Python tools.Logbook方法代码示例

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def main():
    pop = toolbox.population(n=5)
    stats = tools.Statistics(lambda ind: ind.fitness.values)
    stats.register("avg", numpy.mean)
    stats.register("std", numpy.std)
    stats.register("min", numpy.min)
    stats.register("max", numpy.max)

    logbook = tools.Logbook()
    logbook.header = ["gen", "evals"] + stats.fields

    GEN = 1000
    best = None

    for g in range(GEN):
        for part in pop:
            part.fitness.values = toolbox.evaluate(part)
            if part.best is None or part.best.fitness < part.fitness:
                part.best = creator.Particle(part)
                part.best.fitness.values = part.fitness.values
            if best is None or best.fitness < part.fitness:
                best = creator.Particle(part)
                best.fitness.values = part.fitness.values
        for part in pop:
            toolbox.update(part, best)

        # Gather all the fitnesses in one list and print the stats
        logbook.record(gen=g, evals=len(pop), **stats.compile(pop))
        print(logbook.stream)
    
    return pop, logbook, best 

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def main():
    pop = toolbox.population(n=5)
    stats = tools.Statistics(lambda ind: ind.fitness.values)
    stats.register("avg", numpy.mean)
    stats.register("std", numpy.std)
    stats.register("min", numpy.min)
    stats.register("max", numpy.max)

    logbook = tools.Logbook()
    logbook.header = ["gen", "evals"] + stats.fields

    GEN = 1000
    best = None

    for g in range(GEN):
        for part in pop:
            part.fitness.values = toolbox.evaluate(part)
            if not part.best or part.best.fitness < part.fitness:
                part.best = creator.Particle(part)
                part.best.fitness.values = part.fitness.values
            if not best or best.fitness < part.fitness:
                best = creator.Particle(part)
                best.fitness.values = part.fitness.values
        for part in pop:
            toolbox.update(part, best)

        # Gather all the fitnesses in one list and print the stats
        logbook.record(gen=g, evals=len(pop), **stats.compile(pop))
        print(logbook.stream)
    
    return pop, logbook, best 

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def main():
    """Implements the One-Fifth rule algorithm as expressed in :
    Kern, S., S.D. Muller, N. Hansen, D. Buche, J. Ocenasek and P. Koumoutsakos (2004). 
    Learning Probability Distributions in Continuous Evolutionary Algorithms - 
    A Comparative Review. Natural Computing, 3(1), pp. 77-112.

    However instead of parent and offspring the algorithm is expressed in terms of
    best and worst. Best is equivalent to the parent, and worst to the offspring.
    Instead of producing a new individual each time, we have defined a function which
    updates the worst individual using the best one as the mean of the gaussian and 
    the sigma computed as the standard deviation.
    """
    random.seed(64)
    
    logbook = tools.Logbook()
    logbook.header = "gen", "fitness"

    interval = (-3,7)
    mu = (random.uniform(interval[0], interval[1]) for _ in range(IND_SIZE))
    sigma = (interval[1] - interval[0])/2.0
    alpha = 2.0**(1.0/IND_SIZE)

    best = creator.Individual(mu)
    best.fitness.values = toolbox.evaluate(best)
    worst = creator.Individual((0.0,)*IND_SIZE)

    NGEN = 1500
    for g in range(NGEN):
        toolbox.update(worst, best, sigma) 
        worst.fitness.values = toolbox.evaluate(worst)
        if best.fitness <= worst.fitness:
            sigma = sigma * alpha
            best, worst = worst, best
        else:
            sigma = sigma * alpha**(-0.25)
            
        logbook.record(gen=g, fitness=best.fitness.values)
        print(logbook.stream)
    
    return best 

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def setUp(self):
        self.logbook = tools.Logbook()
        print 

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def test_pickle_logbook(self):
        stats = tools.Statistics()
        logbook = tools.Logbook()

        stats.register("mean", numpy.mean)
        record = stats.compile([1,2,3,4,5,6,8,9,10])
        logbook.record(**record)

        logbook_s = pickle.dumps(logbook)
        logbook_r = pickle.loads(logbook_s)

        self.assertEqual(logbook, logbook_r, "Unpickled logbook != pickled logbook") 

