#include <neurite_projector.h>

Inheritance diagram for ug::NeuriteProjector:

Classes
struct	BPProjectionHelper

struct	BranchingPoint

struct	BranchingRegion

struct	CompareBranchingRegionEnds

struct	CompareSections

struct	CompareSomaBranchingRegionsEnd

struct	Mapping
	Mapping of model to surface vertices. More...

struct	Neurite

struct	Section

struct	SomaBranchingRegion

struct	SomaPoint

struct	SurfaceParams

Public Member Functions
void	average_pos_from_parent (vector3 &posOut, const IVertexGroup *const parent) const

number	axial_range_around_branching_region (uint32_t nid, size_t brInd, number numberOfRadii=5.0) const

number	axial_range_around_soma_region (const SomaBranchingRegion &sr, size_t numRadii, size_t nid, Vertex *vrt) const

void	debug_neurites () const

void	direction_at_grid_object (vector3 &dirOut, GridObject *o) const
	spline direction at some grid object More...

bool	is_in_axial_range_around_soma_region (const SomaBranchingRegion &sr, size_t nid, Vertex *vrt) const

const Neurite &	neurite (uint32_t nid) const

	NeuriteProjector ()

	NeuriteProjector (SPIGeometry3d geometry)

std::vector< Neurite > &	neurites ()

virtual number	new_vertex (Vertex vrt, Edge parent)
	called when a new vertex was created from an old edge More...

virtual number	new_vertex (Vertex vrt, Face parent)
	called when a new vertex was created from an old face More...

virtual number	new_vertex (Vertex vrt, Vertex parent)
	called when a new vertex was created from an old vertex More...

virtual number	new_vertex (Vertex vrt, Volume parent)
	called when a new vertex was created from an old volume More...

vector3	position (Vertex *vrt) const

void	print_surface_params (const Vertex *const v) const

void	project (Vertex *vrt)
	project a vertex to its model position More...

const std::vector< std::pair< number, number > > &	quadrature_points () const

virtual void	set_geometry (SPIGeometry3d geometry)

std::vector< SomaBranchingRegion > &	somata ()

Grid::VertexAttachmentAccessor< Attachment< SurfaceParams > > &	surface_params_accessor ()

const Grid::VertexAttachmentAccessor< Attachment< SurfaceParams > > &	surface_params_accessor () const

virtual	~NeuriteProjector ()

Public Member Functions inherited from ug::RefinementProjector
virtual SPIGeometry3d	geometry () const

virtual void	refinement_begins (const ISubGrid *sg)
	called before refinement begins More...

virtual bool	refinement_begins_requires_subgrid () const

virtual void	refinement_ends ()
	called when refinement is done More...

	RefinementProjector ()

	RefinementProjector (SPElementCallback cb)

	RefinementProjector (SPIGeometry3d geometry)

	RefinementProjector (SPIGeometry3d geometry, SPElementCallback concernedElems)

virtual void	set_concerned_elements (SPElementCallback cb)

virtual	~RefinementProjector ()

Protected Member Functions
void	attach_surf_params ()

void	average_params (uint32_t &neuriteID, float &t, float &angle, float &radius, const IVertexGroup *parent) const

std::vector< Section >::const_iterator	get_section_iterator (uint32_t nid, float t) const

std::vector< NeuriteProjector::Section >::const_iterator	get_soma_section_iterator (uint32_t nid, float t) const

void	prepare_quadrature ()

number	push_into_place (Vertex vrt, const IVertexGroup parent)

Protected Member Functions inherited from ug::RefinementProjector
IGeometry3d &	geom ()

const IGeometry3d &	geom () const

template<class TElem >
bool	is_concerned (TElem *e)

vector3	pos (Vertex *v) const

void	set_pos (Vertex *v, const vector3 &p)

Private Member Functions
template<class TElem >
bool	IsElementInsideSphere (const TElem *elem, const ug::vector3 &center, const number radius) const
	check if an element is inside a sphere More...

template<class Archive >
void	load (Archive &ar, const unsigned int version)

template<class Archive >
void	save (Archive &ar, const unsigned int version) const

Private Attributes
Grid::VertexAttachmentAccessor< Attachment< SurfaceParams > >	m_aaSurfParams

Attachment< SurfaceParams >	m_aSurfParams

std::vector< std::pair< number, number > >	m_qPoints
	for quadrature when projecting within branching points More...

std::vector< Neurite >	m_vNeurites
	storage for cubic splines: Vector of sorted vectors of sections; each inner vector represents a single neurite. Any complete neurite is parameterized by t in [0,1]. Each section in the neurite vector consists of the parameter t at which the section ends and the sixteen coefficients describing the spline in each dimension (monomial basis {(t_(i+1) - t)^i}_i). More...

