[Pybrainsim-activity] SF.net SVN: pybrainsim:[130] trunk/src/PyBrainSimGUI.pyw
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[Pybrainsim-activity] SF.net SVN: pybrainsim:[130] trunk/src/PyBrainSimGUI.pyw
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From: <rg...@us...> - 2009-09-13 23:37:51
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Revision: 130
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=130&view=rev
Author: rgoj
Date: 2009-09-13 23:37:32 +0000 (Sun, 13 Sep 2009)
Log Message:
-----------
* Added all the content from the PyBrainSim script, preparing PyBrainSimGUI one to be the main executable.
* Removed all the left over code from wxPython tutorials.
Modified Paths:
--------------
trunk/src/PyBrainSimGUI.pyw
Modified: trunk/src/PyBrainSimGUI.pyw
===================================================================
--- trunk/src/PyBrainSimGUI.pyw 2009-09-13 23:11:44 UTC (rev 129)
+++ trunk/src/PyBrainSimGUI.pyw 2009-09-13 23:37:32 UTC (rev 130)
@@ -30,92 +30,252 @@
import wx
from wx import xrc
+import numpy
+import pylab
+from random import random
+from scipy.integrate import ode
+
+from Head import Head
+from HeadModel import HeadModel
+from HeadModelHalfSphere import HeadModelHalfSphere
+from Experiment import Experiment
+from Stimulus import Stimulus
+from StimulusDummy import StimulusDummy
+from GeneratorDummy import GeneratorDummy
+from GeneratorNumberIncrementing import GeneratorNumberIncrementing
+from GeneratorSine import GeneratorSine
+from Connection import Connection
+from ConnectionDummy import ConnectionDummy
+
class PyBrainSimGUI(wx.App):
def OnInit(self):
self.res = xrc.XmlResource("PyBrainSimGUI.xrc")
- #self.InitFrame()
- #self.InitMenu()
- #self.InitEverythingElse()
self.frame = self.res.LoadFrame(None, "menuFrame")
self.frame.Bind(wx.EVT_BUTTON, self.menuButton1, id=xrc.XRCID("menuButton1"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton2, id=xrc.XRCID("menuButton2"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton3, id=xrc.XRCID("menuButton3"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton4, id=xrc.XRCID("menuButton4"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton5, id=xrc.XRCID("menuButton5"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton6, id=xrc.XRCID("menuButton6"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton7, id=xrc.XRCID("menuButton7"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton8, id=xrc.XRCID("menuButton8"))
self.frame.Bind(wx.EVT_BUTTON, self.menuButtonQuit, id=xrc.XRCID("menuButtonQuit"))
- #self.panel = xrc.XRCCTRL(self.frame, "MainPanel")
- #self.first_arg = xrc.XRCCTRL(self.panel, "FirstArg")
- #self.second_arg = xrc.XRCCTRL(self.panel, "SecondArg")
- #self.result = xrc.XRCCTRL(self.panel, "Result")
- #self.first_arg.SetValue("Hi")
- #self.second_arg.SetValue("You")
- #self.result.SetValue("man")
- #self.menuBar = self.res.LoadMenuBar("MenuBar")
- #self.frame.SetMenuBar(self.menuBar)
- #sizer = self.panel.GetSizer()
- #sizer.Fit(self.frame)
- #sizer.SetSizeHints(self.frame)
self.frame.Show()
return True
def menuButton1(self, control):
- print "Hullo World!"
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ exampleHead.setSamplingFrequency(10)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ exampleStimulus = StimulusDummy('Stim', exampleHead)
+ exampleGenerator = GeneratorDummy('Gen', exampleHead)
+ exampleConnection = ConnectionDummy('Con', exampleHead, exampleStimulus, exampleGenerator)
+
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
+ print("\nSimulations resulted in the following recording:")
+ print(exampleExperiment.getRecording())
+ def menuButton2(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ exampleHead.setSamplingFrequency(10)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ exampleStimulus = Stimulus('Stim', exampleHead)
+ exampleStimulus.setStimulusTimes([0.3, 0.6])
+ exampleGenerator = GeneratorNumberIncrementing('Gen', exampleHead)
+ exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
+
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
