def get_video_meta(video_path, one=None):
"""
Return a bunch of video information with the fields ('length', 'fps', 'width', 'height',
'duration', 'size')
:param video_path: A path to the video. May be a file path or URL.
:param one: An instance of ONE
:return: A Bunch of video mata data
"""
is_url = isinstance(video_path, str) and video_path.startswith('http')
cap = VideoStreamer(video_path).cap if is_url else cv2.VideoCapture(str(video_path))
assert cap.isOpened(), f'Failed to open video file {video_path}'
# Get basic properties of video
meta = Bunch()
meta.length = int(cap.get(cv2.CAP_PROP_FRAME_COUNT))
meta.fps = int(cap.get(cv2.CAP_PROP_FPS))
meta.width = int(cap.get(cv2.CAP_PROP_FRAME_WIDTH))
meta.height = int(cap.get(cv2.CAP_PROP_FRAME_HEIGHT))
meta.duration = timedelta(seconds=meta.length / meta.fps) if meta.fps > 0 else 0
if is_url and one:
eid = one.path2eid(video_path)
datasets = one.list_datasets(eid, details=True)
label = label_from_path(video_path)
record = datasets[datasets['rel_path'].str.contains(f'_iblrig_{label}Camera.raw')]
assert len(record) == 1
meta.size = record['file_size'].iloc[0]
elif is_url and not one:
meta.size = None
else:
meta.size = Path(video_path).stat().st_size
cap.release()
return meta
def _sync_to_alf(raw_ephys_apfile, output_path=None, save=False, parts=''):
"""
Extracts sync.times, sync.channels and sync.polarities from binary ephys dataset
:param raw_ephys_apfile: bin file containing ephys data or spike
:param output_path: output directory
:param save: bool write to disk only if True
:param parts: string or list of strings that will be appended to the filename before extension
:return:
"""
# handles input argument: support ibllib.io.spikeglx.Reader, str and pathlib.Path
if isinstance(raw_ephys_apfile, spikeglx.Reader):
sr = raw_ephys_apfile
else:
raw_ephys_apfile = Path(raw_ephys_apfile)
sr = spikeglx.Reader(raw_ephys_apfile)
opened = sr.is_open
if not opened: # if not (opened := sr.is_open) # py3.8
sr.open()
# if no output, need a temp folder to swap for big files
if not output_path:
output_path = raw_ephys_apfile.parent
file_ftcp = Path(output_path).joinpath(
f'fronts_times_channel_polarity{str(uuid.uuid4())}.bin')
# loop over chunks of the raw ephys file
wg = neurodsp.utils.WindowGenerator(sr.ns,
int(SYNC_BATCH_SIZE_SECS * sr.fs),
overlap=1)
fid_ftcp = open(file_ftcp, 'wb')
for sl in wg.slice:
ss = sr.read_sync(sl)
ind, fronts = neurodsp.utils.fronts(ss, axis=0)
# a = sr.read_sync_analog(sl)
sav = np.c_[(ind[0, :] + sl.start) / sr.fs, ind[1, :],
fronts.astype(np.double)]
sav.tofile(fid_ftcp)
# close temp file, read from it and delete
fid_ftcp.close()
tim_chan_pol = np.fromfile(str(file_ftcp))
tim_chan_pol = tim_chan_pol.reshape((int(tim_chan_pol.size / 3), 3))
file_ftcp.unlink()
sync = {
'times': tim_chan_pol[:, 0],
'channels': tim_chan_pol[:, 1],
'polarities': tim_chan_pol[:, 2]
}
# If opened Reader was passed into function, leave open
if not opened:
sr.close()
if save:
out_files = alfio.save_object_npy(output_path,
sync,
'sync',
namespace='spikeglx',
parts=parts)
return Bunch(sync), out_files
else:
return Bunch(sync)
def __init__(self, x, y, z=None, c=None, cmap=None, plot_type='scatter'):
"""
Class for organising data that will be used to create scatter plots. Can be 2D or 3D (if
z given). Can also represent variable through color by specifying c
:param x: x values for data
:param y: y values for data
:param z: z values for data
:param c: values to use to represent color of scatter points
:param cmap: name of colormap to use if c is given
:param plot_type:
"""
data = Bunch({'x': x, 'y': y, 'z': z, 'c': c})