Friends
class	boost::serialization::access

Constructor & Destructor Documentation

◆ NeuriteProjector() [1/2]

ug::NeuriteProjector::NeuriteProjector ( )

References ug::GlobalAttachments::is_declared(), and prepare_quadrature().

◆ NeuriteProjector() [2/2]

ug::NeuriteProjector::NeuriteProjector ( SPIGeometry3d geometry )

References attach_surf_params(), ug::GlobalAttachments::is_declared(), and prepare_quadrature().

◆ ~NeuriteProjector()

ug::NeuriteProjector::~NeuriteProjector ( )

virtual

Member Function Documentation

◆ attach_surf_params()

void ug::NeuriteProjector::attach_surf_params ( )

protected

References ug::RefinementProjector::geometry(), ug::Grid::has_vertex_attachment(), ug::GlobalAttachments::is_declared(), m_aaSurfParams, m_aSurfParams, and UG_COND_THROW.

Referenced by NeuriteProjector(), and set_geometry().

◆ average_params()

void ug::NeuriteProjector::average_params	(	uint32_t &	neuriteID,
		float &	t,
		float &	angle,
		float &	radius,
		const IVertexGroup *	parent
	)		const

protected

◆ average_pos_from_parent()

void ug::NeuriteProjector::average_pos_from_parent	(	vector3 &	posOut,
		const IVertexGroup *const	parent
	)		const

References ug::IVertexGroup::num_vertices(), ug::RefinementProjector::pos(), and ug::IVertexGroup::vertex().

Referenced by ug::bp_newton_start_pos(), and ug::pos_on_surface_tip().

◆ axial_range_around_branching_region()

number ug::NeuriteProjector::axial_range_around_branching_region	(	uint32_t	nid,
		size_t	brInd,
		number	numberOfRadii = `5.0`
	)		const

References ug::compute_first_section_end_points(), get_section_iterator(), m_vNeurites, neurite(), s, ug::NeuriteProjector::BranchingRegion::t, UG_CATCH_THROW, ug::NeuriteProjector::Neurite::vBR, and ug::VecDistance().

Referenced by ug::pos_in_bp(), and push_into_place().

◆ axial_range_around_soma_region()

number ug::NeuriteProjector::axial_range_around_soma_region	(	const SomaBranchingRegion &	sr,
		size_t	numRadii,
		size_t	nid,
		Vertex *	vrt
	)		const

const float somaRad = sr.radius;

References ug::NeuriteProjector::SomaBranchingRegion::bp, ug::compute_first_section_end_points(), get_soma_section_iterator(), position(), s, ug::NeuriteProjector::SomaBranchingRegion::t, UG_CATCH_THROW, and ug::VecDistance().

◆ debug_neurites()

void ug::NeuriteProjector::debug_neurites ( ) const

References m_vNeurites, neurite(), UG_LOGN, and ug::NeuriteProjector::Neurite::vBR.

◆ direction_at_grid_object()

void ug::NeuriteProjector::direction_at_grid_object	(	vector3 &	dirOut,
		GridObject *	o
	)		const

spline direction at some grid object

References average_params(), ug::NeuriteProjector::SurfaceParams::axial, ug::GridObject::base_object_id(), ug::NeuriteProjector::Section::endParam, get_section_iterator(), m_aaSurfParams, ug::NeuriteProjector::SurfaceParams::neuriteID, s, ug::NeuriteProjector::Section::splineParamsX, ug::NeuriteProjector::Section::splineParamsY, ug::NeuriteProjector::Section::splineParamsZ, UG_COND_THROW, and ug::VERTEX.

◆ get_section_iterator()

std::vector< NeuriteProjector::Section >::const_iterator ug::NeuriteProjector::get_section_iterator	(	uint32_t	nid,
		float	t
	)		const

protected

References m_vNeurites, and UG_COND_THROW.

Referenced by axial_range_around_branching_region(), and direction_at_grid_object().

◆ get_soma_section_iterator()

std::vector< NeuriteProjector::Section >::const_iterator ug::NeuriteProjector::get_soma_section_iterator	(	uint32_t	nid,
		float	t
	)		const

protected

References m_vNeurites, and UG_COND_THROW.

Referenced by axial_range_around_soma_region().

◆ is_in_axial_range_around_soma_region()

bool ug::NeuriteProjector::is_in_axial_range_around_soma_region	(	const SomaBranchingRegion &	sr,
		size_t	nid,
		Vertex *	vrt
	)		const

const number radius = axial_range_around_soma_region(sr, 0.1, nid, vrt);

References ug::NeuriteProjector::SomaBranchingRegion::center, and UG_LOGN.

