def init_params(X, K, theta_init=None, parameters=None):
# Here we will initialize the theta parameters of the mixture model
# THETA PARAMETERS OF THE K COMPONENTS
# Give random values to the theta parameters (parameters of the distribution)
# In this case the parameters are theta = (mu, kappa)
# We need at least the number of clusters K and the dimensionality of the
# distirbutoin D.
N, D = X.shape
if (type(theta_init) == type(None)): # If not given an initialization
mus = np.random.randn(D, K)
mus = gf.normalize_module(mus.T).T
# print mus
Kappa_min = parameters["Kappa_min_init"]
Kappa_max = parameters["Kappa_max_init"]
kappas = np.random.uniform(Kappa_min, Kappa_max, K)
kappas = kappas.reshape(1, K)
####### Put theta in the right format ###########
theta = []
for k in range(K):
theta.append([mus[:, [k]], kappas[:, [k]]])
else:
return theta_init
return theta
def plot_trials_for_same_instance(X_data_trials,
X_data_labels,
X_train,
y_train,
colors=["r", "k"],
time_show=100,
normalize=True):
# For a fixed time instant, the plotting of points from several trials of both classes
gl.scatter_3D(0, 0, 0, nf=1, na=0)
for i in range(len(X_data_trials)):
class_i = X_data_labels[i]
if (normalize == True):
caca = gf.normalize_module(X_data_trials[i][[time_show], :])
else:
caca = X_data_trials[i][[time_show], :]
caca = caca.flatten()
gl.scatter_3D(
caca[0],
caca[1],
caca[2],
nf=0,
na=0,
color=colors[class_i],
labels=[
"Trials for the same time instant for different classes", "D1",
"D2", "D3"
])
def init_params(X, K, theta_init = None, parameters = None):
# Here we will initialize the theta parameters of the mixture model
# THETA PARAMETERS OF THE K COMPONENTS
# Give random values to the theta parameters (parameters of the distribution)
# In this case the parameters are theta = (mu, kappa)
# We need at least the number of clusters K and the dimensionality of the
# distirbutoin D.
# print X.shape
N,D = X.shape
if (type(theta_init) == type(None)): # If not given an initialization
mus = np.random.randn(D,K);
mus = gf.normalize_module(mus.T).T
# print mus
Kappa_min = parameters["Kappa_min_init"]
Kappa_max = parameters["Kappa_max_init"]
kappas = np.random.uniform(Kappa_min,Kappa_max,K)
kappas = kappas.reshape(1,K)
####### Put theta in the right format ###########
theta = []
for k in range(K):
theta.append([mus[:,[k]],kappas[:,[k]]])
else:
return theta_init
return theta
def init_EM_params(D,K, pi_init = None, theta_init = None, Kappa_max = 20):
# Here we will initialize the parameters of the mixture model, that is,the
# theta vectors of the K components and mixing coefficients %
# MIXING COEFICIENTS
# We set the mixing coefficients with uniform discrete distribution, this
# way, the a priori probability of any vector to belong to any component is
# the same.
if (type(pi_init) == type(None)): # If not given an initialization
pimix = np.ones((1,K));
pimix = pimix*(1/float(K));
else:
pimix = np.array(pi_init).reshape(1,K)
# print "grgerhbwe"
# THETA PARAMETERS OF THE K COMPONENTS
# Give random values to the theta parameters (parameters of the distribution)
# In this case the parameters are theta = (mu, kappa)
if (type(theta_init) == type(None)): # If not given an initialization
mus = np.random.randn(D,K);
mus = gf.normalize_module(mus.T).T
# print mus
kappas = np.random.uniform(-1,1,K) * Kappa_max
kappas = kappas.reshape(1,K)
else:
mus = np.array(theta_init[0]).reshape((D,K))
kappas = np.array(theta_init[1]).reshape((1,K))
theta = [mus, kappas]
return pimix, theta
def get_X_trials_EM(X_All_labels,
label_classes,
max_trials=100,
channel_sel=[1, 4, 10]):
max_trials = max_trials # Maximum trials, preprocessed per class, to reduce computation
Nclasses = len(label_classes)
X_data_ave_EM_plus = [] # List of trials :)
X_data_ave_EM_minus = []
# Every label will have set of clusters,
# this is the parameters of the clusters [K][[pimix], [thetas]]
Ninit = 5
K = 2
verbose = 0
T = 20
############# Preprocess by class ? ###################
for i in range(Nclasses):
Ntrials, Nsamples, Ndim = X_All_labels[i].shape
Ntrials = np.min([Ntrials, max_trials])
