NETWORK SIMULATION LOG (started at "+str(time.time())+")<\\title>\n") logFile.write("\nNetwork Parameters:\n") for item in parameterDictionary.items(): logFile.write("<"+str(item[0])+"="+str(item[1])+">") logFile.write("\n") logFile.write("\n<\\head>\n<body>\n") elif fromWhere=="simEnd": logFile.write("<P>NETWORK SIMULATION LOG (ended at "+str(time.time())+")\n") logFile.write("<\\body>\n<\\html>") def logIC(logFile,network,fromWhere,ic): logFile.write("<IC>\n<label="+fromWhere+">\n") outputList(logFile,ic) logFile.write("\n<\IC>\n") def logNetwork(logFile,network,fromWhere): logFile.write("<N>\n<label="+fromWhere+">\n") c=network.connectivityMatrix outputMatrix(logFile,c) logFile.write("<\N>\n") def logToFile(logFile,network,what,fromWhere,parameterDictionary=""): if what=="sim": logSimulation(logFile,fromWhere,parameterDictionary) elif what=="network": logNetwork(logFile,network,fromWhere) elif what=="ic": logIC(logFile,network,fromWhere,network.currentState) def outputList(targetFile,lst): i=0 while i<len(lst): targetFile.write(str(lst[i])+ " ") i=i+1 targetFile.write("\n") def outputMatrix(targetFile,matrix): #only applicable for 2-d arrays dimensions=matrix.shape rows=dimensions[0] cols=dimensions[1] i=0 while i<rows: j=0 while j<cols: targetFile.write(str(matrix[i][j])+ " ") j=j+1 targetFile.write("\n") i=i+1 def inputMatrix(targetFile): f=open(targetFile) #matrix will contain a list of rows matrix=[] for line in f: columns=line.split() i=0 thisRow=[] while i<len(columns): thisRow.append(float(columns[i])) i=i+1 if (len(thisRow)!=0): matrix.append(thisRow) matrixArray=array(matrix) f.close() return matrixArray def getActivity(fileName,transients=0): m=array(inputMatrix(fileName)).sum(1) #calculate row sum return m def getTransients(fileName): f=open(fileName) matrix=[] iteration=0 transients=0 iterationsToNullActivity=0 for line in f: entries=line.split() if int(max(entries))==1: iteration=iteration+1 j=0 while j<len(matrix): if (line==matrix[j] and transients==0): transients=j j=j+1 matrix.append(line) else: iterationsToNullActivity=iteration break #stop parsing this file; it's all zeroes from now on f.close() return transients,iterationsToNullActivity #-----------------------------------------------------------------------# # getFileList: generates list of strings containing data file names # # to analyze; queries user if no parameters passed # #-----------------------------------------------------------------------# def getFileList(baseName="",simNum="",icRange=""): if baseName=="": baseName=raw_input("Enter base file name [timeSeries]: ") if baseName=="": baseName="timeSeries" if simNum=="": simNum=raw_input("Enter simulation number [0]: ") if simNum=="": simNum=0 if icRange=="": icRange=raw_input("Enter number of ICs to analyze [10]: ") if icRange=="": icRange=10 icRange=range(int(icRange)) fileList=[] for ic in icRange: fileList.append(baseName+"_"+str(simNum)+"_ic"+str(ic)) return fileList def transientStatistics(): t,z=getTransients() print "Mean: "+str(average(t)) print "SD: "+str(standardDeviation(t)) dead=[] for i in z: if i>0: dead.append(i) print "Percent Dead Runs: "+str(len(dead)/float(len(z))) if dead!=[]: print "Mean Transients to Dead: "+str(average(dead)) def getSingleNetworkStats(baseName="",simNum="",icRange=""): files=getFileList(baseName,simNum,icRange) transientList=[] deadList=[] for x in files: t,z=getTransients(x) transientList.append(t) if z>0: deadList.append(z) dic={"MeanTransients":average(transientList),"SDTransients":standardDeviation(transientList), "PercentDead":(len(deadList)/float(len(transientList))), "MeanTimeToDead":0} if deadList!