{"action":"created","comment":{"url":"https://api.github.com/repos/nest/nest-simulator/pulls/comments/77787399","id":77787399,"diff_hunk":"@@ -0,0 +1,423 @@\n+/*\n+ *  gif_psc_exp.h\n+ *\n+ *  This file is part of NEST.\n+ *\n+ *  Copyright (C) 2004 The NEST Initiative\n+ *\n+ *  NEST is free software: you can redistribute it and/or modify\n+ *  it under the terms of the GNU General Public License as published by\n+ *  the Free Software Foundation, either version 2 of the License, or\n+ *  (at your option) any later version.\n+ *\n+ *  NEST is distributed in the hope that it will be useful,\n+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n+ *  GNU General Public License for more details.\n+ *\n+ *  You should have received a copy of the GNU General Public License\n+ *  along with NEST.  If not, see <http://www.gnu.org/licenses/>.\n+ *\n+ */\n+\n+#ifndef GIF_PSC_EXP_H\n+#define GIF_PSC_EXP_H\n+\n+// Includes from nestkernel:\n+#include \"event.h\"\n+#include \"archiving_node.h\"\n+#include \"ring_buffer.h\"\n+#include \"connection.h\"\n+#include \"universal_data_logger.h\"\n+\n+#include \"nest.h\"\n+\n+/* BeginDocumentation\n+  Name: gif_psc_exp - Current based generalized integrate-and-fire neuron\n+  model according to Mensi et al. (2012) and Pozzorini et al. (2015).\n+\n+  Description:\n+\n+  gif_psc_exp is the generalized integrate-and-fire neuron according to\n+  Mensi et al. (2012) and Pozzorini et al. (2015), with exponential shaped\n+  postsynaptic currents.\n+\n+  This model features both an adaptation current and a dynamic threshold for\n+  spike-frequency adaptation. The membrane potential (V) is described by the\n+  differential equation:\n+\n+  C*dV(t)/dt = -g_L*(V(t)-E_L) - eta_1(t) - eta_2(t) - ... - eta_n(t) + I(t)\n+\n+  where each eta_i is a spike-triggered current (stc), and the neuron model can\n+  have arbitrary number of them.\n+  Dynamic of each eta_i is described by:\n+\n+  tau_eta_i*d{eta_i}/dt = -eta_i\n+\n+  and in case of spike emission, its value increased by a constant (which can be\n+  positive or negative):\n+\n+  eta_i = eta_i + q_eta_i  (in case of spike emission).\n+\n+  Neuron produces spikes STOCHASTICALLY according to a point process with the\n+  firing intensity:\n+\n+  lambda(t) = lambda_0 * exp[(V(t)-V_T(t)/Delta_V)]\n+\n+  where V_T(t) is a time-dependent firing threshold:\n+\n+  V_T(t) = V_T_star + gamma_1(t) + gamma_2(t) + ... + gamma_m(t)\n+\n+  where gamma_i is a kernel of spike-frequency adaptation (sfa), and the neuron\n+  model can have arbitrary number of them.\n+  Dynamic of each gamma_i is described by:\n+\n+  tau_gamma_i*d{gamma_i}/dt = -gamma_i\n+\n+  and in case of spike emission, its value increased by a constant (which can be\n+  positive or negative):\n+\n+  gamma_i = gamma_i + q_gamma_i  (in case of spike emission).\n+\n+  Note that in the current implementation of the model (as described in [1] and\n+  [2]) the values of eta_i and gamma_i are affected immediately after spike\n+  emission. However, GIF toolbox (http://wiki.epfl.ch/giftoolbox) which fits\n+  the model using experimental data, requires a different set of eta_i and\n+  gamma_i. It applies the jump of eta_i and gamma_i after the refractory period.\n+  One can easily convert between q_eta/gamma of these two approaches:\n+  q_eta_giftoolbox = q_eta_NEST * (1 - exp( -tau_ref / tau_eta ))\n+  The same formula applies for q_gamma.\n+\n+  The shape of post synaptic current is exponential.\n+\n+  Parameters:\n+  The following parameters can be set in the status dictionary.