本文整理汇总了Python中mne.decoding.GeneralizationAcrossTime.predict方法的典型用法代码示例。如果您正苦于以下问题:Python GeneralizationAcrossTime.predict方法的具体用法?Python GeneralizationAcrossTime.predict怎么用?Python GeneralizationAcrossTime.predict使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类mne.decoding.GeneralizationAcrossTime
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在下文中一共展示了GeneralizationAcrossTime.predict方法的7个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_circular_classifiers
# 需要导入模块: from mne.decoding import GeneralizationAcrossTime [as 别名]
# 或者: from mne.decoding.GeneralizationAcrossTime import predict [as 别名]
def test_circular_classifiers():
from mne.decoding import GeneralizationAcrossTime
from ..scorers import scorer_angle
from sklearn.linear_model import Ridge, RidgeCV
epochs, angles = make_circular_data()
clf_list = [PolarRegression, AngularRegression,
SVR_polar, SVR_angle] # XXX will be deprecated
for clf_init in clf_list:
for independent in [False, True]:
if clf_init in [SVR_polar, SVR_angle]:
if (not independent):
continue
clf = clf_init(clf=Ridge(random_state=0))
else:
clf = clf_init(clf=Ridge(random_state=0),
independent=independent)
print clf_init, independent
gat = GeneralizationAcrossTime(clf=clf, scorer=scorer_angle)
gat.fit(epochs, y=angles)
gat.predict(epochs)
gat.score(y=angles)
assert_true(np.abs(gat.scores_[0][0]) < .5) # chance level
assert_true(gat.scores_[1][1] > 1.) # decode
assert_true(gat.scores_[2][2] > 1.) # decode
assert_true(gat.scores_[1][2] < -1.) # anti-generalize
# Test args
gat = GeneralizationAcrossTime(clf=RidgeCV(alphas=[1., 2.]),
scorer=scorer_angle)
gat.fit(epochs, y=angles)
gat = GeneralizationAcrossTime(clf=RidgeCV(), scorer=scorer_angle)
gat.fit(epochs, y=angles)
示例2: test_generalization_across_time
# 需要导入模块: from mne.decoding import GeneralizationAcrossTime [as 别名]
# 或者: from mne.decoding.GeneralizationAcrossTime import predict [as 别名]
def test_generalization_across_time():
"""Test time generalization decoding
"""
from sklearn.svm import SVC
from sklearn.base import is_classifier
# KernelRidge is used for testing 1) regression analyses 2) n-dimensional
# predictions.
from sklearn.kernel_ridge import KernelRidge
from sklearn.preprocessing import LabelEncoder
from sklearn.metrics import roc_auc_score, mean_squared_error
epochs = make_epochs()
y_4classes = np.hstack((epochs.events[:7, 2], epochs.events[7:, 2] + 1))
if check_version('sklearn', '0.18'):
from sklearn.model_selection import (KFold, StratifiedKFold,
ShuffleSplit, LeaveOneLabelOut)
cv_shuffle = ShuffleSplit()
cv = LeaveOneLabelOut()
# XXX we cannot pass any other parameters than X and y to cv.split
# so we have to build it before hand
cv_lolo = [(train, test) for train, test in cv.split(
X=y_4classes, y=y_4classes, labels=y_4classes)]
# With sklearn >= 0.17, `clf` can be identified as a regressor, and
# the scoring metrics can therefore be automatically assigned.
scorer_regress = None
else:
from sklearn.cross_validation import (KFold, StratifiedKFold,
ShuffleSplit, LeaveOneLabelOut)
cv_shuffle = ShuffleSplit(len(epochs))
cv_lolo = LeaveOneLabelOut(y_4classes)
