def run_main():
initialPopulationSize = 51
generations = 1500
conf = LoadSystemConfiguration() #TODO make an object to encapsulate this kind of information
# Genome instance
genome = G2DList.G2DList(400, 18)
genome.setParams(rangemin=0, rangemax=360)
# The evaluator function (objective function)
genome.evaluator.set(eval_func)
genome.crossover.set(Crossovers.G2DListCrossoverSingleHPoint)
#genome.mutator.set(Mutators.G2DListMutatorIntegerRange)
genome.mutator.set(Mutators.G2DListMutatorIntegerGaussian)
# Genetic Algorithm Instance
ga = GSimpleGA.GSimpleGA(genome)
ga.setGenerations(generations) #TODO class atribute
ga.setPopulationSize(initialPopulationSize) #TODO class atribute
ga.setMutationRate(0.2)
ga.selector.set(Selectors.GRankSelector)
#ga.selector.set(Selectors.GTournamentSelector)
#ga.selector.set(Selectors.GRouletteWheel)
ga.setElitism(True)
ga.setElitismReplacement(initialPopulationSize/3)
#ga.terminationCriteria.set(ConvergenceCriteria)
# Create DB Adapter and set as adapter
sqlite_adapter = DBAdapters.DBSQLite(identify="Lucy walk", resetDB=True)
ga.setDBAdapter(sqlite_adapter)
#callback to persist best individual of each generation
ga.stepCallback.set(generationCallback)
#keep a reference to the genetic algorithm engine
global gaEngine
gaEngine = ga
# Do the evolution, with stats dump
# frequency of 2 generations
ga.evolve(freq_stats=1)
# Best individual
best = ga.bestIndividual()
score = best.getRawScore()
timestr = time.strftime("%Y%m%d-%H%M%S")
filename = str(score) + "-" + timestr + "-" + str(generations) + ".xml"
prop = DTIndividualPropertyVanilla() #TODO create a vanilla property as default argument in Individual constructor
bestIndividual = Individual(prop, DTIndividualGeneticMatrix(chromosomeToLucyGeneticMatrix(best)))
geneticPoolDir = os.getcwd()+conf.getDirectory("Genetic Pool")
bestIndividual.persist(geneticPoolDir + filename)
#TODO store all the population, not only the fitest
print ga.getStatistics()
def setInitialPopulation (ga_engine):
prop = DTIndividualPropertyCMUDaz()
propVanilla = DTIndividualPropertyVanilla()
balieroProp = DTIndividualPropertyBaliero()
conf = LoadSystemConfiguration()
CMUxmlDir = os.getcwd()+conf.getDirectory("Transformed CMU mocap Files")
GAwalkDir = os.getcwd()+conf.getDirectory("GAWalk Files")
UIBLHDir = os.getcwd()+conf.getDirectory("UIBLH mocap Files")
BalieroDir = os.getcwd()+conf.getDirectory("Baliero transformed walk Files")
ADHOCDir = os.getcwd()+conf.getDirectory("ADHOC Files")
geneticPoolDir = os.getcwd()+conf.getDirectory("Genetic Pool")
population = ga_engine.getPopulation()
popSize = len(population)
individualCounter = 0
# if individualCounter < popSize:
# for filename in glob.glob(os.path.join(GAwalkDir, '*.xml')):
# print individualCounter, " individuals processed!"
# print 'inserting individual: ' + filename + " into the initial population"
# walk = Individual(propVanilla, DTIndividualGeneticTimeSerieFile(filename))
# geneticMatrix = walk.getGenomeMatrix()
# if individualCounter < popSize:
# adan = population[individualCounter]
# for i in xrange(adan.getHeight()):
# if i == len(geneticMatrix):
# break
# for j in xrange(adan.getWidth()):
# adan.setItem(i,j,geneticMatrix[i][j])
# population[individualCounter]=adan
# individualCounter = individualCounter + 1
# else:
# break
if individualCounter < popSize:
for filename in glob.glob(os.path.join(CMUxmlDir, '*.xml')):
print individualCounter, " individuals processed!"