+ print("\nSimulations resulted in the following recording:")
+ print exampleExperiment.getRecording()
+
+ def menuButton3(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ exampleHead.setSamplingFrequency(10)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0)
+ exampleExperiment.setStimulusTimes([[0.3, 0.6], [0.5]])
+
+ exampleStimulus1 = Stimulus('Stim1', exampleHead)
+ exampleStimulus2 = Stimulus('Stim2', exampleHead)
+ exampleStimulus1.setStimulusTimes(exampleExperiment.getStimulusTimes()[0])
+ exampleStimulus2.setStimulusTimes(exampleExperiment.getStimulusTimes()[1])
+
+ exampleGenerator1 = GeneratorNumberIncrementing('Gen1', exampleHead)
+ exampleGenerator2 = GeneratorNumberIncrementing('Gen2', exampleHead)
+ exampleConnection1 = Connection('Con1', exampleHead, exampleStimulus1, exampleGenerator1)
+ exampleConnection2 = Connection('Con2', exampleHead, exampleStimulus2, exampleGenerator2)
+
+ exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
+ print("\nSimulations resulted in the following recording:")
+ print exampleExperiment.getRecording()
+
+ def menuButton4(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ exampleHead.setSamplingFrequency(128)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 10.0)
+ exampleExperiment.setStimulusTimes([[0.3, 1.75, 2.16, 3.87, 4.31, 5.183, 6.34, 7.13]])
+
+ exampleStimulus = Stimulus('Stim', exampleHead)
+ print exampleExperiment.getStimulusTimes()[0]
+ exampleStimulus.setStimulusTimes(exampleExperiment.getStimulusTimes()[0])
+ exampleGenerator = GeneratorSine('Gen', exampleHead)
+ exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
+
+ exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
+ print("\nSimulations resulted in the following recording:")
+ print exampleExperiment.getRecording()
+ exampleExperiment.plotRecording()
+
+ def menuButton5(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ exampleHead.setSamplingFrequency(256)
+ exampleHead.addRegistrationSite([0, 0, 0])
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 100.0)
+
+ # Randomizing stimuli times
+ stimuli = []
+ for i in range(100):
+ stimuli.append( i + 0.2 +random()/2 )
+ exampleExperiment.setStimulusTimes([stimuli])
+ exampleStimulus = Stimulus('Stim', exampleHead)
+ exampleStimulus.setStimulusTimes(exampleExperiment.getStimulusTimes()[0])
+
+ # Creating many generators with random frequencies in the range 2-20 Hz and
+ # random phases. Connecting some of them to the stimulus generator
+ exampleGenerators = []
+ exampleConnections = []
+ for i in range(100):
+ randomFrequency = 2.0 + random() * 18
+ randomPhaseShift = random()
+ exampleGenerators.append(GeneratorSine('Gen', exampleHead, frequency=randomFrequency, phaseShift=randomPhaseShift))
+ if(random() > 0.75):
+ exampleConnections.append(Connection('Con', exampleHead, exampleStimulus, exampleGenerators[i]))
+
+ exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
+ exampleExperiment.plotRecording()
+
+ def menuButton6(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModelHalfSphere(exampleHead)
+ exampleHead.setSamplingFrequency(128)
+ exampleHead.addRegistrationSite([ 0.5, 0.0, 0.866])
+ exampleHead.addRegistrationSite([ 0.0, 0.0, 0.866])
+ exampleHead.addRegistrationSite([-0.5, 0.0, 0.866])
+
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 10.0)
+ exampleExperiment.setStimulusTimes([[0.3, 1.75, 2.16, 3.87, 4.31, 5.183, 6.34, 7.13]])
+
+ exampleStimulus = Stimulus('Stim', exampleHead)
+ exampleStimulus.setStimulusTimes(exampleExperiment.getStimulusTimes()[0])
+ exampleGenerator = GeneratorSine('Gen', exampleHead, position = [0.5, 0, 0.366], frequency = 7)
+ exampleGenerator = GeneratorSine('Gen', exampleHead, position = [-0.5, 0, 0.366], frequency = 4)
+ exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
+
+ exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
+ exampleExperiment.plotRecording()
+
+ def menuButton7(self, control):
+ exampleHead = Head()
+ exampleHead.displayHead()
+
+ def menuButton8(self, control):
+ # This class will produce noise that will be fed into the modelled
+ # cortical area as input.
