Improved getting of numerical initial values (#1272)

Author: clinssen

pynestml/codegeneration/nest_desktop_code_generator.py

@@ -69,6 +69,6 @@ def _get_neuron_model_namespace(self, neuron: ASTModel) -> Dict:
         namespace["nestml_version"] = pynestml.__version__
         namespace["neuronName"] = neuron.get_name()
         namespace["neuron"] = neuron
-        namespace["parameters"], namespace["state"] = PythonStandaloneTargetTools.get_neuron_parameters_and_state(neuron.file_path)
+        namespace["parameters"], namespace["state"] = PythonStandaloneTargetTools.get_neuron_numerical_initial_values(neuron.file_path)
 
         return namespace

pynestml/codegeneration/python_standalone_target_tools.py

@@ -19,6 +19,8 @@
 # You should have received a copy of the GNU General Public License
 # along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 
+from typing import Mapping, Tuple
+
 import importlib
 import multiprocessing
 import os
@@ -65,23 +67,28 @@ def _get_model_parameters_and_state(cls, nestml_file_name: str):
         parameters_list = [p for p in dir(neuron.Parameters_) if not "__" in p]
         parameters = {p: getattr(neuron, "get_" + p)() for p in parameters_list}
 
+        internals_list = [p for p in dir(neuron.Variables_) if not "__" in p]
+        internals = {p: getattr(neuron, "get_" + p)() for p in internals_list}
+
         if "ode_state_variable_name_to_index" in dir(neuron.State_):
             state_list = neuron.State_.ode_state_variable_name_to_index.keys()
         else:
             state_list = [p for p in dir(neuron.State_) if not "__" in p]
         state_vars = {p: getattr(neuron, "get_" + p)() for p in state_list}
 
-        return parameters, state_vars
+        return parameters, internals, state_vars
 
     @classmethod
-    def get_neuron_parameters_and_state(cls, nestml_file_name: str) -> tuple[dict, dict]:
+    def get_neuron_numerical_initial_values(cls, nestml_file_name: str) -> Tuple[Mapping[str, float], Mapping[str, float], Mapping[str, float]]:
         r"""
-        Get the parameters for the given neuron model. The code is generated for the model for Python standalone target
-        The parameters and state variables are then queried by creating the neuron in Python standalone simulator.
+        Get the numerical values of the parameters, internals, and state variables for the given neuron model.
+
+        Internally, code is generated for the model for the Python standalone target, and then the value is read off by instantiating the resulting code.
+
         :param nestml_file_name: File name of the neuron model
-        :return: A dictionary of parameters and state variables
+        :return: Dictionaries mapping parameters, internals and state variables to their numerical initial values
         """
-        parameters, state = cls._get_model_parameters_and_state(nestml_file_name)
+        parameters, internals, state = cls._get_model_parameters_and_state(nestml_file_name)
 
         if not parameters or not state:
             Logger.log_message(None, -1,

pynestml/codegeneration/resources_python_standalone/point_neuron/@NEURON_NAME@.py.jinja2

@@ -127,29 +127,30 @@ class Neuron_{{neuronName}}(Neuron):
     self.S_ = self.State_()
     self.V_ = self.Variables_()
     self.B_ = self.Buffers_()
+    self._timestep = timestep
 
-{%- if parameter_vars_with_iv|length > 0 %}
+{%  if parameter_vars_with_iv|length > 0 %}
     # initial values for parameters
-{%- filter indent(4) %}
-{%- for variable in parameter_vars_with_iv %}
-{%-   set variable_symbol = neuron.get_scope().resolve_to_symbol(variable.get_name(), SymbolKind.VARIABLE) %}
-{%-   include "directives_py/MemberInitialization.jinja2" %}
-{%- endfor %}
-{%- endfilter %}
+{%-     filter indent(4) %}
+{%-         for variable in parameter_vars_with_iv %}
+{%-             set variable_symbol = neuron.get_scope().resolve_to_symbol(variable.get_name(), SymbolKind.VARIABLE) %}
+{%-             include "directives_py/MemberInitialization.jinja2" %}
+{%-         endfor %}
+{%-     endfilter %}
 {%- endif %}
 
-{%- if neuron.get_state_symbols()|length > 0 %}
+    # initial values for internals
+    self.recompute_internal_variables(self._timestep)
+{%  if neuron.get_state_symbols()|length > 0 %}
     # initial values for state variables
-{%- filter indent(4) %}
-{%- for variable_symbol in neuron.get_state_symbols() %}
-{%-   set variable = utils.get_variable_by_name(astnode, variable_symbol.get_symbol_name()) %}
-{%-   include "directives_py/MemberInitialization.jinja2" %}
-{%- endfor %}
-{%- endfilter %}
+{%-     filter indent(4) %}
+{%-         for variable_symbol in neuron.get_state_symbols() %}
+{%-             set variable = utils.get_variable_by_name(astnode, variable_symbol.get_symbol_name()) %}
+{%-             include "directives_py/MemberInitialization.jinja2" %}
+{%-         endfor %}
+{%-     endfilter %}
 {%- endif %}
 
-    self._timestep = timestep
-    self.recompute_internal_variables(self._timestep)
 
   def get_model(self) -> str:
     return "{{neuronName}}"