=[]: dic["MeanTimeToDead"]=average(deadList) return dic def networkActivityHistogram(dataDict,key,bins=20): if not(dataDict.has_key(key)): return [] hg=Histogram(dataDict[key],bins) return hg def plotNetworkActivityHistogram(dataDict,key="",bins=""): if key=="": key=interactiveList(dataDict.keys(),"Data") if bins=="": bins=raw_input("Enter number of bins [20]: ") if bins=="": bins=20 bins=int(bins) print key figure(1,(8,6)) TitleString = 'Histogram of '+key title(TitleString) xlabel(key) # set x-axis label ylabel('Count('+key+')') # set y-axis label hg=networkActivityHistogram(dataDict,key,bins) x=[] y=[] for i in hg: x.append(i[0]) y.append(i[1]) plot(x,y,'ro') show() #-----------------------------------------------------------------------# # Plot activity v time # #-----------------------------------------------------------------------# def plotGlobalActivity(baseName="",simNum="",icRange=""): if baseName=="": baseName=raw_input("Enter base file name [timeSeriesD]: ") if baseName=="": baseName="timeSeriesD" if simNum=="": simNum=raw_input("Enter simulation number [0]: ") if simNum=="": simNum=0 if icRange=="": icRange=raw_input("Enter number of ICs to analyze [10]: ") if icRange=="": icRange=10 icRange=range(int(icRange)) for ic in icRange: rowSumArray=getActivity(baseName+"_"+str(simNum)+"_ic"+str(ic)) plot(arange(len(rowSumArray)),rowSumArray,label='activity over time') title(baseName+"_"+str(simNum)+"_ic"+str(ic)) legend() show() #-----------------------------------------------------------------------# # Plot average activity v time # #-----------------------------------------------------------------------# def plotAverageActivity(baseName="",simNum="",icRange=""): if baseName=="": baseName=raw_input("Enter base file name [timeSeriesD]: ") if baseName=="": baseName="timeSeriesD" if simNum=="": simNum=raw_input("Enter simulation number [0]: ") if simNum=="": simNum=0 if icRange=="": icRange=raw_input("Enter number of ICs to analyze [10]: ") if icRange=="": icRange=10 icRange=range(int(icRange)) for ic in icRange: rowSumArray=getActivity(baseName+"_"+str(simNum)+"_ic"+str(ic)) j=0 averageActivity=[] while j<len(rowSumArray)-1: z=(rowSumArray[j]+rowSumArray[j+1])/2.0 averageActivity.append(z) j=j+1 plot(arange(len(averageActivity)),averageActivity,label='Average activity over time') title(baseName+"_"+str(simNum)+"_ic"+str(ic)) legend() show() #-----------------------------------------------------------------------# # Retrieve basic stats about series of simulations # #-----------------------------------------------------------------------# def getMultiNetworkStats(): baseName=raw_input("Enter base file name [timeSeries]: ") if baseName=="": baseName="timeSeries" simNumRange=raw_input("Enter number of simulations to analyze [1]: ") if simNumRange=="": simNumRange=1 icRange=raw_input("Enter number of ICs to analyze [10]: ") if icRange=="": icRange=10 multiStats={} for sim in range(int(simNumRange)): singleStats=getSingleNetworkStats(baseName,sim,icRange) for key in singleStats.keys(): if multiStats.has_key(key): multiStats[key].append(singleStats[key]) else: multiStats[key]=[] multiStats[key].append(singleStats[key]) return multiStats

""" nnUtils.py Created by Daniel Wuellner on 2007-05-15. Last edited on 2007-06-08 Utility functions to test neuronal network simulation. Requires nnGenericUtilityFunctions.py """ import sys import os from nnGenericUtilityFunctions import * from pylab import * from numpy import * from Scientific.Statistics import average, standardDeviation from Scientific.Statistics.Histogram import Histogram import time #-----------------------------------------------------------------------# # TOOLS FOR ANALYZING SIMULATION # #-----------------------------------------------------------------------# def