def tryLinearDiscriminantAnalysis(goFast):
from sklearn.datasets import dump_svmlight_file, load_svmlight_file
if goFast:
training_data, training_labels = load_svmlight_file("dt1_1500.trn.svm", n_features=253659, zero_based=True)
validation_data, validation_labels = load_svmlight_file("dt1_1500.vld.svm", n_features=253659, zero_based=True)
testing_data, testing_labels = load_svmlight_file("dt1_1500.tst.svm", n_features=253659, zero_based=True)
else:
training_data, training_labels = load_svmlight_file("dt1.trn.svm", n_features=253659, zero_based=True)
validation_data, validation_labels = load_svmlight_file("dt1.vld.svm", n_features=253659, zero_based=True)
testing_data, testing_labels = load_svmlight_file("dt1.tst.svm", n_features=253659, zero_based=True)
from sklearn.lda import LDA
from sklearn.metrics import accuracy_score
from sklearn.grid_search import ParameterGrid
from sklearn.decomposition import RandomizedPCA
rpcaDataGrid = [{"n_components": [10,45,70,100],
"iterated_power": [2, 3, 4],
"whiten": [True]}]
for rpca_parameter_set in ParameterGrid(rpcaDataGrid):
rpcaOperator = RandomizedPCA(**rpca_parameter_set)
rpcaOperator.fit(training_data,training_labels)
new_training_data = rpcaOperator.transform(training_data,training_labels)
new_validation_data = rpcaOperator.transform(validation_data,validation_labels)
ldaOperator = LDA()
ldaOperator.fit(new_training_data,training_labels)
print "Score = " + str(accuracy_score(validation_labels,ldaOperator.predict(new_validation_data)))
class Ensemble: def __init__(self, data): self.rf = RandomForestClassifier(n_estimators=80, n_jobs=-1, min_samples_split=45, criterion='entropy') self.lda = LDA() self.dec = DecisionTreeClassifier(criterion='entropy') self.ada = AdaBoostClassifier(n_estimators=500, learning_rate=0.25) self.make_prediction(data) def make_prediction(self, data): ''' Make an ensemble prediction ''' self.rf.fit(data.features_train, data.labels_train) self.lda.fit(data.features_train, data.labels_train) self.dec.fit(data.features_train, data.labels_train) self.ada.fit(data.features_train, data.labels_train) pre_pred = [] self.pred = [] ada_pred = self.ada.predict(data.features_test) rf_pred = self.rf.predict(data.features_test) lda_pred = self.lda.predict(data.features_test) dec_pred = self.dec.predict(data.features_test) for i in range(len(rf_pred)): pre_pred.append([ rf_pred[i], lda_pred[i], dec_pred[i], ada_pred[i] ]) for entry in pre_pred: pred_list = sorted(entry, key=entry.count, reverse=True) self.pred.append(pred_list[0])
def test_twomethods(self):
key_y_pred = 'y' + conf.SEP + conf.PREDICTION
X, y = datasets.make_classification(n_samples=20, n_features=5,
n_informative=2)
# = With EPAC
wf = Methods(LDA(), SVC(kernel="linear"))
r_epac = wf.run(X=X, y=y)
# = With SKLEARN
lda = LDA()
svm = SVC(kernel="linear")
lda.fit(X, y)
svm.fit(X, y)
r_sklearn = [lda.predict(X), svm.predict(X)]
# Comparison
for i_cls in range(2):
comp = np.all(np.asarray(r_epac[i_cls][key_y_pred]) ==
np.asarray(r_sklearn[i_cls]))
self.assertTrue(comp, u'Diff Methods')
# test reduce
r_epac_reduce = [wf.reduce().values()[0][key_y_pred],
wf.reduce().values()[1][key_y_pred]]
comp = np.all(np.asarray(r_epac_reduce) == np.asarray(r_sklearn))
self.assertTrue(comp, u'Diff Perm / CV: EPAC reduce')
def LDAmeanScore(X, Y, n_folds, dim_reduction=0):
"""
:param X: matrice d'entree du classifieur, n_samples*n_parameters, n_paramters>=2, n_samples>0. DONNES COHERENTES POUR CLASSIFICATION LDA
:param Y: matrice des labels, n_samples
:param n_folds: nombre de tests pour le KFold, >1
:param dim_reduction: si egale a 0, pas de reduction, si inferieur a 0, best_reduction, sinon on fait une reduction PCA (on reduit a dim_reduction dimensions)
:return: le score moyen de la validation croisee, affiche ce score. Si n_folds>n_samples, renvoie -1
"""
if dim_reduction > 0 and X.shape[1] > dim_reduction:
X = dim_reduction_PCA(X, dim_reduction)
if dim_reduction == -1:
dim_reduction = best_dimension(X)
print "Best dimension : " + str(dim_reduction)
X = dim_reduction_PCA(X, dim_reduction)
if X.shape[0] > n_folds:
# Cross validation pour estimer la performance d'un classifieur LDA
kf = KFold(n=len(Y), n_folds=n_folds, shuffle=True, random_state=None)
scores = []
for train_index, test_index in kf:
X_train, X_test = X[train_index, :], X[test_index, :]
Y_train, Y_test = Y[train_index], Y[test_index]
cl = LDA()
cl.fit(X_train, Y_train)
scores.append(cl.score(X_test, Y_test))
print "Score moyen : ", np.mean(np.array(scores))
return 100.0 * np.mean(np.array(scores))
else:
return -1
def LDA模型(self, 問題, 答案):
lda = LDA()
# clf = svm.NuSVC()
print('訓練LDA')
lda.fit(問題, 答案)
print('訓練了')
return lambda 問:lda.predict(問)
def test_all_methods(self):
x_cols = ["Lag2"]
formula = "Direction~Lag2"
# print self.df.shape[0]
train_data = self.df.ix[(self.df["Year"] >= 1990) & (self.df["Year"] <= 2008), :]
# print train_data.shape[0]
""" (d) logistic"""
model = smf.glm(formula, data=train_data, family=sm.families.Binomial())
result = model.fit()
test_data = self.df.ix[self.df["Year"] > 2008, :]
probs = Series(result.predict(sm.add_constant(test_data[["Lag2"]])))
pred_values = probs.map(lambda x: "Down" if x > 0.5 else "Up")
tp.output_table(pred_values.values, test_data[self.y_col].values)
train_X = train_data[x_cols].values
train_y = train_data[self.y_col].values
test_X = test_data[x_cols].values
test_y = test_data[self.y_col].values
""" (e) LDA """
lda_res = LDA().fit(train_X, train_y)
pred_y = lda_res.predict(test_X)
tp.output_table(pred_y, test_y)
""" (f) QDA """
qda_res = QDA().fit(train_X, train_y)
pred_y = qda_res.predict(test_X)
tp.output_table(pred_y, test_y)
""" (g) KNN """
clf = neighbors.KNeighborsClassifier(1, weights="uniform")
clf.fit(train_X, train_y)
pred_y = clf.predict(test_X)
tp.output_table(pred_y, test_y)
""" (h) logistic and LDA """
""" (i) Is the purpose of the last question going through all methods with no direction?"""
def score(train_X, train_y):
X_train, X_valid, y_train, y_valid = train_test_split(train_X, train_y, test_size=0.01, random_state=10)
clf = LDA()
clf.fit(X_train, y_train)
y_pred = clf.predict_proba(X_valid)
return log_loss(y_valid, y_pred)
def test_classification():
from read import read
import numpy, tfidf
from sklearn.decomposition import TruncatedSVD
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import Normalizer
m, files = read("training.json")
y_map = [str(file["topic"]) for file in files]
map = []
for i in range(len(y_map)):
if(len(map) == 0 or not map.__contains__(y_map[i])):
map.append(y_map[i])
y = numpy.array([map.index(y_map[i]) for i in range(len(y_map))])
print("Construindo TF-IDF...")
X, vectorizer = tfidf.vectorizeTFIDF(files)
print X.shape
print("Performing dimensionality reduction using LDA...")
lda = LDA(n_components=9)
X = X.toarray()
lda.fit(X, y)
X = lda.transform(X)
mlp = MLPClassifier()
mlp.fit(X, y)
training_score = mlp.score(X, y)
print("training accuracy: %f" % training_score)
def main():
for question in range(3,18):
print("Question ", question, " Percent Accuracy")
trainingSet_features, trainingSet_labels, testSet_features, testSet_labels = loadTrainingAndTestData(question)
#print(len(trainingSet_features))
#print(trainingSet_labels)
#print(len(testSet_features))
#print(len(testSet_labels))
#print(trainingSet_labels)
nnC = KNeighborsClassifier(n_neighbors=5)
nnC.fit(trainingSet_features, trainingSet_labels)
nnC_predictions = nnC.predict(testSet_features)
print("Nearest Neighbor: %.2f" % (100*accuracy_score(testSet_labels,nnC_predictions)),"%")
svmC = svm.SVC()
svmC.fit(trainingSet_features, trainingSet_labels)
svmCpredictions = svmC.predict(testSet_features)
print("Support Vector Machines: %.2f" % (100*accuracy_score(testSet_labels,svmCpredictions)),"%")
rfC = RandomForestClassifier(n_estimators=100)
rfC.fit(trainingSet_features, trainingSet_labels)
rfC_predictions = rfC.predict(testSet_features)
print("Random Forrest: %.2f" % (100*accuracy_score(testSet_labels,rfC_predictions)),"%")
ldaC = LDA(solver='lsqr')
ldaC.fit(trainingSet_features, trainingSet_labels)
ldaC_predictions = ldaC.predict(testSet_features)
print("Linear Discriminant Analysis Classifier: %.2f" % (100*accuracy_score(testSet_labels,ldaC_predictions)),"%")
def main():
logging.basicConfig(format='[%(asctime)s] %(levelname)7s: %(message)s', level=logging.DEBUG)
all_image_numbers = generate_all_image_numbers(no_of_persons, samples_person)
classes = all_image_numbers[:, 0]
all_face_vectors = load_face_vectors_from_disk(all_image_numbers, image_size)
classifier = LDA()
logging.debug("Training..")
