[med-svn] [python-mne] 339/353: pyflakes + pep8
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:25:28 UTC 2015
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yoh pushed a commit to tag 0.4
in repository python-mne.
commit d3c80dc02822df89f720ea05ef20aa08350112c7
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date: Fri Aug 3 22:27:21 2012 +0200
pyflakes + pep8
---
mne/artifacts/stim.py | 2 +-
mne/artifacts/tests/test_ecg.py | 1 -
mne/artifacts/tests/test_peak_finder.py | 1 -
mne/cov.py | 2 +-
mne/epochs.py | 9 ++++++---
mne/fiff/matrix.py | 2 +-
mne/fiff/tests/test_evoked.py | 1 +
mne/fiff/tests/test_pick.py | 1 -
mne/filter.py | 2 ++
mne/mixed_norm/debiasing.py | 2 +-
mne/selection.py | 1 -
mne/simulation/evoked.py | 2 +-
mne/source_space.py | 1 +
mne/stats/tests/test_permutations.py | 2 +-
mne/tests/test_epochs.py | 12 ++++++------
mne/tests/test_misc.py | 1 +
mne/tests/test_selection.py | 1 -
mne/tests/test_utils.py | 1 +
mne/time_frequency/tests/test_psd.py | 7 ++++---
mne/time_frequency/tfr.py | 4 ++--
mne/utils.py | 10 +++++-----
21 files changed, 35 insertions(+), 30 deletions(-)
diff --git a/mne/artifacts/stim.py b/mne/artifacts/stim.py
index 5f65ddd..84717ec 100644
--- a/mne/artifacts/stim.py
+++ b/mne/artifacts/stim.py
@@ -48,7 +48,7 @@ def eliminate_stim_artifact(raw, events, event_id, tmin=-0.005,
picks = pick_types(raw.info, meg=True, eeg=True)
if mode == 'window':
- window = 1 - np.r_[signal.hann(4)[:2], np.ones(s_end + s_start - 4), \
+ window = 1 - np.r_[signal.hann(4)[:2], np.ones(s_end + s_start - 4),
signal.hann(4)[-2:]].T
for k in range(len(event_start)):
diff --git a/mne/artifacts/tests/test_ecg.py b/mne/artifacts/tests/test_ecg.py
index 5777136..4c994e0 100644
--- a/mne/artifacts/tests/test_ecg.py
+++ b/mne/artifacts/tests/test_ecg.py
@@ -1,7 +1,6 @@
import os.path as op
from nose.tools import assert_true
-from numpy.testing import assert_array_almost_equal
from mne.fiff import Raw
from mne.artifacts.ecg import find_ecg_events
diff --git a/mne/artifacts/tests/test_peak_finder.py b/mne/artifacts/tests/test_peak_finder.py
index 276427a..5d60719 100644
--- a/mne/artifacts/tests/test_peak_finder.py
+++ b/mne/artifacts/tests/test_peak_finder.py
@@ -1,4 +1,3 @@
-import numpy as np
from numpy.testing import assert_array_equal
from mne.artifacts.peak_finder import peak_finder
diff --git a/mne/cov.py b/mne/cov.py
index 518a403..ef1872c 100644
--- a/mne/cov.py
+++ b/mne/cov.py
@@ -94,7 +94,7 @@ class Covariance(dict):
"""Add Covariance taking into account number of degrees of freedom"""
_check_covs_algebra(self, cov)
this_cov = copy.deepcopy(cov)
- this_cov['data'] = ((this_cov['data'] * this_cov['nfree']) + \
+ this_cov['data'] = ((this_cov['data'] * this_cov['nfree']) +
(self['data'] * self['nfree'])) / \
(self['nfree'] + this_cov['nfree'])
this_cov['nfree'] += self['nfree']
diff --git a/mne/epochs.py b/mne/epochs.py
index 944153f..8b6dc75 100644
--- a/mne/epochs.py
+++ b/mne/epochs.py
@@ -16,6 +16,7 @@ from .fiff.proj import activate_proj, make_eeg_average_ref_proj
from .baseline import rescale
from .utils import check_random_state
+
class Epochs(object):
"""List of Epochs
@@ -181,7 +182,8 @@ class Epochs(object):
# Select the desired events
self.events = events
if event_id is not None:
- selected = np.logical_and(events[:, 1] == 0, events[:, 2] == event_id)
+ selected = np.logical_and(events[:, 1] == 0,
+ events[:, 2] == event_id)
self.events = self.events[selected]
n_events = len(self.events)
@@ -519,8 +521,9 @@ def _is_good(e, ch_names, channel_type_idx, reject, flat):
delta = deltas[idx_min_delta]
if delta < thresh:
ch_name = ch_names[idx[idx_min_delta]]
- print (' Rejecting flat epoch based on %s : %s (%s < %s).'
