def test_lda_transform():
# Test LDA transform.
clf = lda.LDA(solver="svd", n_components=1)
X_transformed = clf.fit(X, y).transform(X)
assert_equal(X_transformed.shape[1], 1)
clf = lda.LDA(solver="eigen", n_components=1)
X_transformed = clf.fit(X, y).transform(X)
assert_equal(X_transformed.shape[1], 1)
def test_lda_transform():
# Test LDA transform.
clf = lda.LDA(solver="svd", n_components=1)
X_transformed = clf.fit(X, y).transform(X)
assert_equal(X_transformed.shape[1], 1)
clf = lda.LDA(solver="eigen", n_components=1)
X_transformed = clf.fit(X, y).transform(X)
assert_equal(X_transformed.shape[1], 1)
clf = lda.LDA(solver="lsqr", n_components=1)
clf.fit(X, y)
msg = "transform not implemented for 'lsqr'"
assert_raise_message(NotImplementedError, msg, clf.transform, X)
def binary_lda(training_feature_array, training_label_array,
test_feature_array, test_label_array):
"""
2クラス分類LDA（しかし多クラス分類で代用可能だった現実...）
@param training_feature_array: トレーニング用データ
@param training_label_array: トレーニング用データラベル
@param test_feature_array: テスト用データ
@param test_label_array: テスト用データラベル
@return: 識別率, 識別結果のリスト, 識別されたクラスへの所属確率のリスト, LDAオブジェクト
動作確認済
"""
lda_obj = slda.LDA()
lda_obj.fit(training_feature_array, training_label_array)
print "test..."
class_result = lda_obj.predict(test_feature_array)
proba_result = lda_obj.predict_proba(test_feature_array)
proba_max_result = np.max(proba_result, axis=1)
try:
precision = smet.accuracy_score(test_label_array, class_result)
#precision, recall, fmeasure, sup = smet.precision_recall_fscore_support(test_label_array, class_result,
# average='micro')
except DeprecationWarning, e:
pass
def buildModelQDA(self, outputFile, priorProbs=[0.5, 0.5]):
classifier = lda.LDA(priors=priorProbs)
classifier.fit(self.instances, self.classes)
modelData = pickle.dumps(classifier)
f = open(outputFile, "w")
f.write(modelData)
f.close()
def LDAclassification(train_set,test_set,train_ann,test_ann):
global path, train_perc
#Create z-scored data
normalized_train = zscore(train_set)
classifier = lda.LDA('lsqr')
#train the LDA classifier
classifier.fit(train_set, train_ann)
#store the trained classifier
if train_perc<1.0:
pickle.dump( classifier, open(path+"LDA_classifier.p", "wb+" ) )
results = classifier.predict(test_set)
#res2 = classifier.predict()
cm = confusion_matrix(test_ann, results)
print 'CONFUSION MATRIX = {}'.format(cm)
return metrics(cm)
def fit_model(df, model='logistic_regression', max_depth=5): # split the target attribute from the explanatory variables y = df['clicks'] x = df.drop(['clicks', 'paying_price'], axis=1) # fit the model if model == 'logistic_regression': m = linear_model.LogisticRegression() m.fit(x, y) df_coef = pd.DataFrame(columns=['attribute','logreg_coef']) df_coef['attribute'] = x.columns.values df_coef['logreg_coef'] = np.ravel(m.coef_) df_coef.to_csv(TABLES_DIR_PATH + 'logreg_coef.csv') print 'Logistic regression coefficients:' print df_coef elif model == 'tree': m = tree.DecisionTreeClassifier(max_depth=max_depth) m.fit(x, y) elif model == 'lda': m = lda.LDA() m.fit(x, y) elif model == 'naivebayes': m = naive_bayes.GaussianNB() m.fit(x, y) return m
def visualize(X, y, name):
X2 = X.copy()
X2.flat[::X.shape[1] + 1] += 0.01 # Make X invertible
t0 = time()
X_lda = lda.LDA(n_components=2).fit_transform(X2, y)
plot_embedding(X_lda, y, name, "haha", True)
plt.show()
def test_lda_predict():
"""
LDA classification.
