def getOrigSpec(path=None, preProcess=False):
from pyspec.spectrum import spectrum
mainPath = getCurMainDir(path)
origSpec = spectrum(os.path.join(mainPath, "spectra", "origspect.dat"))
if preProcess:
origSpec = initialize.preProcessOrigSpec(origSpec)
return origSpec
def evolve(conn, SNSpecID, GARunID=None, description=None, generations=20, populationSize=150,
breedFunc = breed, selectFunc=geneticDalekAlgo.selectRoulette,
crossFunc=geneticDalekAlgo.crossSingle,
randomParamFunc = geneticDalekAlgo.createRandomLogNormalValueW7):
#Run the GA
startTime = datetime.datetime.now()
#Initializing cursor
curs = conn.cursor()
#trying to remove existing break and debug switches
try:
os.remove('break_after_loop')
except:
pass
try:
os.remove('debug_after_loop')
except:
pass
#Initializing random seed
random.seed(config.GAConfDict['seed'])
#Initializing mode dependent constants:
generationGapNo=int(populationSize * config.GAConfDict['generationGapFraction'])
subPopulationNo=int(populationSize * config.GAConfDict['generationGapFraction']
* config.GAConfDict['subPopulationFraction'])
#Launching the gateways
gws=elauncher.gateways()
#getting origSpec and preparing it
rawOrigSpec = curs.execute('select SPECTRUM from SN_SPECTRA where ID=%d' % SNSpecID).fetchall()[0]
origSpec = initialize.preProcessOrigSpec(rawOrigSpec[0])
breedSource = dalekDB.makeZipPickle(inspect.getsource(breedFunc))
GAConfSource = dalekDB.makeZipPickle(config.GAConfDict)
crossSource = dalekDB.makeZipPickle(inspect.getsource(crossFunc))
selectSource = dalekDB.makeZipPickle(inspect.getsource(selectFunc))
fitSource = dalekDB.makeZipPickle(inspect.getsource(genFitness.fitFunc))
#Getting SNConfigDict
SNConfigDict = config.getSNConfigDict(conn)
SNConfigDict['t'] = config.getTimeFromExplosion(conn, SNSpecID, SNConfigDict)
#setting time
param.SNConfigDict = SNConfigDict
#Checking for continue or new
if GARunID!=None:
raise NotImplementedError('soon.....')
if GARunID == None: #or GA_CUR_GEN=0
#creating new GA_RUN entry and inserting the code of various functions
curs.execute('insert into GA_RUN(DESCRIPTION, SN_ID, START_TIME,'
'SN_SPECTRUM, GA_POP_SIZE, GA_GENERATION_SIZE, GA_CONF_DICT, GA_BREED_FUNC,'
'GA_CROSS_FUNC, GA_SELECT_FUNC, GA_FITNESS_FUNC)'
' VALUES(?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)',
(description, SNSpecID, startTime,
origSpec, populationSize, generations, GAConfSource, breedSource,
crossSource, selectSource, fitSource))
GARunID = curs.lastrowid
curs.execute('insert into GA_GENERATION(GA_RUN_ID) VALUES(?)', (GARunID,))
generationID = curs.lastrowid
curGenerationSet = geneticDalekAlgo.createRandomParamSet(populationSize)
#Inserting the dica into the database, this dica will be used throughout the run
dicaID = dalekDB.insertDica(conn, curGenerationSet.paramGrid[0].dica)
firstGeneration = 0
# Checking availability on gateways
gws.checkAvailability()
pp.pprint(gws.availability)
#Launching
curGenerationModel = elauncher.cloudLaunch(curGenerationSet.paramGrid, gws.getAvailGateWays(), origSpec=origSpec)
#getting fitnesses from the model
fitness = curGenerationModel['fitness']
fitnessIDX = np.argsort(fitness)[::-1]
keepChildren = param.multiParam()
keepChildren.grid = np.array([])
keepModelIDs = np.array([])
keepFitness = np.array([])
for i in range(firstGeneration,generations):
#getting current time
curTime=time.time()
#saving model to db
modelIDs = curGenerationModel.toDB(conn, dicaID=dicaID, storeLList=False, storeWParam=False)
#main link between models and the GA for the keeping
dalekDB.insertGAIndividual(conn, generationID, keepModelIDs, keepFitness)
#main link between models and the GA
dalekDB.insertGAIndividual(conn, generationID, modelIDs, fitness)
curs.execute('update GA_RUN set GA_CUR_GEN=? where ID=?', (generationID, GARunID))
#getting new generation
curs.execute('insert into GA_GENERATION(GA_RUN_ID) VALUES(?)', (GARunID,))
generationID = curs.lastrowid
#uniting old keepChildren and current generation model
curGenerationModel.grid=np.concatenate((keepChildren.grid,curGenerationModel.grid))
curGenerationModel._initSpecs()
modelIDs = np.concatenate((keepModelIDs, modelIDs))
#getting fitnesses from the model
fitness = curGenerationModel['fitness']
fitnessIDX = np.argsort(fitness)[::-1]
#Checking for break conditions
if os.path.exists('break_after_loop'): break
if os.path.exists('debug_after_loop'):
try:
os.remove('debug_after_loop')
except:
pass
pdb.set_trace()
#start selective breeding
#First the children that are kept for the subpopulation are put into a seperate variable
if config.GAConfDict['mode'] == 'subpopulation':
if populationSize==subPopulationNo:
keepChildren=param.multiParam()
keepChildren.grid=np.array([])
else:
keepChildren = model.modelGrid(paramList=curGenerationModel.
grid[fitnessIDX[:(populationSize-subPopulationNo)]],
origSpec=origSpec)
keepModelIDs = modelIDs[fitnessIDX[:(populationSize - subPopulationNo)]]
keepFitness = fitness[fitnessIDX[:(populationSize - subPopulationNo)]]
keepChildren._initSpecs()
elif config.GAConfDict['mode'] == 'elitism':
keepChildren = model.modelGrid(paramList=curGenerationModel.
grid[fitnessIDX[:int(populationSize * config.GAConfDict['elitism'])]],
origSpec=origSpec)
keepModelIDs = modelIDs[fitnessIDX[:(populationSize * config.GAConfDict['elitism'])]]
keepFitness = fitness[fitnessIDX[:(populationSize * config.GAConfDict['elitism'])]]
keepChildren._initSpecs()
#Now we get the population that is used for breeding and submit it to the breed function
breedPopulation=model.modelGrid(paramList=curGenerationModel.
grid[fitnessIDX[:generationGapNo]],
origSpec=origSpec)
if config.GAConfDict['mode'] == 'subpopulation':
curGenerationSet=breed(breedPopulation,
popNum=subPopulationNo, select=selectFunc, cross=crossFunc)
elif config.GAConfDict['mode'] == 'elitism':
curGenerationSet=breed(breedPopulation,
popNum=int(populationSize*(1-config.GAConfDict['elitism'])), select=selectFunc, cross=crossFunc)
del curGenerationModel
#Time is kept
ficaTime=time.time()
#Network check for available nodes
gws.checkAvailability()
pp.pprint(gws.availability)
#Calculating the new generation with elauncher
curGenerationModel = elauncher.cloudLaunch(curGenerationSet.paramGrid, gws.getAvailGateWays(), origSpec=origSpec)
conn.commit()
#Printing time statements
print "Took %.3f for the fica runs" % (time.time()-ficaTime)
print "Took %.3f seconds for last loop" % (time.time()-curTime)
curs.execute('update GA_RUN set END_TIME=? where ID=?', (datetime.datetime.now(), GARunID))