# With sklearn < 0.17, `clf` cannot be identified as a regressor, and
# therefore the scoring metrics cannot be automatically assigned.
scorer_regress = mean_squared_error
# Test default running
gat = GeneralizationAcrossTime(picks='foo')
assert_equal("<GAT | no fit, no prediction, no score>", "%s" % gat)
assert_raises(ValueError, gat.fit, epochs)
with warnings.catch_warnings(record=True):
# check classic fit + check manual picks
gat.picks = [0]
gat.fit(epochs)
# check optional y as array
gat.picks = None
gat.fit(epochs, y=epochs.events[:, 2])
# check optional y as list
gat.fit(epochs, y=epochs.events[:, 2].tolist())
assert_equal(len(gat.picks_), len(gat.ch_names), 1)
assert_equal("<GAT | fitted, start : -0.200 (s), stop : 0.499 (s), no "
"prediction, no score>", '%s' % gat)
assert_equal(gat.ch_names, epochs.ch_names)
# test different predict function:
gat = GeneralizationAcrossTime(predict_method='decision_function')
gat.fit(epochs)
# With classifier, the default cv is StratifiedKFold
assert_true(gat.cv_.__class__ == StratifiedKFold)
gat.predict(epochs)
assert_array_equal(np.shape(gat.y_pred_), (15, 15, 14, 1))
gat.predict_method = 'predict_proba'
gat.predict(epochs)
assert_array_equal(np.shape(gat.y_pred_), (15, 15, 14, 2))
gat.predict_method = 'foo'
assert_raises(NotImplementedError, gat.predict, epochs)
gat.predict_method = 'predict'
gat.predict(epochs)
assert_array_equal(np.shape(gat.y_pred_), (15, 15, 14, 1))
assert_equal("<GAT | fitted, start : -0.200 (s), stop : 0.499 (s), "
"predicted 14 epochs, no score>",
"%s" % gat)
gat.score(epochs)
assert_true(gat.scorer_.__name__ == 'accuracy_score')
# check clf / predict_method combinations for which the scoring metrics
# cannot be inferred.
gat.scorer = None
gat.predict_method = 'decision_function'
assert_raises(ValueError, gat.score, epochs)
# Check specifying y manually
gat.predict_method = 'predict'
gat.score(epochs, y=epochs.events[:, 2])
gat.score(epochs, y=epochs.events[:, 2].tolist())
assert_equal("<GAT | fitted, start : -0.200 (s), stop : 0.499 (s), "
"predicted 14 epochs,\n scored "
"(accuracy_score)>", "%s" % gat)
with warnings.catch_warnings(record=True):
gat.fit(epochs, y=epochs.events[:, 2])
old_mode = gat.predict_mode
gat.predict_mode = 'super-foo-mode'
assert_raises(ValueError, gat.predict, epochs)
gat.predict_mode = old_mode
gat.score(epochs, y=epochs.events[:, 2])
assert_true("accuracy_score" in '%s' % gat.scorer_)
epochs2 = epochs.copy()
# check _DecodingTime class
assert_equal("<DecodingTime | start: -0.200 (s), stop: 0.499 (s), step: "
"0.050 (s), length: 0.050 (s), n_time_windows: 15>",
"%s" % gat.train_times_)
#.........这里部分代码省略.........
示例3: test_generalization_across_time
# 需要导入模块: from mne.decoding import GeneralizationAcrossTime [as 别名]
# 或者: from mne.decoding.GeneralizationAcrossTime import predict [as 别名]
def test_generalization_across_time():
"""Test time generalization decoding
"""
from sklearn.svm import SVC
from sklearn.preprocessing import LabelEncoder
from sklearn.metrics import mean_squared_error
raw = io.Raw(raw_fname, preload=False)
events = read_events(event_name)
picks = pick_types(raw.info, meg='mag', stim=False, ecg=False,