assert len(data['x']) == len(data['y']), 'dimensions must agree'
if data['z'] is not None:
assert len(data['z']) == len(data['x']), 'dimensions must agree'
if data['c'] is not None:
assert len(data['c']) == len(data['x']), 'dimensions must agree'
super().__init__(plot_type, data)
self._set_init_style()
self.set_xlim()
self.set_ylim()
# If we have 3D data
if data['z'] is not None:
self.set_zlim()
# If we want colorbar associated with scatter plot
self.set_clim()
self.cmap = self._set_default(cmap, 'viridis')
def __init__(self, img, x=None, y=None, cmap=None):
"""
Class for organising data that will be used to create 2D image plots
:param img: 2D image data
:param x: x coordinate of each image voxel in x dimension
:param y: y coordinate of each image voxel in y dimension
:param cmap: name of colormap to use
"""
data = Bunch({
'x': self._set_default(x, np.arange(img.shape[0])),
'y': self._set_default(y, np.arange(img.shape[1])),
'c': img
})
# Make sure dimensions agree
assert data['c'].shape[0] == data['x'].shape[
0], 'dimensions must agree'
assert data['c'].shape[1] == data['y'].shape[
0], 'dimensions must agree'
# Initialise default plot class with data
super().__init__('image', data)
self.scale = None
self.offset = None
self.cmap = self._set_default(cmap, 'viridis')
self.set_xlim()
self.set_ylim()
self.set_clim()
def __init__(self, img, x, y, cmap=None):
"""
Class for organising data that will be used to create 2D probe plots. Use function
plot_base.arrange_channels2bank to prepare data in correct format before using this class
:param img: list of image data for each bank of probe
:param x: list of x coordinate for each bank of probe
:param y: list of y coordinate for each bank or probe
:param cmap: name of cmap
"""
# Make sure we have inputs as lists, can get input from arrange_channels2banks
assert (type(img) == list)
assert (type(x) == list)
assert (type(y) == list)
data = Bunch({'x': x, 'y': y, 'c': img})
super().__init__('probe', data)
self.cmap = self._set_default(cmap, 'viridis')
self.set_xlim()
self.set_ylim()
self.set_clim()
self.set_scale()
self.set_offset()
def combine_behaviour_data(self, wheel, dlc_left, dlc_right):
behav = Bunch()
behav_options = []
aligned = [True]
if all([val in wheel.keys() for val in ['timestamps', 'position']]):
behav['wheel'] = wheel
behav_options = behav_options + ['wheel']
if all([val in dlc_left.keys() for val in ['times', 'dlc']]):
dlc = get_dlc_everything(dlc_left, 'left')
behav['leftCamera'] = dlc
keys = [f'leftCamera_{key}' for key in dlc.dlc.keys() if 'speed' in key]
behav_options = behav_options + keys
keys = [f'leftCamera_{key}' for key in dlc.keys() if
any([key in name for name in ['licks', 'sniffs']])]
behav_options = behav_options + keys
aligned.append(dlc['aligned'])
if all([val in dlc_right.keys() for val in ['times', 'dlc']]):
dlc = get_dlc_everything(dlc_right, 'right')
behav['rightCamera'] = dlc
keys = [f'rightCamera_{key}' for key in dlc.dlc.keys() if 'speed' in key]
behav_options = behav_options + keys
keys = [f'rightCamera_{key}' for key in dlc.keys() if
any([key in name for name in ['licks', 'sniffs']])]
behav_options = behav_options + keys
aligned.append(dlc['aligned'])
aligned = all(aligned)
return behav, behav_options, aligned
def get_qc_info(self, eid, one):
data = Bunch()
sess = one.alyx.rest('sessions', 'read', id=eid)['extended_qc']
for qc in SESS_QC:
data[qc] = sess.get(qc, '')
return data
def __init__(self,
eid=None,
one=None,
log=logging.getLogger('ibllib'),
**kwargs):
self.one = one or ONE()
self.eid = eid
self.session_path = kwargs.pop('session_path',
None) or self.one.eid2path(eid)