- % (name, ch_name, delta, thresh))
+ print (' Rejecting flat epoch based on '
+ '%s : %s (%s < %s).' % (name, ch_name, delta,
+ thresh))
return False
return True
diff --git a/mne/fiff/matrix.py b/mne/fiff/matrix.py
index 8f883a2..df01757 100644
--- a/mne/fiff/matrix.py
+++ b/mne/fiff/matrix.py
@@ -7,7 +7,7 @@ import copy
from .constants import FIFF
from .tag import find_tag, has_tag
from .write import write_int, start_block, end_block, write_float_matrix, \
- write_string, write_name_list
+ write_name_list
def _transpose_named_matrix(mat):
diff --git a/mne/fiff/tests/test_evoked.py b/mne/fiff/tests/test_evoked.py
index 7feca2c..248526d 100644
--- a/mne/fiff/tests/test_evoked.py
+++ b/mne/fiff/tests/test_evoked.py
@@ -6,6 +6,7 @@ from mne.fiff import read_evoked, write_evoked
fname = op.join(op.dirname(__file__), 'data', 'test-ave.fif')
+
def test_io_evoked():
"""Test IO for evoked data
"""
diff --git a/mne/fiff/tests/test_pick.py b/mne/fiff/tests/test_pick.py
index ce4ef37..d574c34 100644
--- a/mne/fiff/tests/test_pick.py
+++ b/mne/fiff/tests/test_pick.py
@@ -8,4 +8,3 @@ def test_pick_channels_regexp():
assert_array_equal(pick_channels_regexp(ch_names, 'MEG ...1'), [0])
assert_array_equal(pick_channels_regexp(ch_names, 'MEG ...[2-3]'), [1, 2])
assert_array_equal(pick_channels_regexp(ch_names, 'MEG *'), [0, 1, 2])
-
diff --git a/mne/filter.py b/mne/filter.py
index 55f82a4..cd68046 100644
--- a/mne/filter.py
+++ b/mne/filter.py
@@ -5,6 +5,7 @@ from scipy.signal import freqz
from .utils import firwin2 # back port for old scipy
+
def is_power2(num):
"""Test if number is a power of 2
@@ -148,6 +149,7 @@ def _filter_attenuation(h, freq, gain):
return att_db, att_freq
+
def _filter(x, Fs, freq, gain, filter_length=None):
"""Filter signal using gain control points in the frequency domain.
diff --git a/mne/mixed_norm/debiasing.py b/mne/mixed_norm/debiasing.py
index 95d7f47..439af2d 100755
--- a/mne/mixed_norm/debiasing.py
+++ b/mne/mixed_norm/debiasing.py
@@ -7,7 +7,7 @@ from math import sqrt
import numpy as np
from scipy import linalg
-from ..utils import check_random_state
+from ..utils import check_random_state
def power_iteration_kron(A, C, max_iter=1000, tol=1e-3, random_state=0):
diff --git a/mne/selection.py b/mne/selection.py
index ba52262..558e7ca 100644
--- a/mne/selection.py
+++ b/mne/selection.py
@@ -95,4 +95,3 @@ def read_selection(name, fname=None):
sel.sort()
return sel
-
diff --git a/mne/simulation/evoked.py b/mne/simulation/evoked.py
index cf127dd..f7b9895 100644
--- a/mne/simulation/evoked.py
+++ b/mne/simulation/evoked.py
@@ -47,7 +47,7 @@ def generate_evoked(fwd, stc, evoked, cov, snr=3, tmin=None, tmax=None,
The simulated evoked data
"""
evoked = apply_forward(fwd, stc, evoked)
- noise = generate_noise_evoked(evoked, cov, fir_filter, random_state)
+ noise = generate_noise_evoked(evoked, cov, iir_filter, random_state)
evoked_noise = add_noise_evoked(evoked, noise, snr, tmin=tmin, tmax=tmax)
return evoked_noise
diff --git a/mne/source_space.py b/mne/source_space.py
index a75df95..e5a8388 100644
--- a/mne/source_space.py
+++ b/mne/source_space.py
@@ -382,6 +382,7 @@ def _get_vertno(src):
vertno.append(s['vertno'])
return vertno
