def test_MDM_transform():
"""Test transform of MDM"""
covset = generate_cov(100, 3)
labels = np.array([0, 1]).repeat(50)
mdm = MDM(metric='riemann')
mdm.fit(covset, labels)
mdm.transform(covset)
def test_MDM_transform():
"""Test transform of MDM"""
covset = generate_cov(100,3)
labels = np.array([0,1]).repeat(50)
mdm = MDM(metric='riemann')
mdm.fit(covset,labels)
mdm.transform(covset)
def test_MDM_predict():
"""Test prediction of MDM"""
covset = generate_cov(100, 3)
labels = np.array([0, 1]).repeat(50)
mdm = MDM(metric='riemann')
mdm.fit(covset, labels)
mdm.predict(covset)
# test fit_predict
mdm = MDM(metric='riemann')
mdm.fit_predict(covset, labels)
# test transform
mdm.transform(covset)
# predict proba
mdm.predict_proba(covset)
# test n_jobs
mdm = MDM(metric='riemann', n_jobs=2)
mdm.fit(covset, labels)
mdm.predict(covset)
def test_MDM_predict():
"""Test prediction of MDM"""
covset = generate_cov(100, 3)
labels = np.array([0, 1]).repeat(50)
mdm = MDM(metric='riemann')
mdm.fit(covset, labels)
mdm.predict(covset)
# test fit_predict
mdm = MDM(metric='riemann')
mdm.fit_predict(covset, labels)
# test transform
mdm.transform(covset)
# predict proba
mdm.predict_proba(covset)
# test n_jobs
mdm = MDM(metric='riemann', n_jobs=2)
mdm.fit(covset, labels)
mdm.predict(covset)
class DistanceCalculatorRafal(BaseEstimator, TransformerMixin):
"""Distance Calulator Based on MDM Rafal style."""
def __init__(self,
metric_mean='logeuclid',
metric_dist=['riemann'],
n_jobs=12,
subsample=10):
"""Init."""
self.metric_mean = metric_mean
self.metric_dist = metric_dist
self.n_jobs = n_jobs
self.subsample = subsample
def fit(self, X, y):
"""Fit."""
self.mdm = MDM(metric=self.metric_mean, n_jobs=self.n_jobs)
labels = y[::self.subsample]
pCalcMeans = partial(mean_covariance, metric=self.metric_mean)
pool = Pool(processes=6)
mc1 = pool.map(pCalcMeans,
[X[labels[:, i] == 1] for i in range(N_EVENTS)])
pool.close()
pool = Pool(processes=6)
mc0 = pool.map(pCalcMeans,
[X[labels[:, i] == 0] for i in range(N_EVENTS)])
pool.close()
self.mdm.covmeans = mc1 + mc0
return self
def transform(self, X, y=None):
"""Transform."""
feattr = []
for metric in self.metric_dist:
self.mdm.metric_dist = metric
feat = self.mdm.transform(X)
# print 'feat', feat, feat.shape
# substract distance of the class 0
feat = feat[:, 0:N_EVENTS] - feat[:, N_EVENTS:]
feattr.append(feat)
feattr = np.concatenate(feattr, axis=1)
feattr[np.isnan(feattr)] = 0
return feattr
def fit_transform(self, X, y):
"""Fit and transform."""
self.fit(X, y)
return self.transform(X)
class DistanceCalculatorRafal(BaseEstimator, TransformerMixin):
"""Distance Calulator Based on MDM Rafal style."""
def __init__(self, metric_mean='logeuclid', metric_dist=['riemann'],
n_jobs=12, subsample=10):
"""Init."""
self.metric_mean = metric_mean
self.metric_dist = metric_dist
self.n_jobs = n_jobs
self.subsample = subsample
def fit(self, X, y):
"""Fit."""
self.mdm = MDM(metric=self.metric_mean, n_jobs=self.n_jobs)
labels = y[::self.subsample]
pCalcMeans = partial(mean_covariance, metric=self.metric_mean)
pool = Pool(processes=6)
mc1 = pool.map(pCalcMeans, [X[labels[:, i] == 1] for i in range(6)])
pool.close()
pool = Pool(processes=6)
mc0 = pool.map(pCalcMeans, [X[labels[:, i] == 0] for i in range(6)])
pool.close()
self.mdm.covmeans = mc1 + mc0
return self
def transform(self, X, y=None):
"""Transform."""