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def varOr(population, toolbox, lambda_, cxpb, mutpb):
    """Part of an evolutionary algorithm applying only the variation part
    (crossover, mutation **or** reproduction). The modified individuals have
    their fitness invalidated. The individuals are cloned so returned
    population is independent of the input population.
    :param population: A list of individuals to vary.
    :param toolbox: A :class:`~deap.base.Toolbox` that contains the evolution
                    operators.
    :param lambda\_: The number of children to produce
    :param cxpb: The probability of mating two individuals.
    :param mutpb: The probability of mutating an individual.
    :returns: The final population
    :returns: A class:`~deap.tools.Logbook` with the statistics of the
              evolution
    The variation goes as follow. On each of the *lambda_* iteration, it
    selects one of the three operations; crossover, mutation or reproduction.
    In the case of a crossover, two individuals are selected at random from
    the parental population :math:`P_\mathrm{p}`, those individuals are cloned
    using the :meth:`toolbox.clone` method and then mated using the
    :meth:`toolbox.mate` method. Only the first child is appended to the
    offspring population :math:`P_\mathrm{o}`, the second child is discarded.
    In the case of a mutation, one individual is selected at random from
    :math:`P_\mathrm{p}`, it is cloned and then mutated using using the
    :meth:`toolbox.mutate` method. The resulting mutant is appended to
    :math:`P_\mathrm{o}`. In the case of a reproduction, one individual is
    selected at random from :math:`P_\mathrm{p}`, cloned and appended to
    :math:`P_\mathrm{o}`.
    This variation is named *Or* beceause an offspring will never result from
    both operations crossover and mutation. The sum of both probabilities
    shall be in :math:`[0, 1]`, the reproduction probability is
    1 - *cxpb* - *mutpb*.
    """
    offspring = []

    for _ in range(lambda_):
        op_choice = np.random.random()
        if op_choice < cxpb:  # Apply crossover
            ind1, ind2 = pick_two_individuals_eligible_for_crossover(population)
            if ind1 is not None:
                ind1, _ = toolbox.mate(ind1, ind2)
                del ind1.fitness.values
            else:
                # If there is no pair eligible for crossover, we still want to
                # create diversity in the population, and do so by mutation instead.
                ind1 = mutate_random_individual(population, toolbox)
            offspring.append(ind1)
        elif op_choice < cxpb + mutpb:  # Apply mutation
            ind = mutate_random_individual(population, toolbox)
            offspring.append(ind)
        else:  # Apply reproduction
            idx = np.random.randint(0, len(population))
            offspring.append(toolbox.clone(population[idx]))

    return offspring 

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def eaSimpleWithElitism(population, toolbox, cxpb, mutpb, ngen, stats=None,
             halloffame=None, verbose=__debug__):
    """This algorithm is similar to DEAP eaSimple() algorithm, with the modification that
    halloffame is used to implement an elitism mechanism. The individuals contained in the
    halloffame are directly injected into the next generation and are not subject to the
    genetic operators of selection, crossover and mutation.
    """
    logbook = tools.Logbook()
    logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])

    # Evaluate the individuals with an invalid fitness
    invalid_ind = [ind for ind in population if not ind.fitness.valid]
    fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
    for ind, fit in zip(invalid_ind, fitnesses):
        ind.fitness.values = fit

    if halloffame is None:
        raise ValueError("halloffame parameter must not be empty!")

    halloffame.update(population)
    hof_size = len(halloffame.items) if halloffame.items else 0

    record = stats.compile(population) if stats else {}
    logbook.record(gen=0, nevals=len(invalid_ind), **record)
    if verbose:
        print(logbook.stream)

    # Begin the generational process
    for gen in range(1, ngen + 1):

        # Select the next generation individuals
        offspring = toolbox.select(population, len(population) - hof_size)

        # Vary the pool of individuals
        offspring = algorithms.varAnd(offspring, toolbox, cxpb, mutpb)

        # Evaluate the individuals with an invalid fitness
        invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
        fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
        for ind, fit in zip(invalid_ind, fitnesses):
            ind.fitness.values = fit

        # add the best back to population:
        offspring.extend(halloffame.items)

        # Update the hall of fame with the generated individuals
        halloffame.update(offspring)

        # Replace the current population by the offspring
        population[:] = offspring

        # Append the current generation statistics to the logbook
        record = stats.compile(population) if stats else {}
        logbook.record(gen=gen, nevals=len(invalid_ind), **record)
        if verbose:
            print(logbook.stream)

    return population, logbook 

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def main():
    # create the population of particle population:
    population = toolbox.populationCreator(n=POPULATION_SIZE)