Referenced by push_into_place().

◆ IsElementInsideSphere()

template<class TElem >

bool ug::NeuriteProjector::IsElementInsideSphere	(	const TElem *	elem,
		const ug::vector3 &	center,
		const number	radius
	)		const

inlineprivate

check if an element is inside a sphere

Parameters

[in]	elem
[in]	center
[in]	radius

Returns: true if element is inside or on sphere else false

References ug::aPosition, ug::CalculateCenter(), ug::RefinementProjector::geometry(), s, ug::SMALL, ug::sq(), ug::VecPow(), and ug::VecSubtract().

◆ load()

template<class Archive >

void ug::NeuriteProjector::load	(	Archive &	ar,
		const unsigned int	version
	)

inlineprivate

References ug::NeuriteProjector::BranchingRegion::bp, m_vNeurites, neurite(), UG_ASSERT, UG_EMPTY_BASE_CLASS_SERIALIZATION, SmartPtr< T, FreePolicy >::valid(), and ug::NeuriteProjector::Neurite::vBR.

◆ neurite()

const NeuriteProjector::Neurite & ug::NeuriteProjector::neurite ( uint32_t nid ) const

References m_vNeurites, and UG_COND_THROW.

Referenced by axial_range_around_branching_region(), ug::bp_newton_start_pos(), debug_neurites(), load(), ug::pos_in_bp(), and push_into_place().

◆ neurites()

std::vector< NeuriteProjector::Neurite > & ug::NeuriteProjector::neurites ( )

References m_vNeurites.

◆ new_vertex() [1/4]

number ug::NeuriteProjector::new_vertex	(	Vertex *	vrt,
		Edge *	parent
	)

virtual

called when a new vertex was created from an old edge

Reimplemented from ug::RefinementProjector.

References push_into_place().

◆ new_vertex() [2/4]

number ug::NeuriteProjector::new_vertex	(	Vertex *	vrt,
		Face *	parent
	)

virtual

called when a new vertex was created from an old face

Reimplemented from ug::RefinementProjector.

References push_into_place().

◆ new_vertex() [3/4]

number ug::NeuriteProjector::new_vertex	(	Vertex *	vrt,
		Vertex *	parent
	)

virtual

called when a new vertex was created from an old vertex

Reimplemented from ug::RefinementProjector.

References m_aaSurfParams, ug::RefinementProjector::pos(), and ug::RefinementProjector::set_pos().

◆ new_vertex() [4/4]

number ug::NeuriteProjector::new_vertex	(	Vertex *	vrt,
		Volume *	parent
	)

virtual

called when a new vertex was created from an old volume

Reimplemented from ug::RefinementProjector.

References push_into_place().

◆ position()

vector3 ug::NeuriteProjector::position ( Vertex * vrt ) const

References ug::RefinementProjector::pos().

Referenced by average_params(), axial_range_around_soma_region(), and push_into_place().

◆ prepare_quadrature()

void ug::NeuriteProjector::prepare_quadrature ( )

protected

points

weights

References ug::cmpQPairs(), and m_qPoints.

Referenced by NeuriteProjector().

◆ print_surface_params()

void ug::NeuriteProjector::print_surface_params ( const Vertex *const v ) const

References ug::NeuriteProjector::SurfaceParams::angular, ug::NeuriteProjector::SurfaceParams::axial, m_aaSurfParams, ug::NeuriteProjector::SurfaceParams::neuriteID, ug::NeuriteProjector::SurfaceParams::radial, and UG_LOGN.

◆ project()

void ug::NeuriteProjector::project ( Vertex * vrt )

project a vertex to its model position

References push_into_place().

◆ push_into_place()

number ug::NeuriteProjector::push_into_place	(	Vertex *	vrt,
		const IVertexGroup *	parent
	)

protected

UG_LOGN("Number of soma branching regions for neurite with id: " << plainNID << ": " << vSBR.size());

This works due to the fact that vBR is sorted ascending

This works due to the fact that vSBR is sorted ascending

This should integrate along the neurite [0, END_SOMA_BRANCHING_REGION] but not [-range, range] to avoid dints in the soma interior close to the surface. A new position for the vertex based on the average of the (first) neurite section and the soma sphere position and radius will be calculated based on the SomaRegion information stored in a struct. FIXME: Optimize iteration: Find better starting position for iteration start pos_on_surface_soma_bp(pos, neurite, neuriteID, t, angle, parent, this, rad, vrt, *it2, m_aaSurfParams);

pos_on_surface_soma(pos, neurite, this, parent);

References average_params(), axial_range_around_branching_region(), is_in_axial_range_around_soma_region(), m_aaSurfParams, m_vNeurites, neurite(), ug::RefinementProjector::pos(), ug::pos_in_bp(), ug::pos_in_neurite(), ug::pos_on_surface_tip(), position(), ug::RefinementProjector::set_pos(), UG_CATCH_THROW, UG_COND_THROW, UG_LOGN, ug::NeuriteProjector::Neurite::vBR, and ug::NeuriteProjector::Neurite::vSBR.

