#include <neurite_element.h>

Inheritance diagram for bdm::neuroscience::NeuriteElement:

Collaboration diagram for bdm::neuroscience::NeuriteElement:

Classes
struct	MechanicalForcesFunctor

Public Member Functions
	NeuriteElement ()

void	Initialize (const NewAgentEvent &event) override

void	Update (const NewAgentEvent &event) override

const AgentUid &	GetUid () const override

Spinlock *	GetLock () override

void	CriticalRegion (std::vector< AgentPointer<>> *aptrs) override

Shape	GetShape () const override

std::set< std::string >	GetRequiredVisDataMembers () const override

void	SetDiameter (real_t diameter) override

void	SetDensity (real_t density)

const Real3 &	GetPosition () const override

void	SetPosition (const Real3 &position) override

void	UpdatePosition ()

const Real3 &	GetMassLocation () const
	return end of neurite element position More...

void	SetMassLocation (const Real3 &mass_location)

real_t	GetAdherence () const

void	SetAdherence (real_t adherence)

const Real3 &	GetXAxis () const

const Real3 &	GetYAxis () const

const Real3 &	GetZAxis () const

real_t	GetVolume () const

real_t	GetDiameter () const override

real_t	GetDensity () const

real_t	GetMass () const

Real3	OriginOf (const AgentUid &daughter_uid) const override

StructureIdentifierSWC	GetIdentifierSWC () const override

void	RetractTerminalEnd (real_t speed)

void	ElongateTerminalEnd (real_t speed, const Real3 &direction)

bool	BranchPermitted () const

NeuriteElement *	Branch (real_t new_branch_diameter, const Real3 &direction, real_t length=1.0)
	Create a branch for this neurite element. More...

NeuriteElement *	Branch (const Real3 &direction)
	Create a branch for this neurite element. More...

NeuriteElement *	Branch (real_t diameter)
	Create a branch for this neurite element. More...

NeuriteElement *	Branch ()
	Create a branch for this neurite element. More...

bool	BifurcationPermitted () const

std::array< NeuriteElement *, 2 >	Bifurcate (real_t length, real_t diameter_1, real_t diameter_2, const Real3 &direction_1, const Real3 &direction_2)
	Growth cone bifurcation. More...

std::array< NeuriteElement *, 2 >	Bifurcate (real_t diameter_1, real_t diameter_2, const Real3 &direction_1, const Real3 &direction_2)
	Growth cone bifurcation. More...

std::array< NeuriteElement *, 2 >	Bifurcate (const Real3 &direction_1, const Real3 &direction_2)
	Growth cone bifurcation. More...

std::array< NeuriteElement *, 2 >	Bifurcate ()
	Growth cone bifurcation. More...

void	RemoveDaughter (const AgentPointer< NeuriteElement > &daughter) override

void	UpdateRelative (const NeuronOrNeurite &old_relative, const NeuronOrNeurite &new_relative) override

Real3	ForceTransmittedFromDaugtherToMother (const NeuronOrNeurite &mother)

void	RunDiscretization () override

void	MovePointMass (real_t speed, const Real3 &direction)

void	SetRestingLengthForDesiredTension (real_t tension)

void	ChangeVolume (real_t speed)

void	ChangeDiameter (real_t speed)

Real3	CalculateDisplacement (const InteractionForce *force, real_t squared_radius, real_t dt) override

void	ApplyDisplacement (const Real3 &displacement) override

void	UpdateLocalCoordinateAxis ()

void	UpdateDiameter ()
	Recomputes diameter after volume has changed. More...

void	UpdateVolume ()
	Recomputes volume, after diameter has been changed. More...

Real3	TransformCoordinatesGlobalToLocal (const Real3 &position) const

Real3	TransformCoordinatesLocalToGlobal (const Real3 &position) const

Real3	TransformCoordinatesLocalToPolar (const Real3 &position) const

Real3	TransformCoordinatesPolarToLocal (const Real3 &position) const

Real3	TransformCoordinatesPolarToGlobal (const std::array< real_t, 2 > &position) const
	P -> G : P -> L, then L -> G. More...

Real3	TransformCoordinatesGlobalToPolar (const Real3 &position) const
	G -> L : G -> L, then L -> P. More...

bool	IsAxon () const

void	SetAxon (bool is_axon)

AgentPointer< NeuronOrNeurite > &	GetMother ()

const AgentPointer< NeuronOrNeurite > &	GetMother () const

void	SetMother (const AgentPointer< NeuronOrNeurite > &mother)

const AgentPointer< NeuriteElement > &	GetDaughterLeft () const

void	SetDaughterLeft (const AgentPointer< NeuriteElement > &daughter)

const AgentPointer< NeuriteElement > &	GetDaughterRight () const

void	SetDaughterRight (const AgentPointer< NeuriteElement > &daughter)

int	GetBranchOrder () const

void	SetBranchOrder (int branch_order)

real_t	GetActualLength () const

void	SetActualLength (real_t actual_length)
	Should not be used, since the actual length depends on the geometry. More...

real_t	GetRestingLength () const

void	SetRestingLength (real_t resting_length)

const Real3 &	GetSpringAxis () const

void	SetSpringAxis (const Real3 &axis)

real_t	GetSpringConstant () const

void	SetSpringConstant (real_t spring_constant)

real_t	GetTension () const

void	SetTension (real_t tension)

Real3	GetUnitaryAxisDirectionVector () const

bool	IsTerminal () const

Real3	ProximalEnd () const

const Real3 &	DistalEnd () const
	Returns the position of the distal end == position_. More...

real_t	LengthToProximalBranchingPoint () const

real_t	GetLength () const

const Real3 &	GetAxis () const
	Returns the axis direction of a neurite element. More...

