def periodicOrbitTest():
numGenes = 25
network = gn.geneNetwork(preset="RANDOM", numNodes=numGenes, connectionsPerNode=int(0.2*numGenes))
#print network.findPeriodicOrbit(threshold = 0)
#print network.countAttractors(numICs=100, threshold=0)
network.generateAttractorsVsThreshold(thresholdMin=-10, thresholdMax=15,
thresholdStep=0.25, numICsPerThreshold=400)
def timingGEDTest():
#Testing expression diversity code
nStart = 200
nEnd = 1600
times = []
for numGenes in xrange(nStart, nEnd, 100):
network = gn.geneNetwork(preset="RANDOM", numNodes=numGenes, connectionsPerNode=int(0.01*numGenes))
t1 = time.time()
network.generateExpDivVsThreshold(thresholdMin=0, thresholdMax=1,
thresholdStep=1, numICsPerThreshold=10)
t2 = time.time()
times.append(t2 - t1)
#Plot the timings
plt.clf()
plt.plot(xrange(nStart, nEnd, 100), times)
plt.ylabel('Time to compute (s)')
plt.xlabel('Number of nodes')
plt.grid(True)
plt.savefig("GEDBenchmark4.jpg")
def diversityTest():
numGenes = 25
network = gn.geneNetwork(preset="RANDOM", numNodes=numGenes, connectionsPerNode=int(0.2*numGenes))
network.generateDiversityVsThreshold(thresholdMin=-3, thresholdMax=4,
thresholdStep=0.1, numICsPerThreshold = 200)
def hammingDistanceTest():
numGenes = 1000
network = gn.geneNetwork(preset="RANDOM", numNodes=numGenes, connectionsPerNode=int(0.2*numGenes))
network.generateHammingDistVsThreshold(thresholdMin=-4, thresholdMax=5,
thresholdStep=0.2, numICsPerThreshold = 10,
numTimeStepsToSaturate=10, diffPermutation=0.1)
def geneExpressionDiversityTest():
numGenes = 25
network = gn.geneNetwork(preset="RANDOM", numNodes=numGenes, connectionsPerNode=int(0.2*numGenes))
network.generateExpDivVsThreshold(thresholdMin=-10, thresholdMax=15,
thresholdStep=0.25, numICsPerThreshold = 400)