    # prepare the statistics object:
    stats = tools.Statistics(lambda ind: ind.fitness.values)
    stats.register("min", np.min)
    stats.register("avg", np.mean)

    logbook = tools.Logbook()
    logbook.header = ["gen", "evals"] + stats.fields

    best = None

    for generation in range(MAX_GENERATIONS):

        # evaluate all particles in polulation:
        for particle in population:

            # find the fitness of the particle:
            particle.fitness.values = toolbox.evaluate(particle)

            # particle best needs to be updated:
            if particle.best is None or particle.best.size == 0 or particle.best.fitness < particle.fitness:
                particle.best = creator.Particle(particle)
                particle.best.fitness.values = particle.fitness.values

            # global best needs to be updated:
            if best is None or best.size == 0 or best.fitness < particle.fitness:
                best = creator.Particle(particle)
                best.fitness.values = particle.fitness.values

        # update each particle's speed and position:
        for particle in population:
            toolbox.update(particle, best)

        # record the statistics for the current generation and print it:
        logbook.record(gen=generation, evals=len(population), **stats.compile(population))
        print(logbook.stream)

    # print info for best solution found:
    print("-- Best Particle = ", best)
    print("-- Best Fitness = ", best.fitness.values[0]) 

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def eaSimpleModified(population, toolbox, cxpb, mutpb, ngen, stats=None,
             halloffame=None, verbose=__debug__):
    logbook = tools.Logbook()
    logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])

    # Evaluate the individuals with an invalid fitness
    invalid_ind = [ind for ind in population if not ind.fitness.valid]
    fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
    for ind, fit in zip(invalid_ind, fitnesses):
        ind.fitness.values = fit

    if halloffame is not None:
        halloffame.update(population)

    record = stats.compile(population) if stats else {}
    logbook.record(gen=0, nevals=len(invalid_ind), **record)
    if verbose:
        print(logbook.stream)

    best = []

    best_ind = max(population, key=attrgetter("fitness"))
    best.append(best_ind)

    # Begin the generational process
    for gen in range(1, ngen + 1):
        # Select the next generation individuals
        offspring = toolbox.select(population, len(population))

        # Vary the pool of individuals
        offspring = algorithms.varAnd(offspring, toolbox, cxpb, mutpb)

        # Evaluate the individuals with an invalid fitness
        invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
        fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
        for ind, fit in zip(invalid_ind, fitnesses):
            ind.fitness.values = fit

        # Save the best individual from the generation
        best_ind = max(offspring, key=attrgetter("fitness"))
        best.append(best_ind)

        # Update the hall of fame with the generated individuals
        if halloffame is not None:
            halloffame.update(offspring)

        # Replace the current population by the offspring
        population[:] = offspring

        # Append the current generation statistics to the logbook
        record = stats.compile(population) if stats else {}
        logbook.record(gen=gen, nevals=len(invalid_ind), **record)
        if verbose:
            print(logbook.stream)

    return population, logbook, best 

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def main():
    # Differential evolution parameters
    MU = NDIM * 10
    NGEN = 200    
    
    pop = toolbox.population(n=MU);
    hof = tools.HallOfFame(1)
    stats = tools.Statistics(lambda ind: ind.fitness.values)
    stats.register("avg", numpy.mean)
    stats.register("std", numpy.std)
    stats.register("min", numpy.min)
    stats.register("max", numpy.max)
    
    logbook = tools.Logbook()
    logbook.header = "gen", "evals", "std", "min", "avg", "max"
    
    # Evaluate the individuals
    fitnesses = toolbox.map(toolbox.evaluate, pop)
    for ind, fit in zip(pop, fitnesses):
        ind.fitness.values = fit
    
    record = stats.compile(pop)
    logbook.record(gen=0, evals=len(pop), **record)
    print(logbook.stream)

    for g in range(1, NGEN):
        children = []
        for agent in pop:
            # We must clone everything to ensure independance
            a, b, c = [toolbox.clone(ind) for ind in toolbox.select(pop)]
            x = toolbox.clone(agent)
            y = toolbox.clone(agent)
            y = toolbox.mutate(y, a, b, c)
            z = toolbox.mate(x, y)
            del z.fitness.values
            children.append(z)
            
        fitnesses = toolbox.map(toolbox.evaluate, children)
        for (i, ind), fit in zip(enumerate(children), fitnesses):
            ind.fitness.values = fit
            if ind.fitness > pop[i].fitness:
                pop[i] = ind
        
        hof.update(pop)
        record = stats.compile(pop)
        logbook.record(gen=g, evals=len(pop), **record)
        print(logbook.stream)
    
    print("Best individual is ", hof[0])
    print("with fitness", hof[0].fitness.values[0])
    return logbook 

