def test_neoviewer():
#TODO make autorun neo tdtrawio test before
from neo.rawio.tdtrawio import TdtRawIO
dirname = '/tmp/files_for_testing_neo/tdt/aep_05/'
neorawio = TdtRawIO(dirname=dirname)
neorawio.parse_header()
print(neorawio)
sources = ephyviewer.get_sources_from_neo_rawio(neorawio)
app = ephyviewer.mkQApp()
win = ephyviewer.MainViewer(debug=True, show_auto_scale=True)
for i, sig_source in enumerate(sources['signal']):
view = ephyviewer.TraceViewer(source=sig_source, name='signal {}'.format(i))
win.add_view(view)
for i, ep_source in enumerate(sources['epoch']):
view = ephyviewer.EpochViewer(source=ep_source, name='epochs')
win.add_view(view)
win.show()
app.exec_()
def test_neoviewer(interactive=False):
#~ from neo.rawio.tdtrawio import TdtRawIO
#~ local_tdt_folder = get_tdt_test_files()
#~ neorawio = TdtRawIO(dirname=local_tdt_folder)
#~ neorawio.parse_header()
#~ print(neorawio)
from neo.rawio.blackrockrawio import BlackrockRawIO
filename = get_blackrock_files()
neorawio = BlackrockRawIO(filename=filename)
neorawio.parse_header()
print(neorawio)
sources = ephyviewer.get_sources_from_neo_rawio(neorawio)
print(sources)
app = ephyviewer.mkQApp()
win = ephyviewer.MainViewer(debug=True, show_auto_scale=True)
for i, sig_source in enumerate(sources['signal']):
view = ephyviewer.TraceViewer(source=sig_source,
name='signal {}'.format(i))
win.add_view(view)
for i, ep_source in enumerate(sources['epoch']):
view = ephyviewer.EpochViewer(source=ep_source, name='epochs')
win.add_view(view)
if interactive:
win.show()
app.exec_()
else:
# close thread properly
win.close()
def test_neoviewer(interactive=False):
from neo.rawio.tdtrawio import TdtRawIO
local_test_dir = get_tdt_test_files()
dirname = os.path.join(local_test_dir, 'aep_05')
neorawio = TdtRawIO(dirname=dirname)
neorawio.parse_header()
print(neorawio)
sources = ephyviewer.get_sources_from_neo_rawio(neorawio)
app = ephyviewer.mkQApp()
win = ephyviewer.MainViewer(debug=True, show_auto_scale=True)
for i, sig_source in enumerate(sources['signal']):
view = ephyviewer.TraceViewer(source=sig_source,
name='signal {}'.format(i))
win.add_view(view)
for i, ep_source in enumerate(sources['epoch']):
view = ephyviewer.EpochViewer(source=ep_source, name='epochs')
win.add_view(view)
if interactive:
win.show()
app.exec_()
else:
# close thread properly
win.close()
def test_mainviewer2():
from ephyviewer.tests.testing_tools import make_fake_video_source
from ephyviewer.tests.testing_tools import make_fake_signals
from ephyviewer.tests.testing_tools import make_fake_event_source
from ephyviewer.tests.testing_tools import make_fake_epoch_source
app = ephyviewer.mkQApp()
view1 = ephyviewer.TraceViewer(source=make_fake_signals(), name='signals')
view2 = ephyviewer.VideoViewer(source=make_fake_video_source(), name='video')
view3 = ephyviewer.EventList(source=make_fake_event_source(), name='events')
view4 = ephyviewer.EpochViewer(source=make_fake_epoch_source(), name='epoch')
view5 = ephyviewer.TimeFreqViewer(source=make_fake_signals(), name='timefreq')
win = ephyviewer.MainViewer(debug=True, settings_name='test1', show_global_xsize=True, show_auto_scale=True)
#TODO bug because new params!!!!!!!
