#include <neuron_soma.h>

Inheritance diagram for bdm::neuroscience::NeuronSoma:

Collaboration diagram for bdm::neuroscience::NeuronSoma:

Public Member Functions
	NeuronSoma ()

	~NeuronSoma () override

	NeuronSoma (const Real3 &position)

	NeuronSoma (const NeuronSoma &other)

void	Initialize (const NewAgentEvent &event) override
	This method is used to initialise the values of daughter 2 for a cell division event. More...

void	Update (const NewAgentEvent &event) override
	This method is used to update attributes after a cell division. or new neurite branching event. More...

const AgentUid &	GetUid () const override

Spinlock *	GetLock () override

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

NeuriteElement *	ExtendNewNeurite (const Real3 &direction, NeuriteElement *prototype=nullptr)
	Extend a new neurite from this soma. More...

NeuriteElement *	ExtendNewNeurite (real_t diameter, real_t phi, real_t theta, NeuriteElement *prototype=nullptr)
	Extend a new neurite from this soma. More...

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

Real3	OriginOf (const AgentUid &daughter_uid) const override

void	UpdateDependentPhysicalVariables () override

void	UpdateRelative (const NeuronOrNeurite &old_rel, const NeuronOrNeurite &new_rel) override

const std::vector< AgentPointer< NeuriteElement > > &	GetDaughters () const

void	PrintSWC (std::ostream &out) const
	Exports the soma and the attached neurite elements to the SWC file format. More...

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

	Cell (real_t diameter)

	Cell (const Real3 &position)

	~Cell () override=default

Shape	GetShape () const override

virtual Cell *	Divide ()
	Divide this cell. More...

virtual Cell *	Divide (real_t volume_ratio)
	Divide this cell. More...

virtual Cell *	Divide (const Real3 &axis)
	Divide this cell. More...

virtual Cell *	Divide (real_t volume_ratio, const Real3 &axis)
	Divide this cell. More...

virtual Cell *	Divide (real_t volume_ratio, real_t phi, real_t theta)
	Divide this cell. More...

real_t	GetAdherence () const

real_t	GetDiameter () const override

real_t	GetMass () const

real_t	GetDensity () const

const Real3 &	GetPosition () const override

const Real3 &	GetTractorForce () const

real_t	GetVolume () const

void	SetAdherence (real_t adherence)

void	SetDiameter (real_t diameter) override

void	SetVolume (real_t volume)

void	SetMass (real_t mass)

void	SetDensity (real_t density)

void	SetPosition (const Real3 &position) override

void	SetTractorForce (const Real3 &tractor_force)

void	ChangeVolume (real_t speed)

void	UpdateDiameter ()

void	UpdateVolume ()

void	UpdatePosition (const Real3 &delta)

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

void	ApplyDisplacement (const Real3 &displacement) override

void	MovePointMass (const Real3 &normalized_dir, real_t speed)

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

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

virtual void	RunDiscretization ()

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

virtual StructureIdentifierSWC	GetIdentifierSWC () const
	Returns the SWC classification of the object. More...

bool	IsNeuronSoma () const

bool	IsNeuriteElement () const

Protected Attributes
std::vector< AgentPointer< NeuriteElement > >	daughters_

std::unordered_map< AgentUid, Real3 >	daughters_coord_

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...

Private Member Functions
	BDM_AGENT_HEADER (NeuronSoma, Cell, 1)

Additional Inherited Members
Static Public Attributes inherited from bdm::Cell
static const Real3	kXAxis = {1.0, 0.0, 0.0}
	First axis of the local coordinate system. More...

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

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

Protected Member Functions inherited from bdm::Cell
Real3	TransformCoordinatesGlobalToPolar (const Real3 &coord) const

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

Detailed Description

Definition at line 30 of file neuron_soma.h.

Constructor & Destructor Documentation

◆ NeuronSoma() [1/3]

bdm::neuroscience::NeuronSoma::NeuronSoma ( )

default

◆ ~NeuronSoma()

bdm::neuroscience::NeuronSoma::~NeuronSoma ( )

overridedefault

◆ NeuronSoma() [2/3]

bdm::neuroscience::NeuronSoma::NeuronSoma ( const Real3 & position )

explicit

Definition at line 33 of file neuron_soma.cc.

◆ NeuronSoma() [3/3]

bdm::neuroscience::NeuronSoma::NeuronSoma ( const NeuronSoma & other )

inline

Definition at line 39 of file neuron_soma.h.

Member Function Documentation

◆ BDM_AGENT_HEADER()

bdm::neuroscience::NeuronSoma::BDM_AGENT_HEADER	(	NeuronSoma	,
		Cell	,
		1
	)

private

◆ CriticalRegion()

void bdm::neuroscience::NeuronSoma::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 69 of file neuron_soma.cc.

◆ ExtendNewNeurite() [1/2]

NeuriteElement * bdm::neuroscience::NeuronSoma::ExtendNewNeurite	(	const Real3 &	direction,
		NeuriteElement *	prototype = `nullptr`
	)

Extend a new neurite from this soma.

