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wonambi-python/wonambi | wonambi/widgets/overview.py | Overview.display_markers | def display_markers(self):
"""Mark all the markers, from the dataset.
This function should be called only when we load the dataset or when
we change the settings.
"""
for rect in self.idx_markers:
self.scene.removeItem(rect)
self.idx_markers = []
mar... | python | def display_markers(self):
"""Mark all the markers, from the dataset.
This function should be called only when we load the dataset or when
we change the settings.
"""
for rect in self.idx_markers:
self.scene.removeItem(rect)
self.idx_markers = []
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wonambi-python/wonambi | wonambi/widgets/overview.py | Overview.mark_stages | def mark_stages(self, start_time, length, stage_name):
"""Mark stages, only add the new ones.
Parameters
----------
start_time : int
start time in s of the epoch being scored.
length : int
duration in s of the epoch being scored.
stage_name : str
... | python | def mark_stages(self, start_time, length, stage_name):
"""Mark stages, only add the new ones.
Parameters
----------
start_time : int
start time in s of the epoch being scored.
length : int
duration in s of the epoch being scored.
stage_name : str
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wonambi-python/wonambi | wonambi/widgets/overview.py | Overview.mark_quality | def mark_quality(self, start_time, length, qual_name):
"""Mark signal quality, only add the new ones.
Parameters
----------
start_time : int
start time in s of the epoch being scored.
length : int
duration in s of the epoch being scored.
qual_name ... | python | def mark_quality(self, start_time, length, qual_name):
"""Mark signal quality, only add the new ones.
Parameters
----------
start_time : int
start time in s of the epoch being scored.
length : int
duration in s of the epoch being scored.
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wonambi-python/wonambi | wonambi/widgets/overview.py | Overview.mark_cycles | def mark_cycles(self, start_time, length, end=False):
"""Mark cycle bound, only add the new one.
Parameters
----------
start_time: int
start time in s of the bounding epoch
length : int
duration in s of the epoch being scored.
end: bool
... | python | def mark_cycles(self, start_time, length, end=False):
"""Mark cycle bound, only add the new one.
Parameters
----------
start_time: int
start time in s of the bounding epoch
length : int
duration in s of the epoch being scored.
end: bool
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wonambi-python/wonambi | wonambi/widgets/overview.py | Overview.mousePressEvent | def mousePressEvent(self, event):
"""Jump to window when user clicks on overview.
Parameters
----------
event : instance of QtCore.QEvent
it contains the position that was clicked.
"""
if self.scene is not None:
x_in_scene = self.mapToScene(event.... | python | def mousePressEvent(self, event):
"""Jump to window when user clicks on overview.
Parameters
----------
event : instance of QtCore.QEvent
it contains the position that was clicked.
"""
if self.scene is not None:
x_in_scene = self.mapToScene(event.... | [
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wonambi-python/wonambi | wonambi/widgets/overview.py | Overview.reset | def reset(self):
"""Reset the widget, and clear the scene."""
self.minimum = None
self.maximum = None
self.start_time = None # datetime, absolute start time
self.idx_current = None
self.idx_markers = []
self.idx_annot = []
if self.scene is not None:
... | python | def reset(self):
"""Reset the widget, and clear the scene."""
self.minimum = None
self.maximum = None
self.start_time = None # datetime, absolute start time
self.idx_current = None
self.idx_markers = []
self.idx_annot = []
if self.scene is not None:
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wonambi-python/wonambi | wonambi/viz/plot_3d.py | _prepare_colors | def _prepare_colors(color, values, limits_c, colormap, alpha, chan=None):
"""Return colors for all the channels based on various inputs.
Parameters
----------
color : tuple
3-, 4-element tuple, representing RGB and alpha, between 0 and 1
values : ndarray
array with values for each c... | python | def _prepare_colors(color, values, limits_c, colormap, alpha, chan=None):
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----------
color : tuple
3-, 4-element tuple, representing RGB and alpha, between 0 and 1
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wonambi-python/wonambi | wonambi/viz/plot_3d.py | Viz3.add_surf | def add_surf(self, surf, color=SKIN_COLOR, vertex_colors=None,
values=None, limits_c=None, colormap=COLORMAP, alpha=1,
colorbar=False):
"""Add surfaces to the visualization.
Parameters
----------
surf : instance of wonambi.attr.anat.Surf
sur... | python | def add_surf(self, surf, color=SKIN_COLOR, vertex_colors=None,
values=None, limits_c=None, colormap=COLORMAP, alpha=1,
colorbar=False):
"""Add surfaces to the visualization.
Parameters
----------
surf : instance of wonambi.attr.anat.Surf
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wonambi-python/wonambi | wonambi/viz/plot_3d.py | Viz3.add_chan | def add_chan(self, chan, color=None, values=None, limits_c=None,
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"""Add channels to visualization
Parameters
----------
chan : instance of Channels
channels to plot
color : tuple
3-, 4-... | python | def add_chan(self, chan, color=None, values=None, limits_c=None,
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"""Add channels to visualization
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chan : instance of Channels
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wonambi-python/wonambi | wonambi/trans/select.py | select | def select(data, trial=None, invert=False, **axes_to_select):
"""Define the selection of trials, using ranges or actual values.
Parameters
----------
data : instance of Data
data to select from.
trial : list of int or ndarray (dtype='i'), optional
index of trials of interest
**a... | python | def select(data, trial=None, invert=False, **axes_to_select):
"""Define the selection of trials, using ranges or actual values.
Parameters
----------
data : instance of Data
data to select from.
trial : list of int or ndarray (dtype='i'), optional
index of trials of interest
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wonambi-python/wonambi | wonambi/trans/select.py | resample | def resample(data, s_freq=None, axis='time', ftype='fir', n=None):
"""Downsample the data after applying a filter.
Parameters
----------
data : instance of Data
data to downsample
s_freq : int or float
desired sampling frequency
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"""Downsample the data after applying a filter.
