fix: add missing L2 soma v_init, remove old init

This fixes what I think is a bug currently present in jonescompneurolab#1168, where the
L2's `soma` section did not have its universal voltage-initialization
value applied (but the dendrites did).

Additionally, @katduecker , I think the same bug is present in your
`_get_interneuron_soma()` function (which I've removed in this commit
since it's not relevant to the voltage-initialization). Your
`_get_interneuron_soma` takes a `v_init` value, but does not apply it in
`Section` creation. This was probably missed.

This also removes `NetworkBuilder.state_init()` like KD did, since it is
no longer needed, as the voltage initialization is completely moved over
to `cells_default.py` now.

With this, I think the voltage-initialization stuff has been completely
extracted from jonescompneurolab#1168. The only remaining work is to write new tests
specifically for the `v_init` where it is used.

Author: asoplata

hnn_core/cells_default.py

@@ -104,6 +104,8 @@ def _cell_L2Pyr(override_params, pos=(0.0, 0.0, 0), gid=0.0):
         assert isinstance(override_params, dict)
         p_all = compare_dictionaries(p_all, override_params)
 
+    all_v_init = -71.46
+
     section_names = [
         "apical_trunk",
         "apical_1",
@@ -118,9 +120,15 @@ def _cell_L2Pyr(override_params, pos=(0.0, 0.0, 0), gid=0.0):
         p_all,
         cell_type="L2Pyr",
         section_names=section_names,
-        v_init={"all": -71.46},
+        v_init={
+            "all": all_v_init,
+        },
+    )
+    sections["soma"] = _get_pyr_soma(
+        p_all,
+        "L2Pyr",
+        v_init=all_v_init,
     )
-    sections["soma"] = _get_pyr_soma(p_all, "L2Pyr")
 
     end_pts = {
         "soma": [[-50, 0, 765], [-50, 0, 778]],
@@ -302,13 +310,14 @@ def _cell_L5Pyr(override_params, pos=(0.0, 0.0, 0), gid=0.0):
 
 def _get_basket_soma(cell_name, v_init=-64.9737):
     end_pts = [[0, 0, 0], [0, 0, 39.0]]
-    return Section(L=39.0, diam=20.0, cm=0.85, Ra=200.0, end_pts=end_pts)
-
-
-# values from Chamberland et al 2023
-def _get_interneuron_soma(cell_name, v_init=-75):
-    end_pts = [[0, 0, 0], [0, 0, 20.0]]
-    return Section(L=20.0, diam=20.0, cm=1, Ra=200.0, end_pts=end_pts)
+    return Section(
+        L=39.0,
+        diam=20.0,
+        cm=0.85,
+        Ra=200.0,
+        v=v_init,
+        end_pts=end_pts,
+    )
 
 
 def _get_pyr_syn_props(p_all, cell_type):

hnn_core/network_builder.py

@@ -371,8 +371,6 @@ def _build(self):
             record_ca=record_ca,
         )
 
-        self.state_init()
-
         # set to record spikes, somatic voltages, and extracellular potentials
         self._spike_times = h.Vector()
         self._spike_gids = h.Vector()
@@ -649,37 +647,6 @@ def aggregate_data(self, n_samples):
 
         _PC.barrier()  # get all nodes to this place before continuing
 
-    def state_init(self):
-        """Initializes the state closer to baseline."""
-
-        for cell in self._cells:
-            seclist = h.SectionList()
-            seclist.wholetree(sec=cell._nrn_sections["soma"])
-            src_type = self.net.gid_to_type(cell.gid)
-            cell_metadata = self.net.cell_types[src_type]["cell_metadata"]
-            # initializing segment voltages from cell_metadata
-            for sect in seclist:
-                for seg in sect:
-                    if (
-                        cell_metadata.get("morpho_type") == "pyramidal"
-                        and cell_metadata.get("layer") == "2"
-                    ):
-                        seg.v = -71.46
-                    elif (
-                        cell_metadata.get("morpho_type") == "pyramidal"
-                        and cell_metadata.get("layer") == "5"
-                    ):
-                        if sect.name() == f"{_short_name(src_type)}_apical_1":
-                            seg.v = -71.32
-                        elif sect.name() == f"{_short_name(src_type)}_apical_2":
-                            seg.v = -69.08
-                        elif sect.name() == f"{_short_name(src_type)}_apical_tuft":
-                            seg.v = -67.30
-                        else:
-                            seg.v = -72.0
-                    elif cell_metadata.get("morpho_type") == "basket":
-                        seg.v = -64.9737
-
     def _clear_neuron_objects(self):
         """Clear up NEURON internal gid and reference information.
 

hnn_core/param/jones2009_base.json

@@ -32,7 +32,7 @@
                             ]
                         ],
                         "nseg": 1,
-                        "v": -65,
+                        "v": -64.9737,
                         "mechs": {
                             "hh2": {}
                         },
@@ -370,7 +370,7 @@
                             ]
                         ],
                         "nseg": 1,
-                        "v": -65,
+                        "v": -71.46,
                         "mechs": {
                             "km": {
                                 "gbar_km": 250.0
@@ -503,7 +503,7 @@
                             ]
                         ],
                         "nseg": 1,
-                        "v": -65,
+                        "v": -64.9737,
                         "mechs": {
                             "hh2": {}
                         },

hnn_core/tests/assets/jones2009_3x3_drives.json

@@ -32,7 +32,7 @@
                             ]
                         ],
                         "nseg": 1,
-                        "v": -65,
+                        "v": -64.9737,
                         "mechs": {
                             "hh2": {}
                         },
@@ -370,7 +370,7 @@
                             ]
                         ],
                         "nseg": 1,
-                        "v": -65,
+                        "v": -71.46,
                         "mechs": {
                             "km": {
                                 "gbar_km": 250.0
@@ -503,7 +503,7 @@
                             ]
                         ],
                         "nseg": 1,
-                        "v": -65,
+                        "v": -64.9737,
                         "mechs": {
                             "hh2": {}
                         },