def rereference(raw, ref_new, ref_old=None):
"""
Reference to new channels. raw object is modified in-place for efficiency.
raw: mne.io.RawArray
ref_new: None | list of str (RawArray) | list of int (numpy array)
Channel(s) to re-reference, e.g. M1, M2.
Average of these channel values are substracted from all channel values.
ref_old: None | str
Channel to recover, assuming this channel was originally used as a reference.
"""
# Re-reference and recover the original reference channel values if possible
if type(raw) == np.ndarray:
if raw_ch_old is not None:
logger.error('Recovering original reference channel is not yet supported for numpy arrays.')
raise NotImplementedError
if type(raw_ch_new[0]) is not int:
logger.error('Channels must be integer values for numpy arrays')
raise ValueError
raw -= np.mean(raw[ref_new], axis=0)
else:
if ref_old is not None:
# Add a blank (zero-valued) channel
mne.io.add_reference_channels(raw, ref_old, copy=False)
# Re-reference
mne.io.set_eeg_reference(raw, ref_new, copy=False)
return True
def get_decoder_info(classifier):
"""
Get the classifier information from a .pkl file.
Parameters
----------
classifier : str
The (absolute) path to the classifier file (.pkl)
Returns
-------
dict : Classifier info
"""
with open(classifier, 'rb') as f:
model = pickle.load(f)
if model is None:
logger.error('>> Error loading %s' % model)
raise ValueError
cls = model['cls']
psde = model['psde']
labels = list(cls.classes_)
w_seconds = model['w_seconds']
w_frames = model['w_frames']
wstep = model['wstep']
sfreq = model['sfreq']
psd_temp = psde.transform(np.zeros((1, len(model['picks']), w_frames)))
psd_shape = psd_temp.shape
psd_size = psd_temp.size
info = dict(labels=labels, cls=cls, psde=psde, w_seconds=w_seconds, w_frames=w_frames,\
wstep=wstep, sfreq=sfreq, psd_shape=psd_shape, psd_size=psd_size)
return info
def check_config(cfg):
"""
Ensure that the config file contains the parameters
"""
critical_vars = {
'COMMON': [
'TRIGGER_DEVICE', 'TRIGGER_FILE', 'SCREEN_SIZE', 'START_VOICE',
'END_VOICE'
],
}
optional_vars = {
'GLOBAL_TIME': 2 * 60,
'SCREEN_POS': (0, 0),
'GLASS_USE': False,
}
for key in critical_vars['COMMON']:
if not hasattr(cfg, key):
logger.error('%s is a required parameter' % key)
raise RuntimeError
for key in optional_vars:
if not hasattr(cfg, key):
setattr(cfg, key, optional_vars[key])
logger.warning('Setting undefined parameter %s=%s' %
(key, getattr(cfg, key)))
def move(self,
dir,
dx,
overlay=False,
barcolor=None,
caption='',
caption_color='W'):
if barcolor is None:
if dx == self.xl2:
c = 'G'
else:
c = 'R'
else:
c = barcolor
self.glass.fullbar_color(c)
color = self.color[c]
if dir == 'L':
if self.pc_feedback:
self.img = self.left_images[dx]
if self.glass_feedback:
self.glass.move_bar(dir, dx, overlay)
elif dir == 'R':
if self.pc_feedback:
self.img = self.right_images[dx]
if self.glass_feedback:
self.glass.move_bar(dir, dx, overlay)
else:
logger.error('Unknown direction %s' % dir)
self.put_text(caption, caption_color)
self.update()
def any2fif(filename, interactive=False, outdir=None, channel_file=None):
"""
Generic file format converter
"""
p = qc.parse_path(filename)
if outdir is not None:
qc.make_dirs(outdir)
if p.ext == 'pcl':
eve_file = '%s/%s.txt' % (p.dir, p.name.replace('raw', 'eve'))
if os.path.exists(eve_file):
logger.info('Adding events from %s' % eve_file)
else:
eve_file = None
pcl2fif(filename,
interactive=interactive,
outdir=outdir,
external_event=eve_file)
elif p.ext == 'eeg':
eeg2fif(filename, interactive=interactive, outdir=outdir)
elif p.ext in ['edf', 'bdf']:
bdf2fif(filename, interactive=interactive, outdir=outdir)
elif p.ext == 'gdf':
gdf2fif(filename,
interactive=interactive,
outdir=outdir,
channel_file=channel_file)
elif p.ext == 'xdf':
xdf2fif(filename, interactive=interactive, outdir=outdir)
else: # unknown format
logger.error(
'Ignored unrecognized file extension %s. It should be [.pcl | .eeg | .gdf | .bdf]'
% p.ext)
def _check_cfg_selected(cfg, optional_vars, select):
"""
Used in case of dict attributes containing subparams
Check that the selected cfg params is valid and that its
subparameters are defined.
