neuron_soma.h

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// -----------------------------------------------------------------------------
//
// Copyright (C) 2021 CERN & University of Surrey for the benefit of the
// BioDynaMo collaboration. All Rights Reserved.
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
//
// See the LICENSE file distributed with this work for details.
// See the NOTICE file distributed with this work for additional information
// regarding copyright ownership.
//
// -----------------------------------------------------------------------------
 
#ifndef NEUROSCIENCE_NEURON_SOMA_H_
#define NEUROSCIENCE_NEURON_SOMA_H_
 
#include <unordered_map>
#include <vector>
 
#include "core/agent/cell.h"
#include "core/container/math_array.h"
#include "neuroscience/neuron_or_neurite.h"
 
namespace bdm {
namespace neuroscience {
 
class NeuriteElement;
 
class NeuronSoma : public Cell, public NeuronOrNeurite {
  BDM_AGENT_HEADER(NeuronSoma, Cell, 1);
 
 public:
  NeuronSoma();
  ~NeuronSoma() override;
 
  explicit NeuronSoma(const Real3& position);
 
  NeuronSoma(const NeuronSoma& other)
      : Base(other),
        daughters_(other.daughters_),
        daughters_coord_(other.daughters_coord_) {}
 
  void Initialize(const NewAgentEvent& event) override;
 
  void Update(const NewAgentEvent& event) override;
 
  const AgentUid& GetUid() const override { return Base::GetUid(); }
 
  Spinlock* GetLock() override { return Base::GetLock(); }
 
  void CriticalRegion(std::vector<AgentPointer<>>* aptrs) override;
 
  // ***************************************************************************
  //      METHODS FOR NEURON TREE STRUCTURE *
  // ***************************************************************************
 
  NeuriteElement* ExtendNewNeurite(const Real3& direction,
                                   NeuriteElement* prototype = nullptr);
 
  NeuriteElement* ExtendNewNeurite(real_t diameter, real_t phi, real_t theta,
                                   NeuriteElement* prototype = nullptr);
 
  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;
 
 protected:
  std::vector<AgentPointer<NeuriteElement>> daughters_;
 
  std::unordered_map<AgentUid, Real3> daughters_coord_;
};
 
}  // namespace neuroscience
}  // namespace bdm
 
#endif  // NEUROSCIENCE_NEURON_SOMA_H_