def fit(self, X, y):
"""Fit.
Estimate spatial filters and prototyped response for each classes.
Parameters
----------
X : ndarray, shape (n_trials, n_channels, n_samples)
ndarray of trials.
y : ndarray shape (n_trials,)
labels corresponding to each trial.
Returns
-------
self : XdawnCovariances instance
The XdawnCovariances instance.
"""
yb = continuous2discrete(y, self.bins)
self.Xd_ = Xdawn(nfilter=self.nfilter,
classes=self.classes,
estimator=self.xdawn_estimator,
baseline_cov=self.baseline_cov)
self.Xd_.fit(X, yb)
self.P_ = self.Xd_.evokeds_
return self
def test_xdawn_baselinecov(rndstate, get_labels):
"""Test cov precomputation"""
n_matrices, n_channels, n_times = 6, 5, 100
n_classes, default_nfilter = 2, 4
x = rndstate.randn(n_matrices, n_channels, n_times)
labels = get_labels(n_matrices, n_classes)
baseline_cov = np.identity(n_channels)
xd = Xdawn(baseline_cov=baseline_cov)
xd.fit(x, labels).transform(x)
assert len(xd.filters_) == n_classes * default_nfilter
for sfilt in xd.filters_:
assert sfilt.shape == (n_channels, )
def ml_classifier(inputs, targets, classifier=None, pipeline=None):
"""Uses sklearn to fit a model given inputs and targets
Args:
inputs: list containing (N trials * M channels) data segments of length(number of features).
targets: list containing (N trials * M channels) of marker data (0 or 1).
classifier: pre-trained lda classifier; if None train from scratch
pipeline: name of pipeline to create if classifier is None
Returns:
classifier: classifier object
"""
pipeline_dict = {
'vect_lr':
make_pipeline(Vectorizer(), StandardScaler(), LogisticRegression()),
'vecct_reglda':
make_pipeline(Vectorizer(), LDA(shrinkage='auto', solver='eigen')),
'xdawn_reglda':
make_pipeline(Xdawn(2, classes=[1]), Vectorizer(),
LDA(shrinkage='auto', solver='eigen')),
'erpcov_ts':
make_pipeline(ERPCovariances(), TangentSpace(), LogisticRegression()),
'erpcov_mdm':
make_pipeline(ERPCovariances(), MDM())
}
if not classifier and pipeline:
classifier = pipeline_dict[pipeline.lower()]
classifier.fit(inputs, targets)
return classifier
def P300_test(session_id):
markers = P300_MARKERS
epochs = get_session_erp_epochs(session_id, markers)
conditions = OrderedDict()
for i in range(len(markers)-1):
conditions[markers[i]] = [i+1]
clfs = OrderedDict()
clfs['Vect + LR'] = make_pipeline(Vectorizer(), StandardScaler(), LogisticRegression())
clfs['Vect + RegLDA'] = make_pipeline(Vectorizer(), LDA(shrinkage='auto', solver='eigen'))
clfs['Xdawn + RegLDA'] = make_pipeline(Xdawn(2, classes=[1]), Vectorizer(), LDA(shrinkage='auto', solver='eigen'))
clfs['ERPCov + TS'] = make_pipeline(ERPCovariances(), TangentSpace(), LogisticRegression())
clfs['ERPCov + MDM'] = make_pipeline(ERPCovariances(), MDM())
methods_list = ['Vect + LR','Vect + RegLDA','Xdawn + RegLDA','ERPCov + TS','ERPCov + MDM']
# format data
epochs.pick_types(eeg=True)
X = epochs.get_data() * 1e6
times = epochs.times
y = epochs.events[:, -1]
# define cross validation
cv = StratifiedShuffleSplit(n_splits=20, test_size=0.25, random_state=42)
# run cross validation for each pipeline
auc = []
methods = []
print('Calcul in progress...')
