[Pybrainsim-activity] SF.net SVN: pybrainsim:[86] trunk/src/Experiment.py

[<rg...@us...>]

Revision: 86
          http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=86&view=rev
Author:   rgoj
Date:     2009-08-05 11:59:20 +0000 (Wed, 05 Aug 2009)

Log Message:
-----------
* Changes to Experiment class:
** timePoints is now a member of the class
** added baseline and epochDuration as members
** added the findNearestTimeIndex method
** added the getRecordingSlice method
** added the getERP method

Modified Paths:
--------------
    trunk/src/Experiment.py

Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py	2009-08-05 11:54:07 UTC (rev 85)
+++ trunk/src/Experiment.py	2009-08-05 11:59:20 UTC (rev 86)
@@ -27,12 +27,16 @@
 from pylab import *
 
 class Experiment:
-    def __init__(self, samplingFrequency = 128, duration = 1,  recording = [], stimulusTimes = []):
+    def __init__(self, samplingFrequency = 128, duration = 1,  recording = [], stimulusTimes = [], baseline = 0.1, epochDuration = 0.3):
         self.samplingFrequency = samplingFrequency
         self.duration = duration
         self.recording = recording
         self.stimulusTimes = stimulusTimes
+        self.baseline = baseline
+        self.epochDuration = epochDuration
 
+        self.timePoints = list(arange( 1.0/self.samplingFrequency, self.duration + 1.0/self.samplingFrequency, 1.0/self.samplingFrequency ))
+
     def setSamplingFrequency(self, samplingFrequency):
         self.samplingFrequency = samplingFrequency
 
@@ -52,14 +56,44 @@
         return self.recording
 
     def setStimulusTimes(self, stimulusTimes):
+        #TODO: If dimension of stimulusTimes is 1... it needs to be two :/
         self.stimulusTimes = stimulusTimes
 
     def getStimulusTimes(self):
         return self.stimulusTimes
 
+    def findNearestTimeIndex(self, timePoint):
+        """ Returns the index of the closest time point within timePoints that
+        is smaller than the given value timePoint"""
+        if timePoint in self.timePoints:
+            return self.timePoints.index(timePoint)
+        else:
+            for i in range(len(self.timePoints)):
+                if timePoint < self.timePoints[i]:
+                    if timePoint > self.timePoints[i-1]:
+                        return i-1
+
+    def getRecordingSlice(self, sliceStart, sliceDuration, sliceChannel=0):
+        startIndex = self.findNearestTimeIndex(sliceStart)
+        endIndex = self.findNearestTimeIndex(sliceStart + sliceDuration)
+        #print str(startIndex) + "   " + str(endIndex)
+        return self.recording[sliceChannel][startIndex:endIndex]
+
+    def getERP(self, stimulusNumber=0):
+        stimuli = self.stimulusTimes[stimulusNumber]
+        epochs = []
+        for i in range(len(stimuli)):
+            epochs.append(self.getRecordingSlice(stimuli[i] - self.baseline, self.epochDuration))
+        
+        average = list(zeros(len(epochs[0])))
+        for i in range(len(epochs)):
+            for j in range(len(epochs[i])):
+                average[j] += epochs[i][j]
+
+        return average        
+
     def plotRecording(self):
-        timePoints = arange( 1.0/self.samplingFrequency, self.duration + 1.0/self.samplingFrequency, 1.0/self.samplingFrequency )
-        plot(timePoints, self.recording[0], linewidth=1.0)
+        plot(self.timePoints, self.recording[0], linewidth=1.0)
 
         xlabel('Time (s)')
         ylabel('Amplitude')


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