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def main():
    # Differential evolution parameters
    CR = 0.25
    F = 1  
    MU = 300
    NGEN = 200    
    
    pop = toolbox.population(n=MU);
    hof = tools.HallOfFame(1)
    stats = tools.Statistics(lambda ind: ind.fitness.values)
    stats.register("avg", numpy.mean)
    stats.register("std", numpy.std)
    stats.register("min", numpy.min)
    stats.register("max", numpy.max)
    
    logbook = tools.Logbook()
    logbook.header = "gen", "evals", "std", "min", "avg", "max"
    
    # Evaluate the individuals
    fitnesses = toolbox.map(toolbox.evaluate, pop)
    for ind, fit in zip(pop, fitnesses):
        ind.fitness.values = fit
    
    record = stats.compile(pop)
    logbook.record(gen=0, evals=len(pop), **record)
    print(logbook.stream)
    
    for g in range(1, NGEN):
        for k, agent in enumerate(pop):
            a,b,c = toolbox.select(pop)
            y = toolbox.clone(agent)
            index = random.randrange(NDIM)
            for i, value in enumerate(agent):
                if i == index or random.random() < CR:
                    y[i] = a[i] + F*(b[i]-c[i])
            y.fitness.values = toolbox.evaluate(y)
            if y.fitness > agent.fitness:
                pop[k] = y
        hof.update(pop)
        record = stats.compile(pop)
        logbook.record(gen=g, evals=len(pop), **record)
        print(logbook.stream)

    print("Best individual is ", hof[0], hof[0].fitness.values[0]) 

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def main(seed=None):
    random.seed(seed)

    # Initialize statistics object
    stats = tools.Statistics(lambda ind: ind.fitness.values)
    stats.register("avg", numpy.mean, axis=0)
    stats.register("std", numpy.std, axis=0)
    stats.register("min", numpy.min, axis=0)
    stats.register("max", numpy.max, axis=0)

    logbook = tools.Logbook()
    logbook.header = "gen", "evals", "std", "min", "avg", "max"

    pop = toolbox.population(n=MU)

    # Evaluate the individuals with an invalid fitness
    invalid_ind = [ind for ind in pop if not ind.fitness.valid]
    fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
    for ind, fit in zip(invalid_ind, fitnesses):
        ind.fitness.values = fit

    # Compile statistics about the population
    record = stats.compile(pop)
    logbook.record(gen=0, evals=len(invalid_ind), **record)
    print(logbook.stream)

    # Begin the generational process
    for gen in range(1, NGEN):
        offspring = algorithms.varAnd(pop, toolbox, CXPB, MUTPB)

        # Evaluate the individuals with an invalid fitness
        invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
        fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
        for ind, fit in zip(invalid_ind, fitnesses):
            ind.fitness.values = fit

        # Select the next generation population from parents and offspring
        pop = toolbox.select(pop + offspring, MU)

        # Compile statistics about the new population
        record = stats.compile(pop)
        logbook.record(gen=gen, evals=len(invalid_ind), **record)
        print(logbook.stream)

    return pop, logbook 

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def main(seed=None):
    random.seed(seed)

    NGEN = 250
    MU = 100
    CXPB = 0.9

    stats = tools.Statistics(lambda ind: ind.fitness.values)
    # stats.register("avg", numpy.mean, axis=0)
    # stats.register("std", numpy.std, axis=0)
    stats.register("min", numpy.min, axis=0)
    stats.register("max", numpy.max, axis=0)
    
    logbook = tools.Logbook()
    logbook.header = "gen", "evals", "std", "min", "avg", "max"
    
    pop = toolbox.population(n=MU)

    # Evaluate the individuals with an invalid fitness
    invalid_ind = [ind for ind in pop if not ind.fitness.valid]
    fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
    for ind, fit in zip(invalid_ind, fitnesses):
        ind.fitness.values = fit

    # This is just to assign the crowding distance to the individuals
    # no actual selection is done
    pop = toolbox.select(pop, len(pop))
    
    record = stats.compile(pop)
    logbook.record(gen=0, evals=len(invalid_ind), **record)
    print(logbook.stream)

