def get_synchronized_frame_times(session_sync_file: Path,
sync_line_label_keys: Tuple[str, ...]) -> pd.Series:
"""Get experimental frame times from an experiment session sync file.
Parameters
----------
session_sync_file : Path
Path to an ephys session sync file.
The sync file contains rising/falling edges from a daq system which
indicates when certain events occur (so they can be related to
each other).
sync_line_label_keys : Tuple[str, ...]
Line label keys to get times for. See class attributes of
allensdk.brain_observatory.sync_dataset.Dataset for a listing of
possible keys.
Returns
-------
pd.Series
An array of times when frames for the eye tracking camera were acquired.
"""
sync_dataset = Dataset(str(session_sync_file))
frame_times = sync_dataset.get_edges(
"rising", sync_line_label_keys, units="seconds"
)
# Occasionally an extra set of frame times are acquired after the rest of
# the signals. We detect and remove these.
frame_times = trim_discontiguous_times(frame_times)
return pd.Series(frame_times)
def __init__(self,
sync_file,
scanner=None,
dff_file=None,
stimulus_pkl=None,
eye_video=None,
behavior_video=None,
long_stim_threshold=LONG_STIM_THRESHOLD):
self.scanner = scanner if scanner is not None else "SCIVIVO"
self._dataset = Dataset(sync_file)
self._keys = get_keys(self._dataset)
self.long_stim_threshold = long_stim_threshold
self._monitor_delay = None
self._clipped_stim_ts_delta = None
self._clipped_stim_timestamp_values = None
if dff_file is not None:
self.ophys_data_length = get_ophys_data_length(dff_file)
else:
self.ophys_data_length = None
if stimulus_pkl is not None:
self.stim_data_length = get_stim_data_length(stimulus_pkl)
else:
self.stim_data_length = None
if eye_video is not None:
self.eye_data_length = get_video_length(eye_video)
else:
self.eye_data_length = None
if behavior_video is not None:
self.behavior_data_length = get_video_length(behavior_video)
else:
self.behavior_data_length = None
def main(stimulus_pkl_path, sync_h5_path, output_path, wheel_radius,
subject_position, use_median_duration, **kwargs):
stim_file = pd.read_pickle(stimulus_pkl_path)
sync_dataset = Dataset(sync_h5_path)
# Why the rising edge? See Sweepstim.update in camstim. This method does:
# 1. updates the stimuli
# 2. updates the "items", causing a running speed sample to be acquired
# 3. sets the vsync line high
# 4. flips the buffer
frame_times = sync_dataset.get_edges("rising",
Dataset.FRAME_KEYS,
units="seconds")
# occasionally an extra set of frame times are acquired after the rest of
# the signals. We detect and remove these
frame_times = sync_utilities.trim_discontiguous_times(frame_times)
num_raw_timestamps = len(frame_times)
dx_deg = running_from_stim_file(stim_file, "dx", num_raw_timestamps)
if num_raw_timestamps != len(dx_deg):
raise ValueError(
f"found {num_raw_timestamps} rising edges on the vsync line, "
f"but only {len(dx_deg)} rotation samples")
vsig = running_from_stim_file(stim_file, "vsig", num_raw_timestamps)
vin = running_from_stim_file(stim_file, "vin", num_raw_timestamps)
velocities = extract_running_speeds(
frame_times=frame_times,
dx_deg=dx_deg,
vsig=vsig,
vin=vin,
wheel_radius=wheel_radius,
subject_position=subject_position,
use_median_duration=use_median_duration)
raw_data = pd.DataFrame({
"vsig": vsig,
"vin": vin,
"frame_time": frame_times,
"dx": dx_deg
})
store = pd.HDFStore(output_path)
store.put("running_speed", velocities)
store.put("raw_data", raw_data)
store.close()
return {"output_path": output_path}
def get_ophys_frames(dataset: SyncDataset,
permissive: bool = False) -> np.ndarray:
""" Report the timestamps of each optical physiology video frame
Parameters
----------
dataset : describes experiment timing
Returns
-------
array of timestamps (floating point; seconds; relative to experiment start).
permissive : If True, None will be returned if timestamps are not found. If
False, a KeyError will be raised
Notes
-----
use rising edge for Scientifica, falling edge for Nikon
http://confluence.corp.alleninstitute.org/display/IT/Ophys+Time+Sync
This function uses rising edges
"""
try:
return dataset.get_edges("rising", '2p_vsync', "seconds")
except KeyError:
if not permissive:
raise
return
def get_trigger(dataset: SyncDataset,
permissive: bool = False) -> Optional[np.ndarray]:
""" Returns (as a 1-element array) the time at which optical physiology
acquisition was started.