print 'inserting individual: ' + filename + " into the initial population"
walk = Individual(prop, DTIndividualGeneticTimeSerieFile(filename))
geneticMatrix = walk.getGenomeMatrix()
if individualCounter < popSize:
adan = population[individualCounter]
for i in xrange(adan.getHeight()):
if i == len(geneticMatrix):
break
for j in xrange(adan.getWidth()):
adan.setItem(i,j,geneticMatrix[i][j])
population[individualCounter]=adan
individualCounter = individualCounter + 1
else:
break
global initialPopulationSetted
initialPopulationSetted = True
def generationCallback(ga_engine):
# persist best individual at the moment
conf = LoadSystemConfiguration() #TODO make an object to encapsulate this kind of information
geneticPoolDir = os.getcwd()+conf.getDirectory("Genetic Pool")
gen = ga_engine.getCurrentGeneration()
best = ga_engine.bestIndividual()
score = best.getRawScore()
timestr = time.strftime("%Y%m%d-%H%M%S")
filename = str(score) + "-" + timestr + "-" + str(gen) + ".xml"
prop = DTIndividualPropertyVanilla() #TODO create a vanilla property as default argument in Individual constructor
bestIndividual = Individual(prop, DTIndividualGeneticMatrix(chromosomeToLucyGeneticMatrix(best)))
bestIndividual.persist(geneticPoolDir + filename)
ga_engine.getDBAdapter().commit()
##population = ga_engine.getPopulation()
##averagePopulation = getPopulationAverage(population)
#averageGeneration = getPopulationAverage(gen)
##print "current population raw score average: ", averagePopulation
#print "current generation raw score average: ", averageGeneration
return False
def generationCallback(ga_engine):
# persist best individual at the moment
conf = LoadSystemConfiguration() #TODO make an object to encapsulate this kind of information
geneticPoolDir = os.getcwd()+conf.getDirectory("Genetic Pool")
gen = ga_engine.getCurrentGeneration()
best = ga_engine.bestIndividual()
score = best.getRawScore()
#check if the convergence criteria has been reached
global max_score, max_score_generation, convergenceCriteria
if score > max_score:
max_score = score
max_score_generation = gen
else:
#if the score doesn't improve in NUMBER_GENERATIONS_CONVERGENCE_CRITERIA generations then there is no reason to continue and we have reach a convergence
if gen - max_score_generation > NUMBER_GENERATIONS_CONVERGENCE_CRITERIA:
convergenceCriteria = True
timestr = time.strftime("%Y%m%d-%H%M%S")
filename = str(score) + "-" + timestr + "-" + str(gen) + ".xml"
#at generation 0 is the firs time to create de directory and store the GA parameters
if gen == 0:
global experimentDir
experimentDir = geneticPoolDir + timestr
global experimentTime
experimentTime = timestr
os.mkdir(experimentDir)
storeExperimentGAparameters()
prop = DTIndividualPropertyVanilla()
bestIndividual = Individual(prop, DTIndividualGeneticMatrix(chromosomeToLucyGeneticMatrix(best)))
bestIndividual.persist(os.path.join(experimentDir, filename))
ga_engine.getDBAdapter().commit()
#population = ga_engine.getPopulation()
#popSize = len(population)
print "generation executed!, best fit of generation: ", score, "fittest: ", max_score, "reached in generation: ", max_score_generation
return False
from datatypes.DTIndividualGeneticMaterial import DTIndividualGeneticTimeSerieFile, \
DTIndividualGeneticTimeSerieFileWalk
from datatypes.DTIndividualProperty import DTIndividualPropertyCMUDaz, DTIndividualPropertyVanilla, DTIndividualPropertyBaliero, DTIndividualPropertyVanillaEvolutive, DTIndividualPropertyPhysicalBioloid, DTIndividualPropertyVanillaEvolutiveNoAvoid
from Individual import Individual
propCMUDaz = DTIndividualPropertyCMUDaz()
propVanilla = DTIndividualPropertyVanilla()
balieroProp = DTIndividualPropertyBaliero()
physicalProp = DTIndividualPropertyPhysicalBioloid()
geneticVanillaProp = DTIndividualPropertyVanillaEvolutive()
geneticVanillaPropNothingToAvoid = DTIndividualPropertyVanillaEvolutiveNoAvoid()
conf = LoadSystemConfiguration()
CMUxmlDir = os.getcwd()+conf.getDirectory("Transformed CMU mocap Files")
GAwalkDir = os.getcwd()+conf.getDirectory("GAWalk Files")
UIBLHDir = os.getcwd()+conf.getDirectory("UIBLH mocap Files")
BalieroDir = os.getcwd()+conf.getDirectory("Baliero transformed walk Files")
ADHOCDir = os.getcwd()+conf.getDirectory("ADHOC Files")
geneticPoolDir = os.pardir+conf.getDirectory("Genetic Pool")
arguments = len(sys.argv)
def createIndividual(filename):
if int(conf.getProperty("Lucy simulated?"))==1:
if int(conf.getProperty("Concatenate walk cycles?")):
walkEmbryo = DTIndividualGeneticTimeSerieFileWalk(os.getcwd()+"/"+filename)
else:
walkEmbryo = DTIndividualGeneticTimeSerieFile(os.getcwd()+"/"+filename)
def setInitialPopulation(ga_engine):