This checks that LDA implements fit and predict and returns
correct values for a simple toy dataset.
"""
clf = lda.LDA()
y_pred = clf.fit(X, y).predict(X)
assert_array_equal(y_pred, y)
# Assure that it works with 1D data
y_pred1 = clf.fit(X1, y).predict(X1)
assert_array_equal(y_pred1, y)
# Test probas estimates
y_proba_pred1 = clf.predict_proba(X1)
assert_array_equal((y_proba_pred1[:, 1] > 0.5) + 1, y)
y_log_proba_pred1 = clf.predict_log_proba(X1)
assert_array_almost_equal(np.exp(y_log_proba_pred1), y_proba_pred1, 8)
# Primarily test for commit 2f34950 -- "reuse" of priors
y_pred3 = clf.fit(X, y3).predict(X)
# LDA shouldn't be able to separate those
assert_true(np.any(y_pred3 != y3))
def run_classification(args, features, labels):
class_weight = {
0: 1.0,
1: float(len(labels) - sum(labels)) / float(sum(labels))
}
# Assemble data
if args.classifier == 'lda':
clf = lda.LDA()
elif args.classifier == 'lsvm':
clf = svm.LinearSVC()
elif args.classifier == 'svm':
clf = svm.SVC(kernel='rbf', class_weight=class_weight)
elif args.classifier == 'rf':
clf = ensemble.RandomForestClassifier()
sensitivity_scorer = make_scorer(sensitivity, greater_is_better=True)
specificity_scorer = make_scorer(specificity, greater_is_better=True)
accuracies = cross_validation.cross_val_score(clf,
features,
labels,
cv=args.num_folds,
scoring='accuracy')
sensitivities = cross_validation.cross_val_score(
clf, features, labels, cv=args.num_folds, scoring=sensitivity_scorer)
specificities = cross_validation.cross_val_score(
clf, features, labels, cv=args.num_folds, scoring=specificity_scorer)
return accuracies.mean(), sensitivities.mean(), specificities.mean()
def applyLDA(finalFeatures, finalAnswers, cvFeatures, testFeatures, n_components=200):
print 'Applying LDA...'
selLda = lda.LDA(n_components=n_components)
finalFeatures = selLda.fit_transform(finalFeatures, finalAnswers)
cvFeatures = selLda.transform(cvFeatures)
testFeatures = selLda.transform(testFeatures)
return (finalFeatures, cvFeatures, testFeatures)
def validate_feature_linear(features,
labels,
classes,
n_folds=5,
print_folds=True,
print_absolute=True,
print_logloss=True):
kfold = cv.LabelKFold(labels, n_folds)
model = lda.LDA()
if print_absolute:
score = cross_validation.cross_val_score(model,
features,
classes,
cv=kfold)
if print_absolute: print("absolute scores")
if print_folds: print("\tfolds:", score)
if print_absolute: print("\tmean:", score.mean(), "std:", numpy.std(score))
scores = score_calculation.loglossKFold(features,
classes,
model,
kfold,
given_kfold=True)
if print_logloss: print("logloss scores")
if print_folds: print("\tfolds", scores)
if print_logloss:
print("\tmean:", numpy.mean(scores), "std:", numpy.std(scores))
def __init__(self, classifier):
if classifier == 'svm':
self.clf = svm.SCV()
elif classifier == 'lda':
self.clf = lda.LDA()
elif classifier == 'qda':
self.clf = qda.QDA()
def test_lda_orthogonality():
# arrange four classes with their means in a kite-shaped pattern
# the longer distance should be transformed to the first component, and
# the shorter distance to the second component.
means = np.array([[0, 0, -1], [0, 2, 0], [0, -2, 0], [0, 0, 5]])