Parameters
----------
data : instance of Data
data to downsample
s_freq : int or float
desired sampling frequency
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wonambi-python/wonambi | wonambi/trans/select.py | fetch | def fetch(dataset, annot, cat=(0, 0, 0, 0), evt_type=None, stage=None,
cycle=None, chan_full=None, epoch=None, epoch_dur=30,
epoch_overlap=0, epoch_step=None, reject_epoch=False,
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"""Create instance of Segments for analysis, complete with info ab... | python | def fetch(dataset, annot, cat=(0, 0, 0, 0), evt_type=None, stage=None,
cycle=None, chan_full=None, epoch=None, epoch_dur=30,
epoch_overlap=0, epoch_step=None, reject_epoch=False,
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wonambi-python/wonambi | wonambi/trans/select.py | get_times | def get_times(annot, evt_type=None, stage=None, cycle=None, chan=None,
exclude=False, buffer=0):
"""Get start and end times for selected segments of data, bundled
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wonambi-python/wonambi | wonambi/trans/select.py | _longer_than | def _longer_than(segments, min_dur):
"""Remove segments longer than min_dur."""
if min_dur <= 0.:
return segments
long_enough = []
for seg in segments:
if sum([t[1] - t[0] for t in seg['times']]) >= min_dur:
long_enough.append(seg)
return long_enough | python | def _longer_than(segments, min_dur):
"""Remove segments longer than min_dur."""
if min_dur <= 0.:
return segments
long_enough = []
for seg in segments:
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wonambi-python/wonambi | wonambi/trans/select.py | _concat | def _concat(bundles, cat=(0, 0, 0, 0)):
"""Prepare event or epoch start and end times for concatenation."""
chan = sorted(set([x['chan'] for x in bundles]))
cycle = sorted(set([x['cycle'] for x in bundles]))
stage = sorted(set([x['stage'] for x in bundles]))
evt_type = sorted(set([x['name'] for x in... | python | def _concat(bundles, cat=(0, 0, 0, 0)):
"""Prepare event or epoch start and end times for concatenation."""
chan = sorted(set([x['chan'] for x in bundles]))
cycle = sorted(set([x['cycle'] for x in bundles]))
stage = sorted(set([x['stage'] for x in bundles]))
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wonambi-python/wonambi | wonambi/trans/select.py | _divide_bundles | def _divide_bundles(bundles):
"""Take each subsegment inside a bundle and put it in its own bundle,
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divided = []
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"""Take each subsegment inside a bundle and put it in its own bundle,
copying the bundle metadata."""
divided = []
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for t in bund['times']:
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"""Divide bundles into segments of a certain duration and a certain step,
discarding any remainder."""
segments = []
for bund in bundles:
beg, end = bund['times'][0][0], bund['times'][-1][1]
if end - beg >= duration:
new_begs = a... | python | def _find_intervals(bundles, duration, step):
"""Divide bundles into segments of a certain duration and a certain step,
discarding any remainder."""
segments = []
for bund in bundles:
beg, end = bund['times'][0][0], bund['times'][-1][1]
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wonambi-python/wonambi | wonambi/trans/select.py | _create_data | def _create_data(data, active_chan, ref_chan=[], grp_name=None):
"""Create data after montage.
Parameters
----------
data : instance of ChanTime
the raw data
active_chan : list of str
the channel(s) of interest, without reference or group
ref_chan : list of str
reference... | python | def _create_data(data, active_chan, ref_chan=[], grp_name=None):
"""Create data after montage.
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----------
data : instance of ChanTime
the raw data
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the channel(s) of interest, without reference or group
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wonambi-python/wonambi | wonambi/trans/select.py | _select_channels | def _select_channels(data, channels):
"""Select channels.
Parameters
----------
data : instance of ChanTime
data with all the channels
channels : list
channels of interest
Returns
-------
instance of ChanTime
data with only channels of interest
Notes
--... | python | def _select_channels(data, channels):
"""Select channels.
Parameters
----------
data : instance of ChanTime
data with all the channels
channels : list
channels of interest
Returns
-------
instance of ChanTime
data with only channels of interest
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wonambi-python/wonambi | wonambi/widgets/creation.py | create_widgets | def create_widgets(MAIN):
"""Create all the widgets and dockwidgets. It also creates actions to
toggle views of dockwidgets in dockwidgets.
"""
""" ------ CREATE WIDGETS ------ """
MAIN.labels = Labels(MAIN)
MAIN.channels = Channels(MAIN)
MAIN.notes = Notes(MAIN)
MAIN.merge_dialog = Mer... | python | def create_widgets(MAIN):
"""Create all the widgets and dockwidgets. It also creates actions to
toggle views of dockwidgets in dockwidgets.
"""
""" ------ CREATE WIDGETS ------ """
MAIN.labels = Labels(MAIN)
MAIN.channels = Channels(MAIN)
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wonambi-python/wonambi | wonambi/widgets/creation.py | create_actions | def create_actions(MAIN):
"""Create all the possible actions."""
actions = MAIN.action # actions was already taken
""" ------ OPEN SETTINGS ------ """
actions['open_settings'] = QAction(QIcon(ICON['settings']), 'Settings',
MAIN)
actions['open_settings'].trigg... | python | def create_actions(MAIN):
"""Create all the possible actions."""
actions = MAIN.action # actions was already taken
""" ------ OPEN SETTINGS ------ """
actions['open_settings'] = QAction(QIcon(ICON['settings']), 'Settings',
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wonambi-python/wonambi | wonambi/widgets/creation.py | create_toolbar | def create_toolbar(MAIN):
"""Create the various toolbars."""
actions = MAIN.action
toolbar = MAIN.addToolBar('File Management')
toolbar.setObjectName('File Management') # for savestate
toolbar.addAction(MAIN.info.action['open_dataset'])
toolbar.addSeparator()
toolbar.addAction(MAIN.channel... | python | def create_toolbar(MAIN):
"""Create the various toolbars."""