Uses default diameter for new neurite

See also: NewNeuriteExtensionEvent

Definition at line 77 of file neuron_soma.cc.

◆ ExtendNewNeurite() [2/2]

NeuriteElement * bdm::neuroscience::NeuronSoma::ExtendNewNeurite	(	real_t	diameter,
		real_t	phi,
		real_t	theta,
		NeuriteElement *	prototype = `nullptr`
	)

Extend a new neurite from this soma.

See also: NewNeuriteExtensionEvent

Definition at line 86 of file neuron_soma.cc.

◆ GetDaughters()

const std::vector< AgentPointer< NeuriteElement > > & bdm::neuroscience::NeuronSoma::GetDaughters ( ) const

Definition at line 136 of file neuron_soma.cc.

◆ GetLock()

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

inlineoverridevirtual

Implements bdm::neuroscience::NeuronOrNeurite.

Definition at line 62 of file neuron_soma.h.

◆ GetUid()

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

inlineoverridevirtual

Implements bdm::neuroscience::NeuronOrNeurite.

Definition at line 60 of file neuron_soma.h.

◆ Initialize()

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

overridevirtual

This method is used to initialise the values of daughter 2 for a cell division event.

Please note that this implementation does not allow division of neuron somas with already attached neurite elements.

See also: CellDivisionEvent

Reimplemented from bdm::Cell.

Definition at line 35 of file neuron_soma.cc.

◆ OriginOf()

Real3 bdm::neuroscience::NeuronSoma::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 105 of file neuron_soma.cc.

◆ PrintSWC()

void bdm::neuroscience::NeuronSoma::PrintSWC ( std::ostream & out ) const

Exports the soma and the attached neurite elements to the SWC file format.

Exports neuron as an SWC file following the conventions of neuromorpho.org. Unfortunately, the file format is not defined without ambiguities in the scientific community. The export follows the following convention: for each element, we export a line containing the information <element id> <type id> <pos x> <pos y> <pos z> <radius> <prev element id>. The <prev element id> resembles the connectivity of the neuron.

Usage:

std::ofstream myfile;
myfile.open(simulation.GetOutputDir() + "/neuron.swc");
soma->PrintSWC(myfile);

See also: pyramidal_cell.h example. Exports can be visualized with various tools, for instance https://neuroinformatics.nl/HBP/morphology-viewer/#, although we recommend the built-in ParaView visualization for this case. SWC files can be used to extract meaningful descriptive features of the morphology with third party software packages.

Definition at line 147 of file neuron_soma.cc.

◆ RemoveDaughter()

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

overridevirtual

Implements bdm::neuroscience::NeuronOrNeurite.

Definition at line 98 of file neuron_soma.cc.

◆ Update()

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

overridevirtual

This method is used to update attributes after a cell division. or new neurite branching event.

Performs the transition mother to daughter 1

See also: Event, CellDivisionEvent

Reimplemented from bdm::Agent.

Definition at line 49 of file neuron_soma.cc.

◆ UpdateDependentPhysicalVariables()

void bdm::neuroscience::NeuronSoma::UpdateDependentPhysicalVariables ( )

overridevirtual

Implements bdm::neuroscience::NeuronOrNeurite.

Definition at line 119 of file neuron_soma.cc.

◆ UpdateRelative()

void bdm::neuroscience::NeuronSoma::UpdateRelative	(	const NeuronOrNeurite &	old_rel,
		const NeuronOrNeurite &	new_rel
	)

overridevirtual

Implements bdm::neuroscience::NeuronOrNeurite.

Definition at line 121 of file neuron_soma.cc.

Member Data Documentation

◆ daughters_

std::vector<AgentPointer<NeuriteElement> > bdm::neuroscience::NeuronSoma::daughters_

protected

Definition at line 123 of file neuron_soma.h.

◆ daughters_coord_

std::unordered_map<AgentUid, Real3> bdm::neuroscience::NeuronSoma::daughters_coord_

protected

Daughter attachment points in local coordinates Key: neurite segment uid Value: position

Definition at line 128 of file neuron_soma.h.

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

neuroscience/neuron_soma.h
neuroscience/neuron_soma.cc

Public Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ NeuronSoma() [1/3]

◆ ~NeuronSoma()

◆ NeuronSoma() [2/3]

◆ NeuronSoma() [3/3]

Member Function Documentation

◆ BDM_AGENT_HEADER()

◆ CriticalRegion()

◆ ExtendNewNeurite() [1/2]

◆ ExtendNewNeurite() [2/2]

◆ GetDaughters()

◆ GetLock()

◆ GetUid()

◆ Initialize()

◆ OriginOf()

◆ PrintSWC()

◆ RemoveDaughter()

◆ Update()

◆ UpdateDependentPhysicalVariables()

◆ UpdateRelative()

Member Data Documentation

◆ daughters_

◆ daughters_coord_