SpineEntry Class Reference

#include <SpineEntry.h>

Collaboration diagram for SpineEntry:

Public Member Functions
void	apex (double &x, double &y, double &z) const
	Return coords of middle of PSD. More...
double	diffusionLength () const
unsigned int	fid () const
	Returns index of self. Only a single voxel. More...
double	headArea () const
Id	headId () const
	Returns Id of shaft electrical compartment. More...
void	matchCubeMeshEntries (const ChemCompt *other, unsigned int myIndex, double granularity, vector< VoxelJunction > &ret)
void	matchCubeMeshEntriesToHead (const ChemCompt *compt, unsigned int myIndex, double granularity, vector< VoxelJunction > &ret) const
	Returns Id of head electrical compartment. More...
void	matchCubeMeshEntriesToPSD (const ChemCompt *compt, unsigned int myIndex, double granularity, vector< VoxelJunction > &ret) const
unsigned int	matchNeuroMeshEntriesToShaft (const ChemCompt *compt, unsigned int myIndex, double &area, double &length) const
void	mid (double &x, double &y, double &z) const
	Return coords of centre of spine head. More...
unsigned int	parent () const
	Returns index of parent entry located on NeuroMesh. More...
void	positionShaftBase (double x, double y, double z)
vector< double >	psdCoords () const
double	rootArea () const
void	setParent (unsigned int parent)
	Assigns index of parent entry located on NeuroMesh. More...
void	setVolume (double volume)
Id	shaftId () const
	SpineEntry (Id shaft, Id head, unsigned int parent)
	SpineEntry ()
double	volume () const
	Return volume of spine. Ignores shaft volume. Virtual func. More...

Private Attributes
CylBase	head_
	Shaft cylinder. More...
Id	headId_
unsigned int	parent_
	head cylinder. More...
CylBase	root_
CylBase	shaft_
	Anchor point on dendrite. More...
Id	shaftId_
	Id of electrical compartment in which this diffusive compt lives. More...

Detailed Description

Helper class for the SpineMesh. Defines a single spine.

Definition at line 17 of file SpineEntry.h.

Constructor & Destructor Documentation

SpineEntry::SpineEntry	(	Id	shaft,
		Id	head,
		unsigned int	parent
	)

This builds the node using info from the compartment.

Helper class for the SpineMesh. Defines the geometry of the spine and provides the innter function for mapping to CubeMeshes.

Definition at line 24 of file SpineEntry.cpp.

References Field< A >::get(), head_, root_, CylBase::setDia(), CylBase::setIsCylinder(), CylBase::setLength(), CylBase::setNumDivs(), CylBase::setX(), CylBase::setY(), CylBase::setZ(), and shaft_.

        :
                parent_( parent ),
                shaftId_( shaft ),
                headId_( head )
{
    double dia = Field< double >::get( shaft, "diameter" );
    double length = Field< double >::get( shaft, "length" );
    double x0 = Field< double >::get( shaft, "x0" );
    double y0 = Field< double >::get( shaft, "y0" );
    double z0 = Field< double >::get( shaft, "z0" );
    double x1 = Field< double >::get( shaft, "x" );
    double y1 = Field< double >::get( shaft, "y" );
    double z1 = Field< double >::get( shaft, "z" );
    double x2 = Field< double >::get( head, "x" );
    double y2 = Field< double >::get( head, "y" );
    double z2 = Field< double >::get( head, "z" );
    double hdia = Field< double >::get( head, "diameter" );
    double hlength = Field< double >::get( head, "length" );

    // cout << "SpineEntry: " << parent_ << " " << x0 << " " << x1 << " " << x2 << " : " << y0 << " " << y1<< " " << y2 << " : " << z0 << " " << z1 << " " << z2 << " " << hdia << endl;

    root_.setX( x0 );
    root_.setY( y0 );
    root_.setZ( z0 );
    shaft_.setX( x1 );
    shaft_.setY( y1 );
    shaft_.setZ( z1 );
    head_.setX( x2 );
    head_.setY( y2 );
    head_.setZ( z2 );

    root_.setDia( dia );
    root_.setLength( length );
    root_.setNumDivs( 0 );
    root_.setIsCylinder( true );
    shaft_.setDia( dia );
    shaft_.setLength( length );
    shaft_.setNumDivs( 1 );
    shaft_.setIsCylinder( true );
    head_.setDia( hdia );
    head_.setLength( hlength );
    head_.setNumDivs( 1 );
    head_.setIsCylinder( true );
}

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SpineEntry::SpineEntry

(

)

Empty constructor for vectors

Definition at line 71 of file SpineEntry.cpp.

References head_, root_, CylBase::setDia(), CylBase::setIsCylinder(), CylBase::setLength(), CylBase::setNumDivs(), CylBase::setX(), CylBase::setY(), CylBase::setZ(), and shaft_.