\n+\n+  Membrane Parameters:\n+    C_m        double - Capacity of the membrane in pF\n+    t_ref      double - Duration of refractory period in ms.\n+    V_reset    double - Reset value after a spike in mV.\n+    E_L        double - Leak reversal potential in mV.\n+    g_L        double - Leak conductance in nS.\n+    I_e        double - Constant external input current in pA.\n+\n+  Spike adaptation and firing intensity parameters:\n+    q_stc      vector of double - Values added to spike-triggered currents (stc)\n+                                  after each spike emission in nA.\n+    tau_stc    vector of double - Time constants of stc variables in ms.\n+    q_sfa      vector of double - Values added to spike-frequency adaptation\n+                                  (sfa) after each spike emission in mV.\n+    tau_sfa    vector of double - Time constants of sfa variables in ms.\n+    Delta_V    double - Stochasticity level in mV.\n+    lambda_0   double - Stochastic intensity at firing threshold V_T in 1/s.\n+    V_T_star   double - Minimum threshold in mV\n+\n+  Synaptic parameters\n+    tau_syn_ex double - Time constant of the excitatory synaptic current in ms.\n+    tau_syn_in double - Time constant of the inhibitory synaptic current in ms.\n+\n+  References:\n+\n+  [1] Mensi S, Naud R, Pozzorini C, Avermann M, Petersen CC, Gerstner W (2012)\n+  Parameter extraction and classification of three cortical neuron types\n+  reveals two distinct adaptation mechanisms. J. Neurophysiol., 107(6),\n+  1756-1775.\n+\n+  [2] Pozzorini C, Mensi S, Hagens O, Naud R, Koch C, Gerstner W (2015)\n+  Automated High-Throughput Characterization of Single Neurons by Means of\n+  Simplified Spiking Models. PLoS Comput. Biol., 11(6), e1004275.\n+\n+  Sends: SpikeEvent\n+\n+  Receives: SpikeEvent, CurrentEvent, DataLoggingRequest\n+\n+  Author: March 2016, Setareh\n+  SeeAlso: pp_psc_delta, gif_psc_exp_multisynapse, gif_cond_exp,\n+  gif_cond_exp_multisynapse\n+\n+*/\n+\n+namespace nest\n+{\n+\n+class gif_psc_exp : public Archiving_Node\n+{\n+\n+public:\n+  gif_psc_exp();\n+  gif_psc_exp( const gif_psc_exp& );\n+\n+  /**\n+   * Import sets of overloaded virtual functions.\n+   * @see Technical Issues / Virtual Functions: Overriding, Overloading, and\n+   * Hiding\n+   */\n+  using Node::handle;\n+  using Node::handles_test_event;\n+\n+  port send_test_event( Node&, rport, synindex, bool );\n+\n+  void handle( SpikeEvent& );\n+  void handle( CurrentEvent& );\n+  void handle( DataLoggingRequest& );\n+\n+  port handles_test_event( SpikeEvent&, rport );\n+  port handles_test_event( CurrentEvent&, rport );\n+  port handles_test_event( DataLoggingRequest&, rport );\n+\n+  void get_status( DictionaryDatum& ) const;\n+  void set_status( const DictionaryDatum& );\n+\n+private:\n+  void init_state_( const Node& proto );\n+  void init_buffers_();\n+  void calibrate();\n+\n+  void update( Time const&, const long_t, const long_t );\n+\n+  // The next two classes need to be friends to access the State_ class/member\n+  friend class RecordablesMap< gif_psc_exp >;\n+  friend class UniversalDataLogger< gif_psc_exp >;\n+\n+  // ----------------------------------------------------------------\n+\n+  /**\n+   * Independent parameters of the model.