actions = MAIN.action
toolbar = MAIN.addToolBar('File Management')
toolbar.setObjectName('File Management') # for savestate
toolbar.addAction(MAIN.info.action['open_dataset'])
toolbar.addSeparator()
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wonambi-python/wonambi | wonambi/widgets/analysis.py | AnalysisDialog.update_evt_types | def update_evt_types(self):
"""Update the event types list when dialog is opened."""
self.event_types = self.parent.notes.annot.event_types
self.idx_evt_type.clear()
self.frequency['norm_evt_type'].clear()
for ev in self.event_types:
self.idx_evt_type.addItem(ev)
... | python | def update_evt_types(self):
"""Update the event types list when dialog is opened."""
self.event_types = self.parent.notes.annot.event_types
self.idx_evt_type.clear()
self.frequency['norm_evt_type'].clear()
for ev in self.event_types:
self.idx_evt_type.addItem(ev)
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wonambi-python/wonambi | wonambi/widgets/analysis.py | AnalysisDialog.toggle_concatenate | def toggle_concatenate(self):
"""Enable and disable concatenation options."""
if not (self.chunk['epoch'].isChecked() and
self.lock_to_staging.get_value()):
for i,j in zip([self.idx_chan, self.idx_cycle, self.idx_stage,
self.idx_evt_type],
... | python | def toggle_concatenate(self):
"""Enable and disable concatenation options."""
if not (self.chunk['epoch'].isChecked() and
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for i,j in zip([self.idx_chan, self.idx_cycle, self.idx_stage,
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wonambi-python/wonambi | wonambi/widgets/analysis.py | AnalysisDialog.toggle_pac | def toggle_pac(self):
"""Enable and disable PAC options."""
if Pac is not None:
pac_on = self.pac['pac_on'].get_value()
self.pac['prep'].setEnabled(pac_on)
self.pac['box_metric'].setEnabled(pac_on)
self.pac['box_complex'].setEnabled(pac_on)
sel... | python | def toggle_pac(self):
"""Enable and disable PAC options."""
if Pac is not None:
pac_on = self.pac['pac_on'].get_value()
self.pac['prep'].setEnabled(pac_on)
self.pac['box_metric'].setEnabled(pac_on)
self.pac['box_complex'].setEnabled(pac_on)
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wonambi-python/wonambi | wonambi/widgets/analysis.py | AnalysisDialog.update_nseg | def update_nseg(self):
"""Update the number of segments, displayed in the dialog."""
self.nseg = 0
if self.one_grp:
segments = self.get_segments()
if segments is not None:
self.nseg = len(segments)
self.show_nseg.setText('Number of segment... | python | def update_nseg(self):
"""Update the number of segments, displayed in the dialog."""
self.nseg = 0
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self.nseg = len(segments)
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wonambi-python/wonambi | wonambi/widgets/analysis.py | AnalysisDialog.check_all_local | def check_all_local(self):
"""Check or uncheck all local event parameters."""
all_local_chk = self.event['global']['all_local'].isChecked()
for buttons in self.event['local'].values():
buttons[0].setChecked(all_local_chk)
buttons[1].setEnabled(buttons[0].isChecked()) | python | def check_all_local(self):
"""Check or uncheck all local event parameters."""
all_local_chk = self.event['global']['all_local'].isChecked()
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wonambi-python/wonambi | wonambi/widgets/analysis.py | AnalysisDialog.check_all_local_prep | def check_all_local_prep(self):
"""Check or uncheck all enabled event pre-processing."""
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"""Check or uncheck all enabled event pre-processing."""
all_local_pp_chk = self.event['global']['all_local_prep'].isChecked()
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wonambi-python/wonambi | wonambi/widgets/analysis.py | AnalysisDialog.uncheck_all_local | def uncheck_all_local(self):
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self.event['global']['all_local'].setChecked(False)
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"""Uncheck 'all local' box when a local event is unchecked."""
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wonambi-python/wonambi | wonambi/widgets/analysis.py | AnalysisDialog.get_segments | def get_segments(self):
"""Get segments for analysis. Creates instance of trans.Segments."""
# Chunking
chunk = {k: v.isChecked() for k, v in self.chunk.items()}
lock_to_staging = self.lock_to_staging.get_value()
epoch_dur = self.epoch_param['dur'].get_value()
epoch_overl... | python | def get_segments(self):
"""Get segments for analysis. Creates instance of trans.Segments."""
# Chunking
chunk = {k: v.isChecked() for k, v in self.chunk.items()}
lock_to_staging = self.lock_to_staging.get_value()
epoch_dur = self.epoch_param['dur'].get_value()
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wonambi-python/wonambi | wonambi/widgets/analysis.py | AnalysisDialog.transform_data | def transform_data(self, data):
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---------
data : instance of Segments
segments including 'data' (ChanTime)
Returns
-------
instance of Segments
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"""Apply pre-processing transformation to data, and add it to data
dict.
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data : instance of Segments
segments including 'data' (ChanTime)
Returns
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instance of Segments
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"""Dialog for getting name, location of data export file."""
filename = splitext(
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filename, _ = QFileDialog.getSaveFileName(self, 'Export analysis data',
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wonambi-python/wonambi | wonambi/widgets/analysis.py | AnalysisDialog.plot_freq | def plot_freq(self, x, y, title='', ylabel=None, scale='semilogy'):
"""Plot mean frequency spectrum and display in dialog.
Parameters
----------
x : list
vector with frequencies
y : ndarray
vector with amplitudes
title : str
plot title... | python | def plot_freq(self, x, y, title='', ylabel=None, scale='semilogy'):
"""Plot mean frequency spectrum and display in dialog.
