Add 'docs/tutorials/' from commit 'a5661a04ca6804aef66b83cd6ddef08efd…

…dcf1a7'

git-subtree-dir: docs/tutorials
git-subtree-mainline: 1b18b2e
git-subtree-split: a5661a0

docs/tutorials/ballandstick.py

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+from neuron import h, gui
+from neuron.units import ms, mV
+h.load_file('stdrun.hoc')
+
+class Cell:
+    def __init__(self, gid, x, y, z, theta):
+        self._gid = gid
+        self._setup_morphology()
+        self.all = self.soma.wholetree()
+        self._setup_biophysics()
+        self.x = self.y = self.z = 0
+        h.define_shape()
+        self._rotate_z(theta)
+        self._set_position(x, y, z)
+
+        # everything below here in this method is NEW
+        self._spike_detector = h.NetCon(self.soma(0.5)._ref_v, None, sec=self.soma)
+        self.spike_times = h.Vector()
+        self._spike_detector.record(self.spike_times)
+
+        self._ncs = []
+
+        self.soma_v = h.Vector().record(self.soma(0.5)._ref_v)
+
+
+    def __repr__(self):
+        return '{}[{}]'.format(self.name, self._gid)
+
+    def _set_position(self, x, y, z):
+        for sec in self.all:
+            for i in range(sec.n3d()):
+                sec.pt3dchange(i,
+                               x - self.x + sec.x3d(i),
+                               y - self.y + sec.y3d(i),
+                               z - self.z + sec.z3d(i),
+                              sec.diam3d(i))
+        self.x, self.y, self.z = x, y, z
+
+    def _rotate_z(self, theta):
+        """Rotate the cell about the Z axis."""
+        for sec in self.all:
+            for i in range(sec.n3d()):
+                x = sec.x3d(i)
+                y = sec.y3d(i)
+                c = h.cos(theta)
+                s = h.sin(theta)
+                xprime = x * c - y * s
+                yprime = x * s + y * c
+                sec.pt3dchange(i, xprime, yprime, sec.z3d(i), sec.diam3d(i))
+
+
+class BallAndStick(Cell):
+    name = 'BallAndStick'
+
+    def _setup_morphology(self):
+        self.soma = h.Section(name='soma', cell=self)
+        self.dend = h.Section(name='dend', cell=self)
+        self.dend.connect(self.soma)
+        self.soma.L = self.soma.diam = 12.6157
+        self.dend.L = 200
+        self.dend.diam = 1
+
+    def _setup_biophysics(self):
+        for sec in self.all:
+            sec.Ra = 100    # Axial resistance in Ohm * cm
+            sec.cm = 1      # Membrane capacitance in micro Farads / cm^2
+        self.soma.insert('hh')                                          
+        for seg in self.soma:
+            seg.hh.gnabar = 0.12  # Sodium conductance in S/cm2
+            seg.hh.gkbar = 0.036  # Potassium conductance in S/cm2
+            seg.hh.gl = 0.0003    # Leak conductance in S/cm2
+            seg.hh.el = -54.3     # Reversal potential in mV
+        # Insert passive current in the dendrite
+        self.dend.insert('pas')                 
+        for seg in self.dend:
+            seg.pas.g = 0.001  # Passive conductance in S/cm2
+            seg.pas.e = -65    # Leak reversal potential mV
+
+        # NEW: the synapse
+        self.syn = h.ExpSyn(self.dend(0.5))
+        self.syn.tau = 2 * ms
+