# We construct perfectly symmetric distributions, so the LDA can estimate
# precise means.
scatter = np.array([[0.1, 0, 0], [-0.1, 0, 0], [0, 0.1, 0], [0, -0.1, 0],
[0, 0, 0.1], [0, 0, -0.1]])
X = (means[:, np.newaxis, :] + scatter[np.newaxis, :, :]).reshape((-1, 3))
y = np.repeat(np.arange(means.shape[0]), scatter.shape[0])
# Fit LDA and transform the means
clf = lda.LDA(solver="svd").fit(X, y)
means_transformed = clf.transform(means)
d1 = means_transformed[3] - means_transformed[0]
d2 = means_transformed[2] - means_transformed[1]
d1 /= np.sqrt(np.sum(d1**2))
d2 /= np.sqrt(np.sum(d2**2))
# the transformed within-class covariance should be the identity matrix
assert_almost_equal(np.cov(clf.transform(scatter).T), np.eye(2))
# the means of classes 0 and 3 should lie on the first component
assert_almost_equal(np.abs(np.dot(d1[:2], [1, 0])), 1.0)
# the means of classes 1 and 2 should lie on the second component
assert_almost_equal(np.abs(np.dot(d2[:2], [0, 1])), 1.0)
def run_classification(args, features1, features2, features3=None):
# Assemble data
if features3 is None:
features = np.concatenate((features1, features2))
labels = np.concatenate(
(np.zeros(len(features1)), np.ones(len(features2))))
else:
features = np.concatenate((features1, features2, features3))
labels = np.concatenate(
(np.zeros(len(features1)), np.ones(len(features2)),
2 * np.ones(len(features3))))
if args.classifier == 'lda':
# priors_second = float(sum(labels)) / float(len(labels))
# priors = [1 - priors_second, priors_second]
# clf = lda.LDA(priors=priors)
clf = lda.LDA()
elif args.classifier == 'lsvm':
clf = svm.LinearSVC()
elif args.classifier == 'svm':
class_weight = {
0: 1.0,
1: float(len(labels) - sum(labels)) / float(sum(labels))
}
clf = svm.SVC(kernel='rbf', class_weight=class_weight)
elif args.classifier == 'rf':
clf = ensemble.RandomForestClassifier()
sensitivity_scorer = make_scorer(sensitivity, greater_is_better=True)
specificity_scorer = make_scorer(specificity, greater_is_better=True)
accuracies = 0.0
sensitivities = 0.0
specificities = 0.0
for _ in range(args.num_runs):
accuracies += cross_validation.cross_val_score(clf,
features,
labels,
cv=args.num_folds,
scoring='accuracy')
sensitivities += cross_validation.cross_val_score(
clf,
features,
labels,
cv=args.num_folds,
scoring=sensitivity_scorer)
specificities += cross_validation.cross_val_score(
clf,
features,
labels,
cv=args.num_folds,
scoring=specificity_scorer)
accuracies /= args.num_runs
sensitivities /= args.num_runs
specificities /= args.num_runs
return accuracies.mean(), sensitivities.mean(), specificities.mean()
def get_classifier(classifier_str):
'''
This functions maps the classifier string classifier_str to the
corresponding classifier object with the default paramers set.