X_ave_EM_class_plus = []
X_ave_EM_class_minus = []
for i_trial in range(Ntrials):
print "%i / %i " % (i_trial, Ntrials)
# TODO no entiendo por que pelotas tengo que transformar aqui
X_trial_samples = X_All_labels[i][i_trial, :, channel_sel].T
# print X_trial_samples.shape
# print channel_sel
X_trial_samples = gf.normalize_module(X_trial_samples)
# print X_trial_samples.shape
# print X_trial_samples.shape
logl, theta_list, pimix_list = EMl.run_several_EM(X_trial_samples,
K=K,
delta=0.1,
T=T,
Ninit=Ninit,
verbose=verbose)
good_cluster_indx_plus = np.argmax(theta_list[-1][1])
good_cluster_indx_minus = np.argmin(theta_list[-1][1])
mu_plus = theta_list[-1][0][:, [good_cluster_indx_plus]]
mu_minus = theta_list[-1][0][:, [good_cluster_indx_minus]]
# print mu.shape
X_ave_EM_class_plus.append(mu_plus.T)
X_ave_EM_class_minus.append(mu_minus.T)
X_ave_EM_class_plus = np.concatenate(X_ave_EM_class_plus, axis=0)
X_ave_EM_class_minus = np.concatenate(X_ave_EM_class_minus, axis=0)
# print X_ave_EM_class.shape
X_data_ave_EM_plus.append(X_ave_EM_class_plus)
X_data_ave_EM_minus.append(X_ave_EM_class_minus)
return X_data_ave_EM_plus, X_data_ave_EM_minus
def init_HMM_params(D,
I,
pi_init=None,
A_init=None,
B_init=None,
Kappa_max=20):
# Here we will initialize the parameters of the HMM, that is,the initial
# probabilities of the state "pi", the transition probabilities "A" and the
# parameters of the probability functions "B"
# Initial probabilities
# We set the Initial probabilities with uniform discrete distribution, this
# way, the a priori probability of any vector to belong to any component is
# the same.
if (type(pi_init) == type(None)): # If not given an initialization
pi = np.ones((1, I))
pi = pi * (1 / float(I))
else:
pi = np.array(pi_init).reshape(1, I)
# Transition probabilities "A"
# We set the Transition probabilities with uniform discrete distribution, this
# way, the a priori probability of going from a state i to a state j is
# the same, no matter the j.
if (type(A_init) == type(None)): # If not given an initialization
A = np.ones((I, I))
#A(i,j) = aij = P(st = j | st-1 = i) sum(A(i,:)) = 1
for i in range(I):
A[i, :] = A[i, :] * (1 / float(I))
else:
A = A_init
# Parameters of the probability functions "B"
# Give random values to the transit parameters. Since in this case, all
# theta parameters theta(d,k), are the Expected value of a Bernoulli, we
# asign values to them at random accoding to a uniform continuous
# distribution in the support (0,1).
if (type(B_init) == type(None)): # If not given an initialization
mus = np.random.randn(D, I)
mus = gf.normalize_module(mus.T).T
kappas = np.random.uniform(-1, 1, I) * Kappa_max
kappas = kappas.reshape(1, I)
else:
mus = np.array(B_init[0]).reshape((D, I))
kappas = np.array(B_init[1]).reshape((1, I))
# We store the parameter of the clusters in B
B = copy.deepcopy([mus, kappas])
return pi, A, B
def get_X_trials_EM (X_All_labels, label_classes,
max_trials = 100, channel_sel= [1,4,10]):
max_trials = max_trials # Maximum trials, preprocessed per class, to reduce computation
Nclasses = len(label_classes)
X_data_ave_EM_plus = [] # List of trials :)
X_data_ave_EM_minus = []
# Every label will have set of clusters,
# this is the parameters of the clusters [K][[pimix], [thetas]]
Ninit = 5
K = 2
verbose = 0
T = 20
############# Preprocess by class ? ###################
for i in range(Nclasses):
Ntrials, Nsamples, Ndim = X_All_labels[i].shape
Ntrials = np.min([Ntrials,max_trials])
X_ave_EM_class_plus = []
X_ave_EM_class_minus = []
for i_trial in range(Ntrials):
print "%i / %i " %(i_trial, Ntrials)
# TODO no entiendo por que pelotas tengo que transformar aqui
X_trial_samples = X_All_labels[i][i_trial,:,channel_sel].T
# print X_trial_samples.shape
# print channel_sel
X_trial_samples = gf.normalize_module(X_trial_samples)
# print X_trial_samples.shape
# print X_trial_samples.shape
logl,theta_list,pimix_list = EMl.run_several_EM(X_trial_samples, K = K, delta = 0.1, T = T,
Ninit = Ninit, verbose = verbose)
good_cluster_indx_plus = np.argmax(theta_list[-1][1])
good_cluster_indx_minus = np.argmin(theta_list[-1][1])