void	UpdateDependentPhysicalVariables () override

Public Member Functions inherited from bdm::Agent
	Agent ()

	Agent (TRootIOCtor *io_ctor)

	Agent (const Agent &other)

virtual	~Agent ()

virtual Agent *	New () const =0
	Create a new instance of this object using the default constructor. More...

virtual Agent *	NewCopy () const =0
	Create a copy of this object. More...

void	CreateNewAgents (const NewAgentEvent &event, const std::initializer_list< Agent * > &prototypes)

virtual const char *	GetTypeName () const

void	AssignNewUid ()

const AgentUid &	GetUid () const

Spinlock *	GetLock ()

uint32_t	GetBoxIdx () const

void	SetBoxIdx (uint32_t idx)

void	SetStaticnessNextTimestep (bool value) const

bool	GetPropagateStaticness () const

void	SetPropagateStaticness (bool value=true)

void	PropagateStaticness (bool beginning=false)

void	UpdateStaticness ()

bool	IsStatic () const

template<typename TAgent = Agent>
AgentPointer< TAgent >	GetAgentPtr () const
	Return agent pointer. More...

void	AddBehavior (Behavior *behavior)
	Add a behavior to this agent. More...

void	RemoveBehavior (const Behavior *behavior)

void	RunBehaviors ()
	Execute all behaviorsq. More...

const InlineVector< Behavior *, 2 > &	GetAllBehaviors () const
	Return all behaviors. More...

virtual void	RemoveFromSimulation ()

void *	operator new (size_t size)

void	operator delete (void *p)

Public Member Functions inherited from bdm::neuroscience::NeuronOrNeurite
virtual	~NeuronOrNeurite ()

AgentPointer< NeuronOrNeurite >	GetNeuronOrNeuriteAgentPtr () const

bool	IsNeuronSoma () const

bool	IsNeuriteElement () const

Protected Member Functions
void	Copy (const NeuriteElement &rhs)

Protected Member Functions inherited from bdm::Agent
template<typename TFrom , typename TTo >
std::enable_if< std::is_base_of< TFrom, TTo >::value, TTo * >::type	Cast (TFrom *agent) const

template<typename TFrom , typename TTo >
std::enable_if<!std::is_base_of< TFrom, TTo >::value, TTo * >::type	Cast (TFrom *agent) const

Private Member Functions
	BDM_AGENT_HEADER (NeuriteElement, Agent, 1)

NeuriteElement *	SplitNeuriteElement (real_t distal_portion=0.5)
	Split this neurite element into two segments. More...

void	RemoveProximalNeuriteElement ()

NeuriteElement *	ExtendSideNeuriteElement (real_t length, real_t diameter, const Real3 &direction)
	Extend a side neurite element and assign it to daughter right. More...

void	InitializeNewNeuriteExtension (NeuronSoma *soma, real_t diameter, real_t phi, real_t theta)
	TODO. More...

void	InitializeNeuriteBifurcation (NeuriteElement *mother, real_t length, real_t diameter, const Real3 &direction)
	TODO. More...

void	InitializeSplitOrBranching (NeuriteElement *other, real_t distal_portion)

void	InitializeSideExtensionOrBranching (NeuriteElement *mother, real_t length, real_t diameter, const Real3 &direction)

Private Attributes
Real3	mass_location_ = {{0.0, 0.0, 0.0}}

Real3	position_ = {{0.0, 0.0, 0.0}}
	position_ is the middle point of cylinder More...

real_t	volume_

real_t	diameter_ = 1
	NB: Use setter and don't assign values directly. More...

real_t	density_
	NB: Use setter and don't assign values directly. More...

real_t	adherence_
	NB: Use setter and don't assign values directly. More...

Real3	x_axis_ = {{1.0, 0.0, 0.0}}
	First axis of the local coordinate system equal to cylinder axis. More...

Real3	y_axis_ = {{0.0, 1.0, 0.0}}
	Second axis of the local coordinate system. More...

Real3	z_axis_ = {{0.0, 0.0, 1.0}}
	Third axis of the local coordinate system. More...

bool	is_axon_ = false

AgentPointer< NeuronOrNeurite >	mother_

AgentPointer< NeuriteElement >	daughter_left_

AgentPointer< NeuriteElement >	daughter_right_

int	branch_order_ = 0

Real3	force_to_transmit_to_proximal_mass_ = {{0, 0, 0}}
	The part of the inter-object force transmitted to the mother (parent node) More...

Real3	spring_axis_ = {{0, 0, 0}}

real_t	actual_length_ = 1

real_t	tension_

real_t	spring_constant_

real_t	resting_length_

bool	has_neurite_neighbor_ = false
	Helper variable needed in CalculateDisplacement. More...

Friends
std::ostream &	operator<< (std::ostream &str, const NeuriteElement &n)

Additional Inherited Members
Protected Attributes inherited from bdm::Agent
AgentUid	uid_
	unique id More...

uint32_t	box_idx_ = std::numeric_limits<uint32_t>::max()
	Grid box index. More...

InlineVector< Behavior *, 2 >	behaviors_
	collection of behaviors which define the internal behavior More...

Detailed Description

Class defining a neurite element with cylindrical geometry. A cylinder can be seen as a normal cylinder, with two end points and a diameter. It is oriented; the two points are called proximal and distal. The neurite element is be part of a tree-like structure with (one and only) one object at its proximal point and (up to) two neurite elements at its distal end. The proximal end can be a Neurite or Neuron cell body. If there is only one daughter, it is the left one. If daughter_left_ == nullptr, there is no distal neurite element. (it is a terminal neurite element). The presence of a daughter_left_ means that this branch has a bifurcation at its distal end.
All the mass of the neurite element is concentrated at the distal point. Only the distal end is moved. All the forces that are applied to the proximal node are transmitted to the mother element

Definition at line 56 of file neurite_element.h.