Parameters
----------
cfg : python.module
The config module containing the parameters to check
optional_vars :
The optional parameters with predefined values for the param
selected = the cfg parameter (type=dict) containing a key: selected
"""
param = getattr(cfg, select)
selected = param['selected']
if selected not in param:
logger.error('%s not defined in config.' % selected)
raise RuntimeError
for v, vv in optional_vars[selected].items():
if v not in param[selected]:
param[selected].update({v: vv})
setattr(cfg, select, param)
logger.warning(
'Updating internal parameter for classifier %s: %s=%s' %
(selected, v, vv))
def get_timelags(epochs, wlen, wstep, downsample=1, picks=None):
"""
(DEPRECATED FUNCTION)
Get concatenated timelag features
TODO: Unit test.
Input
=====
epochs: input signals
wlen: window length (# time points) in downsampled data
wstep: window step in downsampled data
downsample: downsample signal to be 1/downsample length
picks: ignored for now
Output
======
X: [epochs] x [windows] x [channels*freqs]
y: [epochs] x [labels]
"""
'''
wlen = int(wlen)
wstep = int(wstep)
downsample = int(downsample)
X_data = None
y_data = None
labels = epochs.events[:, -1] # every epoch must have event id
epochs_data = epochs.get_data()
n_channels = epochs_data.shape[1]
# trim to the nearest divisible length
epoch_ds_len = int(epochs_data.shape[2] / downsample)
epoch_len = downsample * epoch_ds_len
range_epochs = np.arange(epochs_data.shape[0])
range_channels = np.arange(epochs_data.shape[1])
range_windows = np.arange(epoch_ds_len - wlen, 0, -wstep)
X_data = np.zeros((len(range_epochs), len(range_windows), wlen * n_channels))
# for each epoch
for ep in range_epochs:
epoch = epochs_data[ep, :, :epoch_len]
ds = qc.average_every_n(epoch.reshape(-1), downsample) # flatten to 1-D, then downsample
epoch_ds = ds.reshape(n_channels, -1) # recover structure to channel x samples
# for each window over all channels
for i in range(len(range_windows)):
w = range_windows[i]
X = epoch_ds[:, w:w + wlen].reshape(1, -1) # our feature vector
X_data[ep, i, :] = X
# fill labels
y = np.empty((1, len(range_windows))) # 1 x windows
y.fill(labels[ep])
if y_data is None:
y_data = y
else:
y_data = np.concatenate((y_data, y), axis=0)
return X_data, y_data
'''
logger.error('This function is deprecated.')