mu_plus = theta_list[-1][0][:,[good_cluster_indx_plus]]
mu_minus = theta_list[-1][0][:,[good_cluster_indx_minus]]
# print mu.shape
X_ave_EM_class_plus.append(mu_plus.T)
X_ave_EM_class_minus.append(mu_minus.T)
X_ave_EM_class_plus = np.concatenate(X_ave_EM_class_plus, axis = 0)
X_ave_EM_class_minus = np.concatenate(X_ave_EM_class_minus, axis = 0)
# print X_ave_EM_class.shape
X_data_ave_EM_plus.append(X_ave_EM_class_plus)
X_data_ave_EM_minus.append(X_ave_EM_class_minus)
return X_data_ave_EM_plus, X_data_ave_EM_minus
def plot_trials_for_same_instance(X_data_trials, X_data_labels, X_train, y_train,
colors = ["r","k"], time_show = 100, normalize = True):
# For a fixed time instant, the plotting of points from several trials of both classes
gl.scatter_3D(0, 0,0, nf = 1, na = 0)
for i in range(len(X_data_trials)):
class_i = X_data_labels[i]
if (normalize == True):
caca = gf.normalize_module(X_data_trials[i][[time_show],:])
else:
caca = X_data_trials[i][[time_show],:]
caca = caca.flatten()
gl.scatter_3D(caca[0],caca[1],caca[2],
nf = 0, na = 0, color = colors[class_i],labels = ["Trials for the same time instant for different classes", "D1","D2","D3"])
def preprocess_data_set(X_All_labels,
label_classes,
max_trials=100,
channel_sel=None,
normalize=True):
# Subselect channels and trials and then normalize modulus
max_trials = max_trials # Maximum trials, preprocessed per class, to reduce computation
channel_sel = channel_sel # Subset of selected channels
Nclasses = len(label_classes)
label_numbers = range(Nclasses)
X_data_trials = [] # List of trials :)
X_data_labels = [] # Labels of the trials :)
# Every label will have set of clusters,
# this is the parameters of the clusters [K][[pimix], [thetas]]
############# Preprocess by class ? ###################
for i in range(Nclasses):
Ntrials, Nsamples, Ndim = X_All_labels[i].shape
# Limit the number of trials processed by labels
Ntrials = np.min([Ntrials, max_trials])
if (type(channel_sel) == type(None)):
channel_sel = range(Ndim)
for nt in range(Ntrials):
################################################################
######## Preprocessing ! ##############################
###############################################################
X_trial = X_All_labels[i][nt, :, :]
X_trial = X_trial[:, channel_sel]
# X_trial = X_trial - np.sum(X_trial, axis = 1).reshape(X_trial.shape[0],1)
# scaler = preprocessing.StandardScaler().fit(X_trial)
# X_trial = scaler.transform(X_trial)
if (normalize == True):
X_trial = gf.normalize_module(X_trial)
X_data_trials.append(X_trial)
X_data_labels.append(i)
# Now have a normal machine learning problem :)
# X_data_trials, X_data_labels
return X_data_trials, X_data_labels
def preprocess_data_set (X_All_labels, label_classes,
max_trials = 100, channel_sel = None,
normalize = True):
# Subselect channels and trials and then normalize modulus
max_trials = max_trials # Maximum trials, preprocessed per class, to reduce computation
channel_sel = channel_sel # Subset of selected channels
Nclasses = len(label_classes)
label_numbers = range(Nclasses)
X_data_trials = [] # List of trials :)
X_data_labels = [] # Labels of the trials :)
# Every label will have set of clusters,
# this is the parameters of the clusters [K][[pimix], [thetas]]
############# Preprocess by class ? ###################
for i in range(Nclasses):
Ntrials, Nsamples, Ndim = X_All_labels[i].shape
# Limit the number of trials processed by labels
Ntrials = np.min([Ntrials,max_trials])
if (type(channel_sel) == type(None)):
channel_sel = range(Ndim)
for nt in range(Ntrials):
################################################################
######## Preprocessing ! ##############################
###############################################################
X_trial = X_All_labels[i][nt,:,:]
X_trial = X_trial[:,channel_sel]
# X_trial = X_trial - np.sum(X_trial, axis = 1).reshape(X_trial.shape[0],1)
# scaler = preprocessing.StandardScaler().fit(X_trial)
# X_trial = scaler.transform(X_trial)
if (normalize == True):
X_trial = gf.normalize_module(X_trial)
X_data_trials.append(X_trial)
X_data_labels.append(i)