\n+   */\n+  struct Parameters_\n+  {\n+    double_t g_L_;\n+    double_t E_L_;\n+    double_t V_reset_;\n+    double_t Delta_V_;\n+    double_t V_T_star_;\n+    double_t lambda_0_; /** 1/ms */\n+\n+    /** Refractory period in ms. */\n+    double_t t_ref_;\n+\n+    /** Membrane capacitance in pF. */\n+    double_t c_m_;\n+\n+    /** We use stc and sfa, respectively instead of eta and gamma\n+    (mentioned in the references). */\n+\n+    /** List of spike triggered current time constant in ms. */\n+    std::vector< double_t > tau_stc_;\n+\n+    /** List of spike triggered current jumps in nA. */\n+    std::vector< double_t > q_stc_;\n+\n+    /** List of adaptive threshold time constant in ms. */\n+    std::vector< double_t > tau_sfa_;\n+\n+    /** List of adaptive threshold jumps in mV. */\n+    std::vector< double_t > q_sfa_;\n+\n+    /** Time constant of excitatory synaptic current in ms. */\n+    double_t tau_ex_;\n+\n+    /** Time constant of inhibitory synaptic current in ms. */\n+    double_t tau_in_;\n+\n+    /** External DC current. */\n+    double_t I_e_;\n+\n+    Parameters_(); //!< Sets default parameter values\n+\n+    void get( DictionaryDatum& ) const; //!< Store current values in dictionary\n+    void set( const DictionaryDatum& ); //!< Set values from dictionary\n+  };\n+\n+  // ----------------------------------------------------------------\n+\n+  /**\n+   * State variables of the model.\n+   */\n+  struct State_\n+  {\n+    double_t y0_; //!< This is piecewise constant external current\n+    double_t\n+      y3_; //!< This is the membrane potential RELATIVE TO RESTING POTENTIAL.\n+    double_t sfa_; //!< This is the change of the 'threshold' due to adaptation.\n+    double_t stc_; //!< Spike triggered current.\n+\n+    std::vector< double_t > sfa_elems_; //!< Vector of adaptation parameters.\n+    std::vector< double_t >\n+      stc_elems_; //!< Vector of spike triggered parameters.\n+\n+    double_t i_syn_ex_; //!< postsynaptic current for exc.\n+    double_t i_syn_in_; //!< postsynaptic current for inh.\n+\n+    int_t r_ref_; //!< absolute refractory counter (no membrane potential\n+    // propagation)\n+\n+    State_(); //!< Default initialization\n+\n+    void get( DictionaryDatum&, const Parameters_& ) const;\n+    void set( const DictionaryDatum&, const Parameters_& );\n+  };\n+\n+  // ----------------------------------------------------------------\n+\n+  /**\n+   * Buffers of the model.\n+   */\n+  struct Buffers_\n+  {\n+    Buffers_( gif_psc_exp& );\n+    Buffers_( const Buffers_&, gif_psc_exp& );\n+\n+    /** buffers and sums up incoming spikes/currents */\n+    RingBuffer spikes_ex_;\n+    RingBuffer spikes_in_;\n+    RingBuffer currents_;\n+\n+    //! Logger for all analog data\n+    UniversalDataLogger< gif_psc_exp > logger_;\n+  };\n+\n+  // ----------------------------------------------------------------\n+\n+  /**\n+   * Internal variables of the model.\n+   */\n+  struct Variables_\n+  {\n+    double_t P30_;\n+    double_t P33_;\n+    double_t P31_;\n+    double_t P11ex_;\n+    double_t P11in_;\n+    double_t P21ex_;\n+    double_t P21in_;","path":"models/gif_psc_exp.h","position":293,"original_position":293,"commit_id":"ffcb78cc3141d26150bf5db54c0dbb5534246e6c","original_commit_id":"ffcb78cc3141d26150bf5db54c0dbb5534246e6c","user":{"login":"Silmathoron","id":8523051,"avatar_url":"https://avatars.githubusercontent.com/u/8523051?v=3","gravatar_id":"","url":"https://api.github.com/users/Silmathoron","html_url":"https://github.com/Silmathoron","followers_url":"https://api.github.com/users/Silmathoron/followers","following_url":"https://api.github.com/users/Silmathoron/following{/other_user}","gists_url":"https://api.github.com/users/Silmathoron/gists{/gist_id}","starred_url":"https://api.github.com/users/Silmathoron/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Silmathoron/subscriptions","organizations_url":"https://api.github.com/users/Silmathoron/orgs","repos_url":"https://api.github.com/users/Silmathoron/repos","events_url":"https://api.github.com/users/Silmathoron/events{/privacy}","received_events_url":"https://api.github.com/users/Silmathoron/received_events","type":"User","site_admin":false},"body":"It