for m in clfs:
try:
res = cross_val_score(clfs[m], X, y==2, scoring='roc_auc', cv=cv, n_jobs=-1)
auc.extend(res)
methods.extend([m]*len(res))
except:
pass
results = pd.DataFrame(data=auc, columns=['AUC'])
results['Method'] = methods
n_row,n_column = results.shape
auc_means = []
for method in methods_list:
auc = []
for i in range(n_row):
if results.loc[i,'Method']== method:
auc.append(results.loc[i,'AUC'])
auc_means.append(np.mean(auc))
counter = 0
for i in range(len(methods_list)):
color = 'green' if auc_means[i]>=0.7 else 'red'
counter = counter +1 if auc_means[i]>=0.7 else counter
return counter > 0, counter
def test_Xdawn_transform():
"""Test transform of Xdawn"""
x = np.random.randn(100,3,10)
labels = np.array([0,1]).repeat(50)
xd = Xdawn()
xd.fit(x,labels)
xd.transform(x)
def test_Xdawn_baselinecov():
"""Test cov precomputation"""
x = np.random.randn(100, 3, 10)
labels = np.array([0, 1]).repeat(50)
baseline_cov = np.identity(3)
xd = Xdawn(baseline_cov=baseline_cov)
xd.fit(x, labels)
xd.transform(x)
from sklearn.cross_validation import KFold
from sklearn.metrics import roc_auc_score
from utils import (DownSampler, EpochsVectorizer, CospBoostingClassifier,
epoch_data)
dataframe1 = pd.read_csv('ecog_train_with_labels.csv')
array_clfs = OrderedDict()
# ERPs models
array_clfs['XdawnCov'] = make_pipeline(XdawnCovariances(6, estimator='oas'),
TangentSpace('riemann'),
LogisticRegression('l2'))
array_clfs['Xdawn'] = make_pipeline(Xdawn(12, estimator='oas'), DownSampler(5),
EpochsVectorizer(),
LogisticRegression('l2'))
# Induced activity models
baseclf = make_pipeline(
ElectrodeSelection(10, metric=dict(mean='logeuclid', distance='riemann')),
TangentSpace('riemann'), LogisticRegression('l1'))
array_clfs['Cosp'] = make_pipeline(
CospCovariances(fs=1000, window=32, overlap=0.95, fmax=300, fmin=1),
CospBoostingClassifier(baseclf))
array_clfs['HankelCov'] = make_pipeline(
DownSampler(2), HankelCovariances(delays=[2, 4, 8, 12, 16],
pipelines = {}
# we have to do this because the classes are called 'Target' and 'NonTarget'
# but the evaluation function uses a LabelEncoder, transforming them
# to 0 and 1
labels_dict = {"Target": 1, "NonTarget": 0}
# Riemannian geometry based classification
pipelines["RG + LDA"] = make_pipeline(
XdawnCovariances(nfilter=5, estimator="lwf", xdawn_estimator="scm"),
TangentSpace(),
LDA(solver="lsqr", shrinkage="auto"),
)
pipelines["Xdw + LDA"] = make_pipeline(
Xdawn(nfilter=2, estimator="scm"), Vectorizer(), LDA(solver="lsqr", shrinkage="auto")
)
##############################################################################
# Evaluation
# ----------
#
# We define the paradigm (P300) and use all three datasets available for it.
# The evaluation will return a dataframe containing AUCs for each permutation
# and dataset size.
paradigm = P300(resample=processing_sampling_rate)
dataset = BNCI2014009()
# Remove the slicing of the subject list to evaluate multiple subjects
dataset.subject_list = dataset.subject_list[1:2]
datasets = [dataset]
class XdawnCovariancesRegression(XdawnCovariances):
"""Estimate special form covariance matrix for ERP combined with Xdawn.
Estimation of special form covariance matrix dedicated to ERP processing
combined with Xdawn spatial filtering. This is similar to `ERPCovariances`
but data are spatially filtered with `Xdawn`. A complete descrition of the
method is available in [1].
The advantage of this estimation is to reduce dimensionality of the
covariance matrices efficiently.
Parameters
----------
nfilter: int (default 4)
number of Xdawn filter per classes.
applyfilters: bool (default True)
if set to true, spatial filter are applied to the prototypes and the
signals. When set to False, filters are applied only to the ERP prototypes
allowing for a better generalization across subject and session at the
expense of dimensionality increase. In that case, the estimation is
similar to ERPCovariances with `svd=nfilter` but with more compact
prototype reduction.
classes : list of int | None (default None)
list of classes to take into account for prototype estimation.
If None (default), all classes will be accounted.
estimator : string (default: 'scm')
covariance matrix estimator. For regularization consider 'lwf' or 'oas'
For a complete list of estimator, see `utils.covariance`.
xdawn_estimator : string (default: 'scm')
covariance matrix estimator for xdawn spatial filtering.
baseline_cov : array, shape(n_chan, n_chan) | None (default)
baseline_covariance for xdawn. see `Xdawn`.
bins : list, len(n_bins+1) | None (default)
for bagging the labels y into bins. Usefull when the labels are continuous
and want to use xdawn with multi-class.
See Also
--------
ERPCovariances
Xdawn
References
----------
[1] Barachant, A. "MEG decoding using Riemannian Geometry and Unsupervised
classification."