Referenced by new_vertex(), and project().

◆ quadrature_points()

const std::vector< std::pair< number, number > > & ug::NeuriteProjector::quadrature_points ( ) const

References m_qPoints.

Referenced by ug::bp_defect_and_gradient().

◆ save()

template<class Archive >

void ug::NeuriteProjector::save	(	Archive &	ar,
		const unsigned int	version
	)		const

inlineprivate

References ug::AT_DATA, ug::AT_GUI, m_vNeurites, and UG_EMPTY_BASE_CLASS_SERIALIZATION.

◆ set_geometry()

void ug::NeuriteProjector::set_geometry ( SPIGeometry3d geometry )

virtual

Reimplemented from ug::RefinementProjector.

References attach_surf_params(), ug::RefinementProjector::geometry(), and ug::RefinementProjector::set_geometry().

◆ somata()

std::vector<SomaBranchingRegion>& ug::NeuriteProjector::somata ( )

◆ surface_params_accessor() [1/2]

Grid::VertexAttachmentAccessor< Attachment< NeuriteProjector::SurfaceParams > > & ug::NeuriteProjector::surface_params_accessor ( )

References m_aaSurfParams.

◆ surface_params_accessor() [2/2]

const Grid::VertexAttachmentAccessor< Attachment< NeuriteProjector::SurfaceParams > > & ug::NeuriteProjector::surface_params_accessor ( ) const

References m_aaSurfParams.

Friends And Related Function Documentation

◆ boost::serialization::access

friend class boost::serialization::access

friend

Member Data Documentation

◆ m_aaSurfParams

Grid::VertexAttachmentAccessor<Attachment<SurfaceParams> > ug::NeuriteProjector::m_aaSurfParams

private

Referenced by attach_surf_params(), average_params(), direction_at_grid_object(), new_vertex(), print_surface_params(), push_into_place(), and surface_params_accessor().

◆ m_aSurfParams

Attachment<SurfaceParams> ug::NeuriteProjector::m_aSurfParams

private

Referenced by attach_surf_params().

◆ m_qPoints

std::vector<std::pair<number, number> > ug::NeuriteProjector::m_qPoints

private

for quadrature when projecting within branching points

Referenced by prepare_quadrature(), and quadrature_points().

◆ m_vNeurites

std::vector<Neurite> ug::NeuriteProjector::m_vNeurites

private

storage for cubic splines: Vector of sorted vectors of sections; each inner vector represents a single neurite. Any complete neurite is parameterized by t in [0,1]. Each section in the neurite vector consists of the parameter t at which the section ends and the sixteen coefficients describing the spline in each dimension (monomial basis {(t_(i+1) - t)^i}_i).

spline information for neurites

Referenced by average_params(), axial_range_around_branching_region(), debug_neurites(), get_section_iterator(), get_soma_section_iterator(), load(), neurite(), neurites(), push_into_place(), and save().

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

ugbase/lib_grid/refinement/projectors/neurite_projector.h
ugbase/lib_grid/refinement/projectors/neurite_projector.cpp

Classes

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Constructor & Destructor Documentation

◆ NeuriteProjector() [1/2]

◆ NeuriteProjector() [2/2]

◆ ~NeuriteProjector()

Member Function Documentation

◆ attach_surf_params()

◆ average_params()

◆ average_pos_from_parent()

◆ axial_range_around_branching_region()

◆ axial_range_around_soma_region()

◆ debug_neurites()

◆ direction_at_grid_object()

◆ get_section_iterator()

◆ get_soma_section_iterator()

◆ is_in_axial_range_around_soma_region()

◆ IsElementInsideSphere()

◆ load()

◆ neurite()

◆ neurites()

◆ new_vertex() [1/4]

◆ new_vertex() [2/4]

◆ new_vertex() [3/4]

◆ new_vertex() [4/4]

◆ position()

◆ prepare_quadrature()

◆ print_surface_params()

◆ project()

◆ push_into_place()

◆ quadrature_points()

◆ save()

◆ set_geometry()

◆ somata()

◆ surface_params_accessor() [1/2]

◆ surface_params_accessor() [2/2]

Friends And Related Function Documentation

◆ boost::serialization::access

Member Data Documentation

◆ m_aaSurfParams

◆ m_aSurfParams

◆ m_qPoints

◆ m_vNeurites