Arbor cable cell exporter and backend

MANIFEST.in

@@ -1,6 +1,9 @@
 include versioneer.py
 include bluepyopt/_version.py
 include bluepyopt/ephys/templates/cell_template.jinja2
+include bluepyopt/ephys/templates/acc/_json_template.jinja2
+include bluepyopt/ephys/templates/acc/decor_acc_template.jinja2
+include bluepyopt/ephys/templates/acc/label_dict_acc_template.jinja2
 
 include.txt
 include AUTHORS.txt

bluepyopt/ephys/create_hoc.py

@@ -112,46 +112,37 @@ def _generate_parameters(parameters):
     return global_params, ordered_section_params, range_params, location_order
 
 
-def create_hoc(
+def _read_template(template_dir, template_filename):
+    """Read Jinja2 hoc template to render"""
+    if template_dir is None:
+        template_dir = os.path.abspath(
+            os.path.join(
+                os.path.dirname(__file__),
+                'templates'))
+
+    template_path = os.path.join(template_dir, template_filename)
+    with open(template_path) as template_file:
+        template = template_file.read()
+        template = jinja2.Template(template)
+    return template
+
+
+def _get_template_params(
         mechs,
         parameters,
-        morphology=None,
         ignored_globals=(),
-        replace_axon=None,
-        template_name='CCell',
-        template_filename='cell_template.jinja2',
-        disable_banner=None,
-        template_dir=None,
-        custom_jinja_params=None,):
-    '''return a string containing the hoc template
+        disable_banner=None):
+    '''return parameters to render Jinja2 templates with simulator descriptions
 
     Args:
         mechs (): All the mechs for the hoc template
         parameters (): All the parameters in the hoc template
-        morpholgy (str): Name of morphology
         ignored_globals (iterable str): HOC coded is added for each
         NrnGlobalParameter
         that exists, to test that it matches the values set in the parameters.
         This iterable contains parameter names that aren't checked
-        replace_axon (str): String replacement for the 'replace_axon' command.
-        Must include 'proc replace_axon(){ ... }
-        template (str): file name of the jinja2 template
-        template_dir (str): dir name of the jinja2 template
-        custom_jinja_params (dict): dict of additional jinja2 params in case
-        of a custom template
     '''
 
-    if template_dir is None:
-        template_dir = os.path.abspath(
-            os.path.join(
-                os.path.dirname(__file__),
-                'templates'))
-
-    template_path = os.path.join(template_dir, template_filename)
-    with open(template_path) as template_file:
-        template = template_file.read()
-        template = jinja2.Template(template)
-
     global_params, section_params, range_params, location_order = \
         _generate_parameters(parameters)
     channels = _generate_channels_by_location(mechs, location_order)
@@ -169,19 +160,57 @@ def create_hoc(
     else:
         banner = None
 
+    return dict(global_params=global_params,
+                ignored_global_params=ignored_global_params,
+                section_params=section_params,
+                range_params=range_params,
+                location_order=location_order,
+                channels=channels,
+                banner=banner)
+
+
+def create_hoc(mechs,
+               parameters,
+               morphology=None,
+               ignored_globals=(),
+               replace_axon=None,
+               template_name='CCell',
+               template_filename='cell_template.jinja2',
+               disable_banner=None,
+               template_dir=None,
+               custom_jinja_params=None):
+    '''return a string containing the hoc template
+
+    Args:
+        mechs (): All the mechs for the hoc template
+        parameters (): All the parameters in the hoc template
+        morpholgy (str): Name of morphology
+        ignored_globals (iterable str): HOC coded is added for each
+        NrnGlobalParameter
+        that exists, to test that it matches the values set in the parameters.
+        This iterable contains parameter names that aren't checked
+        replace_axon (str): String replacement for the 'replace_axon' command.
+        Must include 'proc replace_axon(){ ... }
+        template_filename (str): file name of the jinja2 template
+        template_dir (str): dir name of the jinja2 template
+        custom_jinja_params (dict): dict of additional jinja2 params in case
+        of a custom template
+    '''
+
+    template = _read_template(template_dir, template_filename)
+
+    template_params = _get_template_params(mechs,
+                                           parameters,
+                                           ignored_globals,
+                                           disable_banner)
     re_init_rng = _generate_reinitrng(mechs)
 
     if custom_jinja_params is None:
         custom_jinja_params = {}
 
     return template.render(template_name=template_name,
-                           banner=banner,
-                           channels=channels,
                            morphology=morphology,
-                           section_params=section_params,
-                           range_params=range_params,
-                           global_params=global_params,
-                           re_init_rng=re_init_rng,
                            replace_axon=replace_axon,
-                           ignored_global_params=ignored_global_params,
+                           re_init_rng=re_init_rng,
+                           **template_params,
                            **custom_jinja_params)

bluepyopt/ephys/models.py

@@ -31,7 +31,7 @@
 import collections
 import string
 
-from . import create_hoc
+from . import create_hoc, create_acc
 from . import morphologies
 
 import logging
@@ -223,7 +223,7 @@ def create_empty_cell(
 
         return template_function()
 
-    def instantiate(self, sim=None):
+    def instantiate_morphology(self, sim=None):
         """Instantiate model in simulator"""
 
         # TODO replace this with the real template name
@@ -240,6 +240,11 @@ def instantiate(self, sim=None):
 
         self.morphology.instantiate(sim=sim, icell=self.icell)
 