propCMUDaz = DTIndividualPropertyCMUDaz()
propVanilla = DTIndividualPropertyVanilla()
balieroProp = DTIndividualPropertyBaliero()
conf = LoadSystemConfiguration()
lucyCycles = os.getcwd()+conf.getDirectory("Lucy evolved walk cycles Files")
CMUxmlDir = os.getcwd()+conf.getDirectory("Transformed CMU mocap Files")
GAwalkDir = os.getcwd()+conf.getDirectory("GAWalk Files")
UIBLHDir = os.getcwd()+conf.getDirectory("UIBLH mocap Files")
BalieroDir = os.getcwd()+conf.getDirectory("Baliero transformed walk Files")
ADHOCDir = os.getcwd()+conf.getDirectory("ADHOC Files")
geneticPoolDir = os.getcwd()+conf.getDirectory("Genetic Pool")
population = ga_engine.getPopulation()
popSize = len(population)
individualCounter = 0
walk = Individual(propVanilla, DTIndividualGeneticMatrix()) #dummy individual to initialise the simulator and enable the time step configuration
walk.execute()
print "please set the proper time step in vrep"
dtgenoma = DTGenomeFunctions()
#the random initia population created is replaced by the imitation motion capture database
if individualCounter < popSize:
for filename in glob.glob(os.path.join(CMUxmlDir, '*.xml')):
if individualCounter < popSize:
print individualCounter, " individuals processed!"
print 'inserting individual: ' + filename + " into the initial population"
walk = Individual(propCMUDaz, DTIndividualGeneticTimeSerieFile(filename))
teacherGeneticMatrix = walk.getGenomeMatrix()
adan = population[individualCounter]
adanIndividualLength=dtgenoma.getIndividualLength(adan)
adanJointLength=dtgenoma.getIndividualFrameLength(adan)
for i in xrange(adanIndividualLength):
for j in xrange(adanJointLength):
if i < len(teacherGeneticMatrix): #if the fixed gnoma representation size is less than the teacher size
adan.setItem(i,j,teacherGeneticMatrix[i][j])
else:
#put a sentinel joint value to mark the end of the individual
adan.setItem(i,j,sysConstants.JOINT_SENTINEL)
population[individualCounter]=adan
individualCounter = individualCounter + 1
else:
break
#uncomment this block and comment the one above to use individuals with vainilla format
'''if individualCounter < popSize:
for filename in glob.glob(os.path.join(CMUxmlDir, '*.xml')):
if individualCounter < popSize:
print individualCounter, " individuals processed!"
print 'inserting individual: ' + filename + " into the initial population"
walk = Individual(propVanilla, DTIndividualGeneticTimeSerieFile(filename))
teacherGeneticMatrix = walk.getGenomeMatrix()
adan = population[individualCounter]
adanIndividualLength=dtgenoma.getIndividualLength(adan)
adanJointLength=dtgenoma.getIndividualFrameLength(adan)
for i in xrange(adanIndividualLength):
for j in xrange(adanJointLength):
if i < len(teacherGeneticMatrix): #if the fixed gnoma representation size is less than the teacher size
adan.setItem(i,j,teacherGeneticMatrix[i][j])
else:
#put a sentinel joint value to mark the end of the individual
adan.setItem(i,j,sysConstants.JOINT_SENTINEL)
population[individualCounter]=adan
individualCounter = individualCounter + 1
else:
break
'''
global initialPopulationSetted
initialPopulationSetted = True
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
import os
import glob
import ntpath
from parser.BvhImport import BvhImport
import matplotlib.pyplot as plt
from configuration.LoadSystemConfiguration import LoadSystemConfiguration
import numpy as np
from scipy.signal import argrelextrema
from collections import Counter
sysConf = LoadSystemConfiguration()
BVHDir = os.getcwd() + sysConf.getDirectory("CMU mocap Files")
Y_THREADHOLD = 11 #TODO calculate this as the average of the steps_highs
X_THREADHOLD = 36
def firstMax(values1, values2):
res=0
for i in range(len(values1)-2):
if values1[i] < values1[i+1] and values1[i+1] > values1[i+2]: #i+1 is a local maximun
if (values1[i] - values2[i]) > THREADHOLD:
res=i+1
elif values1[i] < values1[i+1] < values1[i+2]: #i is a local maximun
if (values1[i] - values2[i]) > THREADHOLD:
res=i
return res
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
from parser.JointCalculation import JointCalculation
from parser.MocapLucyMapping import MocapLucyMapping
from simulator.LoadRobotConfiguration import LoadRobotConfiguration
from configuration.LoadSystemConfiguration import LoadSystemConfiguration
from string import rstrip
import os
import glob
import ntpath
sysConf = LoadSystemConfiguration()
BVHDir = os.getcwd() + sysConf.getDirectory("CMU mocap Files")
XMLDir = os.getcwd() + sysConf.getDirectory("Transformed CMU mocap Files")
robotConfiguration = LoadRobotConfiguration()
for filename in glob.glob(os.path.join(BVHDir, '*.bvh')):
print "transforming: " + filename + " ..."