Constructor & Destructor Documentation

◆ NeuriteElement()

bdm::neuroscience::NeuriteElement::NeuriteElement ( )

Definition at line 21 of file neurite_element.cc.

Member Function Documentation

◆ ApplyDisplacement()

void bdm::neuroscience::NeuriteElement::ApplyDisplacement ( const Real3 & displacement )

overridevirtual

Implements bdm::Agent.

Definition at line 624 of file neurite_element.cc.

◆ BDM_AGENT_HEADER()

bdm::neuroscience::NeuriteElement::BDM_AGENT_HEADER	(	NeuriteElement	,
		Agent	,
		1
	)

private

◆ Bifurcate() [1/4]

std::array< NeuriteElement *, 2 > bdm::neuroscience::NeuriteElement::Bifurcate ( )

Growth cone bifurcation.

See also: NeuriteBifurcationEvent

Definition at line 317 of file neurite_element.cc.

◆ Bifurcate() [2/4]

std::array< NeuriteElement *, 2 > bdm::neuroscience::NeuriteElement::Bifurcate	(	const Real3 &	direction_1,
		const Real3 &	direction_2
	)

Growth cone bifurcation.

See also: NeuriteBifurcationEvent

Definition at line 307 of file neurite_element.cc.

◆ Bifurcate() [3/4]

std::array< NeuriteElement *, 2 > bdm::neuroscience::NeuriteElement::Bifurcate	(	real_t	diameter_1,
		real_t	diameter_2,
		const Real3 &	direction_1,
		const Real3 &	direction_2
	)

Growth cone bifurcation.

See also: NeuriteBifurcationEvent

Definition at line 299 of file neurite_element.cc.

◆ Bifurcate() [4/4]

std::array< NeuriteElement *, 2 > bdm::neuroscience::NeuriteElement::Bifurcate	(	real_t	length,
		real_t	diameter_1,
		real_t	diameter_2,
		const Real3 &	direction_1,
		const Real3 &	direction_2
	)

Growth cone bifurcation.

See also: NeuriteBifurcationEvent

Definition at line 282 of file neurite_element.cc.

◆ BifurcationPermitted()

bool bdm::neuroscience::NeuriteElement::BifurcationPermitted ( ) const

Returns true if a bifurcation is physically possible. That is if the neurite element has no daughter and the actual length is bigger than the minimum required.

Definition at line 276 of file neurite_element.cc.

◆ Branch() [1/4]

NeuriteElement * bdm::neuroscience::NeuriteElement::Branch ( )

Create a branch for this neurite element.

Use a random growth direction for the side branch. Diameter of new side branch will be equal to this neurites diameter.

See also: NeuriteBranchingEvent

Definition at line 267 of file neurite_element.cc.

◆ Branch() [2/4]

NeuriteElement * bdm::neuroscience::NeuriteElement::Branch ( const Real3 & direction )

Create a branch for this neurite element.

Diameter of new side branch will be equal to this neurites diameter.

See also: NeuriteBranchingEvent

Definition at line 254 of file neurite_element.cc.

◆ Branch() [3/4]

NeuriteElement * bdm::neuroscience::NeuriteElement::Branch ( real_t diameter )

Create a branch for this neurite element.

Use a random growth direction for the side branch.

See also: NeuriteBranchingEvent

Definition at line 258 of file neurite_element.cc.

◆ Branch() [4/4]

NeuriteElement * bdm::neuroscience::NeuriteElement::Branch	(	real_t	new_branch_diameter,
		const Real3 &	direction,
		real_t	length = `1.0`
	)

Create a branch for this neurite element.

See also: NeuriteBranchingEvent

Definition at line 244 of file neurite_element.cc.

◆ BranchPermitted()

bool bdm::neuroscience::NeuriteElement::BranchPermitted ( ) const

Returns true if a side branch is physically possible. That is if this is not a terminal branch and if there is not already a second daughter.

Definition at line 240 of file neurite_element.cc.

◆ CalculateDisplacement()

Real3 bdm::neuroscience::NeuriteElement::CalculateDisplacement	(	const InteractionForce *	force,
		real_t	squared_radius,
		real_t	dt
	)

overridevirtual

Implements bdm::Agent.

Definition at line 533 of file neurite_element.cc.

◆ ChangeDiameter()

void bdm::neuroscience::NeuriteElement::ChangeDiameter ( real_t speed )

Progressive modification of the diameter. Updates the volume.

Parameters

speed micron/ h

Definition at line 467 of file neurite_element.cc.

◆ ChangeVolume()

void bdm::neuroscience::NeuriteElement::ChangeVolume ( real_t speed )

Progressive modification of the volume. Updates the diameter.

Parameters

speed cubic micron/ h

Definition at line 454 of file neurite_element.cc.

◆ Copy()

void bdm::neuroscience::NeuriteElement::Copy ( const NeuriteElement & rhs )

protected

Definition at line 849 of file neurite_element.cc.

◆ CriticalRegion()

void bdm::neuroscience::NeuriteElement::CriticalRegion ( std::vector< AgentPointer<>> * aptrs )

overridevirtual

If the thread-safety mechanism is set to user-specified this function will be called before the operations are executed for this agent.
Subclasses define the critical region by adding the AgentPointers of all agents that must not be processed in parallel.
Don't forget to add the current agent.
Here an example from NeuronSoma.

void NeuronSoma::CriticalRegion(std::vector<AgentPointer<>>* aptrs) {
  aptrs->reserve(daughters_.size() + 1);
  aptrs->push_back(Agent::GetAgentPtr<>());
  for (auto& daughter : daughters_) {
    aptrs->push_back(daughter);
  }
}

See also: Param::thread_safety_mechanism; AgentPointer; NeuronSoma::CriticalRegion

Reimplemented from bdm::Agent.