self.ref = self.one.dict2ref(self.one.path2ref(self.session_path))
self.log = log
self.trials = self.wheel = self.camera_times = None
raw_cam_path = self.session_path.joinpath('raw_video_data')
camera_path = list(raw_cam_path.glob('_iblrig_*Camera.raw.*'))
self.video_paths = {vidio.label_from_path(x): x for x in camera_path}
self.data = Bunch()
self.alignment = Bunch()
def __init__(self, session_path_or_eid, side, **kwargs):
"""
:param session_path_or_eid: A session eid or path
:param side: The camera to run QC on
:param log: A logging.Logger instance, if None the 'ibllib' logger is used
:param one: An ONE instance for fetching and setting the QC on Alyx
"""
# Make sure the type of camera is chosen
self.side = side
# When an eid is provided, we will download the required data by default (if necessary)
download_data = not is_session_path(session_path_or_eid)
self.download_data = kwargs.pop('download_data', download_data)
super().__init__(session_path_or_eid, **kwargs)
self.data = Bunch()
# QC outcomes map
self.metrics = None
def __init__(self, probe_id, session_path=None, **kwargs):
super().__init__(probe_id, endpoint='insertions', **kwargs)
self.pid = probe_id
self.session_path = session_path
self.stream = kwargs.pop('stream', True)
keys = ('ap', 'ap_meta', 'lf', 'lf_meta')
self.data = Bunch.fromkeys(keys)
self.metrics = {}
self.outcome = 'NOT_SET'
def get_template_for_selection(self):
data = Bunch()
template = (self.clusters.waveforms[self.clust_ids[self.clust], :, 0]) * 1e6
t_template = 1e3 * np.arange(template.shape[0]) / FS
data['vals'] = template
data['time'] = t_template
return data
def _get_raster(self, raster, trials_id):
data = Bunch()
data['raster'] = np.r_[raster.vals[trials_id],
np.full((self.n_trials - trials_id.shape[0],
raster.vals.shape[1]), np.nan)]
data['time'] = raster.time
data['cmap'] = raster.cmap
data['clevels'] = raster.clevels
return data
def sort_clusters(self, sort):
clust_sort = Bunch()
self.clust_ids = self.clusters.clust_ids[self.clusters[sort]]
clust_sort['ids'] = self.clust_ids
clust_sort['amps'] = self.clusters.amps[self.clusters[sort]] * 1e6
clust_sort['depths'] = self.clusters.depths[self.clusters[sort]]
clust_sort['colours_ks'] = self.clusters.colours_ks[self.clusters[sort]]
clust_sort['colours_ibl'] = self.clusters.colours_ibl[self.clusters[sort]]
return clust_sort
def get_sync_fronts(sync, channel_nb, tmin=None, tmax=None):
selection = sync['channels'] == channel_nb
selection = np.logical_and(selection,
sync['times'] <= tmax) if tmax else selection
selection = np.logical_and(selection,
sync['times'] >= tmin) if tmin else selection
return Bunch({
'times': sync['times'][selection],
'polarities': sync['polarities'][selection]
})
def get_sync_fronts(auxiliary_name):
d = Bunch({'times': [], 'nsync': np.zeros(nprobes, )})
# auxiliary_name: frame2ttl or right_camera
for ind, ephys_file in enumerate(ephys_files):
sync = alfio.load_object(ephys_file.ap.parent,
'sync',
namespace='spikeglx',
short_keys=True)
sync_map = get_ibl_sync_map(ephys_file, '3A')
# exits if sync label not found for current probe
if auxiliary_name not in sync_map:
return
isync = np.in1d(sync['channels'],
np.array([sync_map[auxiliary_name]]))
# only returns syncs if we get fronts for all probes
if np.all(~isync):
return
d.nsync[ind] = len(sync.channels)
d['times'].append(sync['times'][isync])
return d
def get_autocorr_for_selection(self):
data = Bunch()
x_corr = xcorr(self.spikes.times[self.spikes.clusters == self.clust_ids[self.clust]],
self.spikes.clusters[self.spikes.clusters == self.clust_ids[self.clust]],
AUTOCORR_BIN, AUTOCORR_WINDOW)