+    def instantiate(self, sim=None):
+        """Instantiate model in simulator"""
+
+        self.instantiate_morphology(sim)
+
         if self.mechanisms is not None:
             for mechanism in self.mechanisms:
                 mechanism.instantiate(sim=sim, icell=self.icell)
@@ -280,11 +285,12 @@ def check_nonfrozen_params(self, param_names):  # pylint: disable=W0613
                     'set before simulation' %
                     param_name)
 
-    def create_hoc(self, param_values,
-                   ignored_globals=(), template='cell_template.jinja2',
-                   disable_banner=False,
-                   template_dir=None):
-        """Create hoc code for this model"""
+    def _create_sim_desc(self, param_values,
+                         ignored_globals=(), template=None,
+                         disable_banner=False,
+                         template_dir=None,
+                         sim_desc_creator=None):
+        """Create simulator description for this model"""
 
         to_unfreeze = []
         for param in self.params.values():
@@ -294,41 +300,89 @@ def create_hoc(self, param_values,
 
         template_name = self.name
         morphology = os.path.basename(self.morphology.morphology_path)
-        if self.morphology.do_replace_axon:
-            replace_axon = self.morphology.replace_axon_hoc
+
+        if sim_desc_creator is create_hoc.create_hoc:
+            if self.morphology.do_replace_axon:
+                replace_axon = self.morphology.replace_axon_hoc
+            else:
+                replace_axon = None
+
+            if (
+                self.morphology.morph_modifiers is not None
+                and self.morphology.morph_modifiers_hoc is None
+            ):
+                logger.warning('You have provided custom morphology'
+                               ' modifiers, but no corresponding hoc files.')
+            elif (
+                self.morphology.morph_modifiers is not None
+                and self.morphology.morph_modifiers_hoc is not None
+            ):
+                if replace_axon is None:
+                    replace_axon = ''
+                for morph_modifier_hoc in self.morphology.morph_modifiers_hoc:
+                    replace_axon += '\n'
+                    replace_axon += morph_modifier_hoc
+        elif sim_desc_creator is create_acc.create_acc:
+            if self.morphology.do_replace_axon:
+                if self.icell is None:
+                    raise ValueError('Need to instantiate_morphology'
+                                     ' on CellModel before creating'
+                                     ' JSON/ACC-description with'
+                                     ' axon replacement.')
+                replace_axon = [dict(nseg=section.nseg,
+                                     length=section.L,
+                                     radius=0.5 * section.diam,
+                                     tag=morphologies._arb_tags['axon'])
+                                for section in self.icell.axon]
+                # Requires safe iteration over myelin section
+                # replace_axon += [dict(nseg=section.nseg,
+                #                      length=section.L,
+                #                      radius=0.5 * section.diam,
+                #                      tag=morphologies._arb_tags['myelin'])
+                #                 for section in self.icell.myelin]
+            else:
+                replace_axon = None
         else:
-            replace_axon = None
-
-        if (
-            self.morphology.morph_modifiers is not None
-            and self.morphology.morph_modifiers_hoc is None
-        ):
-            logger.warning('You have provided custom morphology modifiers, \
-                            but no corresponding hoc files.')
-        elif (
-            self.morphology.morph_modifiers is not None
-            and self.morphology.morph_modifiers_hoc is not None
-        ):
-            if replace_axon is None:
-                replace_axon = ''
-            for morph_modifier_hoc in self.morphology.morph_modifiers_hoc:
-                replace_axon += '\n'
-                replace_axon += morph_modifier_hoc
-
-        ret = create_hoc.create_hoc(mechs=self.mechanisms,
-                                    parameters=self.params.values(),
-                                    morphology=morphology,
-                                    ignored_globals=ignored_globals,
-                                    replace_axon=replace_axon,
-                                    template_name=template_name,
-                                    template_filename=template,
-                                    template_dir=template_dir,
-                                    disable_banner=disable_banner)
+            raise ValueError('Unsupported sim_desc_creator %s '
+                             '(choose either create_hoc.create_hoc or '
+                             'create_acc.create_acc)', str(sim_desc_creator))
+
+        ret = sim_desc_creator(mechs=self.mechanisms,
+                               parameters=self.params.values(),
+                               morphology=morphology,
+                               ignored_globals=ignored_globals,
+                               replace_axon=replace_axon,
+                               template_name=template_name,
+                               template_filename=template,
+                               template_dir=template_dir,
+                               disable_banner=disable_banner)
 
         self.unfreeze(to_unfreeze)
 
         return ret
 
+    def create_hoc(self, param_values,
+                   ignored_globals=(), template='cell_template.jinja2',
+                   disable_banner=False,
+                   template_dir=None):
+        """Create hoc code for this model"""
+        return self._create_sim_desc(param_values,
+                                     ignored_globals, template,
+                                     disable_banner,
+                                     template_dir,
+                                     sim_desc_creator=create_hoc.create_hoc)
+
+    def create_acc(self, param_values,
+                   ignored_globals=(), template='acc/*_template.jinja2',
+                   disable_banner=False,
+                   template_dir=None):
+        """Create hoc code for this model"""
+        return self._create_sim_desc(param_values,
+                                     ignored_globals, template,
+                                     disable_banner,
+                                     template_dir,
+                                     sim_desc_creator=create_acc.create_acc)
+
     def __str__(self):
         """Return string representation"""