Parameters
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x : list
vector with frequencies
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vector with amplitudes
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wonambi-python/wonambi | wonambi/widgets/analysis.py | AnalysisDialog.export_pac | def export_pac(self, xpac, fpha, famp, desc):
"""Write PAC analysis data to CSV."""
filename = splitext(self.filename)[0] + '_pac.csv'
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... | python | def export_pac(self, xpac, fpha, famp, desc):
"""Write PAC analysis data to CSV."""
filename = splitext(self.filename)[0] + '_pac.csv'
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wonambi-python/wonambi | wonambi/widgets/analysis.py | AnalysisDialog.compute_evt_params | def compute_evt_params(self):
"""Compute event parameters."""
ev = self.event
glob = {k: v.get_value() for k, v in ev['global'].items()}
params = {k: v[0].get_value() for k, v in ev['local'].items()}
prep = {k: v[1].get_value() for k, v in ev['local'].items()}
slopes = {k... | python | def compute_evt_params(self):
"""Compute event parameters."""
ev = self.event
glob = {k: v.get_value() for k, v in ev['global'].items()}
params = {k: v[0].get_value() for k, v in ev['local'].items()}
prep = {k: v[1].get_value() for k, v in ev['local'].items()}
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wonambi-python/wonambi | wonambi/widgets/analysis.py | AnalysisDialog.make_title | def make_title(self, chan, cycle, stage, evt_type):
"""Make a title for plots, etc."""
cyc_str = None
if cycle is not None:
cyc_str = [str(c[2]) for c in cycle]
cyc_str[0] = 'cycle ' + cyc_str[0]
title = [' + '.join([str(x) for x in y]) for y in [chan, cyc_str,
... | python | def make_title(self, chan, cycle, stage, evt_type):
"""Make a title for plots, etc."""
cyc_str = None
if cycle is not None:
cyc_str = [str(c[2]) for c in cycle]
cyc_str[0] = 'cycle ' + cyc_str[0]
title = [' + '.join([str(x) for x in y]) for y in [chan, cyc_str,
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wonambi-python/wonambi | wonambi/widgets/analysis.py | PlotCanvas.plot | def plot(self, x, y, title, ylabel, scale='semilogy', idx_lim=(1, -1)):
"""Plot the data.
Parameters
----------
x : ndarray
vector with frequencies
y : ndarray
vector with amplitudes
title : str
title of the plot, to appear above it
... | python | def plot(self, x, y, title, ylabel, scale='semilogy', idx_lim=(1, -1)):
"""Plot the data.
Parameters
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x : ndarray
vector with frequencies
y : ndarray
vector with amplitudes
title : str
title of the plot, to appear above it
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wonambi-python/wonambi | wonambi/widgets/analysis.py | PlotDialog.create_dialog | def create_dialog(self):
"""Create the basic dialog."""
self.bbox = QDialogButtonBox(QDialogButtonBox.Close)
self.idx_close = self.bbox.button(QDialogButtonBox.Close)
self.idx_close.pressed.connect(self.reject)
btnlayout = QHBoxLayout()
btnlayout.addStretch(1)
bt... | python | def create_dialog(self):
"""Create the basic dialog."""
self.bbox = QDialogButtonBox(QDialogButtonBox.Close)
self.idx_close = self.bbox.button(QDialogButtonBox.Close)
self.idx_close.pressed.connect(self.reject)
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wonambi-python/wonambi | wonambi/detect/arousal.py | make_arousals | def make_arousals(events, time, s_freq):
"""Create dict for each arousal, based on events of time points.
Parameters
----------
events : ndarray (dtype='int')
N x 5 matrix with start, end samples
data : ndarray (dtype='float')
vector with the data
time : ndarray (dtype='float')
... | python | def make_arousals(events, time, s_freq):
"""Create dict for each arousal, based on events of time points.
Parameters
----------
events : ndarray (dtype='int')
N x 5 matrix with start, end samples
data : ndarray (dtype='float')
vector with the data
time : ndarray (dtype='float')
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wonambi-python/wonambi | wonambi/dataset.py | _convert_time_to_sample | def _convert_time_to_sample(abs_time, dataset):
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Parameters
----------
abs_time : dat
if it's int or float, it's assumed it's s;
if it's timedelta, it's assumed from the start of the recording;
if it's datetime, it's assumed it's absolute ti... | python | def _convert_time_to_sample(abs_time, dataset):
"""Convert absolute time into samples.
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wonambi-python/wonambi | wonambi/dataset.py | detect_format | def detect_format(filename):
"""Detect file format.
Parameters
----------
filename : str or Path
name of the filename or directory.
Returns
-------
class used to read the data.
"""
filename = Path(filename)
if filename.is_dir():
if list(filename.glob('*.stc')) ... | python | def detect_format(filename):
"""Detect file format.
Parameters
----------
filename : str or Path
name of the filename or directory.
Returns
-------
class used to read the data.
"""
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wonambi-python/wonambi | wonambi/dataset.py | Dataset.read_videos | def read_videos(self, begtime=None, endtime=None):
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Parameters
----------
begtime : int or datedelta or datetime or list
start of the data to read;
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wonambi-python/wonambi | wonambi/dataset.py | Dataset.read_data | def read_data(self, chan=None, begtime=None, endtime=None, begsam=None,
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Parameters
----------
chan : list of strings
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wonambi-python/wonambi | wonambi/ioeeg/moberg.py | _read_dat | def _read_dat(x):
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x : bytes
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numpy vector
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x : bytes
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wonambi-python/wonambi | wonambi/ioeeg/egimff.py | _read_chan_name | def _read_chan_name(orig):
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Parameters
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orig : dict
contains the converted xml information
Returns
-------
list of str
list of channel names
ndarray
vector to indicate to which signal a channel belo... | python | def _read_chan_name(orig):
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wonambi-python/wonambi | wonambi/ioeeg/wonambi.py | write_wonambi | def write_wonambi(data, filename, subj_id='', dtype='float64'):
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Parameters
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data : instance of ChanTime
data with only one trial
filename : path to file
file to export to (the extensions .won and .dat will be added)
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"""Write file in simple Wonambi format.
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filename : path to file
file to export to (the extensions .won and .dat will be added)
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wonambi-python/wonambi | wonambi/attr/anat.py | _read_geometry | def _read_geometry(surf_file):
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surf_file : str
path to surface file
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coords : numpy.ndarray
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faces : numpy.ndarray
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"""Read a triangular format Freesurfer surface mesh.
