# solver for the d-step
solver_d='alternate_adaptive',
solver_d_kwargs={'max_iter': 300},
# Technical parameters
verbose=1,
random_state=0,
n_jobs=6)
###############################################################################
# Here, we load the data from the somato-sensory dataset and preprocess them
# in epochs. The epochs are selected around the stim, starting 2 seconds
# before and finishing 4 seconds after.
from alphacsc.datasets.somato import load_data
t_lim = (-2, 4)
X, info = load_data(epoch=t_lim, sfreq=sfreq)
###############################################################################
# Fit the model and learn rank1 atoms
cdl.fit(X)
###############################################################################
# Display the 4-th atom, which displays a :math:`\mu`-waveform in its temporal
# pattern.
import mne
import numpy as np
import matplotlib.pyplot as plt
i_atom = 4
n_plots = 3
out_iterator = itertools.product(n_times_atom_list, n_atoms_list,
n_channel_list, reg_list)
for params in out_iterator:
n_times_atom, n_atoms, n_channels, reg = params
msg = 'n_times_atom, n_atoms, n_channels, reg = ' + str(params)
print(colorify(msg, RED))
print(colorify('-' * len(msg), RED))
save_name = base_name + str(params)
save_name = os.path.join('figures', save_name)
all_results = []
X, info = load_data(epoch=False, n_jobs=n_jobs, n_trials=2)
if n_channels == 1:
X = X[:, 0, :] # take only one channel
elif n_channels is not None:
X = X[:, :n_channels, :]
assert X.shape[0] > 1 # we need at least two trials for sporco
X_shape = X.shape
if n_channels == 1:
methods = methods_univariate
else:
methods = methods_multivariate
iterator = itertools.product(methods, range(n_states))
help='run the experiment for multivariate')
parser.add_argument('--wohlberg',
action="store_true",
help='run the experiment for wohlberg')
args = parser.parse_args()
# Use the caching utilities from joblib to same intermediate results and
# avoid loosing computations when the interpreter crashes.
mem = Memory(cachedir='.', verbose=0)
cached_one_run = mem.cache(func=one_run)
delayed_one_run = delayed(cached_one_run)
# load somato data
from alphacsc.datasets.somato import load_data
X, info = load_data(epoch=False, n_jobs=args.njobs)
# Set dictionary learning parameters
n_atoms = 2 # K
n_times_atom = 128 # L
# Set the benchmarking parameters.
reg = .005
n_iter = 50
n_states = 5
# Select the method to run and the range of n_channels
n_channels = X.shape[1]
methods = [(run_multichannel, 'rank1', n_iter)]
span_channels = np.unique(
np.floor(np.logspace(0, np.log10(n_channels), 10)).astype(int))
# Plot the psd of the time atom
ax = axes[0, 2]
psd = np.abs(np.fft.rfft(v_hat))**2
frequencies = np.linspace(0, sfreq / 2.0, len(psd))
ax.semilogy(frequencies, psd)
ax.set(xlabel='Frequencies (Hz)', title='Power Spectral Density')
ax.grid(True)
ax.set_xlim(0, 30)
plt.tight_layout()
plt.show()
# Define the parameters
sfreq = 150.
X, info = load_data(epoch=True, sfreq=sfreq)
n_trials, n_channels, n_times = X.shape
# Define the shape of the dictionary
n_atoms = 25
n_times_atom = int(round(sfreq * 1.0)) # 1000. ms
# Set parameter for our dictionary learning algorithm
reg = .2
n_iter = 50
cdl = BatchCDL(n_atoms=n_atoms,
n_times_atom=n_times_atom,
reg=reg,
n_iter=n_iter,
eps=2e3,
solver_d='alternate_adaptive',
solver_d_kwargs={'max_iter': 300},
# sort atoms by explained variances
sort_atoms=True,
# Technical parameters
verbose=1,
random_state=0,
n_jobs=n_jobs)
###############################################################################
# Here, we load the data from the sample datase. The data is not epoched yet,
# but we split it into 12 parts to make the most of multiple processors during
# the model fitting.
from alphacsc.datasets.somato import load_data
X_split, info = load_data(sfreq=sfreq, dataset='sample', n_splits=2 * n_jobs)
###############################################################################
# Fit the model and learn rank1 atoms
cdl.fit(X_split)
###############################################################################
# To avoid artifacts due to the splitting, we can optionally reload the data.
X, info = load_data(sfreq=sfreq, dataset='sample', n_splits=1)
###############################################################################
# Then we call the `transform` method, which returns the sparse codes
# associated with X, without changing the dictionary learned during the `fit`.
z_hat = cdl.transform(X)
###############################################################################