[MRG] Make cell morphology plots reflect actual cell size

doc/whats_new.rst

@@ -18,6 +18,9 @@ Changelog
 - Changed ``conn_seed`` default to ``None`` (from ``3``) in :func:`~hnn_core.network.add_connection`, 
   by `Mattan Pelah`_ in :gh:`492`.
 
+- Add interface to modify attributes of sections in
+ :func:`~hnn_core.Cell.modify_section`, by `Nick Tolley`_ in :gh:`481`
+
 Bug
 ~~~
 - Fix bugs in drives API to enable: rate constant argument as float; evoked drive with
@@ -42,6 +45,9 @@ Bug
 - Add option to plot the averaged dipole in `~hnn_core.viz.plot_dipole` when `dpl`
   is a list of dipoles, by `Huzi Cheng`_ in :gh:`475`.
 
+- Fix bug where :func:`~hnn_core.viz.plot_morphology` did not accurately
+  reflect the shape of the cell being simulated, by `Nick Tolley`_ in :gh:`481`
+
 API
 ~~~
 - Optimization of the evoked drives can be conducted on any :class:`~hnn_core.Network`

hnn_core/cell.py

@@ -11,6 +11,7 @@
 from neuron import h, nrn
 
 from .viz import plot_cell_morphology
+from .externals.mne import _validate_type, _check_option
 
 # Units for e: mV
 # Units for gbar: S/cm^2
@@ -159,11 +160,11 @@ class Section:
     Parameters
     ----------
     L : float
-        length of a section in microns
+        length of a section in microns.
     diam : float
-        diameter of a section in microns
+        diameter of a section in microns.
     cm : float
-        membrane capacitance in micro-Farads
+        membrane capacitance in micro-Farads.
     Ra : float
         axial resistivity in ohm-cm
     end_pts : list of [x, y, z]
@@ -180,20 +181,20 @@ class Section:
     end_pts : list of [x, y, z]
         The start and stop points of the section. Cannot be changed.
     L : float
-        length of a section in microns. Cannot be changed.
+        length of a section in microns.
     diam : float
-        diameter of a section in microns. Cannot be changed.
+        diameter of a section in microns.
     cm : float
-        membrane capacitance in micro-Farads
+        membrane capacitance in micro-Farads.
     Ra : float
-        axial resistivity in ohm-cm
+        axial resistivity in ohm-cm.
     """
     def __init__(self, L, diam, Ra, cm, end_pts=None):
 
         self._L = L
         self._diam = diam
-        self.Ra = Ra
-        self.cm = cm
+        self._Ra = Ra
+        self._cm = cm
         if end_pts is None:
             end_pts = list()
         self._end_pts = end_pts
@@ -212,6 +213,14 @@ def L(self):
     def diam(self):
         return self._diam
 
+    @property
+    def cm(self):
+        return self._cm
+
+    @property
+    def Ra(self):
+        return self._Ra
+
     @property
     def end_pts(self):
         return self._end_pts
@@ -311,6 +320,8 @@ def __init__(self, name, pos, sections, synapses, topology, sect_loc,
         if gid is not None:
             self.gid = gid  # use setter method to check input argument gid
 