t_corr = np.arange(0, AUTOCORR_WINDOW + AUTOCORR_BIN, AUTOCORR_BIN) - AUTOCORR_WINDOW / 2
data['vals'] = x_corr[0, 0, :]
data['time'] = t_corr
return data
def get_cluster_metrics(self):
data = Bunch()
# Only if we have the metrics
if any(self.clusters.get('metrics', [None])):
for qc in CLUSTER_QC:
data[qc] = round((self.clusters.metrics[qc][self.clust_ids[self.clust]]), 3)
else:
for qc in CLUSTER_QC:
data[qc] = None
return data
def test_get_active_wheel_period(self):
"""Check that warning is raised, period is returned None, and QC is NOT_SET
if there is active wheel period to be found"""
wheel_keys = ('timestamps', 'position')
wheel_data = (np.arange(1000), np.ones(1000))
self.qc.data['wheel'] = Bunch(zip(wheel_keys, wheel_data))
with self.assertLogs(logging.getLogger('ibllib'), logging.WARNING):
period = self.qc.get_active_wheel_period(self.qc.data['wheel'])
self.assertEqual(None, period)
outcome = self.qc.check_wheel_alignment()
self.assertEqual('NOT_SET', outcome)
def get(self, ids) -> Bunch:
"""
Get a bunch of the name/id
"""
uid, uind = np.unique(ids, return_inverse=True)
a, iself, _ = np.intersect1d(self.id,
uid,
assume_unique=False,
return_indices=True)
b = Bunch()
for k in self.__dataclass_fields__.keys():
b[k] = self.__getattribute__(k)[iself[uind]]
return b
def detection(data,
fs,
h,
detect_threshold=-4,
time_tol=.002,
distance_threshold_um=70):
"""
Detects and de-duplicates negative voltage spikes based on voltage thresholding.
The de-duplication step locks in maximum amplitude events. To account for collisions the amplitude
is assumed to be decaying from the peak. If this is a multipeak event, each is labeled as a spike.
:param data: 2D numpy array nsamples x nchannels
:param fs: sampling frequency (Hz)
:param h: dictionary with neuropixel geometry header: see. neuropixel.trace_header
:param detect_threshold: negative value below which the voltage is considered to be a spike
:param time_tol: time in seconds for which samples before and after are assumed to be part of the spike
:param distance_threshold_um: distance for which exceeding threshold values are assumed to part of the same spike
:return: spikes dictionary of vectors with keys "time", "trace", "amp" and "ispike"
"""
multipeak = False
time_bracket = np.array([-1, 1]) * time_tol
inds, indtr = np.where(data < detect_threshold)
picks = Bunch(time=inds / fs,
trace=indtr,
amp=data[inds, indtr],
ispike=np.zeros(inds.size))
amp_order = np.argsort(picks.amp)
hxy = h['x'] + 1j * h['y']
spike_id = 1
while np.any(picks.ispike == 0):
# find the first unassigned spike with the highest amplitude
iamp = np.where(picks.ispike[amp_order] == 0)[0][0]
imax = amp_order[iamp]
# look only within the time range
itlims = np.searchsorted(picks.time, picks.time[imax] + time_bracket)
itlims = np.arange(itlims[0], itlims[1])
offset = np.abs(hxy[picks.trace[itlims]] - hxy[picks.trace[imax]])
iit = np.where(offset < distance_threshold_um)[0]
picks.ispike[itlims[iit]] = -1
picks.ispike[imax] = spike_id
# handles collision with a simple amplitude decay model: if amplitude doesn't decay
# as a function of offset, then it's a collision and another spike is set
if multipeak: # noqa
iii = np.lexsort((picks.amp[itlims[iit]], offset[iit]))
sorted_amps_db = 20 * np.log10(np.abs(picks.amp[itlims[iit][iii]]))
idetect = np.r_[0, np.where(np.diff(sorted_amps_db) > 12)[0] + 1]
picks.ispike[itlims[iit[iii[idetect]]]] = np.arange(
idetect.size) + spike_id
spike_id += idetect.size
else:
spike_id += 1
detects = Bunch({k: picks[k][picks.ispike > 0] for k in picks})
return detects
def test_check_timestamps(self):
FPS = 60.