classifier.fit(all_face_vectors, classes)
while True:
function = input(
"0)Exit\n"
"1)Live test\n"
"2)Test image \"test.JPG\"\n"
"3)General test\n"
"\n"
"Choose function:"
)
if function == "1":
test_live(classifier, all_face_vectors)
elif function == "2":
test_one_image(classifier, all_face_vectors)
elif function == "3":
test(all_face_vectors, classes)
elif function == "0":
return
def runLDA(all_kmer_vectors_array,labels):
sklearn_lda = LDA(n_components=4)
X = np.array(all_kmer_vectors_array)
y = np.array(labels)
X_lda_sklearn = sklearn_lda.fit_transform(X,y)
print(X_lda_sklearn)
return X_lda_sklearn
def LDAClassify_Proba(enrollment_id, trainData, trainLabel, testData):
clf = LDA(solver='lsqr')
#clf = LDA()
clf.fit(trainData, ravel(trainLabel))
testLabel = clf.predict_proba(testData)[:,1]
saveResult(enrollment_id, testLabel, 'Proba_sklearn_LDA.csv')
return testLabel
def naive_bayes_with_lda():
train, train_target, test, test_target = load_polluted_spambase()
print "Train data: %s, Train Label: %s" % (train.shape, train_target.shape)
print "Test data: %s, Test Label: %s" % (test.shape, test_target.shape)
start = timeit.default_timer()
lda = LDA(n_components=100)
train = lda.fit_transform(train, train_target)
test = lda.transform(test)
print lda
print "Train data: %s, Train Label: %s" % (train.shape, train_target.shape)
print "Test data: %s, Test Label: %s" % (test.shape, test_target.shape)
cf = GaussianNaiveBayes()
cf.fit(train, train_target)
raw_predicts = cf.predict(test)
predict_class = cf.predict_class(raw_predicts)
cm = confusion_matrix(test_target, predict_class)
print "confusion matrix: TN: %s, FP: %s, FN: %s, TP: %s" % (cm[0, 0], cm[0, 1], cm[1, 0], cm[1, 1])
er, acc, fpr, tpr = confusion_matrix_analysis(cm)
print "Error rate: %f, accuracy: %f, FPR: %f, TPR: %f" % (er, acc, fpr, tpr)
stop = timeit.default_timer()
print "Total Run Time: %s secs" % (stop - start)
def pca_lda(X_train,X_test,y_train,y_test):
pca = PCA(n_components=500)
lda = LDA()
pca.fit(X_train)
scores = np.dot(X_train,np.transpose(pca.components_))
lda.fit(scores, y_train)
return lda.score(scores, y_train, sample_weight=None)
def train_lda():
from sklearn.lda import LDA
data, classes = get_data_and_classes()
classifier = LDA()
classifier.fit(data, classes, store_covariance=True)
return classifier
def read_subpop_data(one_hot=True, fake_data=False, test_size=0.2, undersample=False):
labeled_dic = convert_txt_to_npy(LABELED_RL_PATH)
unlabeled_dic = convert_txt_to_npy(UNLABELED_RL_PATH, labeled=False)
X_train, X_test, y_train, y_test = split_train_test(labeled_dic, test_size=test_size)
class DataSets(object):
pass
data_sets = DataSets()
if undersample:
from unbalanced_dataset import UnderSampler
US = UnderSampler(verbose=True)
X_train, y_train = US.fit_transform(X_train, y_train)
lda = LDA()
lda.fit(X_train, y_train)
score = metrics.accuracy_score(lda.predict(X_test), y_test)
print("Baseline LDA: %f " % score)
if one_hot:
y_train = convert_to_one_hot(y_train)
y_test = convert_to_one_hot(y_test)
data_sets = DataSets()
data_sets.test = DataSet(X_test, y_test)
data_sets.train = SemiDataSet(unlabeled_dic['data'], X_train, y_train)
return data_sets
def ldapredict(trainData,testData,trainOuts,testOuts): clf = LDA() print(clf.fit(trainData,trainOuts)) predictions = clf.predict(testData) print(predictions) misses,error = sup.crunchTestResults(predictions,testOuts,.5) print(1-error)
def do_lda(x, y, folds):
indexes = list(range(len(x)))
shuffle(indexes)
x = list(x[i] for i in indexes)
y = list(y[i] for i in indexes)
fold_size = len(x) / folds
corrects = []
for fold in range(folds):
test_x = []
train_x = []
test_y = []
train_y = []
for i in range(len(x)):
fold_index = i / fold_size
if fold == fold_index:
test_x.append(x[i])
test_y.append(y[i])
else:
train_x.append(x[i])
train_y.append(y[i])
print 'Partitioned data into fold'
test_x, train_x = remove_redundant_dimensions(test_x, train_x)
print 'Removed redundant dimensions'
lda = LDA()
lda.fit(train_x, train_y)
print 'Fit lda'
predictions = lda.predict(test_x)
correct = sum(1 for i in range(len(predictions)) if predictions[i] == test_y[i])
print 'Did fold, correct:', correct
corrects.append(correct)
return corrects
def lda(self, reducedArray = []):
# components vyjadruju pocet stavov / classov medzi ktorymi rozlisujeme.. staci 0/1 pre target a non-target
lda = LDA(n_components=2)
if len(reducedArray) > 0:
self.ldaMat = lda.fit(np.resize(reducedArray,(len(reducedArray),len(reducedArray[0]))), self.targetVals)
else:
self.ldaMat = lda.fit(np.resize(self.signalArray,(len(self.signalArray),len(self.signalArray[0]))), self.targetVals)
def DLDA(self, trainLabel, featureData, testData):
# print featureData == testData
# print testData
clf = LDA()
clf.fit(featureData, trainLabel)
testLabel = clf.predict(testData)
return testLabel
def main_lda(): X,y=fh_lda() lda=LDA() lda.fit(X,y) splot=plot_LDA(lda, X, y, lda.fit(X,y).predict(X)) return splot
def siLDA(X, y):
lda = LDA(n_components=2)
X_r2 = lda.fit(X, y).transform(X)
plt.figure()
for c, i in zip('rgb', [0, 1]):
plt.scatter(X_r2[y == i, 0], X_r2[y == i, 1], c=c)
plt.title('LDA')
plt.show()
def lda(X,y):
lda = LDA(n_components=3)
X_r2 = lda.fit(X,y).transform(X)
plt.figure()
for c, i, target_name in zip("gbr", [0,1, 2], ['others','inhibitory','excitatory']):
plt.scatter(X_r2[y == i, 0], X_r2[y == i, 1], c=c, label=target_name)
plt.legend()
plt.title('LDA')
def reduceDimensionLDA(mat, k): print mat.shape labels = mat[:, -1] mat = mat[:, :-1] lda = LDA(n_components = k) data = lda.fit_transform(mat, labels) data = addLabels(data, labels) print data return data
def classifyLDA(self) :
print self.train_dataset
clf = LDA(n_components=2)
vr_train = clf.fit(self.train_dataset, self.train_label).transform(self.train_dataset)
print vr_train
plt.figure()
for c, i in zip("br", [0, 1]):
plt.scatter(vr_train[self.train_label == i], [0]*len(vr_train[self.train_label == i]), c=c)
plt.show()
def curve_per_subject(subject, data_path, test_labels):
d = load_train_data(data_path, subject)
x, y_10m = d['x'], d['y']
n_train_examples = x.shape[0]
n_timesteps = x.shape[-1]
print 'n_preictal', np.sum(y_10m)
print 'n_inetrictal', np.sum(y_10m - 1)
x, y = reshape_data(x, y_10m)
data_scaler = StandardScaler()
x = data_scaler.fit_transform(x)
lda = LDA()
lda.fit(x, y)
pred_1m = lda.predict_proba(x)[:, 1]
pred_10m = np.reshape(pred_1m, (n_train_examples, n_timesteps))
pred_10m = np.mean(pred_10m, axis=1)
fpr, tpr, threshold = roc_curve(y_10m, pred_10m)
c = np.sqrt((1 - tpr) ** 2 + fpr ** 2)
opt_threshold = threshold[np.where(c == np.min(c))[0]][-1]
print opt_threshold
# ------- TEST ---------------
d = load_test_data(data_path, subject)
x_test, id = d['x'], d['id']
n_test_examples = x_test.shape[0]
n_timesteps = x_test.shape[3]
x_test = reshape_data(x_test)
x_test = data_scaler.transform(x_test)
pred_1m = lda.predict_proba(x_test)[:, 1]
pred_10m = np.reshape(pred_1m, (n_test_examples, n_timesteps))
pred_10m = np.mean(pred_10m, axis=1)
y_pred = np.zeros_like(test_labels)
y_pred[np.where(pred_10m >= opt_threshold)] = 1
cm = confusion_matrix(test_labels, y_pred)
print print_cm(cm, labels=['interictal', 'preictal'])
sn = 1.0 * cm[1, 1] / (cm[1, 1] + cm[1, 0])
sp = 1.0 * cm[0, 0] / (cm[0, 0] + cm[0, 1])
print sn, sp
sn, sp = [], []
t_list = np.arange(0.0, 1.0, 0.01)
for t in t_list:
y_pred = np.zeros_like(test_labels)
y_pred[np.where(pred_10m >= t)] = 1
cm = confusion_matrix(test_labels, y_pred)
sn_t = 1.0 * cm[1, 1] / (cm[1, 1] + cm[1, 0])
sp_t = 1.0 * cm[0, 0] / (cm[0, 0] + cm[0, 1])
sn.append(sn_t)
sp.append(sp_t)
return t_list, sn, sp
def lda(data,labels,n,v_type): train_data,train_labels,test_data,test_labels = split_data(data,labels,v_type) clf = LDA() clf.fit(np.array(train_data,dtype=np.float64), np.array(train_labels,dtype=np.float64)) y_pred = clf.predict(test_data) pure_accuracy_rate = len([y_pred[x] for x in range(len(y_pred)) if y_pred[x] == test_labels[x]])/float(len(test_labels)) report = classification_report(y_pred, test_labels, target_names=rock_names) cm = confusion_matrix(test_labels, y_pred) return pure_accuracy_rate,report,y_pred,test_labels,test_data,clf,cm,"LDA"
def lda(ds, n):
'''
Outputs the projection of the data in the best
discriminant dimension.