feattr = []
for metric in self.metric_dist:
self.mdm.metric_dist = metric
feat = self.mdm.transform(X)
# substract distance of the class 0
feat = feat[:, 0:6] - feat[:, 6:]
feattr.append(feat)
feattr = np.concatenate(feattr, axis=1)
feattr[np.isnan(feattr)] = 0
return feattr
def fit_transform(self, X, y):
"""Fit and transform."""
self.fit(X, y)
return self.transform(X)
class FgMDM2(BaseEstimator, ClassifierMixin, TransformerMixin):
def __init__(self, metric='riemann', tsupdate=False, n_jobs=1):
"""Init."""
self.metric = metric
self.n_jobs = n_jobs
self.tsupdate = tsupdate
if isinstance(metric, str):
self.metric_mean = metric
elif isinstance(metric, dict):
# check keys
for key in ['mean', 'distance']:
if key not in metric.keys():
raise KeyError('metric must contain "mean" and "distance"')
self.metric_mean = metric['mean']
else:
raise TypeError('metric must be dict or str')
def fit(self, X, y):
self.classes_ = unique_labels(y)
self._mdm = MDM(metric=self.metric, n_jobs=self.n_jobs)
self._fgda = FGDA(metric=self.metric_mean, tsupdate=self.tsupdate)
cov = self._fgda.fit_transform(X, y)
self._mdm.fit(cov, y)
return self
def predict(self, X):
cov = self._fgda.transform(X)
return self._mdm.predict(cov)
def predict_proba(self, X):
cov = self._fgda.transform(X)
return self._mdm.predict_proba(cov)
def transform(self, X):
cov = self._fgda.transform(X)
return self._mdm.transform(cov)
class DistanceCalculatorAlex(BaseEstimator, TransformerMixin):
"""Distance Calulator Based on MDM."""
def __init__(self,
metric_mean='logeuclid',
metric_dist=['riemann'],
n_jobs=7,
subsample=10):
"""Init."""
self.metric_mean = metric_mean
self.metric_dist = metric_dist
self.n_jobs = n_jobs
self.subsample = subsample
def fit(self, X, y):
"""Fit."""
self.mdm = MDM(metric=self.metric_mean, n_jobs=self.n_jobs)
labels = np.squeeze(create_sequence(y.T)[::self.subsample])
self.mdm.fit(X, labels)
return self
def transform(self, X, y=None):
"""Transform."""
feattr = []
for metric in self.metric_dist:
self.mdm.metric_dist = metric
feat = self.mdm.transform(X)
# substract distance of the class 0
feat = feat[:, 1:] - np.atleast_2d(feat[:, 0]).T
feattr.append(feat)
feattr = np.concatenate(feattr, axis=1)
feattr[np.isnan(feattr)] = 0
return feattr
def fit_transform(self, X, y):
"""Fit and transform."""
self.fit(X, y)
return self.transform(X)
class DistanceCalculatorAlex(BaseEstimator, TransformerMixin):
"""Distance Calulator Based on MDM."""
def __init__(self, metric_mean='logeuclid', metric_dist=['riemann'],
n_jobs=7, subsample=10):
"""Init."""
self.metric_mean = metric_mean
self.metric_dist = metric_dist
self.n_jobs = n_jobs
self.subsample = subsample
def fit(self, X, y):
"""Fit."""
self.mdm = MDM(metric=self.metric_mean, n_jobs=self.n_jobs)
labels = np.squeeze(create_sequence(y.T)[::self.subsample])
self.mdm.fit(X, labels)
return self
def transform(self, X, y=None):
"""Transform."""
feattr = []
for metric in self.metric_dist:
self.mdm.metric_dist = metric
feat = self.mdm.transform(X)
# substract distance of the class 0
feat = feat[:, 1:] - np.atleast_2d(feat[:, 0]).T
feattr.append(feat)
feattr = np.concatenate(feattr, axis=1)
feattr[np.isnan(feattr)] = 0
return feattr
def fit_transform(self, X, y):
"""Fit and transform."""
self.fit(X, y)
return self.transform(X)
class ERPDistance(BaseEstimator, TransformerMixin):
"""ERP distance cov estimator.
This transformer estimates Riemannian distance for ERP covariance matrices.