Parameters
----------
dataset : describes experiment timing
permissive : If True, None will be returned if timestamps are not found. If
False, a KeyError will be raised
Returns
-------
timestamps (floating point; seconds; relative to experiment start)
or None. If None, no timestamps were found in this sync dataset.
Notes
-----
Ophys frame timestamps can be recorded before acquisition start when
experimenters are setting up the recording session. These do not
correspond to acquired ophys frames.
"""
return dataset.get_edges("rising", ["2p_trigger", "acq_trigger"],
"seconds", permissive)
def build_full_NP_behavior_stim_table(behavior_pkl_path, mapping_pkl_path,
replay_pkl_path, sync_path):
pkl_files = []
for pkl in [behavior_pkl_path, mapping_pkl_path, replay_pkl_path]:
if isinstance(pkl, str):
pkl = pd.read_pickle(pkl)
pkl_files.append(pkl)
behavior_pkl = pkl_files[0]
mapping_pkl = pkl_files[1]
replay_pkl = pkl_files[2]
if isinstance(sync_path, str):
sync_dataset = Dataset(sync_path)
else:
sync_dataset = sync_path
# behavior_pkl = pd.read_pickle(behavior_pkl_path)
# mapping_pkl = pd.read_pickle(mapping_pkl_path)
# replay_pkl = pd.read_pickle(replay_pkl_path)
frame_counts = []
for p in [behavior_pkl, mapping_pkl, replay_pkl]:
total_frames = len(p['intervalsms']) + 1 if 'intervalsms' in p \
else len(p['items']['behavior']['intervalsms']) + 1
frame_counts.append(total_frames)
#mapping_stim_file = CamStimOnePickleStimFile.factory(mapping_pkl_path)
mapping_stim_file = CamStimOnePickleStimFile(mapping_pkl)
frame_offsets = get_frame_offsets(sync_dataset, frame_counts)
stim_table_behavior = generate_behavior_stim_table(
behavior_pkl, sync_dataset, frame_offset=frame_offsets[0])
stim_table_mapping = generate_mapping_stim_table(
mapping_stim_file, sync_dataset, frame_offset=frame_offsets[1])
stim_table_replay = generate_replay_stim_table(
replay_pkl,
sync_dataset,
stim_table_behavior,
frame_offset=frame_offsets[2])
#Rearrange columns to make a bit more readable; the rest of the cols are just alphabetical
stim_table_behavior = sort_columns(stim_table_behavior, [
'stimulus_block', 'active', 'stimulus_name', 'Start', 'End',
'duration', 'start_frame', 'end_frame'
])
stim_table_full = pd.concat(
[stim_table_behavior, stim_table_mapping, stim_table_replay],
sort=False)
stim_table_full.loc[:, 'duration'] = stim_table_full[
'End'] - stim_table_full['Start']
stim_table_full.loc[stim_table_full['stimulus_name'].isnull(),
'stimulus_name'] = 'spontaneous'
stim_table_full['presentation_index'] = np.arange(len(stim_table_full))
return stim_table_full.set_index('presentation_index')
def get_raw_stimulus_frames(
dataset: SyncDataset,
permissive: bool = False
) -> np.ndarray:
""" Report the raw timestamps of each stimulus frame. This corresponds to
the time at which the psychopy window's flip method returned, but not
necessarily to the time at which the stimulus frame was displayed.
Parameters
----------
dataset : describes experiment timing
permissive : If True, None will be returned if timestamps are not found. If
False, a KeyError will be raised
Returns
-------
array of timestamps (floating point; seconds; relative to experiment start).