raise NotImplementedError
def lsl_channel_list(inlet):
"""
Reads XML description of LSL header and returns channel list
Input:
pylsl.StreamInlet object
Returns:
ch_list: [ name1, name2, ... ]
"""
if not type(inlet) is pylsl.StreamInlet:
logger.error('lsl_channel_list(): wrong input type %s' % type(inlet))
raise TypeError
root = ET.fromstring(inlet.info().as_xml())
desc = root.find('desc')
ch_list = []
for ch in desc.find('channels').getchildren():
ch_name = ch.find('label').text
ch_list.append(ch_name)
''' This code may throw access violation error due to bug in pylsl.XMLElement
# for some reason type(inlet) returns 'instance' type in Python 2.
ch = inlet.info().desc().child('channels').first_child()
ch_list = []
for k in range(inlet.info().channel_count()):
ch_name = ch.child_value('label')
ch_list.append(ch_name)
ch = ch.next_sibling()
'''
return ch_list
def get_index_max(seq):
if type(seq) == list:
return max(range(len(seq)), key=seq.__getitem__)
elif type(seq) == dict:
return max(seq, key=seq.__getitem__)
else:
logger.error('Unsupported input %s' % type(seq))
return None
def check_connect(self):
"""
Check connection and automatically connect if not connected
"""
while not self.connected:
logger.error('LSL server not connected yet. Trying to connect automatically.')
self.connect()
time.sleep(1)
def fit_predict_thres(cls,
X_train,
Y_train,
X_test,
Y_test,
cnum,
label_list,
ignore_thres=None,
decision_thres=None):
"""
Any likelihood lower than a threshold is not counted as classification score
Confusion matrix, accuracy and F1 score (macro average) are computed.
Params
======
ignore_thres:
if not None or larger than 0, likelihood values lower than ignore_thres will be ignored
while computing confusion matrix.
"""
timer = qc.Timer()
cls.fit(X_train, Y_train)
assert ignore_thres is None or ignore_thres >= 0
if ignore_thres is None or ignore_thres == 0:
Y_pred = cls.predict(X_test)
score = skmetrics.accuracy_score(Y_test, Y_pred)
cm = skmetrics.confusion_matrix(Y_test, Y_pred, label_list)
f1 = skmetrics.f1_score(Y_test, Y_pred, average='macro')
else:
if decision_thres is not None:
logger.error(
'decision threshold and ignore_thres cannot be set at the same time.'
)
raise ValueError
Y_pred = cls.predict_proba(X_test)
Y_pred_labels = np.argmax(Y_pred, axis=1)
Y_pred_maxes = np.array([x[i] for i, x in zip(Y_pred_labels, Y_pred)])
Y_index_overthres = np.where(Y_pred_maxes >= ignore_thres)[0]
Y_index_underthres = np.where(Y_pred_maxes < ignore_thres)[0]
Y_pred_overthres = np.array(
[cls.classes_[x] for x in Y_pred_labels[Y_index_overthres]])
Y_pred_underthres = np.array(
[cls.classes_[x] for x in Y_pred_labels[Y_index_underthres]])
Y_pred_underthres_count = np.array(
[np.count_nonzero(Y_pred_underthres == c) for c in label_list])
Y_test_overthres = Y_test[Y_index_overthres]
score = skmetrics.accuracy_score(Y_test_overthres, Y_pred_overthres)
cm = skmetrics.confusion_matrix(Y_test_overthres, Y_pred_overthres,
label_list)
cm = np.concatenate((cm, Y_pred_underthres_count[:, np.newaxis]),
axis=1)
f1 = skmetrics.f1_score(Y_test_overthres,
Y_pred_overthres,
average='macro')
logger.info('Cross-validation %d (%.3f) - %.1f sec' %
(cnum, score, timer.sec()))
return score, cm, f1
def run(cfg, state=mp.Value('i', 1), queue=None, logger=logger):
'''
Main function used to run the offline protocol.
Parameters
----------
cfg : python.module
The loaded config module from the corresponding config_offline.py
queue : mp.Queue
If not None, redirect sys.stdout to GUI terminal
logger : logging.logger
The logger to use
'''
# Use to redirect sys.stdout to GUI terminal if GUI usage
redirect_stdout_to_queue(logger, queue, 'INFO')
# Wait the recording to start (GUI)
while state.value == 2: # 0: stop, 1:start, 2:wait
pass
# Protocol start if equals to 1
if not state.value:
sys.exit()
# Load the mapping from int to string for triggers events
cfg.tdef = TriggerDef(cfg.TRIGGER_FILE)
# Refresh rate
refresh_delay = 1.0 / cfg.REFRESH_RATE
# Trigger
trigger = Trigger(lpttype=cfg.TRIGGER_DEVICE, state=state)
if trigger.init(50) == False:
logger.error(
'\n** Error connecting to the trigger device. Use a mock trigger instead?'