analyzeMorphogenesis(logFile,networkLabel): f=open(logFile) startNetwork=array(getNetwork(f,networkLabel+"_start")) f.close() f=open(logFile) endNetwork=array(getNetwork(f,networkLabel+"_end")) f.close() diffArray=(startNetwork-endNetwork) rowSum=diffArray.sum(axis=1) colSum=diffArray.sum(axis=0) return diffArray,rowSum,colSum def getNetwork(lF,networkLabel): networkMatrix=[] match=True k=0 for line in lF: if (match and line.find(networkLabel)>-1): while match: newLine=lF.next() if newLine.find("\N")>-1:match=False if match: temp=newLine.split() #params=[temp,networkMatrix] #programmingPoint(params) networkMatrix.append([]) for y in temp: networkMatrix[k].append(float(y)) k=k+1 return networkMatrix def logSimulation(logFile,fromWhere,parameterDictionary): if fromWhere=="simStart": logFile.write("\n\n") logFile.write("NETWORK SIMULATION LOG (started at "+str(time.time())+")<\\title>\n") logFile.write("\nNetwork Parameters:\n") for item in parameterDictionary.items(): logFile.write("<"+str(item[0])+"="+str(item[1])+">") logFile.write("\n") logFile.write("\n<\\head>\n<body>\n") elif fromWhere=="simEnd": logFile.write("<P>NETWORK SIMULATION LOG (ended at "+str(time.time())+")\n") logFile.write("<\\body>\n<\\html>") def logIC(logFile,network,fromWhere,ic): logFile.write("<IC>\n<label="+fromWhere+">\n") outputList(logFile,ic) logFile.write("\n<\IC>\n") def logNetwork(logFile,network,fromWhere): logFile.write("<N>\n<label="+fromWhere+">\n") c=network.connectivityMatrix outputMatrix(logFile,c) logFile.write("<\N>\n") def logToFile(logFile,network,what,fromWhere,parameterDictionary=""): if what=="sim": logSimulation(logFile,fromWhere,parameterDictionary) elif what=="network": logNetwork(logFile,network,fromWhere) elif what=="ic": logIC(logFile,network,fromWhere,network.currentState) def outputList(targetFile,lst): i=0 while i<len(lst): targetFile.write(str(lst[i])+ " ") i=i+1 targetFile.write("\n") def outputMatrix(targetFile,matrix): #only applicable for 2-d arrays dimensions=matrix.shape rows=dimensions[0] cols=dimensions[1] i=0 while i<rows: j=0 while j<cols: targetFile.write(str(matrix[i][j])+ " ") j=j+1 targetFile.write("\n") i=i+1 def inputMatrix(targetFile): f=open(targetFile) #matrix will contain a list of rows matrix=[] for line in f: columns=line.split() i=0 thisRow=[] while i<len(columns): thisRow.append(float(columns[i])) i=i+1 if (len(thisRow)!=0): matrix.append(thisRow) matrixArray=array(matrix) f.close() return matrixArray def getActivity(fileName,transients=0): m=array(inputMatrix(fileName)).sum(1) #calculate row sum return m def getTransients(fileName): f=open(fileName) matrix=[] iteration=0 transients=0 iterationsToNullActivity=0 for line in f: entries=line.split() if int(max(entries))==1: iteration=iteration+1 j=0 while j<len(matrix): if (line==matrix[j] and transients==0): transients=j j=j+1 matrix.append(line) else: iterationsToNullActivity=iteration break #stop parsing this file; it's all zeroes from now on f.close() return transients,iterationsToNullActivity #-----------------------------------------------------------------------# # getFileList: generates list of strings containing data file names # # to analyze; queries user if no parameters passed # #-----------------------------------------------------------------------# def getFileList(baseName="",simNum="",icRange=""): if baseName=="": baseName=raw_input("Enter base file name [timeSeries]: ") if baseName=="": baseName="timeSeries" if simNum=="": simNum=raw_input("Enter simulation number [0]: ") if simNum=="": simNum=0 if icRange=="": icRange=raw_input("Enter number of ICs to analyze [10]: ") if icRange=="": icRange=10 icRange=range(int(icRange)) fileList=[] for ic in icRange: fileList.append(baseName+"_"+str(simNum)+"_ic"+str(ic)) return fileList def transientStatistics(): t,z=getTransients() print "Mean: "+str(average(t)) print "SD: "+str(standardDeviation(t)) dead=[] for i in z: if i>0: dead.append(i) print "Percent Dead Runs: "+str(len(dead)/float(len(z))) if dead!