'''
# SVC
if (classifier_str == 'linearsvc'):
cl = svm.LinearSVC(**svm_default_param)
elif (classifier_str == 'svc_linear'):
libsvm_default_param['kernel'] = 'linear'
cl = svm.SVC(**libsvm_default_param)
elif (classifier_str == 'svc_rbf'):
libsvm_default_param['kernel'] = 'rbf'
cl = svm.SVC(**libsvm_default_param)
# polynomial, sigmoid kernel
# nuSVC
# Nearest Neighbors (euclidian distance used by default)
elif (classifier_str == 'kn_uniform'):
kn_default_param['weights'] = 'uniform'
cl = neighbors.KNeighborsClassifier(**kn_default_param)
elif (classifier_str == 'kn_distance'):
kn_default_param['weights'] = 'distance'
cl = neighbors.KNeighborsClassifier(**kn_default_param)
elif (classifier_str == 'rn_uniform'):
rn_default_param['weights'] = 'uniform'
cl = neighbors.RadiusNeighborsClassifier(**rn_default_param)
elif (classifier_str == 'rn_distance'):
rn_default_param['weights'] = 'distance'
cl = neighbors.RadiusNeighborsClassifier(**rn_default_param)
elif (classifier_str == 'nc'):
cl = neighbors.NearestCentroid()
# LDA and QDA, priors are by default set to 1/len(class) for each class
elif (classifier_str == 'lda'):
cl = lda.LDA()
elif (classifier_str == 'qda'):
cl = qda.QDA()
# Gaussion naive bayes
# from the code it is unclear how priors are set
elif (classifier_str == 'gnb'):
cl = naive_bayes.GaussianNB()
elif (classifier_str == 'mnb'):
cl = naive_bayes.MultinomialNB()
elif (classifier_str == 'bnb'):
cl = naive_bayes.BernoulliNB()
# Decision tree
elif (classifier_str == 'dtree'):
cl = tree.DecisionTreeClassifier()
elif (classifier_str == 'rforest'):
cl = ensemble.RandomForestClassifier()
else:
# raise error if classifier not found
raise ValueError('Classifier not implemented: %s' % (classifier_str))
return (cl)
def lda_predict(self, unlabelled):
''' Use Linear Discriminant Analysis for classification.
WARNING: Will only work when we have multiple data samples
for each dataset (i.e., two for left, two for right, etc.)'''
self.clf = lda.LDA()
self.clf.fit(self.dataset, self.targets)
unlabelled = np.array(unlabelled)
unlabelled = unlabelled.flatten()
target = self.clf.predict(unlabelled)
return self.positions[target[0]]
def test_lda_coefs():
# Test if the coefficients of the solvers are approximately the same.
n_features = 2
n_classes = 2
n_samples = 1000
X, y = make_blobs(n_samples=n_samples,
n_features=n_features,
centers=n_classes,
random_state=11)
clf_lda_svd = lda.LDA(solver="svd")
clf_lda_lsqr = lda.LDA(solver="lsqr")
clf_lda_eigen = lda.LDA(solver="eigen")
clf_lda_svd.fit(X, y)
clf_lda_lsqr.fit(X, y)
clf_lda_eigen.fit(X, y)
assert_array_almost_equal(clf_lda_svd.coef_, clf_lda_lsqr.coef_, 1)
assert_array_almost_equal(clf_lda_svd.coef_, clf_lda_eigen.coef_, 1)
assert_array_almost_equal(clf_lda_eigen.coef_, clf_lda_lsqr.coef_, 1)
def svmf(index_train , index_test):
cnt = 0
err = 0
clf = lda.LDA(gamma = 'scale')
X = fea_copy[index_train]
y = gnd[index_train]
clf.fit(X, y.ravel())
for i in range(len(index_test)):
if clf.predict(fea_copy[[index_test[i]]]) != gnd[index_test[i]]:
err += 1
cnt += 1
return cnt,err
def test_lda_predict():
"""Test LDA classification.
This checks that LDA implements fit and predict and returns correct values
for simple toy data.