Maximum of 2 dimensions for our binary case (values of n greater than this will be ignored by sklearn)
'''
selector = LDA(n_components=n)
selector.fit(ds.data, ds.target)
new_data = selector.transform(ds.data)
return Dataset(new_data, ds.target)
def lda(df, samples, sample_labels, plot_name='lda_plot.png'):
df = df.copy()
df = df.transpose()
df = df.ix[samples]
df_nrm = normalize_min_max(df)
X = df_nrm.values
label_dict, y = encode_labels(sample_labels)
ldas = LDA(n_components=2)
X_lda = ldas.fit_transform(X, y)
plot_scikit_lda(X_lda, y, label_dict, samples)
def __call__(self, x, y, inputs, labels):
classes = numpy.unique(labels)
if len(classes) == 1:
if y == classes[0]:
return 1
else:
return -1
lda = LDA().fit(inputs, labels)
prob = lda.predict_proba([x])[0][lda.classes_.tolist().index(y)]
return 2 * prob - 1
def new_clf(self, classifier="Decision Tree"):
names = [
"Decision Tree", "Random Forest", "AdaBoost",
"Gaussian Naive Bayes", "Multinomial Naive Bayes",
"Bernoulli Naive Bayes", "LDA"
]
classifiers = [
DecisionTreeClassifier(max_depth=5),
RandomForestClassifier(max_depth=5,
n_estimators=10,
max_features=1),
AdaBoostClassifier(),
GaussianNB(),
MultinomialNB(),
BernoulliNB(),
LDA()
]
dic = dict(zip(names, classifiers))
return dic[classifier]
def test_all_estimators():
estimators = all_estimators()
clf = LDA()
for name, E in estimators:
# some can just not be sensibly default constructed
if E in dont_test:
continue
# test default-constructibility
# get rid of deprecation warnings
with warnings.catch_warnings(record=True) as w:
if E in meta_estimators:
e = E(clf)
else:
e = E()
#test cloning
clone(e)
# test __repr__
repr(e)
def checkeachClassfier(train_x, train_y, test_x, test_y):
classifiers = [
KNeighborsClassifier(3),
SVC(kernel="linear", C=0.025),
SVC(class_weight='auto'),
SVC(gamma=2, C=1),
DecisionTreeClassifier(max_depth=5),
DecisionTreeClassifier(class_weight='auto'),
RandomForestClassifier(max_depth=5, n_estimators=10, max_features=1),
RandomForestClassifier(class_weight='auto'),
AdaBoostClassifier(),
GaussianNB(),
LDA(),
QDA()
]
classtitle = [
"KNeighborsClassifier", "SVC", "SVC weighted", "SVC(gamma=2, C=1)",
"DecisionTreeClassifier", "DecisionTreeClassifier weighted",
"RandomForestClassifier", "RandomForestClassifier weighted",
"AdaBoostClassifier", "GaussianNB", "LDA", "QDA"
]
for i in range(len(classtitle)):
try:
ctitle = classtitle[i]
clf = classifiers[i]
clf.fit(train_x, train_y)
train_pdt = clf.predict(train_x)
MCC, Acc_p, Acc_n, Acc_all = get_Accs(train_y, train_pdt)
print ctitle + ":"
print "MCC, Acc_p , Acc_n, Acc_all(train): "
print "%s,%s,%s,%s" % (str(MCC), str(Acc_p), str(Acc_n),
str(Acc_all))
test_pdt = clf.predict(test_x)
MCC, Acc_p, Acc_n, Acc_all = get_Accs(test_y, test_pdt)
print "MCC, Acc_p , Acc_n, Acc_all(test): "
print "%s,%s,%s,%s" % (str(MCC), str(Acc_p), str(Acc_n),
str(Acc_all))
except:
print ctitle + ": error"
print
def get_classification_r2(ticker_data):
data_len = len(ticker_data)
split_line = int(data_len * 0.8)
X = ticker_data.drop('close',1)[:-1]
y = Series(ticker_data['close'].shift(-1).dropna(),dtype='|S6')
X_train = X.ix[:split_line]
X_test = X.ix[split_line:]
y_train = y.ix[:split_line]
y_test = y.ix[split_line:]
models = [("LR", LogisticRegression()),
("LDA", LDA()),
# ("QDA", QDA()),
("LSVC", LinearSVC()),
("RSVM", SVC(
C=1000000.0, cache_size=200, class_weight=None,
coef0=0.0, degree=3, gamma=0.0001, kernel='rbf',
max_iter=-1, probability=False, random_state=None,
shrinking=True, tol=0.001, verbose=False)
),
("RF", RandomForestClassifier(
n_estimators=1000, criterion='gini',
max_depth=None, min_samples_split=2,
min_samples_leaf=1, max_features='auto',
bootstrap=True, oob_score=False, n_jobs=1,
random_state=None, verbose=0)
)]
best = (0,0)
for m in models:
m[1].fit(X_train, y_train)
pred = m[1].predict(X_test)
name = m[0]
score = m[1].score(X_test, y_test)
if score > best[1]:
best = (name,score)
print 'the best cluster is:' , best
return best
def main():
(X, Y, Ynames) = load_magic_data()
X = StandardScaler().fit_transform(X)
Xtrain, Xtest, Ytrain, Ytest = train_test_split(X,
Y,
test_size=0.33,
random_state=None)
C = 5.0
classifiers = {
'L1 logistic': LogisticRegression(C=C, penalty='l1'),
'L2 logistic': LogisticRegression(C=C, penalty='l2'),
'KNN': KNeighborsClassifier(n_neighbors=11),
'NB': GaussianNB(),
'RF5': RandomForestClassifier(n_estimators=5),
'RF50': RandomForestClassifier(n_estimators=50),
'AdaBoost': AdaBoostClassifier(),
'LDA': LDA(),
'QDA': QDA()
}
plt.figure(figsize=(8, 8))
n_classifiers = len(classifiers)
for index, (name, clf) in enumerate(classifiers.iteritems()):
clf.fit(Xtrain, Ytrain)
probs = clf.predict_proba(Xtest)
fpr, tpr, thresholds = roc_curve(Ytest, probs[:, 1])
roc_auc = auc(fpr, tpr)
print 'For model', name, 'accuracy =', clf.score(Xtest, Ytest)
plt.plot(fpr, tpr, label='%s (area = %0.2f)' % (name, roc_auc))
plt.plot([0, 1], [0, 1], 'k--')
plt.xlim([0.0, 1.0])
plt.ylim([0.0, 1.0])
plt.xlabel('False Positive Rate')
plt.ylabel('True Positive Rate')
plt.title('ROC Curve')
plt.legend(loc="lower right")
plt.show()
def train(args):
print("Loading embeddings.")
fname = "{}/labels.csv".format(args.workDir)
labels = pd.read_csv(fname, header=None).as_matrix()[:, 1]
labels = map(itemgetter(1), map(os.path.split,
map(os.path.dirname,
labels))) # Get the directory.