lucyFileConversion = MocapLucyMapping(filename, robotConfiguration)
newFile = ntpath.basename(filename)
transformedFileName = newFile
newFile = rstrip(newFile[:-4]) + ".xml"
newFile = XMLDir + newFile
lucyFileConversion.generateFile(newFile)
print "file: " + newFile + " generated!"
os.rename(filename, os.path.join(BVHDir)+"/transformed/"+transformedFileName)
import sys
import time
from configuration.LoadSystemConfiguration import LoadSystemConfiguration
from datatypes.DTIndividualGeneticMaterial import DTIndividualGeneticTimeSerieFile, DTIndividualGeneticMatrix
from datatypes.DTIndividualProperty import DTIndividualPropertyBaliero, DTIndividualPropertyPhysicalBioloid
from Individual import Individual
balieroProp = DTIndividualPropertyBaliero()
physicalProp = DTIndividualPropertyPhysicalBioloid()
conf = LoadSystemConfiguration()
BalieroDir = os.getcwd()+conf.getDirectory("Baliero transformed walk Files")
arguments = len(sys.argv)
def createIndividual(filename):
if int(conf.getProperty("Lucy simulated?"))==1:
walk = Individual(balieroProp, DTIndividualGeneticTimeSerieFile(os.getcwd()+"/"+filename))
else:
walk = Individual(physicalProp, DTIndividualGeneticTimeSerieFile(os.getcwd()+"/"+filename))
return walk
walk = Individual(balieroProp, DTIndividualGeneticMatrix()) #dummy individual to initialise the simulator and enable the time step configuration
walk.execute()
print "please set the proper time step in vrep"
time.sleep(5)
if arguments > 1:
from parser.LoadPoses import LoadPoses
from datatypes.DTIndividualProperty import DTIndividualProperty, DTIndividualPropertyCMUDaz, DTIndividualPropertyVanilla, DTIndividualPropertyBaliero, DTIndividualPropertyVanillaEvolutive, DTIndividualPropertyPhysicalBioloid
from datatypes.DTIndividualGeneticMaterial import DTIndividualGeneticMaterial, DTIndividualGeneticTimeSerieFile, DTIndividualGeneticMatrix
from Pose import Pose
from configuration.LoadSystemConfiguration import LoadSystemConfiguration
from simulator.LoadRobotConfiguration import LoadRobotConfiguration
from Individual import Individual
import os
import glob
import time
import sys
propCMUDaz = DTIndividualPropertyCMUDaz()
propVanilla = DTIndividualPropertyVanilla()
balieroProp = DTIndividualPropertyBaliero()
physicalProp = DTIndividualPropertyPhysicalBioloid()
geneticVanillaProp = DTIndividualPropertyVanillaEvolutive()
conf = LoadSystemConfiguration()
CMUxmlDir = os.getcwd()+conf.getDirectory("Transformed CMU mocap Files")
for filename in glob.glob(os.path.join(CMUxmlDir, '*.xml')):
walk = Individual(propCMUDaz, DTIndividualGeneticTimeSerieFile(filename))
fitness = walk.execute()
length = walk.getLength()
walk.persist("/tmp/"+str(fitness)+".xml")
print "individual: ", filename, "fitness: ", fitness, "length: ", length