# Now have a normal machine learning problem :)
# X_data_trials, X_data_labels
return X_data_trials, X_data_labels
for i in range(Nsa):
probs.append([])
for j in range(Nsa):
XdataSample = [np.sin(Xthetta[i])*np.cos(Xfi[j]),
np.sin(Xthetta[i])*np.sin(Xfi[j]),
np.cos(Xthetta[i])]
probs[i].append(Wad.Watson_pdf(XdataSample,mu,kappa ))
probs = np.array(probs).T
## Plotting
gl.set_subplots(1,3)
## Plot it in terms of (angle, prob)
gl.plot_3D(Xthetta,Xfi, np.array(probs))
gl.plot_3D(Xthetta,Xfi, np.array(probs), project = "spher")
mu = np.random.randn(5,1);
mu = gf.normalize_module(mu.T).flatten()
## Generate samples
RandWatson = Was.randWatson(Nsampling, mu, kappa)
gl.scatter_3D(RandWatson[:,0],RandWatson[:,1], RandWatson[:,2])
mu_est = Wae.get_MLmean(RandWatson)
kappa_est = Wae.get_MLkappa(mu_est, RandWatson)
mu_est2, kappa_est2 = Wae.get_Watson_muKappa_ML(RandWatson)
print "Real: ", mu, kappa
print "Estimate: ", mu_est2, kappa_est2
Xdata = np.concatenate((Xdata, copy.deepcopy(Xdata_chain)), axis=0)
k = 1
################################################################
######## Perform the EM !! ###############
###############################################################
perform_EM = 1
if (perform_EM):
K = 3
D = Xdata.shape[1]
pi_init = np.ones((1, K))
pi_init = pi_init * (1 / float(K))
mus_init = np.random.randn(D, K)
mus_init = gf.normalize_module(mus_init.T).T
kappas_init = np.random.uniform(-1, 1, K) * 10
kappas_init = kappas_init.reshape(1, K)
theta_init = [mus_init, kappas_init]
## RUN only one !!
logl, theta_list, pimix_list = EMl.EM(Xdata,
K=K,
delta=0.1,
T=100,
pi_init=pi_init,
theta_init=theta_init)
## RUN several !!
def normalize_trialList(tL):
# Normalize all the trials in a list
tL_norm = []
for i in range(len(tL)): # Put the data in the sphere.
tL_norm.append(gf.normalize_module(tL[i]))
return tL_norm
import general_func as gf
plt.close("all")
################################################################
######## Load and combine 3 sets ##############################
###############################################################
folder = "./HMM_data/"
HMM_list = pkl.load_pickle(folder + "HMM_datapoints.pkl", 1)
HMM_list2 = pkl.load_pickle(folder + "HMM2_datapoints.pkl", 1)
for i in range(len(HMM_list)):
chain = HMM_list[i]
Nsamples, Ndim = HMM_list[i].shape
chain_noise = np.random.rand(Nsamples, Ndim) / 10
HMM_list[i] = gf.normalize_module(chain + chain_noise)
for i in range(len(HMM_list2)):
chain = HMM_list2[i]
Nsamples, Ndim = HMM_list2[i].shape
chain_noise = np.random.rand(Nsamples, Ndim) / 10
HMM_list2[i] = gf.normalize_module(chain + chain_noise)
D = HMM_list[0].shape[1]
## Examples Crosvalidation fot HMM
CV_HMM = 0
if (CV_HMM):
## Run 1
States = [1, 2, 3, 4, 5, 6, 7]
###############################################################
max_trials = 100 # Number of trials per class
Ntrials, NtimeSamples, Ndim = X_All_labels[0].shape
possible_channels = range(Ndim)
Nchannels_chosen = 5 # We select this number of channels
channel_sel = np.random.permutation(possible_channels)[0:Nchannels_chosen].flatten().tolist() # Randomize the array of index
#channel_sel = [20, 21, 22]
X_data_trials, X_data_labels = dp.preprocess_data_set (
X_All_labels, label_classes,
max_trials = max_trials, channel_sel= channel_sel)
X_data_ave = dp.get_timeSeries_average_by_label(X_All_labels, channel_sel = channel_sel)
for i in range (len(X_data_ave)): # Put the data in the sphere.
X_data_ave[i] = gf.normalize_module(X_data_ave[i])
################# Separate in train and validation ############
X_train, X_test, y_train, y_test = train_test_split(X_data_trials, X_data_labels, test_size=0.50, random_state = 0, stratify = X_data_labels)
#######################################################
######################### EM ###########################
#######################################################
EM_flag = 1
if (EM_flag):
Ninit = 10
K = 6
verbose = 0
def normalize_trialList(tL):
# Normalize all the trials in a list
tL_norm = []
for i in range (len(tL)): # Put the data in the sphere.
tL_norm.append( gf.normalize_module(tL[i]))
return tL_norm