fname = "{}/reps.csv".format(args.workDir)
embeddings = pd.read_csv(fname, header=None).as_matrix()
le = LabelEncoder().fit(labels)
labelsNum = le.transform(labels)
nClasses = len(le.classes_)
print("Training for {} classes.".format(nClasses))
if args.classifier == 'LinearSvm':
clf = SVC(C=1, kernel='linear', probability=True)
elif args.classifier == 'GMM': #Doesn't work best
clf = GMM(n_components=nClasses)
#ref: http://scikit-learn.org/stable/auto_examples/classification/plot_classifier_comparison.html#example-classification-plot-classifier-comparison-py
elif args.classifier == 'RadialSvm': #Radial Basis Function kernel
clf = SVC(C=1000, kernel='rbf', probability=True,
gamma=0.05) #works better with C = 1 and gamma = 2
elif args.classifier == 'DecisionTree': #Doesn't work best
clf = DecisionTreeClassifier(max_depth=20)
if args.ldaDim > 0:
clf_final = clf
clf = Pipeline([('lda', LDA(n_components=args.ldaDim)),
('clf', clf_final)])
print "Embeddings: "
print embeddings.shape
print "\nlabelsNum: "
print labelsNum[-1:][0] + 1
clf.fit(embeddings, labelsNum)
fName = "{}/classifier.pkl".format(args.workDir)
print("Saving classifier to '{}'".format(fName))
with open(fName, 'w') as f:
pickle.dump((le, clf), f)
class LDAFeatures:
def __init__(self, n_comp=3):
self.lda = None
self.n_comp = n_comp
def features(self, pixels, gt=None):
#grab feature stack
fullFeatures = naive_features(pixels)
print fullFeatures.shape
#if the LDA from ground truth exists already, transform new features
if gt == None and self.lda != None:
print self.lda
return self.lda.transform(fullFeatures)
assert gt != None
#otherwise, train LDA
self.lda = LDA(n_components=self.n_comp).fit(fullFeatures, gt)
print self.lda
return self.lda.transform(fullFeatures)
def __init__(self):
self.model = LDA()
self.emgMode = myo.EmgMode.RAW
self.imuMode = myo.ImuMode.RAW
self.features = {'Names': ['MAV', 'RMS','ZC'],'LW': 150,'LI': 1}
self.trainPercent = [0.7, 0.2, 0.1]
self.dataMode = ["emg" , "imu"]
self.emgDataFilePath = None
self.accDataFilePath = None
self.gyroDataFilePath = None
self.quatDataFilePath = None
self.modelFilePath = None
self.fileDict = {}
self.modelFileDict = {}
self.filePathName = "wfyFilePath"
self.modelName = "wfyModel"
self.runCount = 0
def main():
svm = SVC(C=4.0)
clf = Pipeline([('scaler', StandardScaler()), ('svm', svm)])
name = 'SVM'
test_method(clf, name)
clf = RandomForestClassifier(n_estimators=60, n_jobs=-1)
name = 'randforest'
test_method(clf, name)
clf = LDA()
name = 'LDA'
test_method(clf, name)
clf = neighbors.KNeighborsClassifier(n_neighbors=15)
name = 'KNN'
test_method(clf, name)
clf = GradientBoostingClassifier(n_estimators=100)
name = 'gradboosting'
test_method(clf, name)
def evaluate(data, targets):
print "Creating models..."
models = []
models.append(LinearSVC())
models.append(SVC(kernel='rbf'))
models.append(GaussianNB())
models.append(LDA())
models.append(QDA())
models.append(LogisticRegression())
models.append(KNeighborsRegressor())
models.append(
RandomForestClassifier(n_estimators=100,
criterion="entropy",
random_state=1234,
n_jobs=-1))
if sparse.issparse(data):
data = data.toarray()
mc = ModelComparison(data, targets, folds=10, numCV=3, models=models)
mc.evaluate()
def modelSelection(X, y, KFold, test_fraction):
model_arr = [
LDA(),
DecisionTreeClassifier(max_depth=5),
KNeighborsClassifier(3),
SVC(gamma=2, C=1),
SVC(kernel="linear", C=0.025),
GaussianNB(),
LogisticRegression()
]
model_names = [
"LDA()", "DecisionTreeClassifier(max_depth=5)",
"KNeighborsClassifier(3)", "SVC(gamma=2, C=1)",
"SVC(kernel=linear, C=0.025)", "GaussianNB()", "LogisticRegression()"
]
for i, m in enumerate(model_arr):
result = cross_validate(X, y, m, KFold, test_fraction)
print model_names[i]
print result
def classification_learning_curves(X, y, title=''):
""" Computes and plots learning curves of regression models of X and y
"""
# Ridge classification
rdgc = RidgeClassifierCV(alphas=np.logspace(-3, 3, 7))
# Support Vector classification
svc = SVC()
# Linear Discriminant Analysis
lda = LDA()
# Logistic Regression
logit = LogisticRegression(penalty='l2', random_state=42)
estimator_str = ['svc', 'lda', 'rdgc', 'logit']
# train size
train_size = np.linspace(.2, .9, 8)
# Compute learning curves
for e in estimator_str:
estimator = eval(e)
ts, _, scores = learning_curve(estimator, X, y,
train_sizes=train_size, cv=4)
bl = plt.plot(train_size, np.mean(scores, axis=1))
plt.fill_between(train_size,
np.mean(scores, axis=1) - np.std(scores, axis=1),
np.mean(scores, axis=1) + np.std(scores, axis=1),
facecolor=bl[0].get_c(),
alpha=0.1)
plt.xticks(fontsize=16)
plt.yticks(fontsize=16)
plt.legend(estimator_str, loc='best')
plt.xlabel('Train size', fontsize=16)
plt.ylabel('Accuracy', fontsize=16)
plt.ylim([.3, .9])
plt.grid()
plt.title('Classification ' + title, fontsize=16)
def evaluate(data, targets):
prior = numpy.bincount(y.astype(int)) / float(len(targets))
models = [
LDA(priors=prior),
SVC(probability=True, class_weight="auto", kernel="linear"),
LogisticRegression(class_weight="auto"),
GaussianNB(),
KNeighborsClassifier(),
QDA(priors=prior),
RandomForestClassifier(n_estimators=100,
criterion="entropy",
n_jobs=-1,
random_state=123456),
SVC(probability=True, class_weight="auto")
]
model_names = [
"LDA", "Linear SVM", "Logistic Regression", "Naive Bayes", "k-NN",
"QDA", "Random Forest", "SVM w/ RBF"
]
# evaluate using ModelEvaluation class
mevaluator = model_evaluation.TenFoldCrossValidation(
data=data,
targets=targets,
models=models,
model_names=model_names,
scale=True)
start = time.time()
caa_eval = mevaluator.evaluate(metrics.class_averaged_accuracy_score)
for key, value in caa_eval.iteritems():
model_str = key.split("(")[0]
print model_str, (str(numpy.around(numpy.mean(value), decimals=3)) +
" (" +
str(numpy.around(numpy.std(value), decimals=3)) +
")")
mevaluator.evaluate_roc()
print "Overall running time:", (time.time() - start)
def gridSearch(X_train, y_train, angle):
"""
Performs a grid search to find the best classifier hyperparameters using LDA
with a KNN classifier.
"""
component_grid = [5, 10, 20, 50, 75, 100]
neighbor_grid = [2, 3, 4, 5, 6, 7, 9, 11, 15, 20, 25, 30, 40]
estimators = [('reduce_dim', LDA(solver='eigen')),
('knn', KNeighborsClassifier())]
clf = Pipeline(estimators)
params = {
'reduce_dim__n_components': neighbor_grid,
'knn__n_neighbors': component_grid
}
grid_search = GridSearchCV(clf, param_grid=params)
grid_search.fit(X_train, y_train)
pickle.dump(grid_search, open("model" + str(angle) + ".p", "wb"))
return grid_search
def __init__(self, training_path, testing_path):
self.training_path = training_path
self.testing_path = testing_path
self.training_features = None
self.testing_features = None
self.training_image_list = []
self.testing_image_list = []
self.training_labels = []
self.testing_labels = []
self.predicted_testing_labels = []
self.class_map = {}
self.n_classes = len(os.listdir(os.path.join('.', 'data', 'training')))
self.classifiers = {
'knn':
KNeighborsClassifier(3),
'svm_linear':
SVC(kernel="linear", C=0.025),
'svm':
SVC(gamma=2, C=1),
'tree':
DecisionTreeClassifier(max_depth=5),
'rf':
RandomForestClassifier(max_depth=5,
n_estimators=10,
max_features=1),
'adb':
AdaBoostClassifier(),
'gauss':
GaussianNB(),
'lda':
LDA(),
'qda':
QDA(),
'ann':
neuralNetwork(self.n_classes)
}
self.get_training_image_list()
self.get_testing_image_list()
def random_methods(data_train1,target_train1):
rng = np.random.RandomState(96235)
names = ["SGD", "Nearest Neighbors", "ensembel","Decision Tree","Random Forest", "AdaBoost", "Naive Bayes", "LDA", "QDA"]
classifiers = [
SGDClassifier(loss='hinge', penalty='l2', alpha=0.0005, n_iter=200, random_state=42, n_jobs=-1, average=True),
KNeighborsClassifier(10),
AdaBoostRegressor(DecisionTreeRegressor(max_depth=25),n_estimators=300, random_state=rng),
DecisionTreeClassifier(max_depth=11),
RandomForestClassifier(max_depth=21, n_estimators=21, max_features=1),
AdaBoostClassifier(),
GaussianNB(),
LDA(),
QDA()
]
# iterate over classifiers
for name, clf in zip(names, classifiers):
print("Fitting " + name + "...")
clf.fit(data_train1, target_train1)
print("Predicting...")