#~ win = ephyviewer.MainViewer(debug=True, show_global_xsize=True)
win.add_view(view1)
win.add_view(view5)
win.add_view(view2)
win.add_view(view4)
win.add_view(view3, location='bottom', orientation='horizontal')
win.show()
app.exec_()
def test_epoch_viewer():
source = make_fake_epoch_source()
app = ephyviewer.mkQApp()
view = ephyviewer.EpochViewer(source=source, name='epoch')
win = ephyviewer.MainViewer(debug=True)
win.add_view(view)
win.show()
app.exec_()
def test_epoch_viewer(interactive=False):
source = make_fake_epoch_source()
app = ephyviewer.mkQApp()
view = ephyviewer.EpochViewer(source=source, name='epoch')
win = ephyviewer.MainViewer(debug=True)
win.add_view(view)
if interactive:
win.show()
app.exec_()
else:
# close thread properly
win.close()
from ephyviewer.tests.testing_tools import make_fake_signals from ephyviewer.tests.testing_tools import make_fake_event_source from ephyviewer.tests.testing_tools import make_fake_epoch_source sig_source = make_fake_signals() event_source = make_fake_event_source() epoch_source = make_fake_epoch_source() video_source = make_fake_video_source() app = ephyviewer.mkQApp() view1 = ephyviewer.TraceViewer(source=sig_source, name='signals') view2 = ephyviewer.VideoViewer(source=video_source, name='video') view3 = ephyviewer.EventList(source=event_source, name='events') view4 = ephyviewer.EpochViewer(source=epoch_source, name='epoch') view5 = ephyviewer.TimeFreqViewer(source=sig_source, name='timefreq') win = ephyviewer.MainViewer(debug=True, settings_name='test1', show_global_xsize=True, show_auto_scale=True) win.add_view(view1) win.add_view(view5, split_with='signals') win.add_view(view2) win.add_view(view4) win.add_view(view3, location='bottom', orientation='horizontal') win.show() win.auto_scale()
def create_ephyviewer_window(self, theme='light', support_increased_line_width=False, show_datetime=False, datetime_format='%Y-%m-%d %H:%M:%S'):
"""
Load data into each ephyviewer viewer and return the main window.
"""
########################################################################
# DATA SOURCES
seg = self.blk.segments[0]
sigs = seg.analogsignals
sources = {'signal': [], 'epoch': [], 'event': [], 'spike': []}
sources['epoch'].append(ephyviewer.NeoEpochSource(seg.epochs))
sources['event'].append(ephyviewer.NeoEventSource(seg.events))
sources['spike'].append(ephyviewer.NeoSpikeTrainSource(seg.spiketrains))
# filter epoch encoder data out of read-only epoch and event lists
# so they are not presented multiple times, and remove empty channels
sources['epoch'][0].all = [ep for ep in sources['epoch'][0].all if len(ep['time']) > 0 and '(from epoch encoder file)' not in ep['label']]
sources['event'][0].all = [ev for ev in sources['event'][0].all if len(ev['time']) > 0 and '(from epoch encoder file)' not in ev['label']]
########################################################################
# WINDOW
# optionally display the real-world date and time
if show_datetime and self.blk.rec_datetime is not None:
show_label_datetime = True
datetime0 = self.blk.rec_datetime
else:
show_label_datetime = False
datetime0 = None
# create a window that will be populated with viewers
win = ephyviewer.MainViewer(
# settings_name='test2', # remember settings (e.g. xsize) between sessions
show_auto_scale = False,
global_xsize_zoom = True,
play_interval = 0.1, # refresh period in seconds
show_label_datetime = show_label_datetime,
datetime0 = datetime0,
datetime_format = datetime_format,
)
win.setWindowTitle(self.metadata['key'])
win.setWindowIcon(ephyviewer.QT.QIcon(':/neurotic-logo-150.png'))
# delete on close so that memory and file resources are released
win.setAttribute(ephyviewer.QT.WA_DeleteOnClose, True)
########################################################################
# PREPARE TRACE PARAMETERS
_set_defaults_for_plots(self.metadata, self.blk)
plotNameToIndex = {p['channel']:i for i, p in enumerate(self.metadata['plots'])}
########################################################################
# PREPARE SCATTER PLOT PARAMETERS
if not self.lazy:
all_times = sigs[0].times.rescale('s').magnitude # assuming all AnalogSignals have the same sampling rate and start time
spike_indices = {}
spike_channels = {}
for st in seg.spiketrains:
if 'channels' in st.annotations:
c = []
for channel in st.annotations['channels']:
index = plotNameToIndex.get(channel, None)
if index is None:
