MRG: Improve cells

hnn_core/cell.py

@@ -105,32 +105,6 @@ def create_soma(self):
         self.soma.Ra = soma_props['Ra']
         self.soma.cm = soma_props['cm']
 
-    def get3dinfo(self):
-        """Get 3d info."""
-        ls = self.get_sections()
-        lx, ly, lz, ldiam = [], [], [], []
-        for s in ls:
-            for i in range(s.n3d()):
-                lx.append(s.x3d(i))
-                ly.append(s.y3d(i))
-                lz.append(s.z3d(i))
-                ldiam.append(s.diam3d(i))
-        return lx, ly, lz, ldiam
-
-    def getbbox(self):
-        """Get cell's bounding box."""
-        lx, ly, lz, ldiam = self.get3dinfo()
-        minx, miny, minz = 1e9, 1e9, 1e9
-        maxx, maxy, maxz = -1e9, -1e9, -1e9
-        for x, y, z in zip(lx, ly, lz):
-            minx = min(x, minx)
-            miny = min(y, miny)
-            minz = min(z, minz)
-            maxx = max(x, maxx)
-            maxy = max(y, maxy)
-            maxz = max(z, maxz)
-        return ((minx, maxx), (miny, maxy), (minz, maxz))
-
     def translate3d(self, dx, dy, dz):
         """Translate 3d."""
         for s in self.get_sections():
@@ -158,20 +132,27 @@ def move_to_pos(self):
     # 2. a list needs to be created with a Dipole (Point Process) in each
     #    section at position 1
     # In Cell() and not Pyr() for future possibilities
-    def dipole_insert(self, yscale):
-        """Insert dipole into each section of this cell."""
+    def insert_dipole(self, yscale):
+        """Insert dipole into each section of this cell.
+
+        Parameters
+        ----------
+        yscale : dict
+            Dictionary of length scales to calculate dipole without
+            3d shape.
+        """
         # dends must have already been created!!
         # it's easier to use wholetree here, this includes soma
         seclist = h.SectionList()
         seclist.wholetree(sec=self.soma)
         # create a python section list list_all
-        self.list_all = [sec for sec in seclist]
-        for sect in self.list_all:
+        list_all = [sec for sec in seclist]
+        for sect in list_all:
             sect.insert('dipole')
         # Dipole is defined in dipole_pp.mod
-        self.dipole_pp = [h.Dipole(1, sec=sect) for sect in self.list_all]
+        self.dipole_pp = [h.Dipole(1, sec=sect) for sect in list_all]
         # setting pointers and ztan values
-        for sect, dpp in zip(self.list_all, self.dipole_pp):
+        for sect, dpp in zip(list_all, self.dipole_pp):
             # assign internal resistance values to dipole point process (dpp)
             dpp.ri = h.ri(1, sec=sect)
             # sets pointers in dipole mod file to the correct locations
@@ -188,7 +169,7 @@ def dipole_insert(self, yscale):
             pos = np.array([seg.x for seg in sect.allseg()])
             # diff in yvals, scaled against the pos np.array. y_long as
             # in longitudinal
-            y_scale = (yscale[sect.name()] * sect.L) * pos
+            y_scale = (yscale[sect.name().split('_', 1)[1]] * sect.L) * pos
             # y_long = (h.y3d(1, sec=sect) - h.y3d(0, sec=sect)) * pos
             # diff values calculate length between successive section points
             y_diff = np.diff(y_scale)
@@ -244,14 +225,14 @@ def syn_create(self, secloc, e, tau1, tau2):
 
         Parameters
         ----------
-        secloc : float (0. to 1.0)
-            The section location
+        secloc : instance of nrn.Segment
+            The section location. E.g., soma(0.5).
         e: float
-            Reverse potential
+            Reverse potential (in mV)
         tau1: float
-            Rise time
+            Rise time (in ms)
         tau2: float
-            Decay time
+            Decay time (in ms)
 
         Returns
         -------