matplotlib-checkins Mailing List for matplotlib

Revision: 8007
          http://matplotlib.svn.sourceforge.net/matplotlib/?rev=8007&view=rev
Author:   jdh2358
Date:     2009-12-05 17:47:26 +0000 (Sat, 05 Dec 2009)

Log Message:
-----------
add izhikevich neuron ODE example

Modified Paths:
--------------
    trunk/py4science/examples/lotka_volterra.py

Added Paths:
-----------
    trunk/py4science/examples/izhikevich_neurons.py

Added: trunk/py4science/examples/izhikevich_neurons.py
===================================================================
--- trunk/py4science/examples/izhikevich_neurons.py	                        (rev 0)
+++ trunk/py4science/examples/izhikevich_neurons.py	2009-12-05 17:47:26 UTC (rev 8007)
@@ -0,0 +1,165 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.cbook import iterable
+
+def rk4step(derivs, y0, t, dt):
+
+    dt2 = dt/2.0
+
+    k1 = np.asarray(derivs(y0, t))
+    k2 = np.asarray(derivs(y0 + dt2*k1, t+dt2))
+    k3 = np.asarray(derivs(y0 + dt2*k2, t+dt2))
+    k4 = np.asarray(derivs(y0 + dt*k3, t+dt))
+    return y0 + dt/6.0*(k1 + 2*k2 + 2*k3 + k4)
+
+class Izhikevich:
+    def __init__(self, a, b, c, d):
+        self.a = a
+        self.b = b
+        self.c = c
+        self.d = d
+        self.I = 0
+        self.indI = 0
+
+    def __call__(self, state, t):
+        v, u = state
+        if hasattr(self.I, 'shape'):
+            if len(self.I.shape)==2:
+                I = self.I[:,self.indI]
+            else:
+                I = self.I[self.indI]
+        else:
+            I = self.I
+
+
+        dv = 0.04*v**2 + 5*v + 140 -u + I
+        du = self.a*(self.b*v-u)
+        return dv, du
+
+    def reset_if_action_potential(self, state):
+        v, u = state
+        spiked = v>=30.0
+
+        if iterable(spiked):
+            ind = np.nonzero(spiked)
+            v = np.where(spiked, self.c, v)
+            u = np.where(spiked, u + self.d, u)
+        else:
+            ind = None
+            if spiked:
+                v = self.c
+                u += self.d
+        self.indI += 1
+        return ind, v, u
+
+
+def integrate_single(times, abcd, V0, I):
+
+    model = Izhikevich(*abcd)
+
+
+    state = np.array( [V0,0], float)
+    if not iterable(I):
+        I = I*np.ones(times.shape, float)
+
+
+    model.I = I
+    volts = np.zeros(times.shape, float)
+    volts[0] = state[0]
+    for i in range(1, len(times)):
+
+        dt = times[i] - times[i-1]
+        state = rk4step(model, state, times[i], dt)
+        ind, v, u = model.reset_if_action_potential(state)
+        state[0] = v
+        state[1] = u
+        volts[i] = state[0]
+
+    return volts
+
+regular_spiking = 0.02, 0.2, -65, 8
+chattering = 0.02, 0.2, -50, 2
+fast_spiking = 0.1, 0.2, -65, 2
+intrinsically_bursting = 0.02, 0.2, -55, 4
+thalamocortical = 0.02, 0.25, -65, 0.05
+
+lines = []
+texts = []
+labels = []
+
+times = np.arange(0.0, 500.0, 0.1)
+V0 = -65
+I = np.where(times>=100, 10, 0)
+offset = 150
+#ax = plt.subplot(111)
+ax = plt.axes([0.125, .11, 0.725, 0.79], axisbg='w')
+
+num = 0
+v = integrate_single(times, regular_spiking, V0, I)
+l = ax.plot(times/1000.0, v+num*offset, 'k')
+ax.text(0.51, v[0]+num*offset+20, 'RS', fontsize=15)
+lines.extend(l)
+num += 1
+
+v = integrate_single(times, chattering, V0, I)
+l = ax.plot(times/1000.0, v+num*offset, 'k')
+ax.text(0.51, v[0]+num*offset+20, 'CH', fontsize=15)
+lines.extend(l)
+num += 1
+
+v = integrate_single(times, fast_spiking, V0, I)
+l = ax.plot(times/1000.0, v+num*offset, 'k')
+ax.text(0.51, v[0]+num*offset+20, 'FS', fontsize=15)
+lines.extend(l)
+
+num += 1
+
+v = integrate_single(times, intrinsically_bursting, V0, I)
+l = ax.plot(times/1000.0, v+num*offset, 'k')
+ax.text(0.51, v[0]+num*offset+20, 'IB', fontsize=15)
+lines.extend(l)
+num += 1
+
+
+ax.axis([0, 0.5, -100, 900])
+ax.set_yticklabels([])
+ax.set_xlabel('time (s)')
+ax.grid(False)
+
+
+ax = plt.axes([0.25, 0.7, 0.175, 0.175], axisbg='w')
+ax.set_xticks([0.02, 0.1])
+ax.set_yticks([0.2, 0.25])
+ax.plot([0.02, 0.1], [0.2, 0.2], 'o',
+     markerfacecolor='k', markeredgecolor='k', markersize=4)
+texts.append( ax.text(0.01, 0.18, 'RS, IB, CH') )
+texts.append( ax.text(0.1, 0.18, 'FS') )
+
+ax.grid(False)
+
+ax.axis([0, 0.15, 0.15, 0.3])
+labels.append(ax.set_xlabel('parameter a'))
+labels.append(ax.set_ylabel('parameter b'))
+
+ax = plt.axes([0.6, 0.7, 0.175, 0.175], axisbg='w')
+ax.set_xticks([-65, -55, -50])
+ax.set_yticks([2, 4, 8])
+ax.plot([-65, -50, -55, -65], [2, 2, 4, 8], 'o',
+     markerfacecolor='k', markeredgecolor='k', markersize=4)
+
+texts.append( ax.text(-64, 2.5, 'FS') )
+texts.append( ax.text(-49, 2.5, 'CH') )
+texts.append( ax.text(-54, 4.5, 'IB') )
+texts.append( ax.text(-64, 8.5, 'RS') )
+
+for text in texts:
+    text.set_fontsize(10)
+
+labels.append(ax.set_xlabel('parameter c'))
+labels.append(ax.set_ylabel('parameter d'))
+
+ax.axis([-70, -40, 0.05, 10])
+ax.grid(False)
+#plt.savefig('figures/four_neurons.eps')
+
+plt.show()

Modified: trunk/py4science/examples/lotka_volterra.py
===================================================================
--- trunk/py4science/examples/lotka_volterra.py	2009-12-03 20:51:21 UTC (rev 8006)
+++ trunk/py4science/examples/lotka_volterra.py	2009-12-05 17:47:26 UTC (rev 8007)
@@ -22,14 +22,14 @@
 
 def derivs(state, t):
     """
-    Return the derivatives of r and f, stored in the *state* vector::
+    Return the derivatives of R and F, stored in the *state* vector::
 
-       state = [r, f]
+       state = [R, F]
 
-    The return data should be [dr, df] which are the derivatives of r
-    and f at position state and time *t*
+    The return data should be [dR, dF] which are the derivatives of R
+    and F at position state and time *t*
     """
-    r, f = state          # and foxes    #@
+    R, F = state          # and foxes    #@
     deltar = dr(r, f)     # in rabbits   #@
     deltaf = df(r, f)     # in foxes     #@
     return deltar, deltaf                #@


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