Parameters
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surf_file : str
path to surface file
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wonambi-python/wonambi | wonambi/attr/anat.py | import_freesurfer_LUT | def import_freesurfer_LUT(fs_lut=None):
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It's necessary that Freesurfer is installed and that the environmental
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Parameters
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fs_lut : str or Path
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wonambi-python/wonambi | wonambi/attr/anat.py | Freesurfer.find_brain_region | def find_brain_region(self, abs_pos, parc_type='aparc', max_approx=None,
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"""Find the name of the brain region in which an electrode is located.
Parameters
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abs_pos : numpy.ndarray
3x0 vector with the position of inte... | python | def find_brain_region(self, abs_pos, parc_type='aparc', max_approx=None,
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wonambi-python/wonambi | wonambi/attr/anat.py | Freesurfer.read_seg | def read_seg(self, parc_type='aparc'):
"""Read the MRI segmentation.
Parameters
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parc_type : str
'aparc' or 'aparc.a2009s'
Returns
-------
numpy.ndarray
3d matrix with values
numpy.ndarray
4x4 affine matrix
... | python | def read_seg(self, parc_type='aparc'):
"""Read the MRI segmentation.
Parameters
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parc_type : str
'aparc' or 'aparc.a2009s'
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numpy.ndarray
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wonambi-python/wonambi | wonambi/trans/merge.py | concatenate | def concatenate(data, axis):
"""Concatenate multiple trials into one trials, according to any dimension.
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----------
data : instance of DataTime, DataFreq, or DataTimeFreq
axis : str
axis that you want to concatenate (it can be 'trial')
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-------
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data : instance of DataTime, DataFreq, or DataTimeFreq
axis : str
axis that you want to concatenate (it can be 'trial')
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wonambi-python/wonambi | wonambi/ioeeg/lyonrri.py | LyonRRI.return_rri | def return_rri(self, begsam, endsam):
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... | python | def return_rri(self, begsam, endsam):
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interval = endsam - begsam
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wonambi-python/wonambi | wonambi/widgets/labels.py | Labels.update | def update(self, checked=False, labels=None, custom_labels=None):
"""Use this function when we make changes to the list of labels or when
we load a new dataset.
Parameters
----------
checked : bool
argument from clicked.connect
labels : list of str
... | python | def update(self, checked=False, labels=None, custom_labels=None):
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wonambi-python/wonambi | wonambi/trans/peaks.py | peaks | def peaks(data, method='max', axis='time', limits=None):
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----------
method : str, optional
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axis : str, optional
the axis where you want to detect the peaks
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wonambi-python/wonambi | wonambi/trans/analyze.py | export_freq | def export_freq(xfreq, filename, desc=None):
"""Write frequency analysis data to CSV.
Parameters
----------
xfreq : list of dict
spectral data, one dict per segment, where 'data' is ChanFreq
filename : str
output filename
desc : dict of ndarray
descriptives
'"""
... | python | def export_freq(xfreq, filename, desc=None):
"""Write frequency analysis data to CSV.
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wonambi-python/wonambi | wonambi/trans/analyze.py | export_freq_band | def export_freq_band(xfreq, bands, filename):
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wonambi-python/wonambi | wonambi/attr/annotations.py | create_empty_annotations | def create_empty_annotations(xml_file, dataset):
"""Create an empty annotation file.
Notes
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"""
xml_file = Path(xml_file)
root = Element('annotations')
root.set('version', VERSION)
info = SubElement(root, 'dataset')
x = SubElement(info, 'f... | python | def create_empty_annotations(xml_file, dataset):
"""Create an empty annotation file.
Notes
-----
Dates are made time-zone unaware.
"""
xml_file = Path(xml_file)
root = Element('annotations')
root.set('version', VERSION)
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wonambi-python/wonambi | wonambi/attr/annotations.py | create_annotation | def create_annotation(xml_file, from_fasst):
"""Create annotations by importing from FASST sleep scoring file.
Parameters
----------
xml_file : path to xml file
annotation file that will be created
from_fasst : path to FASST file
.mat file containing the scores
Returns
----... | python | def create_annotation(xml_file, from_fasst):
"""Create annotations by importing from FASST sleep scoring file.
Parameters
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xml_file : path to xml file
annotation file that will be created
from_fasst : path to FASST file
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xml_file : path to xml file
annotation file that will be created
from_fasst : path to FASST file
.mat file containing the scores
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instance of Annotations
TODO
----
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wonambi-python/wonambi | wonambi/attr/annotations.py | update_annotation_version | def update_annotation_version(xml_file):
"""Update the fields that have changed over different versions.
Parameters
----------
xml_file : path to file
xml file with the sleep scoring
Notes
-----
new in version 4: use 'marker_name' instead of simply 'name' etc
new in version 5:... | python | def update_annotation_version(xml_file):
"""Update the fields that have changed over different versions.
Parameters
----------
xml_file : path to file
xml file with the sleep scoring
Notes
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new in version 4: use 'marker_name' instead of simply 'name' etc
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.load | def load(self):
"""Load xml from file."""
lg.info('Loading ' + str(self.xml_file))
update_annotation_version(self.xml_file)
xml = parse(self.xml_file)
return xml.getroot() | python | def load(self):
"""Load xml from file."""
lg.info('Loading ' + str(self.xml_file))
update_annotation_version(self.xml_file)
xml = parse(self.xml_file)
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.save | def save(self):
"""Save xml to file."""
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"""Save xml to file."""
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self.rater.set('modified', datetime.now().isoformat())
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.add_bookmark | def add_bookmark(self, name, time, chan=''):
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----------
name : str
name of the bookmark
time : (float, float)
float with start and end time in s
Raises
------
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Parameters
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name : str
name of the bookmark
time : (float, float)
float with start and end time in s
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.remove_bookmark | def remove_bookmark(self, name=None, time=None, chan=None):
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bookmarks = self.rater.find('bookmarks')
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bookmark_name = m.find('bookmark_name').text
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"""if you call it without arguments, it removes ALL the bookmarks."""
bookmarks = self.rater.find('bookmarks')
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bookmark_name = m.find('bookmark_name').text
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.remove_event_type | def remove_event_type(self, name):
"""Remove event type based on name."""