)
input('Press Ctrl+C to stop or Enter to continue.')
trigger = Trigger(lpttype='FAKE')
trigger.init(50)
# timers
timer_refresh = Timer()
trial = 1
num_trials = cfg.TRIALS_NB
# start
while trial <= num_trials:
timer_refresh.sleep_atleast(refresh_delay)
timer_refresh.reset()
#-------------------------------------
# ADD YOUR CODE HERE
#-------------------------------------
with state.get_lock():
state.value = 0
def set_pin(self, pin):
if self.lpttype == 'SOFTWARE':
logger.error('set_pin() not supported for software trigger.')
return False
elif self.lpttype == 'FAKE':
logger.info('FAKE trigger pin %s' % pin)
return True
else:
self.set_data(2**(pin - 1))
def balance_samples(X, Y, balance_type, verbose=False):
if balance_type == 'OVER':
"""
Oversample from classes that lack samples
"""
label_set = np.unique(Y)
max_set = []
X_balanced = np.array(X)
Y_balanced = np.array(Y)
# find a class with maximum number of samples
for c in label_set:
yl = np.where(Y == c)[0]
if len(max_set) == 0 or len(yl) > max_set[1]:
max_set = [c, len(yl)]
for c in label_set:
if c == max_set[0]: continue
yl = np.where(Y == c)[0]
extra_samples = max_set[1] - len(yl)
extra_idx = np.random.choice(yl, extra_samples)
X_balanced = np.append(X_balanced, X[extra_idx], axis=0)
Y_balanced = np.append(Y_balanced, Y[extra_idx], axis=0)
elif balance_type == 'UNDER':
"""
Undersample from classes that are excessive
"""
label_set = np.unique(Y)
min_set = []
# find a class with minimum number of samples
for c in label_set:
yl = np.where(Y == c)[0]
if len(min_set) == 0 or len(yl) < min_set[1]:
min_set = [c, len(yl)]
yl = np.where(Y == min_set[0])[0]
X_balanced = np.array(X[yl])
Y_balanced = np.array(Y[yl])
for c in label_set:
if c == min_set[0]: continue
yl = np.where(Y == c)[0]
reduced_idx = np.random.choice(yl, min_set[1])
X_balanced = np.append(X_balanced, X[reduced_idx], axis=0)
Y_balanced = np.append(Y_balanced, Y[reduced_idx], axis=0)
elif balance_type is None or balance_type is False:
return X, Y
else:
logger.error('Unknown balancing type %s' % balance_type)
raise ValueError
logger.info_green('\nNumber of samples after %ssampling' %
balance_type.lower())
for c in label_set:
logger.info(
'%s: %d -> %d' %
(c, len(np.where(Y == c)[0]), len(np.where(Y_balanced == c)[0])))
return X_balanced, Y_balanced
def move(self,
dir,
dx,
overlay=False,
barcolor=None,
caption='',
caption_color='W'):
if not overlay:
self.draw_cue()
if barcolor is None:
if dx == self.xl2:
c = 'G'
else:
c = 'R'
else:
c = barcolor
self.glass.fullbar_color(c)
color = self.color[c]
if dir == 'L':
if self.pc_feedback:
cv2.rectangle(self.img, (self.xl1 - dx, self.yl1),
(self.xl1, self.yr1), color, -1)
if self.glass_feedback:
self.glass.move_bar(dir, dx, overlay)
elif dir == 'U':
if self.pc_feedback:
cv2.rectangle(self.img, (self.xl1, self.yl1 - dx),
(self.xr1, self.yl1), color, -1)
if self.glass_feedback:
self.glass.move_bar(dir, dx, overlay)
elif dir == 'R':
if self.pc_feedback:
cv2.rectangle(self.img, (self.xr1, self.yl1),
(self.xr1 + dx, self.yr1), color, -1)