"""
for test_case in solver_shrinkage:
solver, shrinkage = test_case
clf = lda.LDA(solver=solver, shrinkage=shrinkage)
y_pred = clf.fit(X, y).predict(X)
assert_array_equal(y_pred, y, 'solver %s' % solver)
# Assert that it works with 1D data
y_pred1 = clf.fit(X1, y).predict(X1)
assert_array_equal(y_pred1, y, 'solver %s' % solver)
# Test probability estimates
y_proba_pred1 = clf.predict_proba(X1)
assert_array_equal((y_proba_pred1[:, 1] > 0.5) + 1, y,
'solver %s' % solver)
y_log_proba_pred1 = clf.predict_log_proba(X1)
assert_array_almost_equal(np.exp(y_log_proba_pred1), y_proba_pred1, 8,
'solver %s' % solver)
# Primarily test for commit 2f34950 -- "reuse" of priors
y_pred3 = clf.fit(X, y3).predict(X)
# LDA shouldn't be able to separate those
assert_true(np.any(y_pred3 != y3), 'solver %s' % solver)
# Test invalid shrinkages
clf = lda.LDA(solver="lsqr", shrinkage=-0.2231)
assert_raises(ValueError, clf.fit, X, y)
clf = lda.LDA(solver="eigen", shrinkage="dummy")
assert_raises(ValueError, clf.fit, X, y)
clf = lda.LDA(solver="svd", shrinkage="auto")
assert_raises(NotImplementedError, clf.fit, X, y)
# Test unknown solver
clf = lda.LDA(solver="dummy")
assert_raises(ValueError, clf.fit, X, y)
def __init__(self, name='default'):
self.clf = lda.LDA()
self.scaler = preprocessing.StandardScaler()
self.selector = None
self.transform = None
self.extractor = HardieExtractor()
self.feature_set = None
self.network = None
self.name = name
self.roi_size = 64
self.dataset_type = 'numpy'
self.file = None # datasets_file
def plot_simple_demo_lda():
pylab.clf()
fig = pylab.figure(num=None, figsize=(10, 4))
pylab.subplot(121)
title = "Original feature space"
pylab.title(title)
pylab.xlabel("$X_1$")
pylab.ylabel("$X_2$")
good = x1 > x2
bad = ~good
x1g = x1[good]
x2g = x2[good]
pylab.scatter(x1g, x2g, edgecolor="blue", facecolor="blue")
x1b = x1[bad]
x2b = x2[bad]
pylab.scatter(x1b, x2b, edgecolor="red", facecolor="white")
pylab.grid(True)
pylab.subplot(122)
X = np.c_[(x1, x2)]
lda_inst = lda.LDA(n_components=1)
Xtrans = lda_inst.fit_transform(X, good)
Xg = Xtrans[good]
Xb = Xtrans[bad]
pylab.scatter(Xg[:, 0],
np.zeros(len(Xg)),
edgecolor="blue",
facecolor="blue")
pylab.scatter(Xb[:, 0],
np.zeros(len(Xb)),
edgecolor="red",
facecolor="white")
title = "Transformed feature space"
pylab.title(title)
pylab.xlabel("$X'$")
fig.axes[1].get_yaxis().set_visible(False)
pylab.grid(True)
pylab.autoscale(tight=True)
filename = "lda_demo.png"
pylab.savefig(os.path.join(CHART_DIR, filename), bbox_inches="tight")
def test_lda_explained_variance_ratio():
# Test if the sum of the normalized eigen vectors values equals 1
n_features = 2
n_classes = 2
n_samples = 1000
X, y = make_blobs(n_samples=n_samples,
n_features=n_features,
centers=n_classes,
random_state=11)
clf_lda_eigen = lda.LDA(solver="eigen")
clf_lda_eigen.fit(X, y)
assert_almost_equal(clf_lda_eigen.explained_variance_ratio_.sum(), 1.0, 3)
def test_lda_scaling():
# Test if classification works correctly with differently scaled features.
n = 100
rng = np.random.RandomState(1234)