print('Note: Spike train {} will not be plotted on channel {} because that channel isn\'t being plotted'.format(st.name, channel))
else:
c.append(index)
if c:
spike_channels[st.name] = c
spike_indices[st.name] = np.where(np.isin(all_times, st.times.magnitude))[0]
########################################################################
# TRACES WITH SCATTER PLOTS
if self.is_shown('traces'):
if self.lazy:
import neo
neorawioclass = neo.rawio.get_rawio_class(_abs_path(self.metadata, 'data_file'))
if neorawioclass is None:
raise ValueError('This file type cannot be read with fast loading (lazy=True): {}'.format(_abs_path(self.metadata, 'data_file')))
neorawio = neorawioclass(_abs_path(self.metadata, 'data_file'))
neorawio.parse_header()
# Intan-specific tricks
if type(neorawio) is neo.rawio.IntanRawIO:
# dirty trick for getting ungrouped channels into a single source
neorawio.header['signal_channels']['group_id'] = 0
# prepare to append custom channel names stored in data file to ylabels
custom_channel_names = {c['native_channel_name']: c['custom_channel_name'] for c in neorawio._ordered_channels}
channel_indexes = [p['index'] for p in self.metadata['plots']]
sources['signal'].append(ephyviewer.AnalogSignalFromNeoRawIOSource(neorawio, channel_indexes))
# modify loaded channel names to use ylabels
for i, p in enumerate(self.metadata['plots']):
ylabel = p['ylabel']
# Intan-specific tricks
if type(neorawio) is neo.rawio.IntanRawIO:
# append custom channel names stored in data file to ylabels
if custom_channel_names[p['channel']] != ylabel:
ylabel += ' ({})'.format(custom_channel_names[p['channel']])
sources['signal'][-1].channels['name'][i] = ylabel
# TODO support scatter
else:
sources['signal'].append(ephyviewer.AnalogSignalSourceWithScatter(
signals = np.concatenate([sigs[p['index']].magnitude for p in self.metadata['plots']], axis = 1),
sample_rate = sigs[0].sampling_rate, # assuming all AnalogSignals have the same sampling rate
t_start = sigs[0].t_start, # assuming all AnalogSignals start at the same time
channel_names = [p['ylabel'] for p in self.metadata['plots']],
scatter_indexes = spike_indices,
scatter_channels = spike_channels,
))
# useOpenGL=True eliminates the extremely poor performance associated
# with TraceViewer's line_width > 1.0, but it also degrades overall
# performance somewhat and is reportedly unstable
if support_increased_line_width:
useOpenGL = True
line_width = 2.0
else:
useOpenGL = None
line_width = 1.0
trace_view = ephyviewer.TraceViewer(source = sources['signal'][0], name = 'signals', useOpenGL = useOpenGL)
win.add_view(trace_view)
trace_view.params['scatter_size'] = 5
trace_view.params['line_width'] = line_width
trace_view.params['display_labels'] = True
trace_view.params['antialias'] = True
# set the theme
if theme != 'original':
trace_view.params['background_color'] = self.themes[theme]['background_color']
trace_view.params['vline_color'] = self.themes[theme]['vline_color']
trace_view.params['label_fill_color'] = self.themes[theme]['label_fill_color']
trace_view.params_controller.combo_cmap.setCurrentText(self.themes[theme]['cmap'])
trace_view.params_controller.on_automatic_color()
# adjust plot range, scaling, and positioning
trace_view.params['ylim_max'] = 0.5
trace_view.params['ylim_min'] = -trace_view.source.nb_channel + 0.5
trace_view.params['scale_mode'] = 'by_channel'
for i, p in enumerate(self.metadata['plots']):
sig_units = sigs[p['index']].units
units_ratio = (pq.Quantity(1, p['units'])/pq.Quantity(1, sig_units)).simplified
assert units_ratio.dimensionality.string == 'dimensionless', f"Channel \"{p['channel']}\" has units {sig_units} and cannot be converted to {p['units']}"
ylim_span = np.ptp(p['ylim'] * units_ratio.magnitude)
ylim_center = np.mean(p['ylim'] * units_ratio.magnitude)
trace_view.by_channel_params['ch{}'.format(i), 'gain'] = 1/ylim_span # rescale [ymin,ymax] across a unit
trace_view.by_channel_params['ch{}'.format(i), 'offset'] = -i - ylim_center/ylim_span # center [ymin,ymax] within the unit
########################################################################
# TRACES OF RAUC
if self.is_shown('traces_rauc') and self.rauc_sigs is not None:
sig_rauc_source = ephyviewer.InMemoryAnalogSignalSource(
signals = np.concatenate([self.rauc_sigs[p['index']].as_array() for p in self.metadata['plots']], axis = 1),
sample_rate = self.rauc_sigs[0].sampling_rate, # assuming all AnalogSignals have the same sampling rate