"""
try:
return dataset.get_edges("falling",'stim_vsync', "seconds")
except KeyError:
if not permissive:
raise
return
def get_synchronized_camera_frame_times(session_sync_file: Path) -> pd.Series:
"""Get eye tracking camera frame times from an experiment session sync file.
Args:
session_sync_file (Path): Path to an ephys session sync file.
The sync file contains rising/falling edges from a daq system which
indicates when certain events occur (so they can be related to
each other).
Returns:
pandas.Series: An array of times when frames for the eye tracking
camera were acquired.
"""
sync_dataset = Dataset(str(session_sync_file))
frame_times = sync_dataset.get_edges("rising",
Dataset.EYE_TRACKING_KEYS,
units="seconds")
# Occasionally an extra set of frame times are acquired after the rest of
# the signals. We detect and remove these.
frame_times = sync_utilities.trim_discontiguous_times(frame_times)
return pd.Series(frame_times)
def get_lick_times(dataset: SyncDataset,
permissive: bool = False) -> Optional[np.ndarray]:
""" Report the timestamps of each detected lick
Parameters
----------
dataset : describes experiment timing
permissive : If True, None will be returned if timestamps are not found. If
False, a KeyError will be raised
Returns
-------
array of timestamps (floating point; seconds; relative to experiment start)
or None. If None, no lick timestamps were found in this sync
dataset.
"""
return dataset.get_edges("rising", ["lick_times", "lick_sensor"],
"seconds", permissive)
def get_eye_tracking(dataset: SyncDataset,
permissive: bool = False) -> Optional[np.ndarray]:
""" Report the timestamps of each frame of the eye tracking video
Parameters
----------
dataset : describes experiment timing
permissive : If True, None will be returned if timestamps are not found. If
False, a KeyError will be raised
Returns
-------
array of timestamps (floating point; seconds; relative to experiment start)
or None. If None, no eye tracking timestamps were found in this sync
dataset.
"""
return dataset.get_edges("rising", ["cam2_exposure", "eye_tracking"],
"seconds", permissive)
def get_stim_photodiode(dataset: SyncDataset,
permissive: bool = False) -> Optional[List[float]]:
""" Report the timestamps of each detected sync square transition (both
black -> white and white -> black) in this experiment.
Parameters
----------
dataset : describes experiment timing
permissive : If True, None will be returned if timestamps are not found. If
False, a KeyError will be raised
Returns
-------
array of timestamps (floating point; seconds; relative to experiment start)
or None. If None, no photodiode timestamps were found in this sync
dataset.
"""
return dataset.get_edges("all", ["stim_photodiode", "photodiode"],
"seconds", permissive)
def build_full_NP_behavior_stim_table(behavior_pkl_path, mapping_pkl_path,
replay_pkl_path, sync_path):
behavior_pkl = pd.read_pickle(behavior_pkl_path)
mapping_pkl = pd.read_pickle(mapping_pkl_path)
replay_pkl = pd.read_pickle(replay_pkl_path)
frame_counts = []
for p in [behavior_pkl, mapping_pkl, replay_pkl]:
total_frames = len(p['intervalsms']) + 1 if 'intervalsms' in p \
else len(p['items']['behavior']['intervalsms']) + 1
frame_counts.append(total_frames)
mapping_stim_file = CamStimOnePickleStimFile.factory(mapping_pkl_path)
sync_dataset = Dataset(sync_path)
frame_offsets = get_frame_offsets(sync_dataset, frame_counts)
stim_table_behavior = generate_behavior_stim_table(
behavior_pkl, sync_dataset, frame_offset=frame_offsets[0])
stim_table_mapping = generate_mapping_stim_table(
mapping_stim_file, sync_dataset, frame_offset=frame_offsets[1])
stim_table_replay = generate_replay_stim_table(
replay_pkl,
sync_dataset,
stim_table_behavior,
frame_offset=frame_offsets[2])
#Rearrange columns to make a bit more readable; the rest of the cols are just alphabetical
stim_table_behavior = sort_columns(stim_table_behavior, [