# use uniform distribution of features to make sure there is absolutely no
# overlap between classes.
x1 = rng.uniform(-1, 1, (n, 3)) + [-10, 0, 0]
x2 = rng.uniform(-1, 1, (n, 3)) + [10, 0, 0]
x = np.vstack((x1, x2)) * [1, 100, 10000]
y = [-1] * n + [1] * n
for solver in ('svd', 'lsqr', 'eigen'):
clf = lda.LDA(solver=solver)
# should be able to separate the data perfectly
assert_equal(
clf.fit(x, y).score(x, y), 1.0, 'using covariance: %s' % solver)
def train(self, labels, data):
self.labels = np.array(labels) # [class, ..., class]
self.classes = np.array(np.unique(labels))
self.data = np.array(data, dtype='float')
self.ints_labels = {}
for i in range(0, len(self.classes)):
self.ints_labels[self.classes[i]] = i
ints = np.zeros([len(self.labels)])
for i in range(0, len(self.labels)):
ints[i] = self.ints_labels[self.labels[i]]
Xnorm = self.normalize(self.data)
self.pca = PCA(n_components=N_COMPONENTS)
self.pca.fit(Xnorm)
self.pca_data = self.pca.transform(Xnorm)
self.classifier = lda.LDA()
self.classifier.fit(self.pca_data, ints)
def apply(self):
transformed = components = None
if self.data:
self.data = Continuize(Impute(self.data))
lda = skl_lda.LDA(solver='eigen', n_components=2)
X = lda.fit_transform(self.data.X, self.data.Y)
dom = Domain([
ContinuousVariable('Component_1'),
ContinuousVariable('Component_2')
], self.data.domain.class_vars, self.data.domain.metas)
transformed = Table(dom, X, self.data.Y, self.data.metas)
transformed.name = self.data.name + ' (LDA)'
dom = Domain(self.data.domain.attributes,
metas=[StringVariable(name='component')])
metas = np.array([[
'Component_{}'.format(i + 1)
for i in range(lda.scalings_.shape[1])
]],
dtype=object).T
components = Table(dom, lda.scalings_.T, metas=metas)
components.name = 'components'
self.send("Transformed data", transformed)
self.send("Components", components)
def multiclass_lda(training_feature_array, training_label_array,
test_feature_array, test_label_array):
"""
多クラス分類LDA
@param training_feature_array: トレーニング用データ
@param training_label_array: トレーニング用データラベル
@param test_feature_array: テスト用データ
@param test_label_array: テスト用データラベル
@return: 全体識別率, 識別結果のリスト, 識別されたクラスへの所属確率のリスト, LDAオブジェクト
動作確認済
"""
multi_lda_obj = OneVsRestClassifier(slda.LDA())
multi_lda_obj.fit(training_feature_array, training_label_array)
print "test..."
class_result = multi_lda_obj.predict(test_feature_array)
proba_result = multi_lda_obj.predict_proba(test_feature_array)
proba_max_result = np.max(proba_result, axis=1)
try:
precision = smet.accuracy_score(test_label_array, class_result)
except DeprecationWarning, e:
pass
client = OSCClient()
client.connect(('127.0.0.1', 9999))
recent = []
window = blackman(N)
vectors = []
labels = []
def getAmplitude(data):
freq = sfft.fft(data * window)
nyquist = len(freq)/2
return np.absolute(freq[:nyquist])
clf = SVC(probability=True, kernel = 'rbf')
model = lda.LDA(n_components=2)
projection = []
p_min = None
p_max = None
predicted = None
def buildLDA(vectors, labels):
global model, projection, p_min, p_max
if not len(vectors):
print('No data to learn from.')
return
t0 = time()
X = np.array(map(getAmplitude, vectors))
y = np.array(labels)
X.flat[::X.shape[1] + 1] += 0.01 # Make X invertible
projection = model.fit_transform(X, y)
def splitMeanAngleFeatures(image, splits = 2, threshold = 10):
result = splitMeanAngle(image, splits, threshold).flatten()
return result
print("Loading images")
#images, classes = loader.loadProblematicImagesAndClasses()
images, classes = loader.loadTrainingAndClasses()
amount = len(images)
print("Making thumbnails")
thumbsize = 50
thumbs = [misc.imresize(x,(thumbsize, thumbsize)) for x in images]
print("Calculating features")
#features = list(map(extractor.calculateNormalizedColorFeatures, images))
splits = 5
features = numpy.zeros([len(images), splits * splits])
for i in range(amount):
if(i%10 ==0):print(i, "/", amount)
features[i] = splitMeanAngleFeatures(thumbs[i], splits)
print("Producing KFold indexes")
kfold = cv.KFold(amount, n_folds = 5, shuffle = True)
#model = neighbors.KNeighborsClassifier(n_neighbors = 1)
model = lda.LDA()
score = cross_validation.cross_val_score(model, features, classes, cv=kfold)
print(score)
print(score.mean())
print "Computing PCA projection"
t0 = time()
X_pca = decomposition.RandomizedPCA(n_components=2).fit_transform(X)
plot_embedding(
X_pca, "Principal Components projection of the digits (time %.2fs)" %
(time() - t0))
#----------------------------------------------------------------------
# Projection on to the first 2 linear discriminant components
print "Computing LDA projection"
X2 = X.copy()
X2.flat[::X.shape[1] + 1] += 0.01 # Make X invertible
t0 = time()
X_lda = lda.LDA(n_components=2).fit_transform(X2, y)
plot_embedding(
X_lda, "Linear Discriminant projection of the digits (time %.2fs)" %
(time() - t0))
#----------------------------------------------------------------------
# Isomap projection of the digits dataset
print "Computing Isomap embedding"
t0 = time()
X_iso = manifold.Isomap(n_neighbors, n_components=2).fit_transform(X)
print "Done."