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lg.info('Event type ' + name + ' was not found.')
events = self.rater.find('events')
# list is necessary so that it does not remove in place
for e in list(eve... | python | def remove_event_type(self, name):
"""Remove event type based on name."""
if name not in self.event_types:
lg.info('Event type ' + name + ' was not found.')
events = self.rater.find('events')
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.remove_event | def remove_event(self, name=None, time=None, chan=None):
"""get events inside window."""
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pattern = "event_type[@type='" + name + "']"
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pattern = "event_type"
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if ... | python | def remove_event(self, name=None, time=None, chan=None):
"""get events inside window."""
events = self.rater.find('events')
if name is not None:
pattern = "event_type[@type='" + name + "']"
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.epochs | def epochs(self):
"""Get epochs as generator
Returns
-------
list of dict
each epoch is defined by start_time and end_time (in s in reference
to the start of the recordings) and a string of the sleep stage,
and a string of the signal quality.
... | python | def epochs(self):
"""Get epochs as generator
Returns
-------
list of dict
each epoch is defined by start_time and end_time (in s in reference
to the start of the recordings) and a string of the sleep stage,
and a string of the signal quality.
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.get_stage_for_epoch | def get_stage_for_epoch(self, epoch_start, window_length=None,
attr='stage'):
"""Return stage for one specific epoch.
Parameters
----------
id_epoch : str
index of the epoch
attr : str, optional
'stage' or 'quality'
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----------
id_epoch : str
index of the epoch
attr : str, optional
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.set_stage_for_epoch | def set_stage_for_epoch(self, epoch_start, name, attr='stage', save=True):
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Parameters
----------
epoch_start : int
start time of the epoch, in seconds
name : str
description of the stage or qualifier.
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Parameters
----------
epoch_start : int
start time of the epoch, in seconds
name : str
description of the stage or qualifier.
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.set_cycle_mrkr | def set_cycle_mrkr(self, epoch_start, end=False):
"""Mark epoch start as cycle start or end.
Parameters
----------
epoch_start: int
start time of the epoch, in seconds
end : bool
If True, marked as cycle end; otherwise, marks cycle start
"""
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"""Mark epoch start as cycle start or end.
Parameters
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epoch_start: int
start time of the epoch, in seconds
end : bool
If True, marked as cycle end; otherwise, marks cycle start
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.remove_cycle_mrkr | def remove_cycle_mrkr(self, epoch_start):
"""Remove cycle marker at epoch_start.
Parameters
----------
epoch_start: int
start time of epoch, in seconds
"""
if self.rater is None:
raise IndexError('You need to have at least one rater')
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"""Remove cycle marker at epoch_start.
Parameters
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epoch_start: int
start time of epoch, in seconds
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.clear_cycles | def clear_cycles(self):
"""Remove all cycle markers in current rater."""
if self.rater is None:
raise IndexError('You need to have at least one rater')
cycles = self.rater.find('cycles')
for cyc in list(cycles):
cycles.remove(cyc)
self.save() | python | def clear_cycles(self):
"""Remove all cycle markers in current rater."""
if self.rater is None:
raise IndexError('You need to have at least one rater')
cycles = self.rater.find('cycles')
for cyc in list(cycles):
cycles.remove(cyc)
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.get_cycles | def get_cycles(self):
"""Return the cycle start and end times.
Returns
-------
list of tuple of float
start and end times for each cycle, in seconds from recording start
and the cycle index starting at 1
"""
cycles = self.rater.find('cycles')
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"""Return the cycle start and end times.
Returns
-------
list of tuple of float
start and end times for each cycle, in seconds from recording start
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"""
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.switch | def switch(self, time=None):
"""Obtain switch parameter, ie number of times the stage shifts."""
stag_to_int = {'NREM1': 1, 'NREM2': 2, 'NREM3': 3, 'REM': 5, 'Wake': 0}
hypno = [stag_to_int[x['stage']] for x in self.get_epochs(time=time) \
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... | python | def switch(self, time=None):
"""Obtain switch parameter, ie number of times the stage shifts."""
stag_to_int = {'NREM1': 1, 'NREM2': 2, 'NREM3': 3, 'REM': 5, 'Wake': 0}
hypno = [stag_to_int[x['stage']] for x in self.get_epochs(time=time) \
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.slp_frag | def slp_frag(self, time=None):
"""Obtain sleep fragmentation parameter, ie number of stage shifts to
a lighter stage."""
epochs = self.get_epochs(time=time)
stage_int = {'Wake': 0, 'NREM1': 1, 'NREM2': 2, 'NREM3': 3, 'REM': 2}
hypno_str = [x['stage'] for x in epochs \
... | python | def slp_frag(self, time=None):
"""Obtain sleep fragmentation parameter, ie number of stage shifts to
a lighter stage."""
epochs = self.get_epochs(time=time)
stage_int = {'Wake': 0, 'NREM1': 1, 'NREM2': 2, 'NREM3': 3, 'REM': 2}
hypno_str = [x['stage'] for x in epochs \
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wonambi-python/wonambi | wonambi/attr/annotations.py | Annotations.export | def export(self, file_to_export, xformat='csv'):
"""Export epochwise annotations to csv file.
Parameters
----------
file_to_export : path to file
file to write to
"""
if 'csv' == xformat:
with open(file_to_export, 'w', newline='') as f:
... | python | def export(self, file_to_export, xformat='csv'):
"""Export epochwise annotations to csv file.
Parameters
----------
file_to_export : path to file
file to write to
"""
if 'csv' == xformat:
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wonambi-python/wonambi | wonambi/widgets/info.py | Info.create | def create(self):
"""Create the widget layout with all the information."""
b0 = QGroupBox('Dataset')
form = QFormLayout()
b0.setLayout(form)
open_rec = QPushButton('Open Dataset...')
open_rec.clicked.connect(self.open_dataset)
open_rec.setToolTip('Click here to o... | python | def create(self):
"""Create the widget layout with all the information."""
b0 = QGroupBox('Dataset')
form = QFormLayout()
b0.setLayout(form)
open_rec = QPushButton('Open Dataset...')