eog=False, exclude='bads')
picks = picks[0:2]
decim = 30
# Test on time generalization within one condition
with warnings.catch_warnings(record=True):
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0), preload=True, decim=decim)
# Test default running
gat = GeneralizationAcrossTime()
assert_equal("<GAT | no fit, no prediction, no score>", "%s" % gat)
assert_raises(ValueError, gat.fit, epochs, picks='foo')
with warnings.catch_warnings(record=True):
# check classic fit + check manual picks
gat.fit(epochs, picks=[0])
# check optional y as array
gat.fit(epochs, y=epochs.events[:, 2])
# check optional y as list
gat.fit(epochs, y=epochs.events[:, 2].tolist())
assert_equal(len(gat.picks_), len(gat.ch_names), 1)
assert_equal("<GAT | fitted, start : -0.200 (s), stop : 0.499 (s), no "
"prediction, no score>", '%s' % gat)
assert_equal(gat.ch_names, epochs.ch_names)
gat.predict(epochs)
assert_equal("<GAT | fitted, start : -0.200 (s), stop : 0.499 (s), "
"predicted 14 epochs, no score>",
"%s" % gat)
gat.score(epochs)
gat.score(epochs, y=epochs.events[:, 2])
gat.score(epochs, y=epochs.events[:, 2].tolist())
assert_equal("<GAT | fitted, start : -0.200 (s), stop : 0.499 (s), "
"predicted 14 epochs,\n scored "
"(accuracy_score)>", "%s" % gat)
with warnings.catch_warnings(record=True):
gat.fit(epochs, y=epochs.events[:, 2])
old_mode = gat.predict_mode
gat.predict_mode = 'super-foo-mode'
assert_raises(ValueError, gat.predict, epochs)
gat.predict_mode = old_mode
gat.score(epochs, y=epochs.events[:, 2])
assert_true("accuracy_score" in '%s' % gat.scorer_)
epochs2 = epochs.copy()
# check _DecodingTime class
assert_equal("<DecodingTime | start: -0.200 (s), stop: 0.499 (s), step: "
"0.047 (s), length: 0.047 (s), n_time_windows: 15>",
"%s" % gat.train_times)
assert_equal("<DecodingTime | start: -0.200 (s), stop: 0.499 (s), step: "
"0.047 (s), length: 0.047 (s), n_time_windows: 15 x 15>",
"%s" % gat.test_times_)
# the y-check
gat.predict_mode = 'mean-prediction'
epochs2.events[:, 2] += 10
gat_ = copy.deepcopy(gat)
assert_raises(ValueError, gat_.score, epochs2)
gat.predict_mode = 'cross-validation'
# Test basics
# --- number of trials
assert_true(gat.y_train_.shape[0] ==
gat.y_true_.shape[0] ==
len(gat.y_pred_[0][0]) == 14)
# --- number of folds
assert_true(np.shape(gat.estimators_)[1] == gat.cv)
# --- length training size
assert_true(len(gat.train_times['slices']) == 15 ==
np.shape(gat.estimators_)[0])
# --- length testing sizes
assert_true(len(gat.test_times_['slices']) == 15 ==
np.shape(gat.scores_)[0])
assert_true(len(gat.test_times_['slices'][0]) == 15 ==
np.shape(gat.scores_)[1])
# Test longer time window
gat = GeneralizationAcrossTime(train_times={'length': .100})
with warnings.catch_warnings(record=True):
gat2 = gat.fit(epochs)
assert_true(gat is gat2) # return self
assert_true(hasattr(gat2, 'cv_'))
assert_true(gat2.cv_ != gat.cv)
scores = gat.score(epochs)
assert_true(isinstance(scores, list)) # type check
assert_equal(len(scores[0]), len(scores)) # shape check
assert_equal(len(gat.test_times_['slices'][0][0]), 2)
# Decim training steps
gat = GeneralizationAcrossTime(train_times={'step': .100})
#.........这里部分代码省略.........