would be nice to have the propagators documented","created_at":"2016-09-07T09:22:07Z","updated_at":"2016-09-07T09:22:07Z","html_url":"https://github.com/nest/nest-simulator/pull/261#discussion_r77787399","pull_request_url":"https://api.github.com/repos/nest/nest-simulator/pulls/261","_links":{"self":{"href":"https://api.github.com/repos/nest/nest-simulator/pulls/comments/77787399"},"html":{"href":"https://github.com/nest/nest-simulator/pull/261#discussion_r77787399"},"pull_request":{"href":"https://api.github.com/repos/nest/nest-simulator/pulls/261"}}},"pull_request":{"url":"https://api.github.com/repos/nest/nest-simulator/pulls/261","id":61817042,"html_url":"https://github.com/nest/nest-simulator/pull/261","diff_url":"https://github.com/nest/nest-simulator/pull/261.diff","patch_url":"https://github.com/nest/nest-simulator/pull/261.patch","issue_url":"https://api.github.com/repos/nest/nest-simulator/issues/261","number":261,"state":"open","locked":false,"title":"Gif models","user":{"login":"hesam-setareh","id":14923377,"avatar_url":"https://avatars.githubusercontent.com/u/14923377?v=3","gravatar_id":"","url":"https://api.github.com/users/hesam-setareh","html_url":"https://github.com/hesam-setareh","followers_url":"https://api.github.com/users/hesam-setareh/followers","following_url":"https://api.github.com/users/hesam-setareh/following{/other_user}","gists_url":"https://api.github.com/users/hesam-setareh/gists{/gist_id}","starred_url":"https://api.github.com/users/hesam-setareh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hesam-setareh/subscriptions","organizations_url":"https://api.github.com/users/hesam-setareh/orgs","repos_url":"https://api.github.com/users/hesam-setareh/repos","events_url":"https://api.github.com/users/hesam-setareh/events{/privacy}","received_events_url":"https://api.github.com/users/hesam-setareh/received_events","type":"User","site_admin":false},"body":"Implementing generalized integrate-and-fire (GIF) neuron model for nest in four versions:\r\ngif_psc_exp\r\ngif_psc_exp_multisynapse\r\ngif_cond_exp\r\ngif_cond_exp_multisynapse\r\n\r\nAnd also a unittest for each version.","created_at":"2016-03-05T16:48:06Z","updated_at":"2016-09-07T09:22:07Z","closed_at":null,"merged_at":null,"merge_commit_sha":"b625ab87792a83300304a780cc22da136d1df671","assignee":{"login":"heplesser","id":1059644,"avatar_url":"https://avatars.githubusercontent.com/u/1059644?v=3","gravatar_id":"","url":"https://api.github.com/users/heplesser","html_url":"https://github.com/heplesser","followers_url":"https://api.github.com/users/heplesser/followers","following_url":"https://api.github.com/users/heplesser/following{/other_user}","gists_url":"https://api.github.com/users/heplesser/gists{/gist_id}","starred_url":"https://api.github.com/users/heplesser/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/heplesser/subscriptions","organizations_url":"https://api.github.com/users/heplesser/orgs","repos_url":"https://api.github.com/users/heplesser/repos","events_url":"https://api.github.com/users/heplesser/events{/privacy}","received_events_url":"https://api.github.com/users/heplesser/received_