Definition at line 122 of file neurite_element.cc.

◆ DistalEnd()

const Real3& bdm::neuroscience::NeuriteElement::DistalEnd ( ) const

inline

Returns the position of the distal end == position_.

Definition at line 432 of file neurite_element.h.

◆ ElongateTerminalEnd()

void bdm::neuroscience::NeuriteElement::ElongateTerminalEnd	(	real_t	speed,
		const Real3 &	direction
	)

Method used for active extension of a terminal branch, representing the steering of a growth cone. The movement should always be forward, otherwise no movement is performed. If direction points in an opposite direction than the axis, i.e. if the dot product is negative, there is no movement (only elongation is possible).

Parameters

speed
direction

Definition at line 233 of file neurite_element.cc.

◆ ExtendSideNeuriteElement()

NeuriteElement * bdm::neuroscience::NeuriteElement::ExtendSideNeuriteElement	(	real_t	length,
		real_t	diameter,
		const Real3 &	direction
	)

private

Extend a side neurite element and assign it to daughter right.

See also: SideNeuriteExtensionEvent

Definition at line 903 of file neurite_element.cc.

◆ ForceTransmittedFromDaugtherToMother()

Real3 bdm::neuroscience::NeuriteElement::ForceTransmittedFromDaugtherToMother ( const NeuronOrNeurite & mother )

Returns the total force that this NeuriteElement exerts on it's mother. It is the sum of the spring force and the part of the inter-object force computed earlier in CalculateDisplacement

Definition at line 369 of file neurite_element.cc.

◆ GetActualLength()

real_t bdm::neuroscience::NeuriteElement::GetActualLength ( ) const

inline

Definition at line 396 of file neurite_element.h.

◆ GetAdherence()

real_t bdm::neuroscience::NeuriteElement::GetAdherence ( ) const

inline

Definition at line 93 of file neurite_element.h.

◆ GetAxis()

const Real3 & bdm::neuroscience::NeuriteElement::GetAxis ( ) const

Returns the axis direction of a neurite element.

Definition at line 789 of file neurite_element.cc.

◆ GetBranchOrder()

int bdm::neuroscience::NeuriteElement::GetBranchOrder ( ) const

inline

Definition at line 392 of file neurite_element.h.

◆ GetDaughterLeft()

const AgentPointer< NeuriteElement > & bdm::neuroscience::NeuriteElement::GetDaughterLeft ( ) const

Returns: the (first) distal neurite element, if it exists, i.e. if this is not the terminal segment (otherwise returns nullptr).

Definition at line 728 of file neurite_element.cc.

◆ GetDaughterRight()

const AgentPointer< NeuriteElement > & bdm::neuroscience::NeuriteElement::GetDaughterRight ( ) const

Returns: the second distal neurite element, if it exists i.e. if there is a branching point just after this element (otherwise returns nullptr).

Definition at line 737 of file neurite_element.cc.

◆ GetDensity()

real_t bdm::neuroscience::NeuriteElement::GetDensity ( ) const

inline

Definition at line 105 of file neurite_element.h.

◆ GetDiameter()

real_t bdm::neuroscience::NeuriteElement::GetDiameter ( ) const

inlineoverridevirtual

Implements bdm::Agent.

Definition at line 103 of file neurite_element.h.

◆ GetIdentifierSWC()

StructureIdentifierSWC bdm::neuroscience::NeuriteElement::GetIdentifierSWC ( ) const

overridevirtual

Returns StructureIdentifierSWC:kAxon if NeuriteElement is an Axon and StructureIdentifierSWC::kApicalDendrite for all other cases.

Reimplemented from bdm::neuroscience::NeuronOrNeurite.

Definition at line 179 of file neurite_element.cc.

◆ GetLength()

real_t bdm::neuroscience::NeuriteElement::GetLength ( ) const

inline

Definition at line 441 of file neurite_element.h.

◆ GetLock()

Spinlock* bdm::neuroscience::NeuriteElement::GetLock ( )

inlineoverridevirtual

Implements bdm::neuroscience::NeuronOrNeurite.

Definition at line 68 of file neurite_element.h.

◆ GetMass()

real_t bdm::neuroscience::NeuriteElement::GetMass ( ) const

inline

Definition at line 107 of file neurite_element.h.

◆ GetMassLocation()

const Real3& bdm::neuroscience::NeuriteElement::GetMassLocation ( ) const

inline

return end of neurite element position

Definition at line 89 of file neurite_element.h.

◆ GetMother() [1/2]

AgentPointer<NeuronOrNeurite>& bdm::neuroscience::NeuriteElement::GetMother ( )

inline

Definition at line 371 of file neurite_element.h.

◆ GetMother() [2/2]

const AgentPointer<NeuronOrNeurite>& bdm::neuroscience::NeuriteElement::GetMother ( ) const

inline

Definition at line 373 of file neurite_element.h.

◆ GetPosition()

const Real3& bdm::neuroscience::NeuriteElement::GetPosition ( ) const

inlineoverridevirtual

Implements bdm::Agent.

Definition at line 82 of file neurite_element.h.

◆ GetRequiredVisDataMembers()

std::set< std::string > bdm::neuroscience::NeuriteElement::GetRequiredVisDataMembers ( ) const

overridevirtual

Returns the data members that are required to visualize this simulation object.

Reimplemented from bdm::Agent.

Definition at line 134 of file neurite_element.cc.

◆ GetRestingLength()

real_t bdm::neuroscience::NeuriteElement::GetRestingLength ( ) const

inline

Definition at line 401 of file neurite_element.h.

◆ GetShape()

Shape bdm::neuroscience::NeuriteElement::GetShape ( ) const

inlineoverridevirtual

Implements bdm::Agent.

Definition at line 72 of file neurite_element.h.