plot_embedding(X_iso,
"Isomap projection of the digits (time %.2fs)" % (time() - t0))
#----------------------------------------------------------------------
# Locally linear embedding of the digits dataset
X_train, Y_train, X_test, Y_test = preprocess_dataset(X_train, Y_train, X_test, Y_test, streams=(self.streams != 'none'), config=self.args.preprocess_dataset, mode='hdf5')
X_train, Y_train = self._split_data_pos_neg(X_train, Y_train)
X_test, Y_test = self._split_data_pos_neg(X_test, Y_test)
std = np.std(X_train[0])
'''
#self.helper_model = ae.swwae_augment(self.network.network, X_train, Y_train, X_test, Y_test, finetune_epochs=nb_epoch, multipliers=self.multipliers, layerwise_epochs=self.lw_epochs, decoder_epochs=self.dec_epochs, lr=self.lr, model_name=self.init)
self.helper_model = ae.swwae_augment_hdf5(self.network.network, self.network.generator, X_train, Y_train, X_test, Y_test, finetune_epochs=nb_epoch, multipliers=self.multipliers, layerwise_epochs=self.lw_epochs, decoder_epochs=self.dec_epochs, lr=self.lr, model_name=self.init)
else:
print "Preprocessor {}".format(self.network.preprocessor)
print "Generator {}".format(self.network.generator)
self.helper_model = ae.swwae_augment_hdf5(self.network.network, self.network.generator, X_train, Y_train, X_test, Y_test, finetune_epochs=nb_epoch, multipliers=self.multipliers, layerwise_epochs=self.lw_epochs, decoder_epochs=self.dec_epochs, lr=self.lr, model_name=self.init)
def fit_transform_bovw(self, rois_tr, pred_blobs_tr, blobs_tr, rois_te, pred_blobs_te, blobs_te, model):
X_tr, Y_tr = classify.create_training_set_from_feature_set(rois_tr, pred_blobs_tr, blobs_tr)
X_te, Y_te = classify.create_training_set_from_feature_set(rois_te, pred_blobs_te, blobs_te)
model.fit(X_tr)
V_tr = []
for rois in rois_tr:
V_tr.append(model.transform(rois))
V_te = []
for rois in rois_te:
V_te.append(model.transform(rois))
return np.array(V_tr), np.array(V_te)
# optimized
opt_classifiers = {'svm':svm.SVC(probability=True, C=0.0373, gamma=0.002), 'lda':lda.LDA()}
# default
classifiers = {'linear-svm':svm.SVC(kernel='linear', C=1, probability=True), 'svm':svm.SVC(kernel='rbf', probability=True), 'lda':lda.LDA(), 'knn': neighbors.KNeighborsRegressor(), 'rf': ensemble.RandomForestClassifier(), 'hik':svm.SVC(kernel=pk.regular.Min(), C=1, probability=True)}
reductors = {'none':None, 'pca':decomposition.PCA(n_components=0.99999999999, whiten=True), 'lda':selection.SelectFromModel(lda.LDA())}