score = clf.score(data_test, target_test)
print(score)
predicted_test = clf.fit(data_train1, target_train1).predict(data_test)
print(metrics.classification_report(target_test, predicted_test))
def LDA10Fold(X, y):
acc = []
kf = KFold(X.shape[0], n_folds=10, shuffle=True)
i = 0
for train_index, test_index in kf:
yTest = y[test_index]
yTrain = y[train_index]
clf = LDA()
clf.fit(X[train_index], yTrain)
newRepTrain = clf.transform(X[train_index])
newRepTest = clf.transform(X[test_index])
nclf = neighbors.KNeighborsClassifier(n_neighbors=2)
nclf.fit(newRepTrain, yTrain)
XPred = nclf.predict(newRepTest)
acc.append(np.sum(XPred == yTest) * 1.0 / yTest.shape[0])
# print i,":",acc[i]
i += 1
return np.mean(acc), np.std(acc)
def create_confidence_matrix_one_vs_one(user_matix, file_number=0):
from sklearn.pipeline import Pipeline
import OneVsOneImproved
lda = LDA()
csp = CSP(n_components=2, transform_into='csp_space')
clf = Pipeline([('CSP', csp), ("LDA", lda)]) #TODO NOTE THIS CHANGE
classifier = OneVsOneImproved.OneVsOneClassifier(clf)
labels = []
data = []
for id, subject in enumerate(user_matix):
if len(subject) > file_number:
labels1 = [id for i in range(len(subject[file_number]))]
if not len(labels):
labels = labels1
data = subject[file_number]
else:
labels = np.concatenate((labels, np.asarray(labels1)))
data = np.concatenate((data, np.asarray(subject[file_number])))
#if len(data) != len(labels):
#print(len(data))
# print(len(labels))
score_matrix = fit_classifier_cross_val_score(data, labels, clf)
classifier.fit(np.asarray(data), np.asarray(labels))
return score_matrix, classifier
def execute(self, i, j):
x_train = self.x_train
y_train = self.y_train
dim_red = LDA()
x_train = dim_red.fit_transform(x_train, y_train)
with open('dumped_dim_red_' + str(i) + '.pkl', 'wb') as fid:
cPickle.dump(dim_red, fid)
stat_obj = self.stat_class() # reflection bitches
stat_obj.train(x_train, y_train)
with open('dumped_' + str(j) + '_' + str(i) + '.pkl', 'wb') as fid:
cPickle.dump(stat_obj, fid)
kf = KFold(len(self.x_train), n_folds=self.k_cross)
own_kappa = []
for train_idx, test_idx in kf:
# print train_idx,test_idx
# exit(0)
x_train, x_test = self.x_train[train_idx], self.x_train[test_idx]
y_train, y_test = self.y_train[train_idx], self.y_train[test_idx]
dim_red = LDA()
x_train = dim_red.fit_transform(x_train, y_train)
x_test = dim_red.transform(x_test)
stat_obj = self.stat_class() # reflection bitches
stat_obj.train(x_train, y_train)
y_pred = [0 for i in xrange(len(y_test))]
for i in range(len(x_test)):
val = int(np.round(stat_obj.predict(x_test[i])))
if val > self.range_max: val = self.range_max
if val < self.range_min: val = self.range_min
y_pred[i] = [val]
y_pred = np.matrix(y_pred)
cohen_kappa_rating = own_wp.quadratic_weighted_kappa(
y_test, y_pred, self.range_min, self.range_max)
self.values.append(cohen_kappa_rating)
return sum(self.values) / self.k_cross
def acc_image(training_data, tarining_label, test_data, test_label):
n_train = training_data.shape[0] # samples for training
n_test = test_data.shape[0] # samples for testing
n_averages = 50 # how often to repeat classification
n_features_max = 5 # maximum number of features
step = 1 # step size for the calculation
acc_clf1, acc_clf2 = [], []
n_features_range = range(1, n_features_max + 1, step)
for n_features in n_features_range:
score_clf1, score_clf2 = 0, 0
for _ in range(n_averages):
X, y = training_data[:, 0:n_features], tarining_label
clf1 = LDA(solver='lsqr', shrinkage='auto').fit(X, y)
clf2 = LDA(solver='lsqr', shrinkage=None).fit(X, y)
X, y = test_data[:, 0:n_features], test_label
score_clf1 += clf1.score(X, y)
score_clf2 += clf2.score(X, y)
acc_clf1.append(score_clf1 / n_averages)
acc_clf2.append(score_clf2 / n_averages)
features_samples_ratio = np.array(n_features_range) / n_train
plt.plot(features_samples_ratio,
acc_clf1,
linewidth=2,
label="LDA with shrinkage",
color='r')
plt.plot(features_samples_ratio,
acc_clf2,
linewidth=2,
label="LDA",
color='g')
plt.xlabel('n_features / n_samples')
plt.ylabel('Classification accuracy')
plt.legend(loc=1, prop={'size': 12})
plt.suptitle('LDA vs. shrinkage LDA (1 discriminative feature)')
plt.show()
def lda(input_file,Output):
lvltrace.lvltrace("LVLEntree dans lda")
ncol=tools.file_col_coma(input_file)
data = np.loadtxt(input_file, delimiter=',', usecols=range(ncol-1))
X = data[:,1:]
y = data[:,0]
n_samples, n_features = X.shape
#lda=LDA(n_components=2)
lda=LDA()
lda.fit(X,y)
X_LDA = lda.transform(X)
y_pred = lda.predict(X)
print "#########################################################################################################\n"
print "Linear Discriminant Analysis Accuracy "
print "classification accuracy:", metrics.accuracy_score(y, y_pred)
print "precision:", metrics.precision_score(y, y_pred)
print "recall:", metrics.recall_score(y, y_pred)
print "f1 score:", metrics.f1_score(y, y_pred)
print "\n"
print "#########################################################################################################\n"
results = Output+"LDA_metrics.txt"
file = open(results, "w")
file.write("Linear Discriminant Analaysis estimator accuracy\n")
file.write("Classification Accuracy Score: %f\n"%metrics.accuracy_score(y, y_pred))
file.write("Precision Score: %f\n"%metrics.precision_score(y, y_pred))
file.write("Recall Score: %f\n"%metrics.recall_score(y, y_pred))
file.write("F1 Score: %f\n"%metrics.f1_score(y, y_pred))
file.write("\n")
file.write("True Value, Predicted Value, Iteration\n")
for n in xrange(len(y)):
file.write("%f,%f,%i\n"%(y[n],y_pred[n],(n+1)))
file.close()
title = "LDA"
save = Output + "LDA_confusion_matrix.png"
plot_confusion_matrix(y, y_pred,title,save)
# plot the results along with the labels
fig, ax = plt.subplots()
im = ax.scatter(X_LDA[:, 0], X_LDA[:, 1], c=y)
fig.colorbar(im);
save_lda = Output + "LDA_plot.png"
plt.savefig(save_lda)
plt.close()
lvltrace.lvltrace("LVLSortie dans lda")
def test():
class1 = np.mat([
(2.9500, 6.6300),
(2.5300, 7.7900),
(3.5700, 5.6500),
(3.1600, 5.4700),
])
class2 = np.mat([
(2.5800, 4.4600),
(2.1600, 6.2200),
(3.2700, 3.5200),
])
test = (2.81, 5.46)
lda = myLDA(class1, class2)
print lda.predict(test)
lda = LDA()
lda.fit(np.concatenate((class1, class2)),
np.concatenate((np.zeros((3, 1)), np.ones((4, 1))), axis=0),
store_covariance=True)
print lda.predict(test)
temp = []
#PLS Dimension Reduction
pls2 = PLSRegression(n_components=n_components)
pls2.fit(features, MA_label)
XScore = pls2.transform(features)
# XScore = features
#LDA Classification
kf = KFold(n_splits=5)
kf.get_n_splits(XScore)
mean_acc = 0
for train_index, test_index in kf.split(XScore):
X_train, X_test = XScore[train_index], XScore[test_index]
y_train, y_test = MA_label[train_index], MA_label[test_index]
clf = LDA()
clf.fit(X_train, y_train)
Y_predict = clf.predict(X_test)
for i in range(len(Y_predict)):
print("Y_Predict {} - Y_Test {}".format(Y_predict[i], y_test[i]))
acc = accuracy_score(Y_predict, y_test)
print("Accuracy = {}".format(acc))
mean_acc = mean_acc + acc
mean_acc = (mean_acc / 5) * 100
print("Accuracy is {}".format(mean_acc))
with open("Results/MLL.csv", 'a') as csvFile:
writer = csv.writer(csvFile)
writer.writerow([numFeatures, mean_acc])
csvfile.close()
def classifier_comparison(X, y):
"""
分类器比较
Args:
X: training samples, size=[n_samples, n_features]
y: class labels, size=[n_samples, 1]
Returns:
None
"""
from sklearn import grid_search
from sklearn.svm import SVC
from sklearn.tree import DecisionTreeClassifier
from sklearn.ensemble import RandomForestClassifier, AdaBoostClassifier
from sklearn.naive_bayes import GaussianNB