示例4: test_generalization_across_time
# 需要导入模块: from mne.decoding import GeneralizationAcrossTime [as 别名]
# 或者: from mne.decoding.GeneralizationAcrossTime import predict [as 别名]
def test_generalization_across_time():
"""Test time generalization decoding
"""
from sklearn.svm import SVC
from sklearn.linear_model import RANSACRegressor, LinearRegression
from sklearn.preprocessing import LabelEncoder
from sklearn.metrics import mean_squared_error
from sklearn.cross_validation import LeaveOneLabelOut
epochs = make_epochs()
# Test default running
gat = GeneralizationAcrossTime(picks='foo')
assert_equal("<GAT | no fit, no prediction, no score>", "%s" % gat)
assert_raises(ValueError, gat.fit, epochs)
with warnings.catch_warnings(record=True):
# check classic fit + check manual picks
gat.picks = [0]
gat.fit(epochs)
# check optional y as array
gat.picks = None
gat.fit(epochs, y=epochs.events[:, 2])
# check optional y as list
gat.fit(epochs, y=epochs.events[:, 2].tolist())
assert_equal(len(gat.picks_), len(gat.ch_names), 1)
assert_equal("<GAT | fitted, start : -0.200 (s), stop : 0.499 (s), no "
"prediction, no score>", '%s' % gat)
assert_equal(gat.ch_names, epochs.ch_names)
gat.predict(epochs)
assert_equal("<GAT | fitted, start : -0.200 (s), stop : 0.499 (s), "
"predicted 14 epochs, no score>",
"%s" % gat)
gat.score(epochs)
gat.score(epochs, y=epochs.events[:, 2])
gat.score(epochs, y=epochs.events[:, 2].tolist())
assert_equal("<GAT | fitted, start : -0.200 (s), stop : 0.499 (s), "
"predicted 14 epochs,\n scored "
"(accuracy_score)>", "%s" % gat)
with warnings.catch_warnings(record=True):
gat.fit(epochs, y=epochs.events[:, 2])
old_mode = gat.predict_mode
gat.predict_mode = 'super-foo-mode'
assert_raises(ValueError, gat.predict, epochs)
gat.predict_mode = old_mode
gat.score(epochs, y=epochs.events[:, 2])
assert_true("accuracy_score" in '%s' % gat.scorer_)
epochs2 = epochs.copy()
# check _DecodingTime class
assert_equal("<DecodingTime | start: -0.200 (s), stop: 0.499 (s), step: "
"0.050 (s), length: 0.050 (s), n_time_windows: 15>",
"%s" % gat.train_times_)
assert_equal("<DecodingTime | start: -0.200 (s), stop: 0.499 (s), step: "
"0.050 (s), length: 0.050 (s), n_time_windows: 15 x 15>",
"%s" % gat.test_times_)
# the y-check
gat.predict_mode = 'mean-prediction'
epochs2.events[:, 2] += 10
gat_ = copy.deepcopy(gat)
assert_raises(ValueError, gat_.score, epochs2)
gat.predict_mode = 'cross-validation'
# Test basics
# --- number of trials
assert_true(gat.y_train_.shape[0] ==
gat.y_true_.shape[0] ==
len(gat.y_pred_[0][0]) == 14)
# --- number of folds
assert_true(np.shape(gat.estimators_)[1] == gat.cv)
# --- length training size
assert_true(len(gat.train_times_['slices']) == 15 ==
np.shape(gat.estimators_)[0])
# --- length testing sizes
assert_true(len(gat.test_times_['slices']) == 15 ==
np.shape(gat.scores_)[0])
assert_true(len(gat.test_times_['slices'][0]) == 15 ==
np.shape(gat.scores_)[1])
# Test longer time window
gat = GeneralizationAcrossTime(train_times={'length': .100})
with warnings.catch_warnings(record=True):
gat2 = gat.fit(epochs)
assert_true(gat is gat2) # return self
assert_true(hasattr(gat2, 'cv_'))
assert_true(gat2.cv_ != gat.cv)
scores = gat.score(epochs)
assert_true(isinstance(scores, list)) # type check
assert_equal(len(scores[0]), len(scores)) # shape check
assert_equal(len(gat.test_times_['slices'][0][0]), 2)
# Decim training steps
gat = GeneralizationAcrossTime(train_times={'step': .100})
with warnings.catch_warnings(record=True):
gat.fit(epochs)
gat.score(epochs)
assert_true(len(gat.scores_) == len(gat.estimators_) == 8) # training time
#.........这里部分代码省略.........