◆ GetSpringAxis()

const Real3& bdm::neuroscience::NeuriteElement::GetSpringAxis ( ) const

inline

Definition at line 405 of file neurite_element.h.

◆ GetSpringConstant()

real_t bdm::neuroscience::NeuriteElement::GetSpringConstant ( ) const

inline

Definition at line 409 of file neurite_element.h.

◆ GetTension()

real_t bdm::neuroscience::NeuriteElement::GetTension ( ) const

inline

Definition at line 413 of file neurite_element.h.

◆ GetUid()

const AgentUid& bdm::neuroscience::NeuriteElement::GetUid ( ) const

inlineoverridevirtual

Implements bdm::neuroscience::NeuronOrNeurite.

Definition at line 66 of file neurite_element.h.

◆ GetUnitaryAxisDirectionVector()

Real3 bdm::neuroscience::NeuriteElement::GetUnitaryAxisDirectionVector ( ) const

NOT A "REAL" GETTER Gets a vector of length 1, with the same direction as the SpringAxis.

Returns: a normalized spring axis

Definition at line 773 of file neurite_element.cc.

◆ GetVolume()

real_t bdm::neuroscience::NeuriteElement::GetVolume ( ) const

inline

Definition at line 101 of file neurite_element.h.

◆ GetXAxis()

const Real3& bdm::neuroscience::NeuriteElement::GetXAxis ( ) const

inline

Definition at line 97 of file neurite_element.h.

◆ GetYAxis()

const Real3& bdm::neuroscience::NeuriteElement::GetYAxis ( ) const

inline

Definition at line 98 of file neurite_element.h.

◆ GetZAxis()

const Real3& bdm::neuroscience::NeuriteElement::GetZAxis ( ) const

inline

Definition at line 99 of file neurite_element.h.

◆ Initialize()

void bdm::neuroscience::NeuriteElement::Initialize ( const NewAgentEvent & event )

overridevirtual

This method is called to initialize new agents that are created during a NewAgentEvent. Override this method to initialize attributes of your own Agent subclasses. NB: Don't forget to call the implementation of the base class first. Base::Initialize(event); Failing to do so will result in errors.

Reimplemented from bdm::Agent.

Definition at line 34 of file neurite_element.cc.

◆ InitializeNeuriteBifurcation()

void bdm::neuroscience::NeuriteElement::InitializeNeuriteBifurcation	(	NeuriteElement *	mother,
		real_t	length,
		real_t	diameter,
		const Real3 &	direction
	)

private

TODO.

Definition at line 954 of file neurite_element.cc.

◆ InitializeNewNeuriteExtension()

void bdm::neuroscience::NeuriteElement::InitializeNewNeuriteExtension	(	NeuronSoma *	soma,
		real_t	diameter,
		real_t	phi,
		real_t	theta
	)

private

TODO.

Definition at line 915 of file neurite_element.cc.

◆ InitializeSideExtensionOrBranching()

void bdm::neuroscience::NeuriteElement::InitializeSideExtensionOrBranching	(	NeuriteElement *	mother,
		real_t	length,
		real_t	diameter,
		const Real3 &	direction
	)

private

Neurite branching is composed of neurite splitting and side neurite extension. To avoid code duplication in constructors, logic has been moved here.

Definition at line 1016 of file neurite_element.cc.

◆ InitializeSplitOrBranching()

void bdm::neuroscience::NeuriteElement::InitializeSplitOrBranching	(	NeuriteElement *	other,
		real_t	distal_portion
	)

private

Neurite branching is composed of neurite splitting and side neurite extension. To avoid code duplication in constructors, logic has been moved here.

See also: SplitNeuriteElementEvent, NeuriteBranchingEvent

Definition at line 995 of file neurite_element.cc.

◆ IsAxon()

bool bdm::neuroscience::NeuriteElement::IsAxon ( ) const

inline

Definition at line 367 of file neurite_element.h.

◆ IsTerminal()

bool bdm::neuroscience::NeuriteElement::IsTerminal ( ) const

inline

Should return yes if the PhysicalCylinder is considered a terminal branch.

Returns: is it a terminal branch

Definition at line 424 of file neurite_element.h.

◆ LengthToProximalBranchingPoint()

real_t bdm::neuroscience::NeuriteElement::LengthToProximalBranchingPoint ( ) const

Returns the total (actual) length of all the neurite elements (including the one in which this method is called) before the previous branching point. Used to decide if long enough to bifurcate or branch, independently of the discretization.

Definition at line 778 of file neurite_element.cc.

◆ MovePointMass()

void bdm::neuroscience::NeuriteElement::MovePointMass	(	real_t	speed,
		const Real3 &	direction
	)

Method used for active extension of a terminal branch, representing the steering of a growth cone. There is no check for real extension (unlike in ExtendCylinder()` ).

Parameters

speed	of the growth rate (microns/hours).
direction	the 3D direction of movement.

Definition at line 418 of file neurite_element.cc.

◆ OriginOf()

Real3 bdm::neuroscience::NeuriteElement::OriginOf ( const AgentUid & daughter_uid ) const

overridevirtual

Returns the absolute coordinates of the location where the daughter is attached.

Parameters

daughter_element_idx element_idx of the daughter

Returns: the coord

Implements bdm::neuroscience::NeuronOrNeurite.

Definition at line 175 of file neurite_element.cc.

◆ ProximalEnd()

Real3 bdm::neuroscience::NeuriteElement::ProximalEnd ( ) const

inline

returns the position of the proximal end, ie the position minus the spring axis. Is mainly used for paint

Definition at line 429 of file neurite_element.h.

◆ RemoveDaughter()

void bdm::neuroscience::NeuriteElement::RemoveDaughter ( const AgentPointer< NeuriteElement > & daughter )

overridevirtual

Implements bdm::neuroscience::NeuronOrNeurite.