+        self._update_end_pts()
+
     def __repr__(self):
         class_name = self.__class__.__name__
         return f'<{class_name} | gid={self._gid}>'
@@ -374,6 +385,8 @@ def _create_sections(self, sections, topology):
         for height and xz plane for depth. This is opposite for model as a
         whole, but convention is followed in this function ease use of gui.
         """
+        if 'soma' not in self.sections:
+            raise KeyError('soma must be defined for cell')
         # shift cell to self.pos and reorient apical dendrite
         # along z direction of self.pos
         dx = self.pos[0] - self.sections['soma'].end_pts[0][0]
@@ -428,8 +441,6 @@ def build(self, sec_name_apical=None):
             with this section. The section should belong to the apical dendrite
             of a pyramidal neuron.
         """
-        if 'soma' not in self.sections:
-            raise KeyError('soma must be defined for cell')
         self._create_sections(self.sections, self.topology)
         self._create_synapses(self.sections, self.synapses)
         self._set_biophysics(self.sections)
@@ -640,3 +651,61 @@ def plot_morphology(self, ax=None, cell_types=None, show=True):
             The matplotlib 3D axis handle.
         """
         return plot_cell_morphology(self, ax=ax, show=show)
+
+    def _update_end_pts(self):
+        """"Create cell and copy coordinates to Section.end_pts"""
+        self._create_sections(self.sections, self.topology)
+        section_names = list(self.sections.keys())
+
+        for name in section_names:
+            nrn_pts = self._nrn_sections[name].psection()['morphology'][
+                'pts3d']
+
+            del self._nrn_sections[name]
+
+            x0, y0, z0 = nrn_pts[0][0], nrn_pts[0][1], nrn_pts[0][2]
+            x1, y1, z1 = nrn_pts[1][0], nrn_pts[1][1], nrn_pts[1][2]
+            self.sections[name]._end_pts = [[x0, y0, z0], [x1, y1, z1]]
+
+        self._nrn_sections = dict()
+
+    def modify_section(self, sec_name, L=None, diam=None, cm=None, Ra=None):
+        """Change attributes of section specified by `sec_name`
+
+        Parameters
+        ----------
+        sec_name : str
+            Name of section to be modified. Must be a key of Cell.sections
+        L : float | int | None
+            length of a section in microns. Default None.
+        diam : float | int | None
+            diameter of a section in microns.
+        cm : float | int | None
+            membrane capacitance in micro-Farads.
+        Ra : float | int | None
+            axial resistivity in ohm-cm.
+
+        Notes
+        -----
+        Leaving default of None produces no change.
+        """
+        valid_sec_names = list(self.sections.keys())
+        _check_option('sec_name', sec_name, valid_sec_names)
+
+        if L is not None:
+            _validate_type(L, (float, int), 'L')
+            self.sections[sec_name]._L = L
+
+        if diam is not None:
+            _validate_type(diam, (float, int), 'diam')
+            self.sections[sec_name]._diam = diam
+
+        if cm is not None:
+            _validate_type(cm, (float, int), 'cm')
+            self.sections[sec_name]._cm = cm
+
+        if Ra is not None:
+            _validate_type(Ra, (float, int), 'Ra')
+            self.sections[sec_name]._Ra = Ra
+
+        self._update_end_pts()

hnn_core/tests/test_cell.py

@@ -1,5 +1,6 @@
 import pytest
 import pickle
+import numpy as np
 
 import matplotlib
 
@@ -15,7 +16,8 @@ def test_cell():
 
     name = 'test'
     pos = (0., 0., 0.)
-    sections = {'blah': Section(L=1, diam=5, Ra=3, cm=100)}
+    sections = {'soma': Section(L=1, diam=5, Ra=3, cm=100,
+                                end_pts=[[0, 0, 0], [0, 39., 0]])}
     synapses = {'ampa': dict(e=0, tau1=0.5, tau2=5.)}
     topology = None
     sect_loc = {'proximal': 'soma'}
@@ -45,8 +47,12 @@ def test_cell():
         cell.syn_create(0.5, e=0., tau1=0.5, tau2=5.)
 
     pickle.dumps(cell)  # check cell object is picklable until built
+
+    bad_sections = {'blah': Section(L=1, diam=5, Ra=3, cm=100,
+                    end_pts=[[0, 0, 0], [0, 39., 0]])}
+    # Check soma must be included in sections
     with pytest.raises(KeyError, match='soma must be defined'):
-        cell.build()
+        cell = Cell(name, pos, bad_sections, synapses, topology, sect_loc)
 
     sections = {
         'soma': Section(
@@ -79,6 +85,24 @@ def test_cell():
     with pytest.raises(ValueError, match='sec_name_apical must be an'):
         cell.build(sec_name_apical='blah')
 
+    # Test section modification
+    sec_name = 'soma'
+    new_L = 1.0
+    new_diam = 2.0
+    new_cm = 3.0
+    new_Ra = 4.0
+    cell.modify_section(sec_name, L=new_L, diam=new_diam, cm=new_cm, Ra=new_Ra)
+
+    # Make sure distance betweeen `Section.end_pts` matches `Section.L`
+    new_pts = np.array(cell.sections[sec_name].end_pts)
+    new_dist = np.linalg.norm(new_pts[0, :] - new_pts[1, :])
+    np.isclose(new_L, new_dist)
+
+    assert cell.sections[sec_name].L == new_L
+    assert cell.sections[sec_name].diam == new_diam
+    assert cell.sections[sec_name].cm == new_cm
+    assert cell.sections[sec_name].Ra == new_Ra
+
 
 def test_artificial_cell():
     """Test artificial cell object."""