=[]: print "Mean Transients to Dead: "+str(average(dead)) def getSingleNetworkStats(baseName="",simNum="",icRange=""): files=getFileList(baseName,simNum,icRange) transientList=[] deadList=[] for x in files: t,z=getTransients(x) transientList.append(t) if z>0: deadList.append(z) dic={"MeanTransients":average(transientList),"SDTransients":standardDeviation(transientList), "PercentDead":(len(deadList)/float(len(transientList))), "MeanTimeToDead":0} if deadList!=[]: dic["MeanTimeToDead"]=average(deadList) return dic def networkActivityHistogram(dataDict,key,bins=20): if not(dataDict.has_key(key)): return [] hg=Histogram(dataDict[key],bins) return hg def plotNetworkActivityHistogram(dataDict,key="",bins=""): if key=="": key=interactiveList(dataDict.keys(),"Data") if bins=="": bins=raw_input("Enter number of bins [20]: ") if bins=="": bins=20 bins=int(bins) print key figure(1,(8,6)) TitleString = 'Histogram of '+key title(TitleString) xlabel(key) # set x-axis label ylabel('Count('+key+')') # set y-axis label hg=networkActivityHistogram(dataDict,key,bins) x=[] y=[] for i in hg: x.append(i[0]) y.append(i[1]) plot(x,y,'ro') show() #-----------------------------------------------------------------------# # Plot activity v time # #-----------------------------------------------------------------------# def plotGlobalActivity(baseName="",simNum="",icRange=""): if baseName=="": baseName=raw_input("Enter base file name [timeSeriesD]: ") if baseName=="": baseName="timeSeriesD" if simNum=="": simNum=raw_input("Enter simulation number [0]: ") if simNum=="": simNum=0 if icRange=="": icRange=raw_input("Enter number of ICs to analyze [10]: ") if icRange=="": icRange=10 icRange=range(int(icRange)) for ic in icRange: rowSumArray=getActivity(baseName+"_"+str(simNum)+"_ic"+str(ic)) plot(arange(len(rowSumArray)),rowSumArray,label='activity over time') title(baseName+"_"+str(simNum)+"_ic"+str(ic)) legend() show() #-----------------------------------------------------------------------# # Plot average activity v time # #-----------------------------------------------------------------------# def plotAverageActivity(baseName="",simNum="",icRange=""): if baseName=="": baseName=raw_input("Enter base file name [timeSeriesD]: ") if baseName=="": baseName="timeSeriesD" if simNum=="": simNum=raw_input("Enter simulation number [0]: ") if simNum=="": simNum=0 if icRange=="": icRange=raw_input("Enter number of ICs to analyze [10]: ") if icRange=="": icRange=10 icRange=range(int(icRange)) for ic in icRange: rowSumArray=getActivity(baseName+"_"+str(simNum)+"_ic"+str(ic)) j=0 averageActivity=[] while j<len(rowSumArray)-1: z=(rowSumArray[j]+rowSumArray[j+1])/2.0 averageActivity.append(z) j=j+1 plot(arange(len(averageActivity)),averageActivity,label='Average activity over time') title(baseName+"_"+str(simNum)+"_ic"+str(ic)) legend() show() #-----------------------------------------------------------------------# # Retrieve basic stats about series of simulations # #-----------------------------------------------------------------------# def getMultiNetworkStats(): baseName=raw_input("Enter base file name [timeSeries]: ") if baseName=="": baseName="timeSeries" simNumRange=raw_input("Enter number of simulations to analyze [1]: ") if simNumRange=="": simNumRange=1 icRange=raw_input("Enter number of ICs to analyze [10]: ") if icRange=="": icRange=10 multiStats={} for sim in range(int(simNumRange)): singleStats=getSingleNetworkStats(baseName,sim,icRange) for key in singleStats.keys(): if multiStats.has_key(key): multiStats[key].append(singleStats[key]) else: multiStats[key]=[] multiStats[key].append(singleStats[key]) return multiStats