+
###############################################################################
# Write routines
diff --git a/mne/stats/tests/test_permutations.py b/mne/stats/tests/test_permutations.py
index 1c40457..8ac0bac 100644
--- a/mne/stats/tests/test_permutations.py
+++ b/mne/stats/tests/test_permutations.py
@@ -12,7 +12,7 @@ def test_permutation_t_test():
np.random.seed(10)
n_samples, n_tests = 30, 5
X = np.random.randn(n_samples, n_tests)
- X[:,:2] += 1
+ X[:, :2] += 1
T_obs, p_values, H0 = permutation_t_test(X, n_permutations=999, tail=0)
is_significant = p_values < 0.05
diff --git a/mne/tests/test_epochs.py b/mne/tests/test_epochs.py
index 584b8ac..459e27e 100644
--- a/mne/tests/test_epochs.py
+++ b/mne/tests/test_epochs.py
@@ -85,8 +85,8 @@ def test_reject_epochs():
def test_preload_epochs():
"""Test of epochs rejection
"""
- epochs_preload = Epochs(raw, events[:16], event_id, tmin, tmax, picks=picks,
- baseline=(None, 0), preload=True,
+ epochs_preload = Epochs(raw, events[:16], event_id, tmin, tmax,
+ picks=picks, baseline=(None, 0), preload=True,
reject=reject, flat=flat)
data_preload = epochs_preload.get_data()
@@ -127,7 +127,7 @@ def test_indexing_slicing():
epochs2_sliced = epochs2[start_index:end_index]
data_epochs2_sliced = epochs2_sliced.get_data()
- assert_array_equal(data_epochs2_sliced, \
+ assert_array_equal(data_epochs2_sliced,
data_normal[start_index:end_index])
# using indexing
@@ -136,16 +136,16 @@ def test_indexing_slicing():
data = epochs2_sliced[pos].get_data()
assert_array_equal(data[0], data_normal[idx])
pos += 1
-
+
# using indexing with an int
data = epochs2[data_epochs2_sliced.shape[0]].get_data()
assert_array_equal(data, data_normal[[idx]])
-
+
# using indexing with an array
idx = np.random.randint(0, data_epochs2_sliced.shape[0], 10)
data = epochs2[idx].get_data()
assert_array_equal(data, data_normal[idx])
-
+
# using indexing with a list of indices
idx = [0]
data = epochs2[idx].get_data()
diff --git a/mne/tests/test_misc.py b/mne/tests/test_misc.py
index d639026..0c1008b 100644
--- a/mne/tests/test_misc.py
+++ b/mne/tests/test_misc.py
@@ -6,6 +6,7 @@ from mne.misc import parse_config
ave_fname = op.join(op.dirname(__file__), '..', 'fiff', 'tests', 'data',
'test.ave')
+
def test_parse_ave():
"""Test parsing of .ave file
"""
diff --git a/mne/tests/test_selection.py b/mne/tests/test_selection.py
index 725f2a3..4272ed0 100644
--- a/mne/tests/test_selection.py
+++ b/mne/tests/test_selection.py
@@ -25,4 +25,3 @@ def test_read_selection():
frontal = read_selection('frontal')
occipital = read_selection('Right-occipital')
assert(len(set(frontal).intersection(set(occipital))) == 0)
-
diff --git a/mne/tests/test_utils.py b/mne/tests/test_utils.py
index 6a7cac6..6606d28 100644
--- a/mne/tests/test_utils.py
+++ b/mne/tests/test_utils.py
@@ -3,6 +3,7 @@ from numpy.testing import assert_equal
from mne.utils import _firwin2 as mne_firwin2
+
def test_firwin2():
"""Test firwin2 backport
"""
diff --git a/mne/time_frequency/tests/test_psd.py b/mne/time_frequency/tests/test_psd.py
index b9b8981..9520b4f 100644
--- a/mne/time_frequency/tests/test_psd.py
+++ b/mne/time_frequency/tests/test_psd.py
@@ -3,19 +3,20 @@ import os.path as op
