[MRG] Add name parameter to tonic bias and add tonic biases to different sections

hnn_core/cell.py

@@ -728,7 +728,8 @@ def _insert_dipole(self, sec_name_apical):
             dpp.ztan = seg_lens_z[-1]
         self.dipole = h.Vector().record(self.dpl_ref)
 
-    def create_tonic_bias(self, amplitude, t0, tstop, loc=0.5):
+    def create_tonic_bias(self, amplitude, t0, tstop, sect_name='soma',
+                          loc=0.5):
         """Create tonic bias at the soma.
 
         Parameters
@@ -742,7 +743,8 @@ def create_tonic_bias(self, amplitude, t0, tstop, loc=0.5):
         loc : float (0 to 1)
             The location of the input in the soma section.
         """
-        stim = h.IClamp(self._nrn_sections['soma'](loc))
+
+        stim = h.IClamp(self._nrn_sections[sect_name](loc))
         stim.delay = t0
         stim.dur = tstop - t0
         stim.amp = amplitude

hnn_core/cells_default.py

@@ -429,6 +429,7 @@ def pyramidal_ca(cell_name, pos, override_params=None, gid=None):
     override_params['L5Pyr_dend_gbar_ca'] = gbar_ca
     override_params['L5Pyr_dend_gnabar_hh2'] = gbar_na
     override_params['L5Pyr_dend_gkbar_hh2'] = gbar_k
+    override_params['L5Pyr_soma_gbar_ca'] = 10.
 
     cell = pyramidal(cell_name, pos, override_params=override_params,
                      gid=gid)

hnn_core/extracellular.py

@@ -272,7 +272,7 @@ class ExtracellularArray:
     measured values of conductivity in rat cortex (note units there are mS/cm)
     """
 
-    def __init__(self, positions, *, conductivity=0.3, method='psa',
+    def __init__(self, positions, *, conductivity=0.3, method='lsa',
                  min_distance=0.5, times=None, voltages=None):
 
         _validate_type(positions, (tuple, list), 'positions')

hnn_core/network.py

@@ -1133,7 +1133,8 @@ def _instantiate_drives(self, tstop, n_trials=1):
                 self.external_drives[
                     drive['name']]['events'].append(event_times)
 
-    def add_tonic_bias(self, *, cell_type=None, amplitude, t0=0, tstop=None):
+    def add_tonic_bias(self, *, cell_type=None, sect_name='soma',
+                       bias_name='tonic', amplitude, t0=0, tstop=None):
         """Attaches parameters of tonic bias input for given cell types
 
         Parameters
@@ -1142,6 +1143,10 @@ def add_tonic_bias(self, *, cell_type=None, amplitude, t0=0, tstop=None):
             The name of the cell type to add a tonic input. When supplied,
             a float value must be provided with the `amplitude` keyword.
             Valid inputs are those listed in  `net.cell_types`.
+        sect_name : str | 'soma'
+            section the bias should be added to.
+        bias_name : str | 'tonic'
+            The name of the bias.
         amplitude: dict | float
             A dictionary of cell type keys (str) to amplitude values (float).
             Valid inputs for cell types are those listed in `net.cell_types`.
@@ -1169,6 +1174,7 @@ def add_tonic_bias(self, *, cell_type=None, amplitude, t0=0, tstop=None):
             _validate_type(amplitude, (float, int), 'amplitude')
 
             _add_cell_type_bias(network=self, cell_type=cell_type,
+                                sect_name=sect_name, bias_name=bias_name,
                                 amplitude=float(amplitude),
                                 t_0=t0, t_stop=tstop)
         else:
@@ -1180,6 +1186,7 @@ def add_tonic_bias(self, *, cell_type=None, amplitude, t0=0, tstop=None):
 
             for _cell_type, _amplitude in amplitude.items():
                 _add_cell_type_bias(network=self, cell_type=_cell_type,
+                                    sect_name=sect_name, bias_name=bias_name,
                                     amplitude=_amplitude,
                                     t_0=t0, t_stop=tstop)
 
@@ -1648,7 +1655,7 @@ def __repr__(self):
 
 
 def _add_cell_type_bias(network: Network, amplitude: Union[float, dict],
-                        cell_type=None,
+                        cell_type=None, sect_name='soma', bias_name='tonic',
                         t_0=0, t_stop=None):
 
     if network is None:
@@ -1665,15 +1672,17 @@ def _add_cell_type_bias(network: Network, amplitude: Union[float, dict],
                              f'{list(network.cell_types.keys())}. '
                              f'Got {cell_type}')
 
-        if 'tonic' not in network.external_biases:
-            network.external_biases['tonic'] = dict()
+        if bias_name not in network.external_biases:
+            network.external_biases[bias_name] = dict()
 
-        if cell_type in network.external_biases['tonic']:
-            raise ValueError(f'Tonic bias already defined for {cell_type}')
+        if cell_type in network.external_biases[bias_name]:
+            raise ValueError(f'Bias named {bias_name} already defined '
+                             f'for {cell_type}')
 
         cell_type_bias = {
             'amplitude': amplitude,
             't0': t_0,
-            'tstop': t_stop
+            'tstop': t_stop,
+            'sect_name': sect_name
         }
-        network.external_biases['tonic'][cell_type] = cell_type_bias
+        network.external_biases[bias_name][cell_type] = cell_type_bias

hnn_core/network_builder.py

@@ -441,10 +441,10 @@ def _create_cells_and_drives(self, threshold, record_vsec=False,
                 else:
                     cell.build()
                 # add tonic biases
-                if ('tonic' in self.net.external_biases and
-                        src_type in self.net.external_biases['tonic']):
-                    cell.create_tonic_bias(**self.net.external_biases
-                                           ['tonic'][src_type])
+                for bias in self.net.external_biases:
+                    if src_type in self.net.external_biases[bias]:
+                        cell.create_tonic_bias(**self.net.external_biases
+                                               [bias][src_type])
                 cell.record(record_vsec, record_isec, record_ca)
 
                 # this call could belong in init of a _Cell (with threshold)?