        :
                parent_( 0 ),
                shaftId_( Id() ),
                headId_( Id() )
{
    const double defaultLength = 1e-6;
    root_.setX( 0 );
    root_.setY( 0 );
    root_.setZ( 0 );
    shaft_.setX( defaultLength );
    shaft_.setY( 0 );
    shaft_.setZ( 0 );
    head_.setX( defaultLength * 2 );
    head_.setY( 0 );
    head_.setZ( 0 );



    root_.setDia( defaultLength );
    root_.setLength( defaultLength );
    root_.setNumDivs( 0 );
    root_.setIsCylinder( true );
    shaft_.setDia( defaultLength );
    shaft_.setLength( defaultLength );
    shaft_.setNumDivs( 1 );
    shaft_.setIsCylinder( true );
    head_.setDia( defaultLength );
    head_.setLength( defaultLength );
    head_.setNumDivs( 1 );
    head_.setIsCylinder( true );
}

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Member Function Documentation

void SpineEntry::apex	(	double &	x,
		double &	y,
		double &	z
	)		const

Return coords of middle of PSD.

double SpineEntry::diffusionLength

(

)

const

Definition at line 179 of file SpineEntry.cpp.

References CylBase::getLength(), and shaft_.

{
    // I've simplified this because a) it doesn't make much sense to add
    // a diffusion length with a different axial size and b) it makes the
    // resizing hugely complicated.
    // return shaft_.getLength() + 0.5 * head_.getLength();
    return shaft_.getLength();
}

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unsigned int SpineEntry::fid

(

)

const

Returns index of self. Only a single voxel.

double SpineEntry::headArea

(

)

const

Id SpineEntry::headId

(

)

const

Returns Id of shaft electrical compartment.

Definition at line 114 of file SpineEntry.cpp.

References headId_.

{
        return headId_;
}

void SpineEntry::matchCubeMeshEntries	(	const ChemCompt *	other,
		unsigned int	myIndex,
		double	granularity,
		vector< VoxelJunction > &	ret
	)

Definition at line 131 of file SpineEntry.cpp.

References head_, CylBase::matchCubeMeshEntries(), and shaft_.

{
        // First flag is for curve, second is for cap of cylinder.
    head_.matchCubeMeshEntries( compt, shaft_, myIndex,
            granularity, ret, true, true );
}

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void SpineEntry::matchCubeMeshEntriesToHead	(	const ChemCompt *	compt,
		unsigned int	myIndex,
		double	granularity,
		vector< VoxelJunction > &	ret
	)		const

Returns Id of head electrical compartment.

Generate list of matching CubeMesh entries to the single Head entry.

Definition at line 145 of file SpineEntry.cpp.

References head_, CylBase::matchCubeMeshEntries(), and shaft_.

Referenced by SpineMesh::matchCubeMeshEntries().

{
    head_.matchCubeMeshEntries( compt, shaft_, myIndex,
            granularity, ret, true, false );
}

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void SpineEntry::matchCubeMeshEntriesToPSD	(	const ChemCompt *	compt,
		unsigned int	myIndex,
		double	granularity,
		vector< VoxelJunction > &	ret
	)		const

Generate list of matching CubeMeshEntries to the single PSD.

Definition at line 153 of file SpineEntry.cpp.

References head_, CylBase::matchCubeMeshEntries(), and shaft_.

{
    // First flag is for curve, second is for cap of cylinder.
    head_.matchCubeMeshEntries( compt, shaft_, myIndex,
            granularity, ret, false, true );
}

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unsigned int SpineEntry::matchNeuroMeshEntriesToShaft	(	const ChemCompt *	compt,
		unsigned int	myIndex,
		double &	area,
		double &	length
	)		const

Find the matching matching NeuroMesh entry index to the root of the shaft of this spine. Also compute the area and diffusion length of the shaft.

Find the matching NeuroMesh entry index to the root of the shaft of this spine. Also compute the area and diffusion length of the shaft.

Definition at line 167 of file SpineEntry.cpp.

{
        return 0;
}

void SpineEntry::mid	(	double &	x,
		double &	y,
		double &	z
	)		const

Return coords of centre of spine head.

Definition at line 124 of file SpineEntry.cpp.

References CylBase::getX(), CylBase::getY(), CylBase::getZ(), head_, and shaft_.

Referenced by SpineMesh::nearest(), and psdCoords().

{
    x = ( shaft_.getX() + head_.getX() ) / 2.0;
    y = ( shaft_.getY() + head_.getY() ) / 2.0;
    z = ( shaft_.getZ() + head_.getZ() ) / 2.0;
}

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unsigned int SpineEntry::parent

(

)

const

Returns index of parent entry located on NeuroMesh.

Definition at line 104 of file SpineEntry.cpp.

References parent_.

Referenced by setParent().

{
        return parent_;
}

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void SpineEntry::positionShaftBase	(	double	x,
		double	y,
		double	z
	)

moves Spine entry so that shaft base is now positioned at xyz.

Definition at line 230 of file SpineEntry.cpp.

References CylBase::getX(), CylBase::getY(), CylBase::getZ(), head_, root_, CylBase::setX(), CylBase::setY(), CylBase::setZ(), and shaft_.