"""
def __init__(self,
nfilter=4,
applyfilters=True,
classes=None,
estimator='scm',
xdawn_estimator='scm',
baseline_cov=None,
bins=None):
"""Init."""
self.applyfilters = applyfilters
self.estimator = estimator
self.xdawn_estimator = xdawn_estimator
self.classes = classes
self.nfilter = nfilter
self.baseline_cov = baseline_cov
self.bins = bins
def fit(self, X, y):
"""Fit.
Estimate spatial filters and prototyped response for each classes.
Parameters
----------
X : ndarray, shape (n_trials, n_channels, n_samples)
ndarray of trials.
y : ndarray shape (n_trials,)
labels corresponding to each trial.
Returns
-------
self : XdawnCovariances instance
The XdawnCovariances instance.
"""
yb = continuous2discrete(y, self.bins)
self.Xd_ = Xdawn(nfilter=self.nfilter,
classes=self.classes,
estimator=self.xdawn_estimator,
baseline_cov=self.baseline_cov)
self.Xd_.fit(X, yb)
self.P_ = self.Xd_.evokeds_
return self
def test_Xdawn_fit():
"""Test Fit of Xdawn"""
x = np.random.randn(100,3,10)
labels = np.array([0,1]).repeat(50)
xd = Xdawn()
xd.fit(x,labels)
def test_Xdawn_init():
"""Test init of Xdawn"""
xd = Xdawn()
X_train[:, channel_2d[i][0], channel_2d[i][1]] -
mu[i]) / std[i]
X_val[:, channel_2d[i][0], channel_2d[i][1]] = (
X_val[:, channel_2d[i][0], channel_2d[i][1]] - mu[i]) / std[i]
return X_train, X_val
results = 0
if __name__ == "__main__":
f = []
auc = []
acc = []
methods = []
clfs = OrderedDict()
clfs['Xdawn + RegLDA'] = make_pipeline(
Xdawn(2), Vectorizer(), LDA(shrinkage='auto', solver='eigen'))
for name in file:
X1 = np.load('data/X_' + name + '.npy')
y1 = np.load('data/Y_' + name + '.npy')
X = X1[:, 4:9, :, 50:150]
X = np.reshape(X, (-1, 9 * 5, 100))
y = y1.flatten()
zero = np.sum(X, axis=-1)[0] != 0
X = X[:, zero, :]
cv = StratifiedKFold(n_splits=10, random_state=0)
for m in clfs:
print name, m
res1 = cross_val_score(clfs[m],
X,
y,
processing_sampling_rate = 128
pipelines = {}
# we have to do this because the classes are called 'Target' and 'NonTarget'
# but the evaluation function uses a LabelEncoder, transforming them
# to 0 and 1
labels_dict = {"Target": 1, "NonTarget": 0}
# Riemannian geometry based classification
pipelines["RG+LDA"] = make_pipeline(
XdawnCovariances(nfilter=5, estimator="lwf", xdawn_estimator="scm"),
TangentSpace(),
LDA(solver="lsqr", shrinkage="auto"),
)
pipelines["Xdw+LDA"] = make_pipeline(Xdawn(nfilter=2, estimator="scm"),
Vectorizer(),
LDA(solver="lsqr", shrinkage="auto"))
##############################################################################
# Evaluation
# ----------
#
# We define the paradigm (P300) and use all three datasets available for it.
# The evaluation will return a dataframe containing AUCs for each permutation
# and dataset size.
paradigm = P300(resample=processing_sampling_rate)
dataset = BNCI2014009()
# Remove the slicing of the subject list to evaluate multiple subjects
dataset.subject_list = dataset.subject_list[1:2]
),
'SVM': (
make_pipeline(Vectorizer(), SVC()),
{
'svc__C': np.exp(np.linspace(-4, 4, 9))
},
),
'CSP LDA': (
make_pipeline(CSP(), LDA(shrinkage='auto', solver='eigen')),
{
'csp__n_components': (6, 9, 13),
'csp__cov_est': ('concat', 'epoch')
},
),
'Xdawn LDA': (
make_pipeline(Xdawn(2, classes=[1]), Vectorizer(),
LDA(shrinkage='auto', solver='eigen')),
{},
),
'ERPCov TS LR': (
make_pipeline(ERPCovariances(estimator='oas'), TangentSpace(),
LogisticRegression()),
{
'erpcovariances__estimator': ('lwf', 'oas')
},
),
'ERPCov MDM': (
make_pipeline(ERPCovariances(), MDM()),
{
'erpcovariances__estimator': ('lwf', 'oas')
},