Definition at line 336 of file neurite_element.cc.

◆ RemoveProximalNeuriteElement()

void bdm::neuroscience::NeuriteElement::RemoveProximalNeuriteElement ( )

private

Merges two neurite elements together. The one in which the method is called phagocytes it's mother.

Definition at line 870 of file neurite_element.cc.

◆ RetractTerminalEnd()

void bdm::neuroscience::NeuriteElement::RetractTerminalEnd ( real_t speed )

Retracts the neurite element, if it is a terminal one. Branch retraction by moving the distal end toward the proximal end (the mother), maintaining the same tension in the neurite element. The method shortens the actual and the resting length so that the result is a shorter neurite element with the same tension.

If this neurite element is longer than the required shortening, it simply retracts.
If it is shorter and its mother has no other daughter, it merges with it's mother and the method is recursively called (this time the cylinder length is bigger because we have a new neurite element that resulted from the fusion of two).
If it is shorter and either the previous neurite element has another daughter or the mother is not a neurite element, it disappears.
Parameters

speed the retraction speed in microns / h

Definition at line 187 of file neurite_element.cc.

◆ RunDiscretization()

void bdm::neuroscience::NeuriteElement::RunDiscretization ( )

overridevirtual

Checks if this NeuriteElement is either too long or too short.

too long: insert another NeuriteElement
too short fuse it with the proximal element or even delete it

Only executed for terminal neurite elements.

Reimplemented from bdm::Agent.

Definition at line 387 of file neurite_element.cc.

◆ SetActualLength()

void bdm::neuroscience::NeuriteElement::SetActualLength ( real_t actual_length )

Should not be used, since the actual length depends on the geometry.

Definition at line 746 of file neurite_element.cc.

◆ SetAdherence()

void bdm::neuroscience::NeuriteElement::SetAdherence ( real_t adherence )

Definition at line 168 of file neurite_element.cc.

◆ SetAxon()

void bdm::neuroscience::NeuriteElement::SetAxon ( bool is_axon )

inline

Definition at line 369 of file neurite_element.h.

◆ SetBranchOrder()

void bdm::neuroscience::NeuriteElement::SetBranchOrder ( int branch_order )

inline

Definition at line 394 of file neurite_element.h.

◆ SetDaughterLeft()

void bdm::neuroscience::NeuriteElement::SetDaughterLeft ( const AgentPointer< NeuriteElement > & daughter )

Definition at line 732 of file neurite_element.cc.

◆ SetDaughterRight()

void bdm::neuroscience::NeuriteElement::SetDaughterRight ( const AgentPointer< NeuriteElement > & daughter )

Definition at line 741 of file neurite_element.cc.

◆ SetDensity()

void bdm::neuroscience::NeuriteElement::SetDensity ( real_t density )

Definition at line 146 of file neurite_element.cc.

◆ SetDiameter()

void bdm::neuroscience::NeuriteElement::SetDiameter ( real_t diameter )

overridevirtual

Implements bdm::Agent.

Definition at line 138 of file neurite_element.cc.

◆ SetMassLocation()

void bdm::neuroscience::NeuriteElement::SetMassLocation ( const Real3 & mass_location )

Definition at line 163 of file neurite_element.cc.

◆ SetMother()

void bdm::neuroscience::NeuriteElement::SetMother ( const AgentPointer< NeuronOrNeurite > & mother )

inline

Definition at line 375 of file neurite_element.h.

◆ SetPosition()

void bdm::neuroscience::NeuriteElement::SetPosition ( const Real3 & position )

overridevirtual

Implements bdm::Agent.

Definition at line 153 of file neurite_element.cc.

◆ SetRestingLength()

void bdm::neuroscience::NeuriteElement::SetRestingLength ( real_t resting_length )

Definition at line 753 of file neurite_element.cc.

◆ SetRestingLengthForDesiredTension()

void bdm::neuroscience::NeuriteElement::SetRestingLengthForDesiredTension ( real_t tension )

Definition at line 443 of file neurite_element.cc.

◆ SetSpringAxis()

void bdm::neuroscience::NeuriteElement::SetSpringAxis ( const Real3 & axis )

Definition at line 757 of file neurite_element.cc.

◆ SetSpringConstant()

void bdm::neuroscience::NeuriteElement::SetSpringConstant ( real_t spring_constant )

Definition at line 762 of file neurite_element.cc.

◆ SetTension()

void bdm::neuroscience::NeuriteElement::SetTension ( real_t tension )

Definition at line 766 of file neurite_element.cc.

◆ SplitNeuriteElement()

NeuriteElement * bdm::neuroscience::NeuriteElement::SplitNeuriteElement ( real_t distal_portion = 0.5 )

private

Split this neurite element into two segments.

See also: SplitNeuriteElementEvent

Definition at line 864 of file neurite_element.cc.

◆ TransformCoordinatesGlobalToLocal()

Real3 bdm::neuroscience::NeuriteElement::TransformCoordinatesGlobalToLocal ( const Real3 & position ) const

3 systems of coordinates :

Global : cartesian coord, defined by orthogonal axis (1,0,0), (0,1,0) and (0,0,1) with origin at (0,0,0). Local : defined by orthogonal axis xAxis (=vect proximal to distal end), yAxis and zAxis, with origin at proximal end Polar : cylindrical coordinates [h,theta,r] with h = first local coord (along xAxis), theta = angle from yAxis, r euclidean distance from xAxis; with origin at proximal end

Note: The methods below transform POSITIONS and not DIRECTIONS !!!

G -> L L -> G

L -> P P -> L

G -> P = G -> L, then L -> P P -> P = P -> L, then L -> G G -> L Returns the position in the local coordinate system (xAxis, yXis, zAxis) of a point expressed in global cartesian coordinates ([1,0,0],[0,1,0],[0,0,1]).

