Save strategy in pickle file

[Carlotta Porcelli]

Hello, 

I am running a cmaes algorithm but after running the first generation I can't figure out how to load the pickle file saved.

The error I get is: 

population = toolbox.generate()

AttributeError: 'Toolbox' object has no attribute 'generate'

It looks like it is not saving the generation even though the .pkl file is created

Can someone help ?

Thanks

This is the code:

1. import datetime
2. import pickle
3. import random
4. import sys
6. import numpy as np
7. from deap import base
9. from deap import cma
10. from deap import creator
11. from deap import tools
13. from evol_experimets_chem import EvolutionaryExperiment
14. from petri_dish_coordinates import petridishes
16. import os
18. sys.path.append('../../api')
19. sys.path.append('../../settings')
21.  
22. IND_SIZE = 2
23. NGEN = 10  # number of generations for which the evolution runs
    number_children = 8  # number of individuals in each population - 8 individuals
    random.seed(30)
24. creator.create("FitnessMax", base.Fitness, weights=(1.0,))
25. creator.create("Individual", list, fitness=creator.FitnessMax)
26. creator.create("Strategy", list)
    
    toolbox = base.Toolbox()
27. toolbox.register("attribute", random.random)
28. toolbox.register("individual", tools.initRepeat, creator.Individual, toolbox.attribute, n=IND_SIZE)
29. toolbox.register("population", tools.initRepeat, list, toolbox.individual)
    
    
30. hall_of_fame = tools.HallOfFame(1)
31. stats = tools.Statistics(lambda individual: individual.fitness.values)
32. stats.register("avg", np.mean)
33. stats.register("std", np.std)
34. stats.register("min", np.min)
35. stats.register("max", np.max)
37. logbook = tools.Logbook()
38. logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
40. experiment = EvolutionaryExperiment()
     
41. def do_stuff_here(petri, individual):
42.    """This function prepares the liquid mix with ph and molarity from the individual """
43.    print "Preparing experiment"
44.    os.system("say 'Preparing experiment'")
45.    ph, molarity = experiment.prepare_experiment(individual, petri)
46.    print "Experiment prepared, starting experiment"
47.    os.system("say 'Experiment prepared, starting experiment'")
49.     petri.clean_flag = False
50.    fitness = experiment.perform_experiment(petri, ph, molarity)
51.    print "Experiment has finished"
52.    os.system("say 'Experiment has finished'")
54.     print "Check that all the vessels have enough reagents!"
55.    os.system("say 'Check that all the vessels have enough reagents!'")
57.     return fitness
59.  
60. def eval_max(individual):
61.    for p in petridishes:
            if p.is_clean():
62.            petri = p
63.            break
64.    else: # We did not find any clean petri dish
    
65.         repeat = True
66.        while repeat:
67.            print "There are no clean petri dishes"
68.            os.system("say 'There are no clean petri dishes'")
69.            print "Check that all the vessels have enough reagents and place clean petri dishes!"
70.            os.system("say 'Check that all the vessels have enough reagents and place clean petri dishes!'")
72.             print "Is everything OK? Type ""y"" to continue"
73.            text = sys.stdin.readline()
74.            if "y" in text:
75.                repeat = False # Take the firs petri dish (all are clean now)
76.        
    

    for petris in petridishes:

77.            petris.clean_flag = True
78.        petri = petridishes[0]
80.     fitness = do_stuff_here(petri, individual)
81.    return fitness
83.  
84. toolbox.register("evaluate", eval_max)
86.  
87. def check_individuals(individual):
88.    """ This function checks if the individual's attributes are in the boundaries: if x or y < 0 -> 0 if x or y > 1
89.   -> 1 """
90.    x, y = individual[0], individual[1]
91.    if x < 0.:
92.        new_x = 0.
93.        individual[0] = new_x
94.    elif x > 1.:
95.        new_x_1 = 1.
96.        individual[0] = new_x_1
97.    if y < 0.:
98.        new_y = 0.
99.        individual[1] = new_y
100.    elif y > 1.:
101.        new_y_1 = 1.
102.        individual[1] = new_y_1
104.     return individual
106.  
107. def main(population_file="population-g0.pkl"):
108.    print "The evolutionary experiments start now!"
109.    os.system("say 'Good afternoon Carlotta! Is everything ready ?'")
110.    os.system("say 'The evolutionary experiments start now!'")
111.    if not population_file:
112.        strategy = cma.Strategy(centroid=[0.5] * IND_SIZE, sigma=0.15, lambda_=number_children)
113.        toolbox.register("generate", strategy.generate, creator.Individual)
114.        toolbox.register("update", strategy.update)
115.        start_gen = 0
116.    else:
117.        cp = pickle.load(open(population_file, "r"))
118.        population = cp["population"]
119.        start_gen = cp["generation"]
120.        random.setstate(cp["rndstate"])
121.        fitnesses = cp["fitness"]
122.        strategy = cp["strat"]
123.        for ind, fit in zip(population, fitnesses):
124.            ind.fitness.values = fit,
126.         print("Start of evolution")
128.     for gen in range(start_gen, NGEN):
129.            print("-- Generation %i --" % gen)
130.            os.system('say "Generation %i"' % gen)
     
     
131.             population = toolbox.generate()
132.            for ind in population:
133.                check_individuals(ind)  # check the attributes of each individual
     
                 fitnesses = toolbox.map(toolbox.evaluate, population)
     
134.             print 'GENERATION: %d' % gen
135.            print 'POPULATION: %s' % population
136.            print 'FITNESSES: %s' % fitnesses
138.             for ind, fit in zip(population, fitnesses):
139.                ind.fitness.values = fit,
140.                hall_of_fame.update(population)
     
                toolbox.update(population)
142.             record = stats.compile(population) if stats is not None else {}
143.            logbook.record(gen=gen, nevals=len(population), **record)
144.            print logbook
146.             import csv
147.            my_list = zip(population, fitnesses)
148.            print my_list
149.            with open('/Users/capo/Documents/data_from_exp/logbook/generation_summary-{}.csv'.format(
150.                    datetime.datetime.now().strftime("%Y-%m-%d %H.%M.%S")), 'wb') as f:
151.                writer = csv.writer(f, delimiter=',')
152.                writer.writerow(['generation %d ' % gen])
153.                writer.writerows([
154.                    my_list
155.                ])
157.             cp = dict(population=population, generation=gen, fitness=fitnesses, rndstate=random.getstate(), strat=strategy)
158.            filename = "population-g" + str(gen) + ".pkl"
159.            pickle.dump(cp, open(filename, "wb"))
161.     print "-- End of (successful) evolution --"
163.     best_ind = tools.selBest(population, 1)[0]
164.    print "Best individual is %s, %s" % (best_ind, best_ind.fitness.values)
166.  
167. if __name__ == "__main__":
168.    if len(sys.argv) > 1:
169.        main(sys.argv[1])
170.    else:
171.        main()

[François-Michel De Rainville]

You have te re-register your function within the toolbox when you are loading your pickle. Something like this

if not population_file:

    # Create and register strategy

else:

    cp = pickle.load(open(population_file, "r"))

    # ...

    strategy = cp["strat"]

    toolbox.register("generate", strategy.generate, creator.Individual)
    toolbox.register("update", strategy.update)

Cheers,

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[Carlotta Porcelli]

that helped, thanks you very much !

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