After estimation of special form ERP covariance matrices using the ERP
transformer, a MDM [1] algorithm is used to compute Riemannian distance.
References:
[1] A. Barachant, S. Bonnet, M. Congedo and C. Jutten, "Multiclass
Brain-Computer Interface Classification by Riemannian Geometry," in IEEE
Transactions on Biomedical Engineering, vol. 59, no. 4, p. 920-928, 2012
"""
def __init__(self,
window=500,
nfilters=3,
subsample=1,
metric='riemann',
n_jobs=1):
"""Init."""
self.window = window
self.nfilters = nfilters
self.subsample = subsample
self.metric = metric
self.n_jobs = n_jobs
self._fitted = False
def fit(self, X, y):
"""fit."""
# Create ERP and get cov mat
self.ERP = ERP(self.window, self.nfilters, self.subsample)
train_cov = self.ERP.fit_transform(X, y)
labels_train = self.ERP.labels_train
# Add rest epochs
rest_cov = self._get_rest_cov(X, y)
train_cov = np.concatenate((train_cov, rest_cov), axis=0)
labels_train = np.concatenate((labels_train, [0] * len(rest_cov)))
# fit MDM
self.MDM = MDM(metric=self.metric, n_jobs=self.n_jobs)
self.MDM.fit(train_cov, labels_train)
self._fitted = True
return self
def transform(self, X, y=None):
"""Transform."""
test_cov = self.ERP.transform(X)
dist = self.MDM.transform(test_cov)
dist = dist[:, 1:] - np.atleast_2d(dist[:, 0]).T
return dist
def update_subsample(self, old_sub, new_sub):
"""update subsampling."""
if self._fitted:
self.ERP.update_subsample(old_sub, new_sub)
def _get_rest_cov(self, X, y):
"""Sample rest epochs from data and compute the cov mat."""
ix = np.where(np.diff(y[:, 0]) == 1)[0]
rest = []
offset = -self.window
for i in ix:
start = i + offset - self.window
stop = i + offset
rest.append(self.ERP.erp_cov(X[slice(start, stop)].T))
return np.array(rest)
class ERPDistance(BaseEstimator, TransformerMixin):
"""ERP distance cov estimator.
This transformer estimates Riemannian distance for ERP covariance matrices.
After estimation of special form ERP covariance matrices using the ERP
transformer, a MDM [1] algorithm is used to compute Riemannian distance.
References:
[1] A. Barachant, S. Bonnet, M. Congedo and C. Jutten, "Multiclass
Brain-Computer Interface Classification by Riemannian Geometry," in IEEE
Transactions on Biomedical Engineering, vol. 59, no. 4, p. 920-928, 2012
"""
def __init__(self, window=500, nfilters=3, subsample=1, metric='riemann',
n_jobs=1):
"""Init."""
self.window = window
self.nfilters = nfilters
self.subsample = subsample
self.metric = metric
self.n_jobs = n_jobs
self._fitted = False
def fit(self, X, y):
"""fit."""
# Create ERP and get cov mat
self.ERP = ERP(self.window, self.nfilters, self.subsample)
train_cov = self.ERP.fit_transform(X, y)
labels_train = self.ERP.labels_train
# Add rest epochs
rest_cov = self._get_rest_cov(X, y)
train_cov = np.concatenate((train_cov, rest_cov), axis=0)
labels_train = np.concatenate((labels_train, [0] * len(rest_cov)))
# fit MDM
self.MDM = MDM(metric=self.metric, n_jobs=self.n_jobs)
self.MDM.fit(train_cov, labels_train)
self._fitted = True
return self
def transform(self, X, y=None):
"""Transform."""
test_cov = self.ERP.transform(X)
dist = self.MDM.transform(test_cov)
dist = dist[:, 1:] - np.atleast_2d(dist[:, 0]).T
return dist
def update_subsample(self, old_sub, new_sub):
"""update subsampling."""
if self._fitted:
self.ERP.update_subsample(old_sub, new_sub)
def _get_rest_cov(self, X, y):
"""Sample rest epochs from data and compute the cov mat."""
ix = np.where(np.diff(y[:, 0]) == 1)[0]
rest = []
offset = - self.window
for i in ix:
start = i + offset - self.window
stop = i + offset
rest.append(self.ERP.erp_cov(X[slice(start, stop)].T))
return np.array(rest)