if self.glass_feedback:
self.glass.move_bar(dir, dx, overlay)
elif dir == 'D':
if self.pc_feedback:
cv2.rectangle(self.img, (self.xl1, self.yr1),
(self.xr1, self.yr1 + dx), color, -1)
if self.glass_feedback:
self.glass.move_bar(dir, dx, overlay)
elif dir == 'B':
if self.pc_feedback:
cv2.rectangle(self.img, (self.xl1 - dx, self.yl1),
(self.xl1, self.yr1), color, -1)
cv2.rectangle(self.img, (self.xr1, self.yl1),
(self.xr1 + dx, self.yr1), color, -1)
if self.glass_feedback:
self.glass.move_bar('S', dx, overlay)
else:
logger.error('Unknown direction %s' % dir)
self.put_text(caption, caption_color)
def get_index_max(seq):
"""
Get the index of the maximum item in a list or dict
"""
if type(seq) == list:
return max(range(len(seq)), key=seq.__getitem__)
elif type(seq) == dict:
return max(seq, key=seq.__getitem__)
else:
logger.error('Unsupported input %s' % type(seq))
return None
def move(self, dir, dx, overlay=False, barcolor=None, caption='', caption_color='W'):
#if barcolor is None:
#if dx == self.xl2:
#c = 'G'
#else:
#c = 'R'
#else:
#c = barcolor
#color = self.color[c]
if dir == 'L':
if self.pc_feedback:
if barcolor is None:
color = ((dx/100) * self.color['B'][0], self.color['B'][1], self.color['B'][2])
else:
color = self.color[barcolor]
# color = ((dx/100) * self.color['B'][0], self.color['B'][1], self.color['B'][2])
# color = ((dx/100) * color[0], color[1], color[2])
cv2.circle(self.img, (self.cx, self.cy), int(self.cx/8) - int(self.outerRadiusThickness-2), color, -1)
# self.draw_fixation_cross()
if not overlay:
self.draw_cue(self.actual_cue)
elif dir == 'R':
if self.pc_feedback:
if barcolor is None:
color = (self.color['R'][0], self.color['R'][1], (dx/100) * self.color['R'][2])
else:
color = self.color[barcolor]
# color = (color[0], color[1], (dx/100) * color[2])
# color = (self.color['R'][0], self.color['R'][1], (dx/100) * self.color['R'][2])
cv2.circle(self.img, (self.cx, self.cy), int(self.cx/8) - int(self.outerRadiusThickness-2), color, -1)
# self.draw_fixation_cross()
if not overlay:
self.draw_cue(self.actual_cue)
#elif dir == 'U':
#if self.pc_feedback:tas
#color = (self.color['R'][0], self.color['R'][1], (dx/100) * self.color['R'][2])
#cv2.circle(self.img, (self.cx, self.cy), int(self.cx/8), color, -1)
#self.draw_fixation_cross()
#elif dir == 'D':
#if self.pc_feedback:
#color = (self.color['R'][0], self.color['R'][1], (dx/100) * self.color['R'][2])
#cv2.circle(self.img, (self.cx, self.cy), int(self.cx/8), color, -1)
#self.draw_fixation_cross()
else:
logger.error('Unknown direction %s' % dir)
self.put_text(caption, caption_color)
def check_cfg_mandatory(cfg, critical_vars, key_var):
"""
Check that the mandatory parameters are defined
cfg = config module containing the parameters to check
critical_vars = critival parameters needed for the protocol
key_var = key to look at in critical_vars
"""
for v in critical_vars[key_var]:
if not hasattr(cfg, v):
logger.error('%s not defined in config.' % v)
raise RuntimeError
def reset(self):
"""
Reset the classifier to its initial state.