{
    double dx = x - root_.getX();
    double dy = y - root_.getY();
    double dz = y - root_.getZ();
    root_.setX( x );
    root_.setY( y );
    root_.setZ( z );
    shaft_.setX( dx + shaft_.getX() );
    shaft_.setY( dy + shaft_.getY() );
    shaft_.setZ( dz + shaft_.getZ() );
    head_.setX( dx + head_.getX() );
    head_.setY( dy + head_.getY() );
    head_.setZ( dz + head_.getZ() );
}

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vector< double > SpineEntry::psdCoords

(

)

const

psdCoords is used to build the PsdMesh. The function returns 8 coords to define the psd: centre xyz direction xyz dia, diffusion distance to middle of spine Head.

Definition at line 188 of file SpineEntry.cpp.

References CylBase::getDia(), CylBase::getX(), CylBase::getY(), CylBase::getZ(), head_, and mid().

Referenced by NeuroMesh::transmitSpineInfo().

{
    vector< double > ret( 8, 0.0 );
    double m0, m1, m2;
    mid( m0, m1, m2 );
    ret[0] = m0;
    ret[1] = m1;
    ret[2] = m2;
    ret[3] = head_.getX() - m0;
    ret[4] = head_.getY() - m1;
    ret[5] = head_.getZ() - m2;
    /*
    ret[0] = head_.getX();
    ret[1] = head_.getY();
    ret[2] = head_.getZ();
    double m0, m1, m2;
    mid( m0, m1, m2 );
    ret[3] = ret[0] - m0;
    ret[4] = ret[1] - m1;
    ret[5] = ret[2] - m2;
    */
    ret[6] = head_.getDia();
    ret[7] = sqrt( ret[3] * ret[3] + ret[4] * ret[4] + ret[5] * ret[5] );

    return ret;
}

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double SpineEntry::rootArea

(

)

const

Definition at line 174 of file SpineEntry.cpp.

References CylBase::getDia(), PI, and root_.

{
    return root_.getDia() * root_.getDia() * PI * 0.25;
}

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void SpineEntry::setParent

(

unsigned int

parent

)

Assigns index of parent entry located on NeuroMesh.

Definition at line 119 of file SpineEntry.cpp.

References parent(), and parent_.

{
    parent_ = parent;
}

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void SpineEntry::setVolume

(

double

volume

)

Resizes SpineEntry. Takes original shaft base and scales up from there. Retains original shaft dimensions, only the head is scaled.

Definition at line 216 of file SpineEntry.cpp.

References CylBase::getDia(), CylBase::getLength(), CylBase::getX(), CylBase::getY(), CylBase::getZ(), head_, CylBase::setDia(), CylBase::setLength(), CylBase::setX(), CylBase::setY(), CylBase::setZ(), shaft_, and CylBase::volume().

{
    double volscale = volume / head_.volume( shaft_ );
    double linscale = pow( volscale, 1.0 / 3.0 );
    head_.setLength( head_.getLength() * linscale );
    head_.setDia( head_.getDia() * linscale );
    double dx = head_.getX() - shaft_.getX();
    double dy = head_.getY() - shaft_.getY();
    double dz = head_.getZ() - shaft_.getZ();
    head_.setX( dx * linscale + shaft_.getX() );
    head_.setY( dy * linscale + shaft_.getY() );
    head_.setZ( dz * linscale + shaft_.getZ() );
}

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Id SpineEntry::shaftId

(

)

const

Definition at line 109 of file SpineEntry.cpp.

References shaftId_.

{
        return shaftId_;
}

double SpineEntry::volume

(

)

const

Return volume of spine. Ignores shaft volume. Virtual func.

Definition at line 140 of file SpineEntry.cpp.

References head_, shaft_, and CylBase::volume().

{
    return head_.volume( shaft_ );
}

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Member Data Documentation

CylBase SpineEntry::head_

private

Shaft cylinder.

Definition at line 106 of file SpineEntry.h.

Referenced by matchCubeMeshEntries(), matchCubeMeshEntriesToHead(), matchCubeMeshEntriesToPSD(), mid(), positionShaftBase(), psdCoords(), setVolume(), SpineEntry(), and volume().

Id SpineEntry::headId_

private

Definition at line 114 of file SpineEntry.h.

Referenced by headId().

unsigned int SpineEntry::parent_

private

head cylinder.

Index of parent entry on NeuroMesh.

Definition at line 110 of file SpineEntry.h.

Referenced by parent(), and setParent().

CylBase SpineEntry::root_

private

Definition at line 104 of file SpineEntry.h.

Referenced by positionShaftBase(), rootArea(), and SpineEntry().

CylBase SpineEntry::shaft_

private

Anchor point on dendrite.

Definition at line 105 of file SpineEntry.h.

Referenced by diffusionLength(), matchCubeMeshEntries(), matchCubeMeshEntriesToHead(), matchCubeMeshEntriesToPSD(), mid(), positionShaftBase(), setVolume(), SpineEntry(), and volume().

Id SpineEntry::shaftId_

private

Id of electrical compartment in which this diffusive compt lives.

Definition at line 113 of file SpineEntry.h.

Referenced by shaftId().

---

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

• moose-core/mesh/SpineEntry.h
• moose-core/mesh/SpineEntry.cpp