t_start = self.rauc_sigs[0].t_start, # assuming all AnalogSignals start at the same time
channel_names = [p['ylabel'] + ' RAUC' for p in self.metadata['plots']],
)
sources['signal_rauc'] = [sig_rauc_source]
trace_rauc_view = ephyviewer.TraceViewer(source = sources['signal_rauc'][0], name = 'signals rauc')
if 'signals' in win.viewers:
win.add_view(trace_rauc_view, tabify_with = 'signals')
else:
win.add_view(trace_rauc_view)
trace_rauc_view.params['line_width'] = line_width
trace_rauc_view.params['display_labels'] = True
trace_rauc_view.params['display_offset'] = True
trace_rauc_view.params['antialias'] = True
# set the theme
if theme != 'original':
trace_rauc_view.params['background_color'] = self.themes[theme]['background_color']
trace_rauc_view.params['vline_color'] = self.themes[theme]['vline_color']
trace_rauc_view.params['label_fill_color'] = self.themes[theme]['label_fill_color']
trace_rauc_view.params_controller.combo_cmap.setCurrentText(self.themes[theme]['cmap'])
trace_rauc_view.params_controller.on_automatic_color()
# adjust plot range
trace_rauc_view.params['ylim_max'] = 0.5
trace_rauc_view.params['ylim_min'] = -trace_rauc_view.source.nb_channel + 0.5
trace_rauc_view.params['scale_mode'] = 'by_channel'
for i, p in enumerate(self.metadata['plots']):
ylim_span = np.median(self.rauc_sigs[p['index']].magnitude) * 10
ylim_center = ylim_span / 2
trace_rauc_view.by_channel_params['ch{}'.format(i), 'gain'] = 1/ylim_span # rescale [ymin,ymax] across a unit
trace_rauc_view.by_channel_params['ch{}'.format(i), 'offset'] = -i - ylim_center/ylim_span # center [ymin,ymax] within the unit
########################################################################
# FREQUENCY (EXPERIMENTAL AND COMPUTATIONALLY EXPENSIVE!)
if self.is_shown('freqs'):
freq_view = ephyviewer.TimeFreqViewer(source = trace_view.source, name = 'timefreqs')
freq_view.params['scale_mode'] = 'by_channel'
freq_view.params['nb_column'] = 1
freq_view.params['colormap'] = 'gray'
freq_view.params.param('timefreq')['deltafreq'] = 100
freq_view.params.param('timefreq')['f_start'] = 1
freq_view.params.param('timefreq')['f_stop'] = 1500
freq_view.by_channel_params['ch0', 'visible'] = False
freq_view.by_channel_params['ch1', 'visible'] = True
freq_view.by_channel_params['ch2', 'visible'] = True
freq_view.by_channel_params['ch3', 'visible'] = True
freq_view.by_channel_params['ch4', 'visible'] = False
# freq_view.params.param('timefreq')['normalisation'] = 1.5
freq_view.by_channel_params['ch1', 'clim'] = 3
freq_view.by_channel_params['ch2', 'clim'] = 5
freq_view.by_channel_params['ch3', 'clim'] = 10
if 'signals' in win.viewers:
win.add_view(freq_view, tabify_with = 'signals')
elif 'signals rauc' in win.viewers:
win.add_view(freq_view, tabify_with = 'signals rauc')
else:
win.add_view(freq_view)
########################################################################
# SPIKE TRAINS
if self.is_shown('spike_trains') and sources['spike'][0].nb_channel > 0:
spike_train_view = ephyviewer.SpikeTrainViewer(source = sources['spike'][0], name = 'spiketrains')
win.add_view(spike_train_view)
# set the theme
if theme != 'original':
spike_train_view.params['background_color'] = self.themes[theme]['background_color']
spike_train_view.params['vline_color'] = self.themes[theme]['vline_color']
spike_train_view.params['label_fill_color'] = self.themes[theme]['label_fill_color']
spike_train_view.params_controller.combo_cmap.setCurrentText(self.themes[theme]['cmap'])
spike_train_view.params_controller.on_automatic_color()
########################################################################
# EPOCHS
if self.is_shown('epochs') and sources['epoch'][0].nb_channel > 0:
epoch_view = ephyviewer.EpochViewer(source = sources['epoch'][0], name = 'epochs')
win.add_view(epoch_view)
# set the theme
if theme != 'original':
epoch_view.params['background_color'] = self.themes[theme]['background_color']
epoch_view.params['vline_color'] = self.themes[theme]['vline_color']
epoch_view.params['label_fill_color'] = self.themes[theme]['label_fill_color']
epoch_view.params_controller.combo_cmap.setCurrentText(self.themes[theme]['cmap'])
epoch_view.params_controller.on_automatic_color()
########################################################################
# EPOCH ENCODER
if self.is_shown('epoch_encoder') and self.metadata['epoch_encoder_file'] is not None:
possible_labels = self.metadata['epoch_encoder_possible_labels']