    # Begin the generational process
    for gen in range(1, NGEN):
        # Vary the population
        offspring = tools.selTournamentDCD(pop, len(pop))
        offspring = [toolbox.clone(ind) for ind in offspring]
        
        for ind1, ind2 in zip(offspring[::2], offspring[1::2]):
            if random.random() <= CXPB:
                toolbox.mate(ind1, ind2)
            
            toolbox.mutate(ind1)
            toolbox.mutate(ind2)
            del ind1.fitness.values, ind2.fitness.values
        
        # Evaluate the individuals with an invalid fitness
        invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
        fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
        for ind, fit in zip(invalid_ind, fitnesses):
            ind.fitness.values = fit

        # Select the next generation population
        pop = toolbox.select(pop + offspring, MU)
        record = stats.compile(pop)
        logbook.record(gen=gen, evals=len(invalid_ind), **record)
        print(logbook.stream)

    print("Final population hypervolume is %f" % hypervolume(pop, [11.0, 11.0]))

    return pop, logbook 

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def main():
    random.seed(64)

    NBR_DEMES = 3
    MU = 300
    NGEN = 40
    CXPB = 0.5
    MUTPB = 0.2
    MIG_RATE = 5    
    
    demes = [toolbox.population(n=MU) for _ in range(NBR_DEMES)]
    hof = tools.HallOfFame(1)
    
    stats = tools.Statistics(lambda ind: ind.fitness.values)
    stats.register("avg", numpy.mean)
    stats.register("std", numpy.std)
    stats.register("min", numpy.min)
    stats.register("max", numpy.max)
    
    logbook = tools.Logbook()
    logbook.header = "gen", "deme", "evals", "std", "min", "avg", "max"
    
    for idx, deme in enumerate(demes):
        for ind in deme:
            ind.fitness.values = toolbox.evaluate(ind)
        logbook.record(gen=0, deme=idx, evals=len(deme), **stats.compile(deme))
        hof.update(deme)
    print(logbook.stream)
    
    gen = 1
    while gen <= NGEN and logbook[-1]["max"] < 100.0:
        for idx, deme in enumerate(demes):
            deme[:] = toolbox.select(deme, len(deme))
            deme[:] = algorithms.varAnd(deme, toolbox, cxpb=CXPB, mutpb=MUTPB)
            
            invalid_ind = [ind for ind in deme if not ind.fitness.valid]
            for ind in invalid_ind:
                ind.fitness.values = toolbox.evaluate(ind)
            
            logbook.record(gen=gen, deme=idx, evals=len(deme), **stats.compile(deme))
            hof.update(deme)
        print(logbook.stream)
            
        if gen % MIG_RATE == 0:
            toolbox.migrate(demes)
        gen += 1
    
    return demes, logbook, hof 

# 需要导入模块: from deap import tools [as 别名]
# 或者: from deap.tools import Logbook [as 别名]
def main(extended=True, verbose=True):
    target_set = []
    species = []
    
    stats = tools.Statistics(lambda ind: ind.fitness.values)
    stats.register("avg", numpy.mean)
    stats.register("std", numpy.std)
    stats.register("min", numpy.min)
    stats.register("max", numpy.max)
    
    logbook = tools.Logbook()
    logbook.header = "gen", "species", "evals", "std", "min", "avg", "max"
    
    ngen = 200
    g = 0
    
    schematas = nicheSchematas(TARGET_TYPE, IND_SIZE)
    for i in range(TARGET_TYPE):
        size = int(TARGET_SIZE/TARGET_TYPE)
        target_set.extend(toolbox.target_set(schematas[i], size))
        species.append(toolbox.species())
    
    # Init with a random representative for each species
    representatives = [random.choice(s) for s in species]
    
    while g < ngen:
        # Initialize a container for the next generation representatives
        next_repr = [None] * len(species)
        for i, s in enumerate(species):
            # Vary the species individuals
            s = algorithms.varAnd(s, toolbox, 0.6, 1.0)
            
            # Get the representatives excluding the current species
            r = representatives[:i] + representatives[i+1:]
            for ind in s:
                ind.fitness.values = toolbox.evaluate([ind] + r, target_set)
            
            record = stats.compile(s)
            logbook.record(gen=g, species=i, evals=len(s), **record)
            
            if verbose: 
                print(logbook.stream)
            
            # Select the individuals
            species[i] = toolbox.select(s, len(s))  # Tournament selection
            next_repr[i] = toolbox.get_best(s)[0]   # Best selection
        
            g += 1
        representatives = next_repr

    if extended:
        for r in representatives:
            print("".join(str(x) for x in r))