from sklearn.lda import LDA
from sklearn.qda import QDA
from sklearn.linear_model import LogisticRegression
import scipy
# Exhaustive Grid Search
exhaustive_parameters = {
'kernel': ['rbf'],
'C': [1, 10, 100, 1000],
'gamma': [1e-3, 1e-4]
}
clf_SVC_exhaustive = grid_search.GridSearchCV(SVC(), exhaustive_parameters)
# Randomized Parameter Optimization
randomized_parameter = {
'kernel': ['rbf'],
'C': scipy.stats.expon(scale=100),
'gamma': scipy.stats.expon(scale=.1)
}
clf_SVC_randomized = grid_search.RandomizedSearchCV(
SVC(), randomized_parameter)
names = [
"Linear SVM", "RBF SVM", "RBF SVM with Grid Search",
"RBF SVM with Random Grid Search", "Decision Tree", "Random Forest",
"AdaBoost", "Naive Bayes", "LDA", "QDA"
]
classifiers = [
SVC(kernel="linear", C=0.025),
SVC(gamma=2, C=1), clf_SVC_exhaustive, clf_SVC_randomized,
DecisionTreeClassifier(max_depth=5),
RandomForestClassifier(max_depth=5, n_estimators=10, max_features=1),
AdaBoostClassifier(),
GaussianNB(),
LDA(),
QDA()
]
for name, clf in zip(names, classifiers):
logger.info('Use %s:' % (name))
train_classifier(clf, X, y)
# 逻辑回归
for C in [0.01, 0.1, 1, 10, 100, 1000, 10000]:
logger.info('Use LR with l1 penalty, C=%s:' % (C))
clf = LogisticRegression(C=C, penalty='l1', tol=0.01)
clf = train_classifier(clf, X, y)
logger.debug('coef matrix: %s' % (clf.coef_))
logger.info('Use LR with l2 penalty, C=%s:' % (C))
clf = LogisticRegression(C=C, penalty='l2', tol=0.01)
clf = train_classifier(clf, X, y)
logger.debug('coef matrix: %s' % (clf.coef_))
########################### Instantiate Classifiers ############################
classifiers = {
"Logistic":LogisticRegression(),
"NearestNeighbors":KNeighborsClassifier(100),
"LinearSVM":SVC(kernel="linear", C=0.025),
"RBFSVM":SVC(gamma=2, C=1),
"DecisionTree":DecisionTreeClassifier(max_depth=32),
"RandomForest":RandomForestClassifier(max_depth=None, n_estimators=200, max_features="auto",random_state=0,n_jobs=4),
"RandomForest2":RandomForestClassifier(max_depth=8, n_estimators=200, max_features="auto",random_state=0,n_jobs=4),
"AdaBoost":AdaBoostClassifier(n_estimators=500,random_state=0),
"GradientBoost":GradientBoostingClassifier(n_estimators=500, learning_rate=1.0,max_depth=None, random_state=0),
"NaiveBayes":GaussianNB(),
"LDA":LDA(),
"QDA":QDA()
}
joblist=[
(classifiers["RandomForest"],'RandomForest_signal','model_var_list_signal.csv'), # suffix and varlist
#(classifiers["RandomForest"],'RandomForest_tmxpayer','model_var_list_tmxpayer.csv'),
#(classifiers["RandomForest"],'RandomForest_tmxpayee','model_var_list_tmxpayee.csv'),
#(classifiers["RandomForest"],'RandomForest_signal_tmxpayer','model_var_list_signal_tmxpayer.csv'),
#(classifiers["RandomForest"],'RandomForest_signal_tmxpayee','model_var_list_signal_tmxpayee.csv'),
#(classifiers["RandomForest"],'RandomForest_tmxpayer_tmxpayee','model_var_list_tmxpayer_tmxpayee.csv'),
#(classifiers["RandomForest"],'RandomForest_tmxpayerpayee_comp','model_var_list_tmxpayerpayee_comp.csv'),
#(classifiers["RandomForest"],'RandomForest_signal_tmxboth','model_var_list_signal_tmxboth.csv'),
#(classifiers["RandomForest"],'RandomForest_signal_tmxboth_120','model_var_list_signal_tmxboth_120.csv'),
#(classifiers["RandomForest"],'RandomForest_signal_tmxboth_800','model_var_list_signal_tmxboth_800.csv'),
#(classifiers["RandomForest2"],'RandomForest_signal_tmxboth_RF2','model_var_list_signal_tmxboth.csv'),
def train(args):
print("Loading embeddings.")
fname = "{}/labels.csv".format(args.workDir)
labels = pd.read_csv(fname, header=None).as_matrix()[:, 1]
labels = map(itemgetter(1), map(os.path.split,
map(os.path.dirname,
labels))) # Get the directory.
fname = "{}/reps.csv".format(args.workDir)
embeddings = pd.read_csv(fname, header=None).as_matrix()
le = LabelEncoder().fit(labels)
labelsNum = le.transform(labels)
nClasses = len(le.classes_)
print("Training for {} classes.".format(nClasses))
if args.classifier == 'LinearSvm':
clf = SVC(C=1, kernel='linear', probability=True)
elif args.classifier == 'GridSearchSvm':
print("""
Warning: In our experiences, using a grid search over SVM hyper-parameters only
gives marginally better performance than a linear SVM with C=1 and
is not worth the extra computations of performing a grid search.
""")
param_grid = [{
'C': [1, 10, 100, 1000],
'kernel': ['linear']
}, {
'C': [1, 10, 100, 1000],
'gamma': [0.001, 0.0001],
'kernel': ['rbf']
}]
clf = GridSearchCV(SVC(C=1, probability=True), param_grid, cv=5)
elif args.classifier == 'GMM': # Doesn't work best
clf = GMM(n_components=nClasses)
# ref:
# http://scikit-learn.org/stable/auto_examples/classification/plot_args.classifier_comparison.html#example-classification-plot-args.classifier-comparison-py
elif args.classifier == 'RadialSvm': # Radial Basis Function kernel
# works better with C = 1 and gamma = 2
clf = SVC(C=1, kernel='rbf', probability=True, gamma=2)
elif args.classifier == 'DecisionTree': # Doesn't work best
clf = DecisionTreeClassifier(max_depth=20)
elif args.classifier == 'GaussianNB':
clf = GaussianNB()
# ref: https://jessesw.com/Deep-Learning/
elif args.classifier == 'DBN':
from nolearn.dbn import DBN
clf = DBN(
[embeddings.shape[1], 500, labelsNum[-1:][0] + 1
], # i/p nodes, hidden nodes, o/p nodes
learn_rates=0.3,
# Smaller steps mean a possibly more accurate result, but the
# training will take longer
learn_rate_decays=0.9,
# a factor the initial learning rate will be multiplied by
# after each iteration of the training
epochs=300, # no of iternation
# dropouts = 0.25, # Express the percentage of nodes that
# will be randomly dropped as a decimal.
verbose=1)
if args.ldaDim > 0:
clf_final = clf
clf = Pipeline([('lda', LDA(n_components=ldaDim)), ('clf', clf_final)])
clf.fit(embeddings, labelsNum)
fName = "{}/classifier.pkl".format(args.workDir)
print("Saving classifier to '{}'".format(fName))
with open(fName, 'w') as f:
pickle.dump((le, clf), f)
def get_gridsearch_classifier(clf_name):
""" add docstring later
"""
#%% "is_sparse" flag
"""note: i included this so method like Lasso, so I can obtain nnz after
model fit. for feature selection methods like ttest, i set this
as False since here I know nnz prehand."""
is_sparse = False # <- set this to True if method is sparse
#%% ***START HUGE ELIF STATEMENT ****
if clf_name == 'sklLogregL1':
""" L1 logistic regression """
np.random.seed(
0) # <- needed to ensure replicability in LogReg fit model
from sklearn.linear_model import LogisticRegression
clf = LogisticRegression(penalty='l1', random_state=0)
param_grid = {'C': 2.**np.arange(-8, 18, 2)}
is_sparse = True
elif clf_name == 'sklLinSvm':
""" Linear SVM (hinge loss) """
from sklearn.svm import LinearSVC
clf = LinearSVC(loss='hinge')
param_grid = {'C': 2.**np.arange(-18, 2, 2)}
# param_grid = {'C':2.**np.arange(-18,-2,1)}
# param_grid = {'C':2.**np.arange(-1,0,1)}
elif clf_name == 'fistaLogregElasticnet':
from tak.core import get_incmat_conn86
from tak.machine_learning.fista import LogRegElasticNetFista
clf = LogRegElasticNetFista(tol=1e-3)
param_grid = {
'alpha': 10.**np.arange(-8, 5, 1),
'l1_ratio': np.arange(0.1, 1.1, 0.1)
}
elif clf_name == 'fistaLogregGraphnet':
""" GraphNet Fista (logistic loss) """
from tak.core import get_incmat_conn86
from tak.machine_learning.fista import LogRegGraphNetFista
C, _ = get_incmat_conn86(radius=50)
clf = LogRegGraphNetFista(tol=1e-3, C=C)
param_grid = {
'alpha': 10.**np.arange(-8, 5, 1),
'l1_ratio': np.arange(0.1, 1.1, 0.1)
}
elif clf_name == 'fistaLogregGraphnet80':
""" GraphNet Fista (logistic loss)with radius of 80 """
from tak.core import get_incmat_conn86