+ class NeuralNoise:
+ def __init__(self, timeSpan, dtime):
+ self.noise = []
+ self.dtime = dtime
+ self.timePoints = range( int(timeSpan//dtime+1) )
+ # Random noise distributed evenly between 120 and 320
+ for i in self.timePoints:
+ self.noise.append( 120+200*random() )
+ def getNoise(self, time):
+ # Searching for the appropriate time point
+ for i in self.timePoints:
+ if time < self.timePoints[i]*self.dtime:
+ # Interpolating between the randomly generated values
+ return self.noise[i] + \
+ (self.noise[i+1]-self.noise[i]) \
+ * ((self.timePoints[i]*self.dtime-time)/self.dtime)
+
+ # The sigmoid function
+ def sigmoidFunction(v):
+ """Constants taken from Jansen and Rit 1995, p. 360"""
+ cEzero = 2.5
+ cR = 0.56
+ cVzero = 6
+
+ """Sigmoid function taken from Jansen and Rit 1995, p. 360"""
+ return 2*cEzero / ( 1 + numpy.exp( cR*( cVzero - v ) ) )
+
+ # Defining the equations
+ def f(t, y, noiseObject, cC):
+ cA=3.25
+ ca=100.0
+ cB=22.0
+ cb=50.0
+ cC1=cC
+ cC2=0.8*cC1
+ cC3=0.25*cC1
+ cC4=0.25*cC1
+ noise = noiseObject.getNoise(t)
+ #print("Time: " + str(t) + " Noise: " + str(noise))
+ return [y[1], cA*ca*( sigmoidFunction(y[2] - y[4]) ) - 2*ca*y[1] -
+ ca**2*y[0], y[3], cA*ca*( noise + cC2*sigmoidFunction(cC1*y[0]) ) -
+ 2*ca*y[3] - ca**2*y[2], y[5], cB*cb*( cC4*sigmoidFunction(cC3*y[0])
+ ) - 2*cb*y[5] - cb**2*y[4]]
+
+ # How many seconds should be modelled and how accurately
+ timeSpan = 3
+ dtime = 0.001
+ firstPointToDisplay = 1000
+
+ # A noise object that will be used as input into the equations
+ someNoise = NeuralNoise(timeSpan+1, dtime*10)
+
+ # Initial conditions
+ y0, t0 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 0
+
+ # Preparing for simulations
+ r = []
+ recording = [ [], [], [], [], [], [] ]
+ parameter = [ 68, 128, 135, 270, 675, 1350 ]
+
+ # Differential equation integration
+ for i in range(len(parameter)):
+ # Preparing the integration
+ r.append(ode(f).set_integrator('vode', method='bdf'))
+ r[i].set_initial_value(y0, t0)
+ r[i].set_f_params( someNoise, parameter[i] )
+ # Integrating
+ print("Performing simulation " + str(i+1) + "/" + str(len(parameter)))
+ while r[i].successful() and r[i].t < timeSpan:
+ r[i].integrate(r[i].t+dtime)
+ recording[i].append(r[i].y[2] - r[i].y[4])
+
+ # Show results of simulations
+ for i in range(len(parameter)):
+ pylab.subplot( len(parameter), 1, i+1)
+ if i==0:
+ pylab.title("Simulations based on Fig. 3 from Jansen and Rit 1995")
+ pylab.ylabel( "C = " + str(parameter[i]) )
+ pylab.plot(recording[i][firstPointToDisplay:])
+ pylab.show()
+
def menuButtonQuit(self, control):
self.Exit()
- #def InitFrame(self):
- # self.frame = self.res.LoadFrame(None, "MainFrame")
- # self.panel = xrc.XRCCTRL(self.frame, "MainPanel")
- # self.first_arg = xrc.XRCCTRL(self.panel, "FirstArg")
- # self.second_arg = xrc.XRCCTRL(self.panel, "SecondArg")
- # self.result = xrc.XRCCTRL(self.panel, "Result")
- # self.first_arg.SetValue("Hi")
- # self.second_arg.SetValue("You")
- # self.result.SetValue("man")
- #def InitMenu(self):
- # self.menuBar = self.res.LoadMenuBar("MenuBar")
- # self.frame.Bind(wx.EVT_MENU, self.Add, id=xrc.XRCID("AddMenuItem"))
- # self.frame.Bind(wx.EVT_MENU, self.Subtract, id=xrc.XRCID("SubtractMenuItem"))
- # self.frame.Bind(wx.EVT_MENU, self.Multiply, id=xrc.XRCID("MultiplyMenuItem"))
- # self.frame.Bind(wx.EVT_MENU, self.Divide, id=xrc.XRCID("DivideMenuItem"))
- # self.frame.SetMenuBar(self.menuBar)
- #def InitEverythingElse(self):
- # sizer = self.panel.GetSizer()
- # sizer.Fit(self.frame)
- # sizer.SetSizeHints(self.frame)
- # self.frame.Show()
- #def InitArgs(self):
- # try:
- # self.first = float(self.first_arg.GetValue())
- # except ValueError:
- # return self.BadFloatValue(self.first_arg)
- # try:
- # self.second = float(self.second_arg.GetValue())
- # except ValueError:
- # return self.BadFloatValue(self.second_arg)
- # return True
- #def BadFloatValue(self, control):
- # dlg = wx.MessageDialog(self.frame, "I can't convert this to float.",
- # 'Conversion error', wx.OK | wx.ICON_ERROR)
- # dlg.ShowModal()
- # dlg.Destroy()
- # control.SetFocus()
- # control.SetSelection(-1, -1)
- # return False
- #def Add(self, evt):
- # if self.InitArgs():
- # self.result.SetValue(str(self.first + self.second))
- #def Subtract(self, evt):
- # if self.InitArgs():
- # self.result.SetValue(str(self.first - self.second))
- #def Multiply(self, evt):
- # if self.InitArgs():
- # self.result.SetValue(str(self.first * self.second))
- #def Divide(self, evt):
- # if self.InitArgs():
- # if self.second != 0:
- # self.result.SetValue(str(self.first / self.second))
- # else:
- # self.result.SetValue("#ERROR")
-
if __name__ == '__main__':
app = PyBrainSimGUI(0)
app.MainLoop()
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