file CubeMesh.cpp.

Referenced by CubeMesh::defineIntersection(), and CubeMesh::updateCoords().

{
    if ( x0 > x1 ) {
        double temp = x0;
        x0 = x1;
        x1 = temp;
    }
}

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Variable Documentation

const Cinfo* cubeMeshCinfo = CubeMesh::initCinfo()

static

Definition at line 256 of file CubeMesh.cpp.

Referenced by CubeMesh::initCinfo().