示例5: EpochsArray
# 需要导入模块: from mne.decoding import GeneralizationAcrossTime [as 别名]
# 或者: from mne.decoding.GeneralizationAcrossTime import predict [as 别名]
epochs = EpochsArray(data, info, events)
# RUN GAT ======================================================================
# SVR
# --- fit & predict separately
cos = lambda angles: np.cos(angle2circle(angles))
sin = lambda angles: np.sin(angle2circle(angles))
gats = list()
for transform in [cos, sin]:
scaler = StandardScaler()
svr = SVR(C=1, kernel='linear')
clf = Pipeline([('scaler', scaler), ('svr', svr)])
gat = GeneralizationAcrossTime(n_jobs=-1, clf=clf)
gat.fit(epochs, y=transform(trial_angles))
gat.predict(epochs)
gats.append(gat)
# --- recombine
predict_angles, true_angles = recombine_svr_prediction(gats[0], gats[1])
# --- score
angle_errors_svr = compute_error_svr(predict_angles, true_angles)
plt.matshow(np.mean(angle_errors_svr,axis=2)), plt.colorbar(), plt.show()
# SVC Gat
scaler = StandardScaler()
svc = SVC(C=1, kernel='linear', probability=True)
clf = Pipeline([('scaler', scaler), ('svc', svc)])
gat = GeneralizationAcrossTime(n_jobs=-1, clf=clf, predict_type='predict_proba')
# --- fit & predict
gat.fit(epochs, y=trial_angles)
示例6: simulate_model
# 需要导入模块: from mne.decoding import GeneralizationAcrossTime [as 别名]
# 或者: from mne.decoding.GeneralizationAcrossTime import predict [as 别名]
def simulate_model(sources, mixin, background, snr=.5, n_trial=100):
"""Run simulations :
1. Takes source activations in two visibility conditions:
dict(high=(n_sources * n_times), low=(n_sources * n_times))
2. Target presence/absence is coded in y vector and corresponds to the
reverse activation in source space.
3. Takes a mixin matrix that project the data from source space to sensor
space
4. Generates multiple low and high visibility trials.
5. Fit target presence (y) across all trials (both high and low visiblity),
6. Score target presence separately for high and low visibility trials
7. Fit and score target visibility (for simplicity reasons, we only have 2
visibility conditions. Consequently, we will fit a logistic regression
and not a ridge like the one used for in empirical part of the paper.)
"""
n_source, n_chan = mixin.shape
# add information
X, y, visibility = list(), list(), list()
for vis, source in sources.iteritems():
n_source, n_time = source.shape
# define present and absent in source space
present = np.stack([source + background] * (n_trial // 2))
absent = np.stack([background] * (n_trial // 2))
source = np.vstack((present, absent))
y_ = np.hstack((np.ones(n_trial // 2), -1 * np.ones(n_trial // 2)))
# transform in sensor space
sensor = np.dot(mixin.T, np.hstack((source)))
sensor = np.reshape(sensor, [n_chan, -1, n_time]).transpose(1, 0, 2)
# add sensor specific noise
sensor += np.random.randn(n_trial, n_chan, n_time) / snr
X.append(sensor)
y.append(y_)
visibility.append(int(vis == 'high') * np.ones(n_trial))
X = np.concatenate(X, axis=0)
y = np.concatenate(y, axis=0)
visibility = np.concatenate(visibility, axis=0)
# shuffle trials
idx = range(n_trial * 2)
np.random.shuffle(idx)
X, y, visibility = X[idx], y[idx], visibility[idx]
# format to MNE epochs
epochs = EpochsArray(X, create_info(n_chan, sfreq, 'mag'), tmin=times[0],
proj=False, baseline=None)
# Temporal generalization pipeline
gat = GeneralizationAcrossTime(clf=analysis['clf'], cv=8,
scorer=scorer_auc, n_jobs=-1,
score_mode='mean-sample-wise')
gat.fit(epochs, y=y)
y_pred = gat.predict(epochs)
y_pred = y_pred[:, :, :, 0].transpose(2, 0, 1)
score = list()
for vis in range(2):
# select all absent trials + present at a given visibility
sel = np.unique(np.hstack((np.where(y == -1)[0],
np.where(visibility == vis)[0])))
score_ = scorer_auc(y[sel], y_pred[sel], n_jobs=-1)
score.append(score_)
# correlation with visibility
sel = np.where(y == 1)[0]
