def generate_points(NMbudget, omodel):
points = [] #Main holder
new_points = genfromelites()
random_points = genrandom(NMbudget)
try:
points = np.vstack([new_points, random_points, mp.saved_points])
print('suceeded')
except:
points = np.vstack([new_points, random_points])
indexlist = []
for point in points:
index = tuple(mp.map.nichefinder(mp.feature_fun(point)))
indexlist.append(index)
points = points[tuple(
[sorted(range(len(indexlist)), key=indexlist.__getitem__)])]
point_values = [myacqMINUS(x, omodel) for x in points]
# Perform twice to get truer acquisition value
point_values = [myacqMINUS(x, omodel) for x in points]
### Now order them by fitness and select the top performing ones.
pv = np.array(point_values)
#index = pv.argsort()[::-1]
#random_points = random_points[index]
#more_points = [np.array(rand_point) for rand_point in random_points]
#points.extend(more_points)
points = points[pv.argsort()[::-1]]
#mp.saved_points = points[:NMbudget]
return (points[:NMbudget])
def myacqKG(x, omodel, observations, net, basefit, fmodel=None):
value = 0
modifier = 1
valid_ranges = mp.domain.valid_ranges
mymap = copy.deepcopy(mp.map)
basevalue = np.sum([item[1] for item in net])
indexes = it.product(*[range(dim) for dim in mp.feature_resolution])
#classprobs = classprobabilities( fmodel, x )
if not validatepoint(x):
x = conformpoint(x)
modifier = 0 #violation_cost( x )
## We calculate the posterior mean of the GP at the current point
#posterior_mean = np.float(omodel(torch.Tensor(x).reshape(-1,len(valid_ranges))).mean.detach().numpy())
posterior_mean = np.double(
omodel(torch.Tensor(x).reshape(
-1, len(valid_ranges))).mean.detach().numpy())
new_point = [x, posterior_mean, mp.feature_fun(x)]
observations.append(new_point)
KG_model, _, _ = buildpymodel(observations)
net_gens = [point[0] for point in net]
for point in net:
#point[1] = np.float(KG_model(torch.Tensor(point[0]).reshape(-1,len(valid_ranges))).mean.detach().numpy())
point[1] = np.double(
KG_model(torch.Tensor(point[0]).reshape(
-1, len(valid_ranges))).mean.detach().numpy())
mymap, _ = niche_compete(net, mymap)
New_fitness = np.nansum(mymap.fitness.flatten())
value = New_fitness - basefit
print(value)
print(x)
return (-value * modifier)
def update_gen_map(map, points):
'''Adds new observations to the map and calculates the
percentage of points that were accepted in to the map
'''
for point in points:
index = tuple(mp.map.nichefinder(mp.feature_fun(point)))
return (map)
def classprobabilities(models, x):
'''Returns a list of probabilities of f(x) being in the classes provided
by calculating the density of the posterior at point x
INPUT :
model : GPy model object
x : a single point. (Currently 1d)
classcutofflist : a list of cutoff points for classes
ylower : a minimum value to include in the lowest class
OUTPUT :
classcutoffprobs : a list of probabilities of being in classes.
EXAMPLE :
classprobabilities(model, 3 , [0.3, 0.5, 1], 0)
example return : [0.2,0.7,0.1]
'''
if models == None:
nicheprobs = np.copy(mp.map.blank_map)
trueindex = nichefinder(mp.feature_fun(x))
indexes = it.product(*[range(dim) for dim in mp.feature_resolution])
for index in indexes:
nicheprobs[index] = 0
#if not validatepoint(x):
# return(nicheprobs)
try:
nicheprobs[tuple(trueindex)] = 1
return (nicheprobs)
except:
return (nicheprobs)
else:
# Provide edges of niches from main map
edges = mp.map.edges
#Reshape input to correct genome length
z = np.array([[x]]).reshape(-1, xdims)
# Provide posterior mean/variance for current x in each feature dimension
mulist, varlist = [model.predict(z) for model in models]
#mulist = [ float(mu) for mu in mulist ] #Convert to floats
#varlist = [ float(var) for var in varlist ] #Convert to floats
mulist = [np.double(mu) for mu in mulist] #Convert to floats
varlist = [np.double(var) for var in varlist] #Convert to floats
probability_list = []
for count, mu in enumerate(mulist):
distro = scipy.stats.norm(loc=mu, scale=np.sqrt(var[count]))
cdfvals = distro.cdf(edges[count])
featdimprobs = [(cdfvals[i + 1] - cdfvals[i])
for i in range(len(cdfvals))]
nicheprobs = np.copy(mp.map.blank_map)
indexes = it.product(*[range(dim) for dim in mp.feature_resolution])
for index in indexes:
probs = [nicheprobs[index[i]] for i in range(len(index))]
nicheprobs[index] = np.prod(probs)