events","type":"User","site_admin":false},"assignees":[{"login":"heplesser","id":1059644,"avatar_url":"https://avatars.githubusercontent.com/u/1059644?v=3","gravatar_id":"","url":"https://api.github.com/users/heplesser","html_url":"https://github.com/heplesser","followers_url":"https://api.github.com/users/heplesser/followers","following_url":"https://api.github.com/users/heplesser/following{/other_user}","gists_url":"https://api.github.com/users/heplesser/gists{/gist_id}","starred_url":"https://api.github.com/users/heplesser/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/heplesser/subscriptions","organizations_url":"https://api.github.com/users/heplesser/orgs","repos_url":"https://api.github.com/users/heplesser/repos","events_url":"https://api.github.com/users/heplesser/events{/privacy}","received_events_url":"https://api.github.com/users/heplesser/received_events","type":"User","site_admin":false}],"milestone":null,"commits_url":"https://api.github.com/repos/nest/nest-simulator/pulls/261/commits","review_comments_url":"https://api.github.com/repos/nest/nest-simulator/pulls/261/comments","review_comment_url":"https://api.github.com/repos/nest/nest-simulator/pulls/comments{/number}","comments_url":"https://api.github.com/repos/nest/nest-simulator/issues/261/comments","statuses_url":"https://api.github.com/repos/nest/nest-simulator/statuses/ffcb78cc3141d26150bf5db54c0dbb5534246e6c","head":{"label":"hesam-setareh:master","ref":"master","sha":"ffcb78cc3141d26150bf5db54c0dbb5534246e6c","user":{"login":"hesam-setareh","id":14923377,"avatar_url":"https://avatars.githubusercontent.com/u/14923377?v=3","gravatar_id":"","url":"https://api.github.com/users/hesam-setareh","html_url":"https://github.com/hesam-setareh","followers_url":"https://api.github.com/users/hesam-setareh/followers","following_url":"https://api.github.com/users/hesam-setareh/following{/other_user}","gists_url":"https://api.github.com/users/hesam-setareh/gists{/gist_id}","starred_url":"https://api.github.com/users/hesam-setareh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hesam-setareh/subscriptions","organizations_url":"https://api.github.com/users/hesam-setareh/orgs","repos_url":"https://api.github.com/users/hesam-setareh/repos","events_url":"https://api.github.com/users/hesam-setareh/events{/privacy}","received_events_url":"https://api.github.com/users/hesam-setareh/received_events","type":"User","site_admin":false},"repo":{"id":53140643,"name":"nest-simulator","full_name":"hesam-setareh/nest-simulator","owner":{"login":"hesam-setareh","id":14923377,"avatar_url":"https://avatars.githubusercontent.com/u/14923377?v=3","gravatar_id":"","url":"https://api.github.com/users/hesam-setareh","html_url":"https://github.com/hesam-setareh","followers_url":"https://api.github.com/users/hesam-setareh/followers","following_url":"https://api.github.com/users/hesam-setareh/following{/other_user}","gists_url":"https://api.github.com/users/hesam-setareh/gists{/gist_id}","starred_url":"https://api.github.com/users/hesam-setareh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hesam-setareh/subscriptions","organizations_url":"https://api.github.com/users/hesam-setareh/orgs","repos_url":"https://api.github.com/users/hesam-setareh/repos","events_url":"https://api.github.com/users/hesam-setareh/events{/privacy}","received_events_url":"https://api.github.com/users/hesam-setareh/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/hesam-setareh/nest-simulator","description":"The 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