def run(self, filename, path):
file = open(
path + "input/" + filename,
"r",
)
sequence = file.readline()
# Clean up data
sequence = sequence.replace(' ', '')
sequence = sequence.upper()
minStem = func.getMinStem(len(sequence))
# # Override rule
minStem = 3
print(sequence)
# Parameters
iteration = 100
popSize = 70
KELossRate = 0.55
MoleColl = 0.30
InitialKE = 0
alpha = 2
beta = 8
buffer = 0
# Timer starts
tictoc.tic()
#----------------------------------------------------------------------------------------------
# Population generation
#----------------------------------------------------------------------------------------------
mole = Molecule()
mole.Mol(sequence, popSize, InitialKE, minStem)
# # Save initial informations
# minEnergy = 99999
# index = 0
# minIndex = 0
# initPop = open(path+"output/initial_population_"+filename,"a")
# for molecule in mole.molecules:
# # initPop.write(population.PrintableMolecule(molecule)
# # initPop.write(str(mole.PE[index]))
# # initPop.write("\n")
# if(mole.moleculeEnergy[index]<minEnergy):
# minIndex = index
# minEnergy=mole.moleculeEnergy[index]
# index+=1
# # endfor
# initPop.write("\n")
#----------------------------------------------------------------------------------------------
# Optimize with CRO
#----------------------------------------------------------------------------------------------
C = CRO()
# C.Init(popSize, KELossRate, MoleColl, InitialKE, alpha, beta, buffer, sequence, mole)
sen, sp, f_m, tp, fp, fn, time, ene = C.CRO(popSize, KELossRate,
MoleColl, InitialKE, alpha,
beta, buffer, sequence,
mole, iteration, path,
filename)
return sen, sp, f_m, tp, fp, fn, time, ene
def run(self):
# path = "../data/sa/"
path = '../data/input/dlp 6-5/'
filename = 'data8.txt'
f = open(path + filename, "r")
iteration = 80
myList = Main().dataClean(f)
department = myList[0] # N = number of departments
period = myList[1] # P = total time period
# print(myList)
shiftCost = Main().shiftCost(myList, department)
flowCost = Main().allflowCost(myList, department)
print(flowCost)
print(shiftCost)
P, N = period, department
# print(department)
# print(period)
print(period)
sequence_object = Sequence()
sequence = sequence_object.sequence_generator_smart(
department, period, filename)
# sequence = [[1,3,5,6,4,2], [1,4,2,5,3,6], [1,5,3,2,4,6], [1,6,4,2,5,3], [3,2,6,4,1,5]]
# sequence = [[6, 2, 25, 29, 22, 9, 17, 4, 11, 10, 18, 7, 5, 12, 21, 3, 28, 19, 20, 24, 27, 1, 8, 13, 14, 15,
# 16, 23, 26, 30], [27, 23, 10, 16, 14, 28, 24, 2, 4, 17, 22, 6, 12, 7, 30, 1, 8, 3, 29, 18, 21, 13, 5, 9, 11, 15, 19, 20, 25, 26], [27, 23, 18, 16, 14, 28, 24, 2, 4, 17, 22, 6, 12, 7, 30, 1, 8, 3, 29, 10, 21, 13, 5, 9, 11, 15, 19, 20, 25, 26], [11, 20, 1, 15, 4, 9, 5, 12, 30, 14, 21, 28, 6, 24, 22, 17, 29, 25, 23, 27, 10, 2, 3, 7, 8, 13, 16, 18, 19, 26], [27, 3, 24, 20, 14, 5, 9, 28, 2, 16, 17, 10, 4, 7, 6, 25, 15, 18, 29, 22, 21, 1, 8, 11, 12, 13, 19, 23, 26, 30], [14, 16, 13, 26, 17, 6, 29, 25, 12, 7, 20, 30, 8, 1, 5, 11, 21, 28, 2, 24, 23, 3, 4, 9, 10, 15, 18, 19, 22, 27], [27, 23, 10, 16, 14, 28, 24, 2, 4, 17, 3, 6, 12, 7, 30, 18, 13, 22, 11, 1, 8, 5, 9, 15, 19, 20, 21, 25, 26, 29], [10, 21, 6, 23, 7, 9, 2, 5, 28, 20, 30, 18, 25, 4, 14, 17, 3, 16, 15, 29, 19, 1, 13, 8, 11, 12, 22, 24, 26, 27], [27, 23, 4, 16, 14, 28, 24, 2, 10, 17, 22, 6, 12, 7, 30, 21, 5, 29, 25, 1, 3, 8, 9, 11, 13, 15, 18, 19, 20, 26], [23, 21, 22, 10, 12, 28, 19, 14, 24, 6, 29, 2, 13, 20, 11, 16, 8, 7, 17, 27, 15, 4, 1, 3, 5, 9, 18, 25, 26, 30]]
# sequence1,testSequence1 = Main().SequenceGenerator(P,N)
# sequence2,testSequence2 = Main().SequenceGenerator(P,N)
# print(sequence)
# Parameters
popSize = 30
KELossRate = 0.45
MoleColl = 0.35
InitialKE = 0
# non negative number tolerance of system accepting worst solution
alpha = 5
beta = 6
buffer = 0
# ----------------------------------------------------------------------------------------------
# Population generation
# ----------------------------------------------------------------------------------------------
# sequence = testSequence
sequence = Main.SequenceGenerator(self, period, department)
mole = Molecule()
mole.Mol(sequence, period, department, shiftCost, flowCost)
# Save initial information
minEnergy = 999999
index = 0
minIndex = 0
# initPop = [[6, 4, 1, 2, 5, 3], [1, 6, 4, 2, 5, 3], [1, 5, 4, 2, 3, 6], [2, 5, 3, 1, 4, 6], [2, 3, 1, 5, 4, 6]]
initPop = Main.SequenceGenerator(period, period, department)
initPop = sequence
# end for
# initPop.write("\n")
# ----------------------------------------------------------------------------------------------
# Optimize with CRO
# ----------------------------------------------------------------------------------------------
c = CRO()
# C.Init(popSize, KELossRate, MoleColl, InitialKE, alpha, beta, buffer, sequence, mole)
c.CRO(popSize, KELossRate, MoleColl, InitialKE, alpha, beta, buffer,
sequence, mole, iteration, initPop, shiftCost, flowCost, N)