return (nicheprobs)
def generate_net(n, omodel):
valid_ranges = mp.constraints
net_points = sobol_sample(n, valid_ranges)
net_points = np.array(net_points).T
#net = [ [point , np.float(omodel(torch.Tensor(point).reshape(-1,len(valid_ranges))).mean.detach().numpy()), mp.feature_fun(point)]
net = [[
point,
np.double(
omodel(torch.Tensor(point).reshape(
-1, len(valid_ranges))).mean.detach().numpy()),
mp.feature_fun(point)
] for point in net_points]
return (net)
# sobolmap,fitness = getpredmap(initial_samples)
# sobol_fit_list.append(fitness)
# pickle.dump(sobol_fit_list, filehandler)
####
### Random Samples
def random_point(n, dims):
x=[]
for i in range(n):
x.append(np.random.uniform(0,1,dims))
return(x)
random_fit_list = []
for i in range(1):
ss.initseed(i)
x = random_point(10,10)
rand_points = [[x[i],mp.fitness_fun(x[i]),mp.feature_fun(x[i])] for i in range(len(x))]
for i in range(len(rand_points)):
rand_points[i][1] = np.nansum(rand_points[i][1])
filehandler = open('Results/Init-Test/Random/fitness.csv', 'wb')
mp.map , edges = create_map(mp.feature_resolution, mp.domain )
initialisemap(rand_points)
randommap,fitness = getpredmap(rand_points)
random_fit_list.append(fitness)
pickle.dump(sobol_fit_list, filehandler)
def additional_sampling(n_add_samples, sobol_set, sobol_point, map):
'''additional_sampling -
Samples are produced using a Sobol sequence that evenly selects elites from
the current acquisition map. Those elites are then evaluated and added to the
observation list (which will improve the surrogate model and also improve the
prediction map)
##TODO If samples are invalid (invalid geometry, or did
not converge in simulator), the next sample in the Sobol sequence is
chosen. Lather, rinse, repeat until all initial samples are clean.
Example: new_points = additional_sampling(100 , my_sobol, current_point , map)
Inputs (arguments):
n_add_samples - [ Integer ] - number of samples to produce
sobol_set - [ List ] - A set of random points in feature space
sobol_point - [ Integer ] - An index for the sobol_set
map - [ Map Class ] - The current acquisition map.
Inputs (from config file):
mp.domain - domain Class object
.valid_ranges - [ List ] - To check validity of samples
Outputs:
valid_points - [ n_initial_samples * [ [ x ] , [ y ] , [ f ] ] ] ]
sample_end - [ Integer ] - An update to sobol_point (an index)
Code Author: Paul Kent
Warwick University
email: [email protected]
Oct 2020; Last revision: 16-Oct-2020
'''
valid_ranges = mp.domain.valid_ranges # Valid Search domain ranges
new_value = []
new_sample = []
n_missing = n_add_samples
new_points = []
# randomly sample from map #########################################
sample_end = sobol_point + 10 * n_add_samples
random_genomes = [
sobol_set[i][sobol_point:sample_end] for i in range(len(sobol_set))
]
random_genomes = np.array(random_genomes).T
#random_genomes = np.reshape(random_genomes , (-1 , len( valid_ranges ) ) )
# identify which niche each point belongs to (in feature space)
niche_index = [
nichefinder(mp.feature_fun(random_genomes[i]), map)
for i in range(len(random_genomes))
]
# Remove duplicates, keep track of the random genomes index (n) and the feature values (i)
niche_index = [
i for n, i in enumerate(niche_index) if i not in niche_index[:n]
]
while n_missing > 0:
niche_id = niche_index[-1]
if not np.isnan(map.fitness[tuple(niche_id)]).any():
new_points.append(map.genomes[tuple(niche_id)])
n_missing -= 1
niche_index.pop()
if len(niche_index) <= 0:
print('Not enough unique samples to make all new evaluations')
print('This can happen on the first few runs')
print('or could indicate a problem with your functions')
n_missing = 0
if n_missing == 0:
print(
f'{Fore.GREEN}Success: {Style.RESET_ALL} New points to evaluate chosen from acquisition map'
)
#Reshaping
# print('value check', validate(new_points[0].T))
#new_points = [new_points[i].T for i in range(len(new_points))]
# print(keep_valid( new_points.T,
# new_points ,
# n_add_samples,
# validate ))
# new_points = np.array(new_points).T
#validating and sample from fitness/feature functions
valid_points = []
valid_points, n_missing = keep_valid(valid_points,
np.array(new_points).T, n_add_samples,
validate)
if len(valid_points) == n_add_samples:
print(f'{Fore.GREEN}Success: {Style.RESET_ALL} New points evaluated')
