Compartment Mechanism-Vectorization [WIP]

doc/nestml_language/neurons_in_nestml.rst

@@ -29,7 +29,7 @@ A neuron model written in NESTML can be configured to receive two distinct types
 
    input:
        AMPA_spikes <- spike
-       I_stim pA <- continuous
+       I_stim <- continuous
 
 The general syntax is:
 
@@ -108,7 +108,7 @@ The current port symbol (here, `I_stim`) is available as a variable and can be u
        V_m' = -V_m/tau_m + ... + I_stim
 
    input:
-       I_stim pA <- continuous
+       I_stim <- continuous
 
 
 Integrating spiking input

doc/tutorials/spike_frequency_adaptation/models/iaf_psc_alpha.nestml

@@ -87,7 +87,7 @@ neuron iaf_psc_alpha:
     input:
         exc_spikes <- excitatory spike
         inh_spikes <- inhibitory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

doc/tutorials/spike_frequency_adaptation/models/iaf_psc_alpha_adapt_curr.nestml

@@ -94,7 +94,7 @@ neuron iaf_psc_alpha_adapt_curr:
     input:
         exc_spikes <- excitatory spike
         inh_spikes <- inhibitory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

doc/tutorials/spike_frequency_adaptation/models/iaf_psc_alpha_adapt_thresh.nestml

@@ -94,7 +94,7 @@ neuron iaf_psc_alpha_adapt_thresh:
     input:
         exc_spikes <- excitatory spike
         inh_spikes <- inhibitory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

doc/tutorials/spike_frequency_adaptation/models/iaf_psc_alpha_adapt_thresh_OU.nestml

@@ -101,7 +101,7 @@ neuron iaf_psc_alpha_adapt_thresh_OU:
     input:
         exc_spikes <- excitatory spike
         inh_spikes <- inhibitory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

extras/convert_cm_default_to_template.py

@@ -37,7 +37,7 @@ def get_replacement_patterns():
         # file names
         'cm_default'            : '{{neuronSpecificFileNamesCmSyns[\"main\"]}}',
         'cm_tree'               : '{{neuronSpecificFileNamesCmSyns[\"tree\"]}}',
-        'cm_compartmentcurrents': '{{neuronSpecificFileNamesCmSyns[\"compartmentcurrents\"]}}',
+        'cm_neuroncurrents': '{{neuronSpecificFileNamesCmSyns[\"neuroncurrents\"]}}',
         # class names
         'CompTree'              : 'CompTree{{cm_unique_suffix}}',
         'Compartment'           : 'Compartment{{cm_unique_suffix}}',

models/neurons/aeif_cond_alpha.nestml

@@ -98,7 +98,7 @@ neuron aeif_cond_alpha:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/aeif_cond_exp.nestml

@@ -93,7 +93,7 @@ neuron aeif_cond_exp:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/hh_cond_exp_destexhe.nestml

@@ -127,7 +127,7 @@ neuron hh_cond_exp_destexhe:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/hh_cond_exp_traub.nestml

@@ -117,7 +117,7 @@ neuron hh_cond_exp_traub:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/hh_moto_5ht.nestml

@@ -111,7 +111,7 @@ neuron hh_moto_5ht:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/hh_psc_alpha.nestml

@@ -109,7 +109,7 @@ neuron hh_psc_alpha:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/hill_tononi.nestml

@@ -186,7 +186,7 @@ neuron hill_tononi:
         NMDA <- spike
         GABA_A <- spike
         GABA_B <- spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/iaf_chxk_2008.nestml

@@ -81,7 +81,7 @@ neuron iaf_chxk_2008:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/iaf_cond_alpha.nestml

@@ -71,7 +71,7 @@ neuron iaf_cond_alpha:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/iaf_cond_beta.nestml

@@ -101,7 +101,7 @@ neuron iaf_cond_beta:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/iaf_cond_exp.nestml

@@ -61,7 +61,7 @@ neuron iaf_cond_exp:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/iaf_cond_exp_sfa_rr.nestml

@@ -84,7 +84,7 @@ neuron iaf_cond_exp_sfa_rr:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim  <- continuous
 
     output:
         spike

models/neurons/iaf_psc_alpha.nestml

@@ -87,7 +87,7 @@ neuron iaf_psc_alpha:
     input:
         exc_spikes <- excitatory spike
         inh_spikes <- inhibitory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/iaf_psc_delta.nestml

@@ -79,7 +79,7 @@ neuron iaf_psc_delta:
 
     input:
         spikes <- spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/iaf_psc_exp.nestml