n = 1000
self.qc.data['video'] = Bunch({'fps': FPS, 'length': n})
self.qc.data['timestamps'] = np.array([round(1 / FPS, 4)] * n).cumsum()
# Verify passes
self.assertEqual('PASS', self.qc.check_timestamps())
# Verify fails
self.qc.data['timestamps'] = np.array([round(1 / 30, 4)] *
100).cumsum()
self.assertEqual('FAIL', self.qc.check_timestamps())
# Verify not set
self.qc.data['video'] = None
self.assertEqual('NOT_SET', self.qc.check_timestamps())
def add_lines(self,
pos,
orientation,
lim=None,
style='--',
width=3,
color='k'):
"""
Method to specify position and style of horizontal or vertical reference lines
:param pos: position of line
:param orientation: either 'v' for vertical line or 'h' for horizontal line
:param lim: extent of lines
:param style: line style
:param width: line width
:param color: line colour
:return:
"""
if orientation == 'v':
lim = self._set_default(lim, self.ylim)
self.vlines.append(
Bunch({
'pos': pos,
'lim': lim,
'style': style,
'width': width,
'color': color
}))
if orientation == 'h':
lim = self._set_default(lim, self.xlim)
self.hlines.append(
Bunch({
'pos': pos,
'lim': lim,
'style': style,
'width': width,
'color': color
}))
def _get_psth(self, raster, trials_id, tbin=1):
data = Bunch()
if len(trials_id) == 0:
data['psth_mean'] = np.zeros((raster.vals.shape[1]))
data['psth_std'] = np.zeros((raster.vals.shape[1]))
data['time'] = raster.time
data['ylabel'] = raster.ylabel
else:
data['psth_mean'] = np.nanmean(raster.vals[trials_id], axis=0) / tbin
data['psth_std'] = ((np.nanstd(raster.vals[trials_id], axis=0) / tbin) /
np.sqrt(trials_id.shape[0]))
data['time'] = raster.time
data['ylabel'] = raster.ylabel
return data
def concatenate_trials(trials):
"""
Concatenate trials from different training sessions
:param trials: dict containing trials objects from three consecutive training sessions,
keys are session dates
:type trials: Bunch
:return: trials object with data concatenated over three training sessions
:rtype: dict
"""
trials_all = Bunch()
for k in TRIALS_KEYS:
trials_all[k] = np.concatenate(
list(trials[kk][k] for kk in trials.keys()))
return trials_all
def __init__(self, session_path_or_eid, camera, **kwargs):
"""
:param session_path_or_eid: A session id or path
:param camera: The camera to run QC on, if None QC is run for all three cameras
:param n_samples: The number of frames to sample for the position and brightness QC
:param stream: If true and local video files not available, the data are streamed from
the remote source.