"""
# share numpy array self.psd between processes.
# to compute the shared memory size, we need to create a temporary decoder object.
if self.fake == True:
psd_size = None
psd_shape = None
psd_ctypes = None
self.psd = None
else:
info = get_decoder_info(self.classifier)
psd_size = info['psd_size']
psd_shape = info['psd_shape'][1:] # we get only the last window
psd_ctypes = sharedctypes.RawArray('d', np.zeros(psd_size))
self.psd = np.frombuffer(psd_ctypes,
dtype=np.float64,
count=psd_size)
self.probs = mp.Array('d', [1.0 / len(self.labels)] * len(self.labels))
self.probs_smooth = mp.Array('d', [1.0 / len(self.labels)] *
len(self.labels))
self.pread = mp.Value('i', 1)
self.t_problast = mp.Value('d', 0)
self.return_psd = mp.Value('i', 0)
self.procs = []
mp.freeze_support()
if self.parallel:
logger.error(
'Parallel decoding is under a rigorous test. Please do not use it for now.'
)
raise NotImplementedError
num_strides = self.parallel['num_strides']
period = self.parallel['period']
self.running = [mp.Value('i', 0)] * num_strides
if num_strides > 1:
stride = period / num_strides
else:
stride = 0
t_start = time.time()
for i in range(num_strides):
self.procs.append(mp.Process(target=self._daemon, args=\
[self.classifier, self.probs, self.probs_smooth, self.pread, self.t_problast,\
self.running[i], self.return_psd, psd_ctypes, self.psdlock,\
dict(t_start=(t_start+i*stride), period=period), self.label]))
else:
self.running = [mp.Value('i', 0)]
self.procs = [mp.Process(target=self._daemon, args=\
[self.classifier, self.probs, self.probs_smooth, self.pread, self.t_problast,\
self.running[0], self.return_psd, psd_ctypes, self.psdlock, None, self.label])]
def make_dirs(dirname, delete=False):
"""
Recusively create directories.
if delete=true, directory will be deleted first if exists.
"""
if os.path.exists(dirname) and delete == True:
try:
shutil.rmtree(dirname)
except OSError:
logger.error(
'Directory was not completely removed. (Perhaps a Dropbox folder?). Continuing.'
)
if not os.path.exists(dirname):
os.makedirs(dirname)
def load_raw(rawfile, spfilter=None, spchannels=None, events_ext=None, multiplier=1, verbose='ERROR'):
"""
Loads data from a fif-format file.
You can convert non-fif files (.eeg, .bdf, .gdf, .pcl) to fif format.
Parameters:
rawfile: (absolute) data file path
spfilter: 'car' | 'laplacian' | None
spchannels: None | list (for CAR) | dict (for LAPLACIAN)
'car': channel indices used for CAR filtering. If None, use all channels except
the trigger channel (index 0).
'laplacian': {channel:[neighbor1, neighbor2, ...], ...}
*** Note ***
Since neurodecode puts trigger channel as index 0, data channel starts from index 1.
events_ext: Add externally recorded events.
[ [sample_index1, 0, event_value1],... ]
multiplier: Multiply all values except triggers (to convert unit).
Returns:
raw: mne.io.RawArray object. First channel (index 0) is always trigger channel.
events: mne-compatible events numpy array object (N x [frame, 0, type])
spfilter= {None | 'car' | 'laplacian'}
"""
if not os.path.exists(rawfile):
logger.error('File %s not found' % rawfile)
raise IOError
if not os.path.isfile(rawfile):
logger.error('%s is not a file' % rawfile)
raise IOError
extension = qc.parse_path(rawfile).ext
assert extension in ['fif', 'fiff'], 'only fif format is supported'
raw = mne.io.Raw(rawfile, preload=True, verbose=verbose)
if spfilter is not None or multiplier is not 1:
preprocess(raw, spatial=spfilter, spatial_ch=spchannels, multiplier=multiplier)
if events_ext is not None:
events = mne.read_events(events_ext)
else:
tch = find_event_channel(raw)
if tch is not None:
events = mne.find_events(raw, stim_channel=raw.ch_names[tch], shortest_event=1, uint_cast=True, consecutive='increasing')
# MNE's annoying hidden cockroach: first_samp
events[:, 0] -= raw.first_samp
else:
events = np.array([], dtype=np.int64)
return raw, events
def convert2mat(filename, matfile):
"""
Convert to mat using MATLAB BioSig sload().