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wonambi-python/wonambi | wonambi/widgets/info.py | Info.open_dataset | def open_dataset(self, recent=None, debug_filename=None, bids=False):
"""Open a new dataset.
Parameters
----------
recent : path to file
one of the recent datasets to read
"""
if recent:
filename = recent
elif debug_filename is not None:
... | python | def open_dataset(self, recent=None, debug_filename=None, bids=False):
"""Open a new dataset.
Parameters
----------
recent : path to file
one of the recent datasets to read
"""
if recent:
filename = recent
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wonambi-python/wonambi | wonambi/widgets/info.py | Info.display_dataset | def display_dataset(self):
"""Update the widget with information about the dataset."""
header = self.dataset.header
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short_filename = short_strings(basename(self.filename))
self.idx_filename.setText(short_filename)
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"""Update the widget with information about the dataset."""
header = self.dataset.header
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short_filename = short_strings(basename(self.filename))
self.idx_filename.setText(short_filename)
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wonambi-python/wonambi | wonambi/widgets/info.py | Info.display_view | def display_view(self):
"""Update information about the size of the traces."""
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"""Update information about the size of the traces."""
self.idx_start.setText(str(self.parent.value('window_start')))
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wonambi-python/wonambi | wonambi/widgets/info.py | Info.reset | def reset(self):
"""Reset widget to original state."""
self.filename = None
self.dataset = None
# about the recordings
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self.idx_s_freq.setText('')
self.idx_n_chan.setText('')
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"""Reset widget to original state."""
self.filename = None
self.dataset = None
# about the recordings
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wonambi-python/wonambi | wonambi/widgets/info.py | ExportDatasetDialog.update | def update(self):
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wonambi-python/wonambi | wonambi/utils/simulate.py | create_channels | def create_channels(chan_name=None, n_chan=None):
"""Create instance of Channels with random xyz coordinates
Parameters
----------
chan_name : list of str
names of the channels
n_chan : int
if chan_name is not specified, this defines the number of channels
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-------
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"""Create instance of Channels with random xyz coordinates
Parameters
----------
chan_name : list of str
names of the channels
n_chan : int
if chan_name is not specified, this defines the number of channels
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wonambi-python/wonambi | wonambi/utils/simulate.py | _color_noise | def _color_noise(x, s_freq, coef=0):
"""Add some color to the noise by changing the power spectrum.
Parameters
----------
x : ndarray
one vector of the original signal
s_freq : int
sampling frequency
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----------
x : ndarray
one vector of the original signal
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sampling frequency
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wonambi-python/wonambi | wonambi/ioeeg/openephys.py | _read_openephys | def _read_openephys(openephys_file):
"""Read the channel labels and their respective files from the
'Continuous_Data.openephys' file
Parameters
----------
openephys_file : Path
path to Continuous_Data.openephys inside the open-ephys folder
Returns
-------
int
sampling f... | python | def _read_openephys(openephys_file):
"""Read the channel labels and their respective files from the
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openephys_file : Path
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wonambi-python/wonambi | wonambi/ioeeg/openephys.py | _read_date | def _read_date(settings_file):
"""Get the data from the settings.xml file
Parameters
----------
settings_file : Path
path to settings.xml inside open-ephys folder
Returns
-------
datetime
start time of the recordings
Notes
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"""Get the data from the settings.xml file
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settings_file : Path
path to settings.xml inside open-ephys folder
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start time of the recordings
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wonambi-python/wonambi | wonambi/ioeeg/openephys.py | _read_n_samples | def _read_n_samples(channel_file):
"""Calculate the number of samples based on the file size
Parameters
----------
channel_file : Path
path to single filename with the header
Returns
-------
int
number of blocks (i.e. records, in which the data is cut)
int
numbe... | python | def _read_n_samples(channel_file):
"""Calculate the number of samples based on the file size
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----------
channel_file : Path
path to single filename with the header
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wonambi-python/wonambi | wonambi/ioeeg/openephys.py | _read_header | def _read_header(filename):
"""Read the text header for each file
Parameters
----------
channel_file : Path
path to single filename with the header
Returns
-------
dict
header
"""
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header... | python | def _read_header(filename):
"""Read the text header for each file
Parameters
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channel_file : Path
path to single filename with the header
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dict
header
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wonambi-python/wonambi | wonambi/ioeeg/openephys.py | _check_header | def _check_header(channel_file, s_freq):
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Parameters
----------
channel_file : Path
path to single filename with the header
s_freq : int
sampling frequency
Returns
-------
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channel_file : Path
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Parameters
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channel_file : Path
path to single filename with the header
s_freq : int
sampling frequency
Returns
-------
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wonambi-python/wonambi | wonambi/detect/agreement.py | MatchedEvents.all_to_annot | def all_to_annot(self, annot, names=['TPd', 'TPs', 'FP', 'FN']):
"""Convenience function to write all events to XML by category, showing
overlapping TP detection and TP standard."""
self.to_annot(annot, 'tp_det', names[0])
self.to_annot(annot, 'tp_std', names[1])
self.to_annot(an... | python | def all_to_annot(self, annot, names=['TPd', 'TPs', 'FP', 'FN']):
"""Convenience function to write all events to XML by category, showing
overlapping TP detection and TP standard."""
self.to_annot(annot, 'tp_det', names[0])
self.to_annot(annot, 'tp_std', names[1])
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wonambi-python/wonambi | wonambi/ioeeg/ktlx.py | convert_sample_to_video_time | def convert_sample_to_video_time(sample, orig_s_freq, sampleStamp,
sampleTime):
"""Convert sample number to video time, using snc information.
Parameters
----------
sample : int
sample that you want to convert in time
orig_s_freq : int
sampling frequ... | python | def convert_sample_to_video_time(sample, orig_s_freq, sampleStamp,
sampleTime):
"""Convert sample number to video time, using snc information.