from tak.machine_learning.fista import LogRegGraphNetFista
C, _ = get_incmat_conn86(radius=80)
clf = LogRegGraphNetFista(tol=1e-3, C=C)
param_grid = {
'alpha': 10.**np.arange(-8, 5, 1),
'l1_ratio': np.arange(0.1, 1.1, 0.1)
}
elif clf_name == 'rbfSvm':
""" RBF Kernel SVM """
from tak.ml import PrecomputedRBFSVM
clf = PrecomputedRBFSVM()
param_grid = {
'C': 10.**np.arange(-1, 10, 2),
'gamma': 10.**np.arange(-12, 1, 1)
}
elif clf_name == 'ttestRbfSvm':
# ttest + RBF Kernel SVM using Pipeline (3 parameters)
from tak.ml import ttest_for_fs, PrecomputedRBFSVM
from sklearn.feature_selection import SelectKBest
from sklearn.pipeline import Pipeline
ttest_fs = SelectKBest(score_func=ttest_for_fs)
# setup pipeline of ttest_filter + RBF_SVM
clf = Pipeline([('ttest', ttest_fs), ('svm', PrecomputedRBFSVM())])
# estimator parameters in a pipeline accessed as: <estimator>__<estimator>
param_grid = {
'ttest__k': (2**np.arange(4, 11, 1)).astype(int),
'svm__C':
10.**np.arange(-8, 11,
2), #^^^^^must be int, or scikit will complain
'svm__gamma': 10.**np.arange(-16, -5, 2)
}
elif clf_name == 'ttestLinSvm':
# ttest + liblinear Pipeline (2 parameters)
from tak.ml import ttest_for_fs
from sklearn.svm import LinearSVC
from sklearn.feature_selection import SelectKBest
from sklearn.pipeline import Pipeline
ttest_fs = SelectKBest(score_func=ttest_for_fs)
clf = Pipeline([
('ttest', ttest_fs),
('liblin', LinearSVC(loss='hinge')),
])
param_grid = {
'ttest__k': (2**np.arange(
4, 11.5,
0.5)).astype(int), # must be int, or scikit will complain
'liblin__C': 2.**np.arange(-18, 1, 1),
}
elif clf_name == 'enetLogRegSpams':
# Elastic-net Logistic Regression using my wrapper on SpamsToolbox (2 parameters)
from tak.ml import SpamFistaFlatWrapper
clf = SpamFistaFlatWrapper(loss='logistic',
regul='elastic-net',
max_it=400,
tol=1e-3)
param_grid = {
'lambda1': 2.**np.arange(-16, 1,
2), # L1 penalty (lambda1 in SPAMS)
'lambda2': 2.**np.arange(-16, 11, 3),
} # L2 penalty (lambda2 in SPAMS)
is_sparse = True
elif clf_name == 'enetLogRegGlmNet':
# Elastic-net Logistic Regression using my wrapper on SpamsToolbox (2 parameters)
from tak.ml import LogisticGlmNet
clf = LogisticGlmNet()
param_grid = {
'alpha': np.arange(0.1, 1.1, 0.1),
'lambdas': 2.**np.arange(1, -14, -1)
}
is_sparse = True
#%% === PCA stuffs...no interpretability, but see if accuracy improves ====
elif clf_name == 'PcaLda':
""" PCA + LDA (1 parameter) """
from sklearn.lda import LDA
from sklearn.decomposition import PCA
from sklearn.pipeline import Pipeline
clf = Pipeline([
('PCA', PCA()),
('LDA', LDA(solver='lsqr', shrinkage='auto')),
])
param_grid = {'PCA__n_components': np.array([2, 5, 10, 20, 40])}
#=== PCA + LINSVM ===
elif clf_name == 'PcaLinSvm':
from sklearn.svm import LinearSVC
from sklearn.decomposition import PCA
from sklearn.pipeline import Pipeline
clf = Pipeline([
('PCA', PCA()),
('SVM', LinearSVC(loss='hinge')),
])
param_grid = {
'PCA__n_components': np.array([5, 10, 20, 40, 100]),
'SVM__C': 2.**np.arange(-14, 3, 2)
}
#%% PCA + RBFSVM
elif clf_name == 'PcaRbfSvm':
from tak.ml import PrecomputedRBFSVM
from sklearn.decomposition import PCA
from sklearn.pipeline import Pipeline
clf = Pipeline([
('PCA', PCA()),
('SVM', PrecomputedRBFSVM()),
])
param_grid = {
'PCA__n_components': np.array([5, 10, 20, 40, 100]),
'SVM__C':
10.**np.arange(-1, 10,
2), #^^^^^must be int, or scikit will complain
'SVM__gamma': 2.**np.arange(-18, -8, 2)
}
#%% ttest + LDA (for interpretability, I guess)
elif clf_name == 'ttestLDA':
from tak.ml import ttest_for_fs
from sklearn.lda import LDA
from sklearn.pipeline import Pipeline
from sklearn.feature_selection import SelectKBest
ttest_fs = SelectKBest(score_func=ttest_for_fs)
clf = Pipeline([
('ttest', ttest_fs),
('LDA', LDA(solver='lsqr', shrinkage='auto')),
])
param_grid = {'ttest__k': (2**np.arange(4, 9.5, 0.5)).astype(int)}
#%%______huge elif above is complete. return ______
return clf, param_grid, is_sparse
n_samples = len(digits)
data = digits[:, :-1]
target = digits[:, -1]
param_grid = {
'pca1__n_components': [16],
'poly__degree': [2],
'pca2__n_components': [0.8],
'lda__n_components': [9],
'lr__penalty': ['l2'],
'lr__C': [0.1, 1]
}
steps = [('pca1', PCA()), ('poly', PolynomialFeatures()), ('pca2', PCA()),
('lda', LDA()), ('lr', LogisticRegression())]
pipeline = Pipeline(steps)
grid_search = GridSearchCV(pipeline, param_grid, n_jobs=-1, verbose=1, cv=2)
n_trains = n_samples / 3 * 2
# We learn the digits on the first half of the digits
grid_search.fit(data[:n_trains], target[:n_trains])
print("Best score: %0.3f" % grid_search.best_score_)
print("Best parameters set:")
best_parameters = grid_search.best_estimator_.get_params()
print best_parameters
def lda(X_train, y_train, X_test, y_test):
# Linear Discriminant Analysis (LDA) additionally maximizes the spread between classes
lda = LDA()
def speakerDiarization(fileName, numOfSpeakers, mtSize = 2.0, mtStep=0.2, stWin=0.05, LDAdim = 35, PLOT = False):
'''
ARGUMENTS:
- fileName: the name of the WAV file to be analyzed
- numOfSpeakers the number of speakers (clusters) in the recording (<=0 for unknown)
- mtSize (opt) mid-term window size
- mtStep (opt) mid-term window step
- stWin (opt) short-term window size
- LDAdim (opt) LDA dimension (0 for no LDA)
- PLOT (opt) 0 for not plotting the results 1 for plottingy
'''
[Fs, x] = audioBasicIO.readAudioFile(fileName)
x = audioBasicIO.stereo2mono(x);
Duration = len(x) / Fs
[Classifier1, MEAN1, STD1, classNames1, mtWin1, mtStep1, stWin1, stStep1, computeBEAT1] = aT.loadKNNModel("data/knnSpeakerAll")
[Classifier2, MEAN2, STD2, classNames2, mtWin2, mtStep2, stWin2, stStep2, computeBEAT2] = aT.loadKNNModel("data/knnSpeakerFemaleMale")
[MidTermFeatures, ShortTermFeatures] = aF.mtFeatureExtraction(x, Fs, mtSize * Fs, mtStep * Fs, round(Fs*stWin), round(Fs*stWin*0.5));
MidTermFeatures2 = numpy.zeros( (MidTermFeatures.shape[0] + len(classNames1) + len(classNames2), MidTermFeatures.shape[1] ) )
for i in range(MidTermFeatures.shape[1]):
curF1 = (MidTermFeatures[:,i] - MEAN1) / STD1
curF2 = (MidTermFeatures[:,i] - MEAN2) / STD2
[Result, P1] = aT.classifierWrapper(Classifier1, "knn", curF1)
[Result, P2] = aT.classifierWrapper(Classifier2, "knn", curF2)
MidTermFeatures2[0:MidTermFeatures.shape[0], i] = MidTermFeatures[:, i]
MidTermFeatures2[MidTermFeatures.shape[0]:MidTermFeatures.shape[0]+len(classNames1), i] = P1 + 0.0001;
MidTermFeatures2[MidTermFeatures.shape[0]+len(classNames1)::, i] = P2 + 0.0001;
MidTermFeatures = MidTermFeatures2 # TODO
# SELECT FEATURES:
#iFeaturesSelect = [8,9,10,11,12,13,14,15,16,17,18,19,20]; # SET 0A
#iFeaturesSelect = [8,9,10,11,12,13,14,15,16,17,18,19,20, 99,100]; # SET 0B
#iFeaturesSelect = [8,9,10,11,12,13,14,15,16,17,18,19,20, 68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98, 99,100]; # SET 0C
iFeaturesSelect = [8,9,10,11,12,13,14,15,16,17,18,19,20,41,42,43,44,45,46,47,48,49,50,51,52,53]; # SET 1A
#iFeaturesSelect = [8,9,10,11,12,13,14,15,16,17,18,19,20,41,42,43,44,45,46,47,48,49,50,51,52,53, 99,100]; # SET 1B
#iFeaturesSelect = [8,9,10,11,12,13,14,15,16,17,18,19,20,41,42,43,44,45,46,47,48,49,50,51,52,53, 68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98, 99,100]; # SET 1C
#iFeaturesSelect = [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53]; # SET 2A
#iFeaturesSelect = [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53, 99,100]; # SET 2B
#iFeaturesSelect = [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53, 68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98, 99,100]; # SET 2C
#iFeaturesSelect = range(100); # SET 3
