instantiate cells in network_builder.py

hnn_core/network.py

@@ -14,7 +14,6 @@
 from .drives import _get_target_populations, _add_drives_from_params
 from .drives import _check_drive_parameter_values, _check_poisson_rates
 from .cells_default import pyramidal, basket
-from .cell import Cell
 from .cell_response import CellResponse
 from .params import _long_name, _short_name
 from .viz import plot_cells, plot_cell_morphology
@@ -189,8 +188,7 @@ def __init__(self, params, add_drives_from_params=False,
         self._update_gid_ranges()
 
         self.cell_properties = dict()
-        self.cells = dict()
-        self._create_cells()
+        self._set_cell_properties()
 
         # set n_cells, EXCLUDING Artificial ones
         self.n_cells = sum(len(self.pos_dict[src]) for src in
@@ -231,7 +229,7 @@ def copy(self):
         net_copy._reset_drives()
         return net_copy
 
-    def _create_cells(self):
+    def _set_cell_properties(self):
         '''Populate the network with cell objects'''
 
         for cell_type in self.pos_dict.keys():
@@ -246,10 +244,6 @@ def _create_cells(self):
                                                    'synapses': p_syn,
                                                    'topology': topology,
                                                    'sect_loc': sect_loc}
-                for cell_idx, pos in enumerate(self.pos_dict[cell_type]):
-                    gid = self.gid_dict[cell_type][cell_idx]
-                    cell = Cell(name=_short_name(cell_type), pos=pos, gid=gid)
-                    self.cells[cell_type].append(cell)
 
     def add_evoked_drive(self, name, *, mu, sigma, numspikes,
                          sync_within_trial=False, location,

hnn_core/network_builder.py

@@ -12,7 +12,7 @@
 if int(__version__[0]) >= 8:
     h.nrnunit_use_legacy(1)
 
-from .cell import _ArtificialCell
+from .cell import Cell, _ArtificialCell
 from .cells_default import pyramidal, basket
 from .params import _long_name, _short_name
 from copy import deepcopy
@@ -380,16 +380,16 @@ def _create_cells_and_drives(self, threshold, record_vsoma=False,
         # have to loop over self._gid_list, since this is what we got
         # on this rank (MPI)
         for gid in self._gid_list:
-            src_type = self.net.gid_to_type(gid)
-            cell = self.net._gid_to_cell(gid)
+            src_type, src_pos, is_cell = self.net._get_src_type_and_pos(gid)
 
-            if cell is not None:
+            if is_cell:
+                cell = Cell(name=_short_name(src_type), pos=src_pos, gid=gid)
                 p_secs = self.net.cell_properties[src_type]['sections']
                 p_syn = self.net.cell_properties[src_type]['synapses']
                 topology = self.net.cell_properties[src_type]['topology']
                 sect_loc = self.net.cell_properties[src_type]['sect_loc']
                 # instantiate NEURON object
-                cell.build(p_secs, p_syn, topology, sect_loc=sect_loc)
+                cell.build(p_secs, p_syn, topology, sect_loc)
                 # insert dipole in pyramidal cells
                 if src_type in ('L2_pyramidal', 'L5_pyramidal'):
                     cell.insert_dipole(p_secs, 'apical_trunk')
@@ -403,6 +403,7 @@ def _create_cells_and_drives(self, threshold, record_vsoma=False,
                 # this call could belong in init of a _Cell (with threshold)?
                 nrn_netcon = cell.setup_source_netcon(threshold)
                 _PC.cell(cell.gid, nrn_netcon)
+                self.cells.append(cell)
 
             # external inputs are special types of artificial-cells
             # 'common': all cells impacted with identical TIMING of spike

hnn_core/tests/test_cells_default.py

@@ -44,4 +44,4 @@ def test_cells_default():
     assert len(times) == len(vsoma)
 
     with pytest.raises(ValueError, match='Unknown basket cell type'):
-        l5p = basket(pos=(0, 0, 0), cell_name='blah')
+        p_secs, p_syn, topology, sect_loc = basket(cell_name='blah')