Parameters
----------
sample : int
sample that you want to convert in time
orig_s_freq : int
sampling frequ... | [
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wonambi-python/wonambi | wonambi/ioeeg/ktlx.py | _find_channels | def _find_channels(note):
"""Find the channel names within a string.
The channel names are stored in the .ent file. We can read the file with
_read_ent and we can parse most of the notes (comments) with _read_notes
however the note containing the montage cannot be read because it's too
complex. So,... | python | def _find_channels(note):
"""Find the channel names within a string.
The channel names are stored in the .ent file. We can read the file with
_read_ent and we can parse most of the notes (comments) with _read_notes
however the note containing the montage cannot be read because it's too
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wonambi-python/wonambi | wonambi/ioeeg/ktlx.py | _find_start_time | def _find_start_time(hdr, s_freq):
"""Find the start time, usually in STC, but if that's not correct, use ERD
Parameters
----------
hdr : dict
header with stc (and stamps) and erd
s_freq : int
sampling frequency
Returns
-------
datetime
either from stc or from e... | python | def _find_start_time(hdr, s_freq):
"""Find the start time, usually in STC, but if that's not correct, use ERD
Parameters
----------
hdr : dict
header with stc (and stamps) and erd
s_freq : int
sampling frequency
Returns
-------
datetime
either from stc or from e... | [
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wonambi-python/wonambi | wonambi/ioeeg/ktlx.py | _read_ent | def _read_ent(ent_file):
"""Read notes stored in .ent file.
This is a basic implementation, that relies on turning the information in
the string in the dict format, and then evaluate it. It's not very flexible
and it might not read some notes, but it's fast. I could not implement a
nice, recursive ... | python | def _read_ent(ent_file):
"""Read notes stored in .ent file.
This is a basic implementation, that relies on turning the information in
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wonambi-python/wonambi | wonambi/ioeeg/ktlx.py | _read_packet | def _read_packet(f, pos, n_smp, n_allchan, abs_delta):
"""
Read a packet of compressed data
Parameters
----------
f : instance of opened file
erd file
pos : int
index of the start of the packet in the file (in bytes from beginning
of the file)
n_smp : int
num... | python | def _read_packet(f, pos, n_smp, n_allchan, abs_delta):
"""
Read a packet of compressed data
Parameters
----------
f : instance of opened file
erd file
pos : int
index of the start of the packet in the file (in bytes from beginning
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n_smp : int
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wonambi-python/wonambi | wonambi/ioeeg/ktlx.py | _read_erd | def _read_erd(erd_file, begsam, endsam):
"""Read the raw data and return a matrix, converted to microvolts.
Parameters
----------
erd_file : str
one of the .erd files to read
begsam : int
index of the first sample to read
endsam : int
index of the last sample (excluded, ... | python | def _read_erd(erd_file, begsam, endsam):
"""Read the raw data and return a matrix, converted to microvolts.
Parameters
----------
erd_file : str
one of the .erd files to read
begsam : int
index of the first sample to read
endsam : int
index of the last sample (excluded, ... | [
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wonambi-python/wonambi | wonambi/ioeeg/ktlx.py | _read_etc | def _read_etc(etc_file):
"""Return information about table of content for each erd.
"""
etc_type = dtype([('offset', '<i'),
('samplestamp', '<i'),
('sample_num', '<i'),
('sample_span', '<h'),
('unknown', '<h')])
wit... | python | def _read_etc(etc_file):
"""Return information about table of content for each erd.
"""
etc_type = dtype([('offset', '<i'),
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('sample_num', '<i'),
('sample_span', '<h'),
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wonambi-python/wonambi | wonambi/ioeeg/ktlx.py | _read_snc | def _read_snc(snc_file):
"""Read Synchronization File and return sample stamp and time
Returns
-------
sampleStamp : list of int
Sample number from start of study
sampleTime : list of datetime.datetime
File time representation of sampleStamp
Notes
-----
The synchronizat... | python | def _read_snc(snc_file):
"""Read Synchronization File and return sample stamp and time
Returns
-------
sampleStamp : list of int
Sample number from start of study
sampleTime : list of datetime.datetime
File time representation of sampleStamp
Notes
-----
The synchronizat... | [
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wonambi-python/wonambi | wonambi/ioeeg/ktlx.py | _read_stc | def _read_stc(stc_file):
"""Read Segment Table of Contents file.
Returns
-------
hdr : dict
- next_segment : Sample frequency in Hertz
- final : Number of channels stored
- padding : Padding
stamps : ndarray of dtype
- segment_name : Name of ERD / ETC file segment
... | python | def _read_stc(stc_file):
"""Read Segment Table of Contents file.
Returns
-------
hdr : dict
- next_segment : Sample frequency in Hertz
- final : Number of channels stored
- padding : Padding
stamps : ndarray of dtype
- segment_name : Name of ERD / ETC file segment
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wonambi-python/wonambi | wonambi/ioeeg/ktlx.py | _read_vtc | def _read_vtc(vtc_file):
"""Read the VTC file.
Parameters
----------
vtc_file : str
path to vtc file
Returns
-------
mpg_file : list of str
list of avi files
start_time : list of datetime
list of start time of the avi files
end_time : list of datetime
... | python | def _read_vtc(vtc_file):
"""Read the VTC file.
Parameters
----------
vtc_file : str
path to vtc file
Returns
-------
mpg_file : list of str
list of avi files
start_time : list of datetime
list of start time of the avi files
end_time : list of datetime
... | [
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wonambi-python/wonambi | wonambi/ioeeg/ktlx.py | Ktlx._read_hdr_dir | def _read_hdr_dir(self):
"""Read the header for basic information.
Returns
-------
hdr : dict
- 'erd': header of .erd file
- 'stc': general part of .stc file
- 'stamps' : time stamp for each file
Also, it adds the attribute
_basename : Path... | python | def _read_hdr_dir(self):
"""Read the header for basic information.
Returns
-------
hdr : dict
- 'erd': header of .erd file
- 'stc': general part of .stc file
- 'stamps' : time stamp for each file
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