"""
basename = '.'.join(filename.split('.')[:-1])
# extension= filename.split('.')[-1]
matfile = basename + '.mat'
if not os.path.exists(matfile):
logger.info('Converting input to mat file')
run = "[sig,header]=sload('%s'); save('%s.mat','sig','header');" % (
filename, basename)
qc.matlab(run)
if not os.path.exists(matfile):
logger.error('mat file convertion error.')
sys.exit()
def set_data(self, value):
if self.lpttype == 'SOFTWARE':
logger.error('set_data() not supported for software trigger.')
return False
elif self.lpttype == 'FAKE':
logger.info('FAKE trigger value %s' % value)
return True
else:
if self.lpttype == 'USB2LPT':
self.lpt.setdata(value)
elif self.lpttype == 'DESKTOP':
self.lpt.setdata(self.portaddr, value)
elif self.lpttype == 'ARDUINO':
self.ser.write(bytes([value]))
else:
raise RuntimeError('Wrong trigger device')
def start(self):
"""
Start the daemon
"""
if self.is_running() > 0:
msg = 'Cannot start. Daemon already running. (PID' + ', '.join(
['%d' % proc.pid for proc in self.procs]) + ')'
logger.error(msg)
return
for proc in self.procs:
proc.start()
if self.wait_init:
for running in self.running:
while running.value == 0:
time.sleep(0.001)
logger.info(self.startmsg)
def check_config(cfg):
critical_vars = {
'COMMON': [
'TRIGGER_DEVICE', 'TRIGGER_FILE', 'SCREEN_SIZE', 'DIRECTIONS',
'DIR_RANDOM', 'TRIALS_EACH'
],
'TIMINGS': [
'INIT', 'GAP', 'CUE', 'READY', 'READY_RANDOMIZE', 'DIR',
'DIR_RANDOMIZE'
]
}
optional_vars = {
'FEEDBACK_TYPE': 'BAR',
'FEEDBACK_IMAGE_PATH': None,
'SCREEN_POS': (0, 0),
'DIR_RANDOM': True,
'GLASS_USE': False,
'TRIAL_PAUSE': False,
'REFRESH_RATE': 30
}
for key in critical_vars['COMMON']:
if not hasattr(cfg, key):
raise RuntimeError('%s is a required parameter' % key)
if not hasattr(cfg, 'TIMINGS'):
logger.error('"TIMINGS" not defined in config.')
raise RuntimeError
for v in critical_vars['TIMINGS']:
if v not in cfg.TIMINGS:
logger.error('%s not defined in config.' % v)
raise RuntimeError
for key in optional_vars:
if not hasattr(cfg, key):
setattr(cfg, key, optional_vars[key])
logger.warning('Setting undefined %s=%s' % (key, optional[key]))
if getattr(cfg, 'TRIGGER_DEVICE') == None:
logger.warning(
'The trigger device is set to None! No events will be saved.')
raise RuntimeError(
'The trigger device is set to None! No events will be saved.')
def bdf2fif(filename, interactive=False, outdir=None):
"""
EDF or BioSemi BDF format
"""
# convert to mat using MATLAB (MNE's edf reader has an offset bug)
fdir, fname, fext = qc.parse_path_list(filename)
if outdir is None:
outdir = fdir
elif outdir[-1] != '/':
outdir += '/'
fiffile = outdir + fname + '.fif'
raw = mne.io.read_raw_edf(filename, preload=True)
# process event channel
if raw.info['chs'][-1]['ch_name'] != 'STI 014':
logger.error(
"The last channel (%s) doesn't seem to be an event channel. Entering debugging mode."