Parameters

position in global coordinates

Definition at line 681 of file neurite_element.cc.

◆ TransformCoordinatesGlobalToPolar()

Real3 bdm::neuroscience::NeuriteElement::TransformCoordinatesGlobalToPolar ( const Real3 & position ) const

G -> L : G -> L, then L -> P.

Definition at line 722 of file neurite_element.cc.

◆ TransformCoordinatesLocalToGlobal()

Real3 bdm::neuroscience::NeuriteElement::TransformCoordinatesLocalToGlobal ( const Real3 & position ) const

L -> G Returns the position in global cartesian coordinates ([1,0,0],[0,1,0],[0,0,1]) of a point expressed in the local coordinate system (xAxis, yXis, zAxis).

Parameters

position in local coordinates

Definition at line 687 of file neurite_element.cc.

◆ TransformCoordinatesLocalToPolar()

Real3 bdm::neuroscience::NeuriteElement::TransformCoordinatesLocalToPolar ( const Real3 & position ) const

L -> P Returns the position in cylindrical coordinates (h,theta,r) of a point expressed in the local coordinate system (xAxis, yXis, zAxis).

Parameters

position in local coordinates

Definition at line 699 of file neurite_element.cc.

◆ TransformCoordinatesPolarToGlobal()

Real3 bdm::neuroscience::NeuriteElement::TransformCoordinatesPolarToGlobal ( const std::array< real_t, 2 > & position ) const

P -> G : P -> L, then L -> G.

Definition at line 711 of file neurite_element.cc.

◆ TransformCoordinatesPolarToLocal()

Real3 bdm::neuroscience::NeuriteElement::TransformCoordinatesPolarToLocal ( const Real3 & position ) const

P -> L Returns the position in the local coordinate system (xAxis, yXis, zAxis) of a point expressed in cylindrical coordinates (h,theta,r).

Parameters

position in local coordinates

Definition at line 705 of file neurite_element.cc.

◆ Update()

void bdm::neuroscience::NeuriteElement::Update ( const NewAgentEvent & event )

overridevirtual

This method is called to update the existing agent at the end of a NewAgentEvent. Override this method to update attributes of your own Agent subclasses. NB: Don't forget to call the implementation of the base class first. Base::Update(event); Failing to do so will result in errors.

Reimplemented from bdm::Agent.

Definition at line 77 of file neurite_element.cc.

◆ UpdateDependentPhysicalVariables()

void bdm::neuroscience::NeuriteElement::UpdateDependentPhysicalVariables ( )

overridevirtual

Updates the spring axis, the actual length, the tension and the volume.

For tension, T = k * (aL - rL) / rL. k = spring constant, rL = resting length, aL = actual length. (Note the division by rL. Otherwise we could have cylinders with big aL and rL = 0).

Implements bdm::neuroscience::NeuronOrNeurite.

Definition at line 794 of file neurite_element.cc.

◆ UpdateDiameter()

void bdm::neuroscience::NeuriteElement::UpdateDiameter ( )

Recomputes diameter after volume has changed.

Definition at line 669 of file neurite_element.cc.

◆ UpdateLocalCoordinateAxis()

void bdm::neuroscience::NeuriteElement::UpdateLocalCoordinateAxis ( )

Defines the three orthonormal local axis so that a cylindrical coordinate system can be used. The x_axis_ is aligned with the spring_axis_. The two other are in the plane perpendicular to spring_axis_. This method to update the axis was suggested by Matt Coock. Although not perfectly exact, it is accurate enough for us to use.

Definition at line 650 of file neurite_element.cc.

◆ UpdatePosition()

void bdm::neuroscience::NeuriteElement::UpdatePosition ( )

Definition at line 158 of file neurite_element.cc.

◆ UpdateRelative()

void bdm::neuroscience::NeuriteElement::UpdateRelative	(	const NeuronOrNeurite &	old_relative,
		const NeuronOrNeurite &	new_relative
	)

overridevirtual

Implements bdm::neuroscience::NeuronOrNeurite.

Definition at line 353 of file neurite_element.cc.

◆ UpdateVolume()

void bdm::neuroscience::NeuriteElement::UpdateVolume ( )

Recomputes volume, after diameter has been changed.

Definition at line 677 of file neurite_element.cc.

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	str,
		const NeuriteElement &	n
	)

friend

Definition at line 809 of file neurite_element.cc.

Member Data Documentation

◆ actual_length_

real_t bdm::neuroscience::NeuriteElement::actual_length_ = 1

private

Real length of the PhysicalCylinder (norm of the springAxis). NB: Use setter and don't assign values directly

Definition at line 509 of file neurite_element.h.

◆ adherence_

real_t bdm::neuroscience::NeuriteElement::adherence_

private

NB: Use setter and don't assign values directly.

Definition at line 474 of file neurite_element.h.

◆ branch_order_

int bdm::neuroscience::NeuriteElement::branch_order_ = 0

private

number of branching points from here to the soma (root of the neuron tree-structure).

Definition at line 497 of file neurite_element.h.

◆ daughter_left_

AgentPointer<NeuriteElement> bdm::neuroscience::NeuriteElement::daughter_left_

private

First child node in the neuron tree structure (can only be a Neurite element)

Definition at line 490 of file neurite_element.h.

◆ daughter_right_

AgentPointer<NeuriteElement> bdm::neuroscience::NeuriteElement::daughter_right_

private

Second child node in the neuron tree structure. (can only be a Neurite element)

Definition at line 493 of file neurite_element.h.

◆ density_

real_t bdm::neuroscience::NeuriteElement::density_

private

NB: Use setter and don't assign values directly.

Definition at line 472 of file neurite_element.h.