corr_vis = scorer_spearman(visibility[sel], y_pred[sel], n_jobs=-1)
# decode visibility
sel = np.where(y == 1)[0] # present trials only
gat.fit(epochs[sel], y=visibility[sel])
score_vis = gat.score(epochs[sel], y=visibility[sel])
return np.array(score), np.squeeze(score_vis), np.squeeze(corr_vis)
示例7: test_generalization_across_time
# 需要导入模块: from mne.decoding import GeneralizationAcrossTime [as 别名]
# 或者: from mne.decoding.GeneralizationAcrossTime import predict [as 别名]
def test_generalization_across_time():
"""Test time generalization decoding
"""
from sklearn.svm import SVC
raw = io.Raw(raw_fname, preload=False)
events = read_events(event_name)
picks = pick_types(raw.info, meg='mag', stim=False, ecg=False,
eog=False, exclude='bads')
picks = picks[0:2]
decim = 30
# Test on time generalization within one condition
with warnings.catch_warnings(record=True):
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0), preload=True, decim=decim)
# Test default running
gat = GeneralizationAcrossTime()
assert_equal("<GAT | no fit, no prediction, no score>", "%s" % gat)
with warnings.catch_warnings(record=True):
gat.fit(epochs)
assert_equal("<GAT | fitted, start : -0.200 (s), stop : 0.499 (s), no "
"prediction, no score>", '%s' % gat)
gat.predict(epochs)
assert_equal("<GAT | fitted, start : -0.200 (s), stop : 0.499 (s), "
"predict_type : 'predict' on 15 epochs, no score>",
"%s" % gat)
gat.score(epochs)
assert_equal("<GAT | fitted, start : -0.200 (s), stop : 0.499 (s), "
"predict_type : 'predict' on 15 epochs,\n scored "
"(accuracy_score)>", "%s" % gat)
with warnings.catch_warnings(record=True):
gat.fit(epochs, y=epochs.events[:, 2])
old_type = gat.predict_type
gat.predict_type = 'foo'
assert_raises(ValueError, gat.predict, epochs)
gat.predict_type = old_type
old_mode = gat.predict_mode
gat.predict_mode = 'super-foo-mode'
assert_raises(ValueError, gat.predict, epochs)
gat.predict_mode = old_mode
gat.score(epochs, y=epochs.events[:, 2])
assert_true("accuracy_score" in '%s' % gat.scorer_)
epochs2 = epochs.copy()
# check _DecodingTime class
assert_equal("<DecodingTime | start: -0.200 (s), stop: 0.499 (s), step: "
"0.047 (s), length: 0.047 (s), n_time_windows: 15>",
"%s" % gat.train_times)
assert_equal("<DecodingTime | start: -0.200 (s), stop: 0.499 (s), step: "
"0.047 (s), length: 0.047 (s), n_time_windows: 15 x 15>",
"%s" % gat.test_times_)
# the y-check
gat.predict_mode = 'mean-prediction'
epochs2.events[:, 2] += 10
assert_raises(ValueError, gat.score, epochs2)
gat.predict_mode = 'cross-validation'
# Test basics
# --- number of trials
assert_true(gat.y_train_.shape[0] ==
gat.y_true_.shape[0] ==
gat.y_pred_.shape[2] == 14)
# --- number of folds
assert_true(np.shape(gat.estimators_)[1] == gat.cv)
# --- length training size
assert_true(len(gat.train_times['slices']) == 15 ==
np.shape(gat.estimators_)[0])
# --- length testing sizes
assert_true(len(gat.test_times_['slices']) == 15 ==
np.shape(gat.scores_)[0])
assert_true(len(gat.test_times_['slices'][0]) == 15 ==
np.shape(gat.scores_)[1])
# Test longer time window
gat = GeneralizationAcrossTime(train_times={'length': .100})
with warnings.catch_warnings(record=True):
gat2 = gat.fit(epochs)
assert_true(gat is gat2) # return self
assert_true(hasattr(gat2, 'cv_'))
assert_true(gat2.cv_ != gat.cv)
scores = gat.score(epochs)
assert_true(isinstance(scores, list)) # type check
assert_equal(len(scores[0]), len(scores)) # shape check
assert_equal(len(gat.test_times_['slices'][0][0]), 2)
# Decim training steps
gat = GeneralizationAcrossTime(train_times={'step': .100})
with warnings.catch_warnings(record=True):
gat.fit(epochs)
gat.score(epochs)
assert_equal(len(gat.scores_), 8)
# Test start stop training
gat = GeneralizationAcrossTime(train_times={'start': 0.090,
#.........这里部分代码省略.........