% raw.info['chs'][-1]['ch_name'])
pdb.set_trace()
raw.info['chs'][-1]['ch_name'] = 'TRIGGER'
events = mne.find_events(raw,
stim_channel='TRIGGER',
shortest_event=1,
uint_cast=True,
consecutive=True)
events[:, 2] -= events[:, 1] # set offset to 0
events[:, 1] = 0
# move the event channel to index 0 (for consistency)
raw._data = np.concatenate(
(raw._data[-1, :].reshape(1, -1), raw._data[:-1, :]))
raw._data[0] *= 0 # init the event channel
raw.info['chs'] = [raw.info['chs'][-1]] + raw.info['chs'][:-1]
# add events
raw.add_events(events, 'TRIGGER')
# save and close
raw.save(fiffile, verbose=False, overwrite=True, fmt='double')
logger.info('Saved to %s' % fiffile)
saveChannels2txt(outdir, ch_names)
def init(self, duration):
if self.lpttype == 'SOFTWARE':
logger.info('Ignoring delay parameter for software trigger.')
return True
elif self.lpttype == 'FAKE':
return True
else:
self.delay = duration / 1000.0
if self.lpttype in ['DESKTOP', 'USB2LPT']:
if self.lpt.init() == -1:
logger.error(
'Connecting to LPT port failed. Check the driver status.'
)
self.lpt = None
return False
self.action = False
self.offtimer = threading.Timer(self.delay, self.signal_off)
return True
def check_config(cfg):
"""
Ensure that the config file contains the parameters
"""
critical_vars = {
'COMMON': ['DATA_PATH'],
}
optional_vars = {
}
for key in critical_vars['COMMON']:
if not hasattr(cfg, key):
logger.error('%s is a required parameter' % key)
raise RuntimeError
for key in optional_vars:
if not hasattr(cfg, key):
setattr(cfg, key, optional_vars[key])
logger.warning('Setting undefined parameter %s=%s' % (key, getattr(cfg, key)))
return cfg
def print_c(msg, color=None, end='\n'):
"""
Colored print using colorama.
Fullset:
https://pypi.python.org/pypi/colorama
Fore: BLACK, RED, GREEN, YELLOW, BLUE, MAGENTA, CYAN, WHITE, RESET.
Back: BLACK, RED, GREEN, YELLOW, BLUE, MAGENTA, CYAN, WHITE, RESET.
Style: DIM, NORMAL, BRIGHT, RESET_ALL
TODO:
Make it using *args and **kwargs to support fully featured print().
"""
if color is None:
print(str(msg), end=end)
return
color = str(color)
if len(color) != 1:
raise ValueError(
'Color parameter must be a single color code, not %s' %
type(color))
if color.upper() == 'B':
c = colorama.Fore.BLUE
elif color.upper() == 'R':
c = colorama.Fore.RED
elif color.upper() == 'G':
c = colorama.Fore.GREEN
elif color.upper() == 'Y':
c = colorama.Fore.YELLOW
elif color.upper() == 'W':
c = colorama.Fore.WHITE
elif color.upper() == 'C':
c = colorama.Fore.CYAN
else:
logger.error('print_c(): Unknown color code %s' % color)
raise ValueError
print(colorama.Style.BRIGHT + c + str(msg) + colorama.Style.RESET_ALL,
end=end)
def check_config(cfg):
"""
Ensure that the config file contains the parameters
"""
critical_vars = {'COMMON': ['DATA_PATH']}
optional_vars = {
'AMP_NAME': None,
'AMP_SERIAL': None,
'GLOBAL_TIME': 1.0 * 60,
'NJOBS': 1,
}
for key in critical_vars['COMMON']:
if not hasattr(cfg, key):
logger.error('%s is a required parameter' % key)
raise RuntimeError
for key in optional_vars:
if not hasattr(cfg, key):
setattr(cfg, key, optional_vars[key])
logger.warning('Setting undefined parameter %s=%s' %
(key, getattr(cfg, key)))