#MidTermFeatures += numpy.random.rand(MidTermFeatures.shape[0], MidTermFeatures.shape[1]) * 0.000000010
MidTermFeatures = MidTermFeatures[iFeaturesSelect,:]
(MidTermFeaturesNorm, MEAN, STD) = aT.normalizeFeatures([MidTermFeatures.T])
MidTermFeaturesNorm = MidTermFeaturesNorm[0].T
numOfWindows = MidTermFeatures.shape[1]
# remove outliers:
DistancesAll = numpy.sum(distance.squareform(distance.pdist(MidTermFeaturesNorm.T)), axis=0)
MDistancesAll = numpy.mean(DistancesAll)
iNonOutLiers = numpy.nonzero(DistancesAll < 1.2*MDistancesAll)[0]
# TODO: Combine energy threshold for outlier removal:
#EnergyMin = numpy.min(MidTermFeatures[1,:])
#EnergyMean = numpy.mean(MidTermFeatures[1,:])
#Thres = (1.5*EnergyMin + 0.5*EnergyMean) / 2.0
#iNonOutLiers = numpy.nonzero(MidTermFeatures[1,:] > Thres)[0]
#print iNonOutLiers
perOutLier = (100.0*(numOfWindows-iNonOutLiers.shape[0])) / numOfWindows
MidTermFeaturesNormOr = MidTermFeaturesNorm
MidTermFeaturesNorm = MidTermFeaturesNorm[:, iNonOutLiers]
# LDA dimensionality reduction:
if LDAdim > 0:
#[mtFeaturesToReduce, _] = aF.mtFeatureExtraction(x, Fs, mtSize * Fs, stWin * Fs, round(Fs*stWin), round(Fs*stWin));
# extract mid-term features with minimum step:
mtWinRatio = int(round(mtSize / stWin));
mtStepRatio = int(round(stWin / stWin));
mtFeaturesToReduce = []
numOfFeatures = len(ShortTermFeatures)
numOfStatistics = 2;
#for i in range(numOfStatistics * numOfFeatures + 1):
for i in range(numOfStatistics * numOfFeatures):
mtFeaturesToReduce.append([])
for i in range(numOfFeatures): # for each of the short-term features:
curPos = 0
N = len(ShortTermFeatures[i])
while (curPos<N):
N1 = curPos
N2 = curPos + mtWinRatio
if N2 > N:
N2 = N
curStFeatures = ShortTermFeatures[i][N1:N2]
mtFeaturesToReduce[i].append(numpy.mean(curStFeatures))
mtFeaturesToReduce[i+numOfFeatures].append(numpy.std(curStFeatures))
curPos += mtStepRatio
mtFeaturesToReduce = numpy.array(mtFeaturesToReduce)
mtFeaturesToReduce2 = numpy.zeros( (mtFeaturesToReduce.shape[0] + len(classNames1) + len(classNames2), mtFeaturesToReduce.shape[1] ) )
for i in range(mtFeaturesToReduce.shape[1]):
curF1 = (mtFeaturesToReduce[:,i] - MEAN1) / STD1
curF2 = (mtFeaturesToReduce[:,i] - MEAN2) / STD2
[Result, P1] = aT.classifierWrapper(Classifier1, "knn", curF1)
[Result, P2] = aT.classifierWrapper(Classifier2, "knn", curF2)
mtFeaturesToReduce2[0:mtFeaturesToReduce.shape[0], i] = mtFeaturesToReduce[:, i]
mtFeaturesToReduce2[mtFeaturesToReduce.shape[0]:mtFeaturesToReduce.shape[0]+len(classNames1), i] = P1 + 0.0001;
mtFeaturesToReduce2[mtFeaturesToReduce.shape[0]+len(classNames1)::, i] = P2 + 0.0001;
mtFeaturesToReduce = mtFeaturesToReduce2
mtFeaturesToReduce = mtFeaturesToReduce[iFeaturesSelect,:]
#mtFeaturesToReduce += numpy.random.rand(mtFeaturesToReduce.shape[0], mtFeaturesToReduce.shape[1]) * 0.0000010
(mtFeaturesToReduce, MEAN, STD) = aT.normalizeFeatures([mtFeaturesToReduce.T])
mtFeaturesToReduce = mtFeaturesToReduce[0].T
#DistancesAll = numpy.sum(distance.squareform(distance.pdist(mtFeaturesToReduce.T)), axis=0)
#MDistancesAll = numpy.mean(DistancesAll)
#iNonOutLiers2 = numpy.nonzero(DistancesAll < 3.0*MDistancesAll)[0]
#mtFeaturesToReduce = mtFeaturesToReduce[:, iNonOutLiers2]
Labels = numpy.zeros((mtFeaturesToReduce.shape[1],));
LDAstep = 1.0
LDAstepRatio = LDAstep / stWin
#print LDAstep, LDAstepRatio
for i in range(Labels.shape[0]):
Labels[i] = int(i*stWin/LDAstepRatio);
clf = LDA(n_components=LDAdim)
clf.fit(mtFeaturesToReduce.T, Labels, tol=0.000001)
MidTermFeaturesNorm = (clf.transform(MidTermFeaturesNorm.T)).T
if numOfSpeakers<=0:
sRange = range(2,10)
else:
sRange = [numOfSpeakers]
clsAll = []; silAll = []; centersAll = []
for iSpeakers in sRange:
cls, means, steps = mlpy.kmeans(MidTermFeaturesNorm.T, k=iSpeakers, plus=True) # perform k-means clustering
#YDist = distance.pdist(MidTermFeaturesNorm.T, metric='euclidean')
#print distance.squareform(YDist).shape
#hc = mlpy.HCluster()
#hc.linkage(YDist)
#cls = hc.cut(14.5)
#print cls
# Y = distance.squareform(distance.pdist(MidTermFeaturesNorm.T))
clsAll.append(cls)
centersAll.append(means)
silA = []; silB = []
for c in range(iSpeakers): # for each speaker (i.e. for each extracted cluster)
clusterPerCent = numpy.nonzero(cls==c)[0].shape[0] / float(len(cls))
if clusterPerCent < 0.020:
silA.append(0.0)
silB.append(0.0)
else:
MidTermFeaturesNormTemp = MidTermFeaturesNorm[:,cls==c] # get subset of feature vectors
Yt = distance.pdist(MidTermFeaturesNormTemp.T) # compute average distance between samples that belong to the cluster (a values)
silA.append(numpy.mean(Yt)*clusterPerCent)
silBs = []
for c2 in range(iSpeakers): # compute distances from samples of other clusters
if c2!=c:
clusterPerCent2 = numpy.nonzero(cls==c2)[0].shape[0] / float(len(cls))
MidTermFeaturesNormTemp2 = MidTermFeaturesNorm[:,cls==c2]
Yt = distance.cdist(MidTermFeaturesNormTemp.T, MidTermFeaturesNormTemp2.T)
silBs.append(numpy.mean(Yt)*(clusterPerCent+clusterPerCent2)/2.0)
silBs = numpy.array(silBs)
silB.append(min(silBs)) # ... and keep the minimum value (i.e. the distance from the "nearest" cluster)
silA = numpy.array(silA);
silB = numpy.array(silB);
sil = []
for c in range(iSpeakers): # for each cluster (speaker)
sil.append( ( silB[c] - silA[c]) / (max(silB[c], silA[c])+0.00001) ) # compute silhouette
silAll.append(numpy.mean(sil)) # keep the AVERAGE SILLOUETTE
#silAll = silAll * (1.0/(numpy.power(numpy.array(sRange),0.5)))
imax = numpy.argmax(silAll) # position of the maximum sillouette value
nSpeakersFinal = sRange[imax] # optimal number of clusters
# generate the final set of cluster labels
# (important: need to retrieve the outlier windows: this is achieved by giving them the value of their nearest non-outlier window)
cls = numpy.zeros((numOfWindows,))
for i in range(numOfWindows):
j = numpy.argmin(numpy.abs(i-iNonOutLiers))
cls[i] = clsAll[imax][j]
# Post-process method 1: hmm smoothing
for i in range(1):
startprob, transmat, means, cov = trainHMM_computeStatistics(MidTermFeaturesNormOr, cls)
hmm = sklearn.hmm.GaussianHMM(startprob.shape[0], "diag", startprob, transmat) # hmm training
hmm.means_ = means; hmm.covars_ = cov
cls = hmm.predict(MidTermFeaturesNormOr.T)
# Post-process method 2: median filtering:
cls = scipy.signal.medfilt(cls, 13)
cls = scipy.signal.medfilt(cls, 11)
sil = silAll[imax] # final sillouette
classNames = ["speaker{0:d}".format(c) for c in range(nSpeakersFinal)];
# load ground-truth if available
gtFile = fileName.replace('.wav', '.segments'); # open for annotated file
if os.path.isfile(gtFile): # if groundturh exists
[segStart, segEnd, segLabels] = readSegmentGT(gtFile) # read GT data
flagsGT, classNamesGT = segs2flags(segStart, segEnd, segLabels, mtStep) # convert to flags
if PLOT:
fig = plt.figure()
if numOfSpeakers>0:
ax1 = fig.add_subplot(111)
else:
ax1 = fig.add_subplot(211)
ax1.set_yticks(numpy.array(range(len(classNames))))
ax1.axis((0, Duration, -1, len(classNames)))
ax1.set_yticklabels(classNames)
ax1.plot(numpy.array(range(len(cls)))*mtStep+mtStep/2.0, cls)
if os.path.isfile(gtFile):
if PLOT:
ax1.plot(numpy.array(range(len(flagsGT)))*mtStep+mtStep/2.0, flagsGT, 'r')
purityClusterMean, puritySpeakerMean = evaluateSpeakerDiarization(cls, flagsGT)
print "{0:.1f}\t{1:.1f}".format(100*purityClusterMean, 100*puritySpeakerMean)
if PLOT:
plt.title("Cluster purity: {0:.1f}% - Speaker purity: {1:.1f}%".format(100*purityClusterMean, 100*puritySpeakerMean) )
if PLOT:
plt.xlabel("time (seconds)")
#print sRange, silAll
if numOfSpeakers<=0:
plt.subplot(212)
plt.plot(sRange, silAll)
plt.xlabel("number of clusters");
plt.ylabel("average clustering's sillouette");
plt.show()