ENH: sec_pts is documented + sect_loc is updated transparently?

hnn_core/cell.py

@@ -74,6 +74,8 @@ class Cell:
 
     Parameters
     ----------
+    name : str
+        The name of the cell.
     pos : tuple
         The (x, y, z) coordinates.
     gid : int or None (optional)
@@ -114,7 +116,8 @@ class Cell:
         names of section locations that are proximal or distal.
     """
 
-    def __init__(self, pos, gid=None):
+    def __init__(self, name, pos, gid=None):
+        self.name = name
         self.pos = pos
         self.soma = None
         self.dends = dict()
@@ -242,7 +245,7 @@ def _create_sections(self, p_secs, topology):
             child_loc = connection[3]
             child_sec.connect(parent_sec, parent_loc, child_loc)
 
-    def build(self, p_secs, p_syn, topology):
+    def build(self, p_secs, p_syn, topology, sect_loc):
         """Build cell in Neuron.
 
         Parameters
@@ -267,6 +270,9 @@ def build(self, p_secs, p_syn, topology):
             specifying the location in the section to connect and
             parent_sec and child_sec are names of the connecting
             sections.
+        sect_loc : dict of list
+            Can have keys 'proximal' or 'distal' each containing
+            names of section locations that are proximal or distal.
 
         Examples
         --------
@@ -277,6 +283,7 @@ def build(self, p_secs, p_syn, topology):
                 'diam': 20,
                 'cm': 0.85,
                 'Ra': 200.,
+                'sec_pts': [[0, 0, 0], [0, 39., 0]],
                 'syns': ['ampa', 'gabaa', 'nmda'],
                 'mechs' : {
                     'ca': {
@@ -289,6 +296,7 @@ def build(self, p_secs, p_syn, topology):
         self._create_sections(p_secs, topology)
         self._create_synapses(p_secs, p_syn)
         self._set_biophysics(p_secs)
+        self.sect_loc = sect_loc
 
     def move_to_pos(self):
         """Move cell to position."""

hnn_core/cells_default.py

@@ -165,9 +165,6 @@ def basket(pos, cell_name='L2Basket', gid=None):
     cell : instance of BasketSingle
         The basket cell.
     """
-    cell = Cell(pos=pos, gid=gid)
-    cell.name = cell_name
-
     p_secs = dict()
     p_secs['soma'] = _get_basket_soma_props(cell_name)
     p_syn = _get_basket_syn_props()
@@ -179,11 +176,12 @@ def basket(pos, cell_name='L2Basket', gid=None):
         p_secs[sec_name]['sec_pts'] = sec_pts[sec_name]
 
     if cell_name == 'L2Basket':
-        cell.sect_loc = dict(proximal=['soma'], distal=['soma'])
+        sect_loc = dict(proximal=['soma'], distal=['soma'])
     elif cell_name == 'L5Basket':
-        cell.sect_loc = dict(proximal=['soma'], distal=[])
+        sect_loc = dict(proximal=['soma'], distal=[])
 
-    cell.build(p_secs, p_syn, topology)
+    cell = Cell(cell_name, pos=pos, gid=gid)
+    cell.build(p_secs, p_syn, topology, sect_loc)
 
     return cell
 
@@ -205,10 +203,9 @@ def pyramidal(pos, celltype, override_params=None, gid=None):
         yet attached to a network. Once the GID is set, it cannot be changed.
     """
 
-    cell = Cell(pos=pos, gid=gid)
     if celltype == 'L5_pyramidal':
         p_all_default = get_L5Pyr_params_default()
-        cell.name = 'L5Pyr'
+        cell_name = 'L5Pyr'
         # units = ['pS/um^2', 'S/cm^2', 'pS/um^2', '??', 'tau', '??']
         mechanisms = {
             'hh2': ['gkbar_hh2', 'gnabar_hh2',
@@ -226,7 +223,7 @@ def pyramidal(pos, celltype, override_params=None, gid=None):
         sec_pts, _, _, yscale, topology = _secs_L5Pyr()
     elif celltype == 'L2_pyramidal':
         p_all_default = get_L2Pyr_params_default()
-        cell.name = 'L2Pyr'
+        cell_name = 'L2Pyr'
         mechanisms = {
             'km': ['gbar_km'],
             'hh2': ['gkbar_hh2', 'gnabar_hh2',
@@ -244,14 +241,14 @@ def pyramidal(pos, celltype, override_params=None, gid=None):
 
     prop_names = ['L', 'diam', 'Ra', 'cm']
     # Get somatic, dendritic, and synapse properties
-    p_soma = _get_pyr_soma_props(p_all, cell.name)
-    p_dend = _get_dend_props(p_all, cell_type=cell.name,
+    p_soma = _get_pyr_soma_props(p_all, cell_name)
+    p_dend = _get_dend_props(p_all, cell_type=cell_name,
                              section_names=section_names,
                              prop_names=prop_names)
-    p_syn = _get_pyr_syn_props(p_all, cell.name)
+    p_syn = _get_pyr_syn_props(p_all, cell_name)
     p_secs = p_dend.copy()
     p_secs['soma'] = p_soma
-    p_mech = _get_mechanisms(p_all, cell.name, ['soma'] + section_names,
+    p_mech = _get_mechanisms(p_all, cell_name, ['soma'] + section_names,
                              mechanisms)
     for key in p_secs:
         p_secs[key]['mechs'] = p_mech[key]
@@ -267,10 +264,11 @@ def pyramidal(pos, celltype, override_params=None, gid=None):
     for sec_name in p_secs:
         p_secs[sec_name]['sec_pts'] = sec_pts[sec_name]
 
-    cell.sect_loc['proximal'] = ['apicaloblique', 'basal2', 'basal3']
-    cell.sect_loc['distal'] = ['apicaltuft']
+    sect_loc = {'proximal': ['apicaloblique', 'basal2', 'basal3'],
+                'distal': ['apicaltuft']}
 
-    cell.build(p_secs, p_syn, topology)
+    cell = Cell(name=cell_name, pos=pos, gid=gid)
+    cell.build(p_secs, p_syn, topology, sect_loc=sect_loc)
 
     # insert dipole
     yscale = yscale

hnn_core/tests/test_cell.py

@@ -11,16 +11,16 @@
 def test_cell():
     """Test cells object."""
     pos = (0., 0., 0.)
-
+    name = 'test'
     # GID is assigned exactly once for each cell, either at initialisation...
-    cell = Cell(pos=pos, gid=42)
+    cell = Cell(name, pos=pos, gid=42)
     assert cell.gid == 42
     with pytest.raises(RuntimeError,
                        match='Global ID for this cell already assigned!'):
         cell.gid += 1
     # ... or later
     # cells can exist fine without gid
-    cell = Cell(pos=pos)
+    cell = Cell(name, pos=pos)
     assert cell.gid is None  # check that it's initialised to None
     with pytest.raises(ValueError,
                        match='gid must be an integer'):
@@ -30,7 +30,7 @@ def test_cell():
     with pytest.raises(ValueError,
                        match='gid must be an integer'):
         # test init checks gid
-        cell = Cell(pos=pos, gid='one')
+        cell = Cell(name, pos=pos, gid='one')
 
     # test that ExpSyn always takes nrn.Segment, not float
     with pytest.raises(TypeError, match='secloc must be instance of'):