:param log: A logging.Logger instance, if None the 'ibllib' logger is used
:param one: An ONE instance for fetching and setting the QC on Alyx
"""
# When an eid is provided, we will download the required data by default (if necessary)
download_data = not is_session_path(session_path_or_eid)
self.download_data = kwargs.pop('download_data', download_data)
self.stream = kwargs.pop('stream', None)
self.n_samples = kwargs.pop('n_samples', 100)
super().__init__(session_path_or_eid, **kwargs)
# Data
self.label = assert_valid_label(camera)
filename = f'_iblrig_{self.label}Camera.raw*.mp4'
raw_video_path = self.session_path.joinpath('raw_video_data')
self.video_path = next(raw_video_path.glob(filename), None)
# If local video doesn't exist, change video path to URL
if not self.video_path and self.stream is not False and self.one is not None:
try:
self.stream = True
self.video_path = self.one.path2url(raw_video_path /
filename.replace('*', ''))
except (StopIteration, ALFObjectNotFound):
_log.error('No remote or local video file found')
self.video_path = None
logging.disable(logging.CRITICAL)
self._type = get_session_extractor_type(self.session_path) or None
logging.disable(logging.NOTSET)
keys = ('count', 'pin_state', 'audio', 'fpga_times', 'wheel', 'video',
'frame_samples', 'timestamps', 'camera_times', 'bonsai_times')
self.data = Bunch.fromkeys(keys)
self.frame_samples_idx = None
# QC outcomes map
self.metrics = None
self.outcome = 'NOT_SET'
def test_check_camera_times(self):
outcome = self.qc.check_camera_times()
self.assertEqual('NOT_SET', outcome)
# Verify passes
self.qc.label = 'body'
ts_path = Path(__file__).parents[1].joinpath('extractors', 'data',
'session_ephys')
ssv_times = load_camera_ssv_times(ts_path, self.qc.label)
self.qc.data.bonsai_times, self.qc.data.camera_times = ssv_times
self.qc.data.video = Bunch({'length': self.qc.data.bonsai_times.size})
outcome, _ = self.qc.check_camera_times()
self.assertEqual('PASS', outcome)
# Verify warning
n_over = 14
self.qc.data.video['length'] -= n_over
outcome, actual = self.qc.check_camera_times()
self.assertEqual('WARNING', outcome)
self.assertEqual(n_over, actual)
def set_labels(self,
title=None,
xlabel=None,
ylabel=None,
zlabel=None,
clabel=None):
"""
Set labels for plot
:param title: title
:param xlabel: x axis label
:param ylabel: y axis label
:param zlabel: z axis label
:param clabel: cbar label
:return:
"""
self.labels = Bunch({
'title': title,
'xlabel': xlabel,
'ylabel': ylabel,
'zlabel': zlabel,
'clabel': clabel
})
def _get_spike_raster(self, trial_ids):
# Ain't most efficient but it will do for now!
data = Bunch()
x = np.empty(0)
y = np.empty(0)
epoch = [0.4, 1]
spk_times = self.spikes.times[self.spikes.clusters == self.clust_ids[self.clust]]
for idx, val in enumerate(self.trials[self.trial_event][trial_ids]):
spks_to_include = np.bitwise_and(spk_times >= val - epoch[0],
spk_times <= val + epoch[1])
trial_spk_times = spk_times[spks_to_include] - val
x = np.append(x, trial_spk_times)
y = np.append(y, np.ones(len(trial_spk_times)) * idx)
data['raster'] = np.c_[x, y]
data['time'] = EPOCH
data['n_trials'] = self.n_trials
return data
subjects = [
'dop_24', 'dop_14', 'dop_13', 'dop_16', 'dop_21', 'dop_22', 'dop_36'
]
fig = rendering.figure()
for subject in subjects:
ba = atlas.AllenAtlas(25)
channels_rest = one.alyx.rest('channels', 'list', subject=subject)
channels = Bunch({
'atlas_id':
np.array([ch['brain_region'] for ch in channels_rest]),
'xyz':
np.c_[np.array([ch['x'] for ch in channels_rest]),
np.array([ch['y'] for ch in channels_rest]),
np.array([ch['z'] for ch in channels_rest])] / 1e6,
'axial_um':
np.array([ch['axial'] for ch in channels_rest]),
'lateral_um':
np.array([ch['lateral'] for ch in channels_rest]),
'trajectory_id':
np.array([ch['trajectory_estimate'] for ch in channels_rest])
})
for m, probe_id in enumerate(np.unique(channels['trajectory_id'])):
traj_dict = one.alyx.rest('trajectories', 'read', id=probe_id)
ses = traj_dict['session']
label = (f"{ses['subject']}/{ses['start_time'][:10]}/"
f"{str(ses['number']).zfill(3)}/{traj_dict['probe_name']}")
print(label)
color = ibllib.plots.color_cycle(m)
def setUp(self):
eid = '8dd0fcb0-1151-4c97-ae35-2e2421695ad7'
one = ONE(**TEST_DB)
self.qc = qcmetrics.HabituationQC(eid, one=one)
self.qc.extractor = Bunch({'data': self.load_fake_bpod_data()
}) # Dummy extractor obj
