def receive(self):
try:
received, address = self.socketConn.recvfrom(2048)
logMessage = "Received message from " + address
Logger.Log(0, logMessage)
except Exception as ex:
Logger.Log(1, "Failed to receive message: " + str(ex))
return ex
def bind(self):
try:
Logger.Log(0, "Binding Socket")
self.socketConn.bind((self.hostIP, self.hostPort))
Logger.Log(0, "Sucessfuly bind")
except Exception as ex:
Logger.Log(1, "Failed to bind:" + str(ex))
return ex
def send(self, message, destination):
try:
logMessage = "Sending Message to " + str(destination)
Logger.Log(0,logMessage)
data = message
self.socketConn.sendto(data.encode('utf-8'),destination)
Logger.Log(0,"Message Sent")
except Exception as ex:
Logger.Log(1, "Failed to send message: " + str(ex))
return ex
def regulate(self, iterations, output=False, log=False):
self.normalize()
for itter in range(iterations):
for i, gene in enumerate(self.genes):
# Save the old output values
# We don't want to regulate the input genes
if gene.type == "I":
continue
enh = 0.
inh = 0.
for j, g_j in enumerate(self.genes):
# We don't want to regulate with the output genes
if g_j.type == "O":
continue
enh += gene.enhImpacts[j] * g_j.concentration
inh += gene.inhImpacts[j] * g_j.concentration
enh /= len(self.genes)
inh /= len(self.genes)
# print("Gene: {} enh: {} inh: {} impact: {}".format(i, enh, inh, enh-inh))
# update the concentrations
impact = gene.concentration * self.delta * (enh - inh)
# print("old: {} impact: {} new: {}".format(gene.concentration, impact, gene.concentration + impact))
gene.concentration += impact
#ToDo:: I hate this
if gene.concentration < 0:
gene.concentration = 0
self.normalize()
self.mapValues()
# ToDo:: Probably need to change this format for logging and outputting for simplifying the network
if output:
print("Iteration {}".format(itter))
for i, gene in enumerate(self.genes):
print("Gene: {} Type: {} Concentration: {}".format(i, gene.type, gene.concentration))
log = True
if log:
if itter == 0:
header = ['time']
for i, gene in enumerate(self.genes):
header.append("{}.{}".format(gene.type, i))
LOG = L.Logger("Task", "regulation.csv", header, True)
LOG2 = L.Logger("Task", "outputs.csv", header, True)
data = "{},".format(itter)
data2 = "{},".format(itter)
for gene in self.genes:
data += "{},".format(gene.concentration)
try:
data2 += "{},".format(gene.extra[0])
except:
raise Exception("can't find extra information about the gene")
LOG.logln(data)
LOG2.logln(data2)
def regulate(self, iterations, output=False, log=False):
self.outputs = []
self.normalize()
# The time loop
for itter in range(iterations):
for i, gene in enumerate(self.genes):
# We don't want to regulate the input genes
if gene.type == "I":
continue
enh = 0.
inh = 0.
for j, g_j in enumerate(self.genes):
# We don't want to regulate with the output genes
if g_j.type == "O":
continue
enh += gene.enhImpacts[j] * g_j.concentration
inh += gene.inhImpacts[j] * g_j.concentration
enh /= (len(self.genes) - self.outputCount)
inh /= (len(self.genes) - self.outputCount)
# update the concentrations
impact = gene.concentration * self.delta * (enh - inh)
# print("old: {} impact: {} new: {}".format(gene.concentration, impact, gene.concentration + impact))
gene.concentration += impact
if gene.concentration < 0:
gene.concentration = 0
self.normalize()
# ToDo:: Probably need to change this format for logging and outputting for simplifying the network
if output:
print("Iteration {}".format(itter))
for i, gene in enumerate(self.genes):
print("Gene: {} Type: {} Concentration: {}".format(
i, gene.type, gene.concentration))
if log:
if itter == 0:
header = ['time']
for i, gene in enumerate(self.genes):
header.append("{}.{}".format(gene.type, i))
LOG = L.Logger("Task", "regulation.csv", header, True)
data = "{},".format(itter)
for gene in self.genes:
data += "{},".format(gene.concentration)
LOG.logln(data)
def regulate(self, iterations, output=False, log=False):
self.outputs = []
oldOutputs = []
# ToDo:: Computational cost can be reduced if we save a list of inputs/outputs
if self.mode == "binaryIncremental":
for gene in self.genes:
if gene.type == "O":
oldOutputs.append(gene.concentration)
elif self.mode == "continuous":
pass
else:
print("ERROR! Mode does not exist!")
exit(1)
for itter in range(iterations):
self.normalize()
for i, gene in enumerate(self.genes):
# Save the old output values
# We don't want to regulate the input genes
if gene.type == "I":
continue
enh = 0.
inh = 0.
for j, g_j in enumerate(self.genes):
# We don't want to regulate with the output genes
if g_j.type == "O":
continue
enh += gene.enhImpacts[j] * g_j.concentration
inh += gene.inhImpacts[j] * g_j.concentration
enh /= len(self.genes)
inh /= len(self.genes)
# print("Gene: {} enh: {} inh: {} impact: {}".format(i, enh, inh, enh-inh))
# update the concentrations
impact = gene.concentration * self.delta * (enh - inh)
# print("old: {} impact: {} new: {}".format(gene.concentration, impact, gene.concentration + impact))
gene.concentration += impact
if gene.concentration < 0:
gene.concentration = 0
self.normalize()
# ToDo:: Probably need to change this format for logging and outputting for simplifying the network
if output:
print("Iteration {}".format(itter))
for i, gene in enumerate(self.genes):
print("Gene: {} Type: {} Concentration: {}".format(
i, gene.type, gene.concentration))
if log:
if itter == 0:
header = ['time']
for i, gene in enumerate(self.genes):
header.append("{}.{}".format(gene.type, i))
LOG = L.Logger("Task", "regulation.csv", header, True)
data = "{},".format(itter)
for gene in self.genes:
data += "{},".format(gene.concentration)
LOG.logln(data)
# ToDo:: To reduce the computational cost, maybe add this to the normalize function? Or even saving a list of outputs might help.
if self.mode == "binaryIncremental":
outputIndex = -1
for gene in self.genes:
if gene.type == "O":
outputIndex += 1
# ExpValue: The equal part for not changing is an experimental value. But this makes sense cause it's the same as rounding up maybe? I don't know this at this point.
# if doesn't change or increases
if gene.concentration >= oldOutputs[outputIndex]:
self.outputs.append(1)
else:
# if becomes less
self.outputs.append(0)
else:
print("ERROR! Mode not coded -.- :( Exiting!")
exit(1)
pass
def __init__(self, hostIP, hostPort):
logMessage = "Initiating socket at " + hostIP +":" + str(hostPort)
Logger.Log(0, logMessage)
self.socketConn = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
self.hostIP = hostIP
self.hostPort = hostPort