elif len(valid_points) == 0:
print(f'{Fore.RED}FAILURE: {Style.RESET_ALL} No new Points selected ')
else:
print(
f'{Fore.YELLOW}Warning: {Style.RESET_ALL} Not all new points evaluated correctly '
)
return (valid_points, sample_end, len(valid_points))
plot_fit_ls()
truedata = np.genfromtxt('Results/AdamParsec/data/fit_true_500.csv',
delimiter=',')
preddata = np.genfromtxt(
'Results/AdamRastrigin/10d/data_10se/data/fit_pred_500.csv', delimiter=',')
true_points = np.genfromtxt('Results/AdamRastrigin/train_input.csv',
delimiter=',')
true_points = np.genfromtxt('Results/AdamResults/genomes_500.csv',
delimiter=',')
#true_points = [point[0] for point in points]
fitness = list(map(mp.fitness_fun, true_points))
behaviour = mp.feature_fun(true_points)
points = [(true_points[i], fitness[i], behaviour[i])
for i in range(len(fitness))]
points
## Set Hypers
variance = 0.01
lengthscale = 0.5
noise_var = 0
GP_params = (variance, lengthscale, noise_var)
hyper = hypers[-1]
fit_gp, hypers = buildpymodel(points, hypers, retrain=True)
###
mp.ME_params = (0.0, 2**6, 0.1, 2**9)
predmap = create_prediction_map(fit_gp, points)
#heatmap(np.array(fitness).reshape(25,25), 'none')
def acquisition_fun(points, give_var=False):
#Check if it's a single observation
xdims = len(mp.domain.valid_ranges)
index = tuple(mp.map.nichefinder(mp.feature_fun(points)))
if np.shape(points) == (xdims, ):
index = pred_map.nichefinder(mp.feature_fun(points))
if index not in mp.modelindex:
mp.modellist.append(
mp.map.adapt_model(omodel, index[0], index[1],
globalmean))
mp.modelindex.append(index)
niche_model = mp.modellist[mp.modelindex.index(index)]
if len(mp.modellist) > 10:
del mp.modellist[0]
del mp.modelindex[0]
libc = ctypes.CDLL("libc.so.6")
libc.malloc_trim(0)
point = torch.tensor(points,
dtype=torch.double).reshape(-1, xdims)
niche_model.eval()
posterior = niche_model.posterior(point)
fitness = posterior.mean
posterior_variance = posterior.variance.clamp_min(1e-9).sqrt()
return (np.double(fitness))
else:
#Process multiple points
n = len(points)
indexes = [
pred_map.nichefinder(mp.feature_fun(point))
for point in points
]
points = np.array([point for point in points])
points = torch.tensor(points,
dtype=torch.double).reshape(-1, xdims)
fitlist = []
varlist = []
for i in range(n):
index = tuple(indexes[i])
if index not in mp.modelindex:
mp.modellist.append(
mp.map.adapt_model(omodel, index[0], index[1],
globalmean))
mp.modelindex.append(index)
niche_model = mp.modellist[mp.modelindex.index(index)]
if len(mp.modellist) > 10:
del mp.modellist[0]
del mp.modelindex[0]
libc = ctypes.CDLL("libc.so.6")
libc.malloc_trim(0)
fun = niche_model
niche_model.eval()
posterior = niche_model.posterior(points[i].reshape(
-1, xdims))
fitness = posterior.mean
pv = posterior.variance.clamp_min(1e-9).sqrt()
fitlist.append(fitness)
varlist.append(pv)
# evaluation = [fun( points[i].reshape(-1,xdims) ) for i in range(n)]
# fitness = [ float( e.mean *mp.std + mp.smean ) for e in evaluation]
# posterior_variance = [ float(e.variance ) for e in evaluation]
# fitlist = [ float( f ) for f in fitness ]
# varlist = [ float( v ) for v in posterior_variance ]
if give_var:
return (fitlist, varlist)
else:
return (np.array(fitlist))
filehandler = open(
'Results/Random_sampling' + '/' + str(seed) + '10x10BDC.csv', 'wb')
pickle.dump(binary_data, filehandler)
seed = 2160
valueranges = [20, 50, 100, 250, 500, 750, 1000]
for i in range(20):
values = []
np.random.seed(seed)
seed += 1
initial_samples = np.array(lhsmdu.sample(1000, 10))
print(str(valueranges[0]) + 'samples')
points = initial_samples[:valueranges[0]]
fitness = mp.fitness_fun(points)
features = mp.feature_fun(points)
observations = [[points[i], fitness[i], features[i]]
for i in range(valueranges[0])]
mp.map, edges = create_map(mp.feature_resolution, mp.domain)
initialisemap(observations)
print('Score = ' + str(np.nansum(mp.map.fitness.flatten())))
values.append(np.nansum(mp.map.fitness.flatten()))
for count, val in enumerate(valueranges[1:]):
new_samples = initial_samples[valueranges[count]:valueranges[count +
1]]
fitness = mp.fitness_fun(new_samples)
features = mp.feature_fun(new_samples)
new_observations = [[new_samples[i], fitness[i], features[i]]
for i in range(len(new_samples))]
updatemapSAIL(new_observations)
observations.append(new_observations)