@@ -66,7 +66,7 @@ neuron iaf_psc_exp:
     input:
         exc_spikes <- excitatory spike
         inh_spikes <- inhibitory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/iaf_psc_exp_dend.nestml

@@ -67,7 +67,7 @@ neuron iaf_psc_exp_dend:
     input:
         exc_spikes <- excitatory spike
         inh_spikes <- inhibitory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/iaf_psc_exp_htum.nestml

@@ -96,7 +96,7 @@ neuron iaf_psc_exp_htum:
     input:
         exc_spikes <- excitatory spike
         inh_spikes <- inhibitory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/izhikevich.nestml

@@ -58,7 +58,7 @@ neuron izhikevich:
 
     input:
         spikes <- spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/izhikevich_psc_alpha.nestml

@@ -76,7 +76,7 @@ neuron izhikevich_psc_alpha:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/mat2_psc_exp.nestml

@@ -83,7 +83,7 @@ neuron mat2_psc_exp:
     input:
         exc_spikes <- excitatory spike
         inh_spikes <- inhibitory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/terub_gpe.nestml

@@ -140,7 +140,7 @@ neuron terub_gpe:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/terub_stn.nestml

@@ -146,7 +146,7 @@ neuron terub_stn:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/traub_cond_multisyn.nestml

@@ -144,7 +144,7 @@ neuron traub_cond_multisyn:
         NMDA <- spike
         GABA_A <- spike
         GABA_B <- spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/traub_psc_alpha.nestml

@@ -86,7 +86,7 @@ neuron traub_psc_alpha:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/wb_cond_exp.nestml

@@ -80,7 +80,7 @@ neuron wb_cond_exp:
     input:
         inh_spikes <- inhibitory spike
         exc_spikes <- excitatory spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

models/neurons/wb_cond_multisyn.nestml

@@ -130,7 +130,7 @@ neuron wb_cond_multisyn:
         NMDA <- spike
         GABA_A <- spike
         GABA_B <- spike
-        I_stim pA <- continuous
+        I_stim <- continuous
 
     output:
         spike

pynestml/cocos/co_co_cm_continuous_input_model.py

@@ -0,0 +1,36 @@
+# -*- coding: utf-8 -*-
+#
+# co_co_cm_continuous_input_model.py
+#
+# This file is part of NEST.
+#
+# Copyright (C) 2004 The NEST Initiative
+#
+# NEST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#
+# NEST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with NEST.  If not, see <http://www.gnu.org/licenses/>.
+
+from pynestml.cocos.co_co import CoCo
+from pynestml.meta_model.ast_neuron import ASTNeuron
+from pynestml.utils.continuous_input_processing import ContinuousInputProcessing
+
+
+class CoCoCmContinuousInputModel(CoCo):
+    @classmethod
+    def check_co_co(cls, neuron: ASTNeuron):
+        """
+        Checks if this compartmental condition applies to the handed over neuron.
+        If yes, it checks the presence of expected functions and declarations.
+        :param neuron: a single neuron instance.
+        :type neuron: ast_neuron
+        """
+        return ContinuousInputProcessing.check_co_co(neuron)

pynestml/cocos/co_cos_manager.py

@@ -26,6 +26,7 @@
 from pynestml.cocos.co_co_inline_expression_not_assigned_to import CoCoInlineExpressionNotAssignedTo
 from pynestml.cocos.co_co_input_port_not_assigned_to import CoCoInputPortNotAssignedTo
 from pynestml.cocos.co_co_cm_channel_model import CoCoCmChannelModel
+from pynestml.cocos.co_co_cm_continuous_input_model import CoCoCmContinuousInputModel
 from pynestml.cocos.co_co_convolve_cond_correctly_built import CoCoConvolveCondCorrectlyBuilt
 from pynestml.cocos.co_co_correct_numerator_of_unit import CoCoCorrectNumeratorOfUnit
 from pynestml.cocos.co_co_correct_order_in_equation import CoCoCorrectOrderInEquation
@@ -148,6 +149,7 @@ def check_compartmental_model(cls, neuron: ASTNeuron) -> None:
         CoCoCmChannelModel.check_co_co(neuron)
         CoCoCmConcentrationModel.check_co_co(neuron)
         CoCoCmSynapseModel.check_co_co(neuron)
+        CoCoCmContinuousInputModel.check_co_co(neuron)
 
     @classmethod
     def check_inline_expressions_have_rhs(cls, neuron: ASTNeuron):