# append labels found in the epoch encoder file but not in the
# epoch_encoder_possible_labels list, preserving the original
# ordering of epoch_encoder_possible_labels
labels_from_file = [ep.name for ep in seg.epochs if len(ep.times) > 0 and '(from epoch encoder file)' in ep.labels]
for label in labels_from_file:
if label not in possible_labels:
possible_labels.append(label)
writable_epoch_source = NeuroticWritableEpochSource(
filename = _abs_path(self.metadata, 'epoch_encoder_file'),
possible_labels = possible_labels,
)
epoch_encoder = ephyviewer.EpochEncoder(source = writable_epoch_source, name = 'epoch encoder')
epoch_encoder.params['exclusive_mode'] = False
win.add_view(epoch_encoder)
# set the theme
if theme != 'original':
epoch_encoder.params['background_color'] = self.themes[theme]['background_color']
epoch_encoder.params['vline_color'] = self.themes[theme]['vline_color']
epoch_encoder.params['label_fill_color'] = self.themes[theme]['label_fill_color']
# TODO add support for combo_cmap
########################################################################
# VIDEO
if self.is_shown('video') and self.metadata['video_file'] is not None:
video_source = ephyviewer.MultiVideoFileSource(video_filenames = [_abs_path(self.metadata, 'video_file')])
# some video files are loaded with an incorrect start time, so
# reset video start to zero
video_source.t_stops[0] -= video_source.t_starts[0]
video_source.t_starts[0] = 0
# apply the video_offset
if self.metadata['video_offset'] is not None:
video_source.t_starts[0] += self.metadata['video_offset']
video_source.t_stops[0] += self.metadata['video_offset']
# correct for videos that report frame rates that are too fast or
# too slow compared to the clock on the data acquisition system
if self.metadata['video_rate_correction'] is not None:
video_source.rates[0] *= self.metadata['video_rate_correction']
if self.metadata['video_jumps'] is not None:
# create an unmodified video_times vector with evenly spaced times
video_times = np.arange(video_source.nb_frames[0])/video_source.rates[0] + video_source.t_starts[0]
# insert repeating times at pause_start to fill pause_duration
# so that that section of the video is skipped over
for pause_start, pause_duration in self.metadata['video_jumps']:
pause_start_index = np.searchsorted(video_times, pause_start)
pause_fill = video_times[pause_start_index] * np.ones(int(np.round(pause_duration*video_source.rates[0])))
video_times = np.insert(video_times, pause_start_index, pause_fill)
video_times = video_times[:video_source.nb_frames[0]]
# add the modified video_times to the video_source
video_source.video_times = [video_times]
video_source.t_starts[0] = min(video_times)
video_source.t_stops[0] = max(video_times)
# update the source-level times from the modified file-level times
video_source._t_start = max(min(video_source.t_starts), 0)
video_source._t_stop = max(video_source.t_stops)
video_view = ephyviewer.VideoViewer(source = video_source, name = 'video')
if theme != 'original':
video_view.graphiclayout.setBackground(self.themes[theme]['background_color'])
win.add_view(video_view, location = 'bottom', orientation = 'horizontal')
########################################################################
# EVENTS
if self.is_shown('event_list') and sources['event'][0].nb_channel > 0:
event_list = ephyviewer.EventList(source = sources['event'][0], name = 'events')
if 'video' in win.viewers:
win.add_view(event_list, split_with = 'video')
else:
win.add_view(event_list, location = 'bottom', orientation = 'horizontal')
########################################################################
# DATAFRAME
annotations_dataframe = _neo_epoch_to_dataframe(seg.epochs, exclude_epoch_encoder_epochs=True)
if self.is_shown('data_frame') and len(annotations_dataframe) > 0:
data_frame_view = ephyviewer.DataFrameView(source = annotations_dataframe, name = 'table')
if 'events' in win.viewers:
win.add_view(data_frame_view, tabify_with = 'events')
elif 'video' in win.viewers:
win.add_view(data_frame_view, split_with = 'video')
else:
win.add_view(data_frame_view, location = 'bottom', orientation = 'horizontal')
########################################################################
# FINAL TOUCHES
# select first tabs
for widget in win.children():
if isinstance(widget, ephyviewer.PyQt5.QtWidgets.QTabBar):
widget.setCurrentIndex(0)
# set amount of time shown initially
win.set_xsize(self.metadata['t_width']) # seconds
return win