from numpy.testing import assert_array_almost_equal
from nose.tools import assert_true
-from mne import fiff, Epochs, read_events
+from mne import fiff
from mne.time_frequency import compute_raw_psd
raw_fname = op.join(op.dirname(__file__), '..', '..', 'fiff', 'tests', 'data',
'test_raw.fif')
+
def test_psd():
"""Test PSD estimation
"""
raw = fiff.Raw(raw_fname)
- exclude = raw.info['bads'] + ['MEG 2443', 'EEG 053'] # bads + 2 more
+ exclude = raw.info['bads'] + ['MEG 2443', 'EEG 053'] # bads + 2 more
# picks MEG gradiometers
picks = fiff.pick_types(raw.info, meg='mag', eeg=False,
@@ -25,7 +26,7 @@ def test_psd():
tmin, tmax = 0, 10 # use the first 60s of data
fmin, fmax = 2, 70 # look at frequencies between 5 and 70Hz
- NFFT = 124 # the FFT size (NFFT). Ideally a power of 2
+ NFFT = 124 # the FFT size (NFFT). Ideally a power of 2
psds, freqs = compute_raw_psd(raw, tmin=tmin, tmax=tmax, picks=picks,
fmin=fmin, fmax=fmax, NFFT=NFFT, n_jobs=1,
proj=False)
diff --git a/mne/time_frequency/tfr.py b/mne/time_frequency/tfr.py
index a0c431e..8b33534 100644
--- a/mne/time_frequency/tfr.py
+++ b/mne/time_frequency/tfr.py
@@ -142,8 +142,8 @@ def _cwt_convolve(X, Ws, mode='same'):
for i, W in enumerate(Ws):
ret = np.convolve(x, W, mode=mode)
if len(W) > len(x):
- raise ValueError('Wavelet is too long for such a short signal. '
- 'Reduce the number of cycles.')
+ raise ValueError('Wavelet is too long for such a short '
+ 'signal. Reduce the number of cycles.')
if mode == "valid":
sz = abs(W.size - n_times) + 1
offset = (n_times - sz) / 2
diff --git a/mne/utils.py b/mne/utils.py
index 187de8e..ec62e83 100644
--- a/mne/utils.py
+++ b/mne/utils.py
@@ -193,7 +193,7 @@ def _firwin2(numtaps, freq, gain, nfreqs=None, window='hamming', nyq=1.0):
if nfreqs is not None and numtaps >= nfreqs:
raise ValueError('ntaps must be less than nfreqs, but firwin2 was '
- 'called with ntaps=%d and nfreqs=%s' % (numtaps, nfreqs))
+ 'called with ntaps=%d and nfreqs=%s' % (numtaps, nfreqs))
if freq[0] != 0 or freq[-1] != nyq:
raise ValueError('freq must start with 0 and end with `nyq`.')
@@ -209,14 +209,14 @@ def _firwin2(numtaps, freq, gain, nfreqs=None, window='hamming', nyq=1.0):
"have zero gain at the Nyquist rate.")
if nfreqs is None:
- nfreqs = 1 + 2 ** int(ceil(log(numtaps,2)))
+ nfreqs = 1 + 2 ** int(ceil(log(numtaps, 2)))
# Tweak any repeated values in freq so that interp works.
eps = np.finfo(float).eps
for k in range(len(freq)):
- if k < len(freq)-1 and freq[k] == freq[k+1]:
+ if k < len(freq) - 1 and freq[k] == freq[k + 1]:
freq[k] = freq[k] - eps
- freq[k+1] = freq[k+1] + eps
+ freq[k + 1] = freq[k + 1] + eps
# Linearly interpolate the desired response on a uniform mesh `x`.
x = np.linspace(0.0, nyq, nfreqs)
@@ -224,7 +224,7 @@ def _firwin2(numtaps, freq, gain, nfreqs=None, window='hamming', nyq=1.0):
# Adjust the phases of the coefficients so that the first `ntaps` of the
# inverse FFT are the desired filter coefficients.
- shift = np.exp(-(numtaps-1)/2. * 1.j * np.pi * x / nyq)
+ shift = np.exp(-(numtaps - 1) / 2. * 1.j * np.pi * x / nyq)
fx2 = fx * shift
# Use irfft to compute the inverse FFT.
--
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