◆ diameter_

real_t bdm::neuroscience::NeuriteElement::diameter_ = 1

private

NB: Use setter and don't assign values directly.

Definition at line 470 of file neurite_element.h.

◆ force_to_transmit_to_proximal_mass_

Real3 bdm::neuroscience::NeuriteElement::force_to_transmit_to_proximal_mass_ = {{0, 0, 0}}

private

The part of the inter-object force transmitted to the mother (parent node)

Definition at line 500 of file neurite_element.h.

◆ has_neurite_neighbor_

bool bdm::neuroscience::NeuriteElement::has_neurite_neighbor_ = false

private

Helper variable needed in CalculateDisplacement.

Definition at line 524 of file neurite_element.h.

◆ is_axon_

bool bdm::neuroscience::NeuriteElement::is_axon_ = false

private

Definition at line 482 of file neurite_element.h.

◆ mass_location_

Real3 bdm::neuroscience::NeuriteElement::mass_location_ = {{0.0, 0.0, 0.0}}

private

mass_location_ is distal end of the cylinder NB: Use setter and don't assign values directly

Definition at line 463 of file neurite_element.h.

◆ mother_

AgentPointer<NeuronOrNeurite> bdm::neuroscience::NeuriteElement::mother_

private

Parent node in the neuron tree structure can be a Neurite element or cell body

Definition at line 486 of file neurite_element.h.

◆ position_

Real3 bdm::neuroscience::NeuriteElement::position_ = {{0.0, 0.0, 0.0}}

private

position_ is the middle point of cylinder

Definition at line 466 of file neurite_element.h.

◆ resting_length_

real_t bdm::neuroscience::NeuriteElement::resting_length_

private

The length of the internal spring where tension would be zero. T = k*(A-R)/R --> R = k*A/(T+K)

Definition at line 521 of file neurite_element.h.

◆ spring_axis_

Real3 bdm::neuroscience::NeuriteElement::spring_axis_ = {{0, 0, 0}}

private

from the attachment point to the mass location (proximal -> distal). NB: Use setter and don't assign values directly

Definition at line 505 of file neurite_element.h.

◆ spring_constant_

real_t bdm::neuroscience::NeuriteElement::spring_constant_

private

Spring constant per distance unit (springConstant restingLength = "real" spring constant).

Definition at line 517 of file neurite_element.h.

◆ tension_

real_t bdm::neuroscience::NeuriteElement::tension_

private

Tension in the cylinder spring. NB: Use setter and don't assign values directly

Definition at line 513 of file neurite_element.h.

◆ volume_

real_t bdm::neuroscience::NeuriteElement::volume_

private

Definition at line 468 of file neurite_element.h.

◆ x_axis_

Real3 bdm::neuroscience::NeuriteElement::x_axis_ = {{1.0, 0.0, 0.0}}

private

First axis of the local coordinate system equal to cylinder axis.

Definition at line 476 of file neurite_element.h.

◆ y_axis_

Real3 bdm::neuroscience::NeuriteElement::y_axis_ = {{0.0, 1.0, 0.0}}

private

Second axis of the local coordinate system.

Definition at line 478 of file neurite_element.h.

◆ z_axis_

Real3 bdm::neuroscience::NeuriteElement::z_axis_ = {{0.0, 0.0, 1.0}}

private

Third axis of the local coordinate system.

Definition at line 480 of file neurite_element.h.

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

neuroscience/neurite_element.h
neuroscience/neurite_element.cc

Classes

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ NeuriteElement()

Member Function Documentation

◆ ApplyDisplacement()

◆ BDM_AGENT_HEADER()

◆ Bifurcate() [1/4]

◆ Bifurcate() [2/4]

◆ Bifurcate() [3/4]

◆ Bifurcate() [4/4]

◆ BifurcationPermitted()

◆ Branch() [1/4]

◆ Branch() [2/4]

◆ Branch() [3/4]

◆ Branch() [4/4]

◆ BranchPermitted()

◆ CalculateDisplacement()

◆ ChangeDiameter()

◆ ChangeVolume()

◆ Copy()

◆ CriticalRegion()

◆ DistalEnd()

◆ ElongateTerminalEnd()

◆ ExtendSideNeuriteElement()

◆ ForceTransmittedFromDaugtherToMother()

◆ GetActualLength()

◆ GetAdherence()

◆ GetAxis()

◆ GetBranchOrder()

◆ GetDaughterLeft()

◆ GetDaughterRight()

◆ GetDensity()

◆ GetDiameter()

◆ GetIdentifierSWC()

◆ GetLength()

◆ GetLock()

◆ GetMass()

◆ GetMassLocation()

◆ GetMother() [1/2]

◆ GetMother() [2/2]

◆ GetPosition()

◆ GetRequiredVisDataMembers()

◆ GetRestingLength()

◆ GetShape()

◆ GetSpringAxis()

◆ GetSpringConstant()

◆ GetTension()

◆ GetUid()

◆ GetUnitaryAxisDirectionVector()

◆ GetVolume()

◆ GetXAxis()

◆ GetYAxis()

◆ GetZAxis()

◆ Initialize()

◆ InitializeNeuriteBifurcation()

◆ InitializeNewNeuriteExtension()

◆ InitializeSideExtensionOrBranching()

◆ InitializeSplitOrBranching()

◆ IsAxon()

◆ IsTerminal()

◆ LengthToProximalBranchingPoint()

◆ MovePointMass()

◆ OriginOf()

◆ ProximalEnd()

◆ RemoveDaughter()

◆ RemoveProximalNeuriteElement()

◆ RetractTerminalEnd()

◆ RunDiscretization()

◆ SetActualLength()

◆ SetAdherence()

◆ SetAxon()

◆ SetBranchOrder()

◆ SetDaughterLeft()