'stimulus_block', 'active', 'stimulus_name', 'Start', 'End',
'duration', 'start_frame', 'end_frame'
])
stim_table_full = pd.concat(
[stim_table_behavior, stim_table_mapping, stim_table_replay],
sort=False)
stim_table_full.loc[:, 'duration'] = stim_table_full[
'End'] - stim_table_full['Start']
return stim_table_full
class OphysTimeAligner(object):
def __init__(self,
sync_file,
scanner=None,
dff_file=None,
stimulus_pkl=None,
eye_video=None,
behavior_video=None,
long_stim_threshold=LONG_STIM_THRESHOLD):
self.scanner = scanner if scanner is not None else "SCIVIVO"
self._dataset = Dataset(sync_file)
self._keys = get_keys(self._dataset)
self.long_stim_threshold = long_stim_threshold
self._monitor_delay = None
self._clipped_stim_ts_delta = None
self._clipped_stim_timestamp_values = None
if dff_file is not None:
self.ophys_data_length = get_ophys_data_length(dff_file)
else:
self.ophys_data_length = None
if stimulus_pkl is not None:
self.stim_data_length = get_stim_data_length(stimulus_pkl)
else:
self.stim_data_length = None
if eye_video is not None:
self.eye_data_length = get_video_length(eye_video)
else:
self.eye_data_length = None
if behavior_video is not None:
self.behavior_data_length = get_video_length(behavior_video)
else:
self.behavior_data_length = None
@property
def dataset(self):
return self._dataset
@property
def ophys_timestamps(self):
"""Get the timestamps for the ophys data."""
ophys_key = self._keys["2p"]
if self.scanner == "SCIVIVO":
# Scientifica data looks different than Nikon.
# http://confluence.corp.alleninstitute.org/display/IT/Ophys+Time+Sync
times = self.dataset.get_rising_edges(ophys_key, units="seconds")
elif self.scanner == "NIKONA1RMP":
# Nikon has a signal that indicates when it started writing to disk
acquiring_key = self._keys["acquiring"]
acquisition_start = self._dataset.get_rising_edges(
acquiring_key, units="seconds")[0]
ophys_times = self._dataset.get_falling_edges(ophys_key,
units="seconds")
times = ophys_times[ophys_times >= acquisition_start]
else:
raise ValueError("Invalid scanner: {}".format(self.scanner))
return times
@property
def corrected_ophys_timestamps(self):
times = self.ophys_timestamps
delta = 0
if self.ophys_data_length is not None:
if len(times) < self.ophys_data_length:
raise ValueError(
"Got too few timestamps ({}) for ophys data length "
"({})".format(len(times), self.ophys_data_length))
elif len(times) > self.ophys_data_length:
logging.info(
"Ophys data of length %s has timestamps of "
"length %s, truncating timestamps", self.ophys_data_length,
len(times))
delta = len(times) - self.ophys_data_length
times = times[:-delta]
else:
logging.info("No data length provided for ophys stream")
return times, delta
@property
def stim_timestamps(self):
stim_key = self._keys["stimulus"]
return self.dataset.get_falling_edges(stim_key, units="seconds")
def _get_clipped_stim_timestamps(self):
timestamps = self.stim_timestamps
delta = 0
if self.stim_data_length is not None and \
self.stim_data_length < len(timestamps):
stim_key = self._keys["stimulus"]
rising = self.dataset.get_rising_edges(stim_key, units="seconds")
# Some versions of camstim caused a spike when the DAQ is first
# initialized. Remove it.
if rising[1] - rising[0] > self.long_stim_threshold:
logging.info("Initial DAQ spike detected from stimulus, "
"removing it")
timestamps = timestamps[1:]
delta = len(timestamps) - self.stim_data_length
if delta != 0:
logging.info(
"Stim data of length %s has timestamps of "
"length %s", self.stim_data_length, len(timestamps))
elif self.stim_data_length is None:
logging.info("No data length provided for stim stream")
return timestamps, delta
@property
def clipped_stim_timestamps(self):
"""
Return the stimulus timestamps with the erroneous initial spike
removed (if relevant)
Returns
-------
timestamps: np.ndarray
An array of stimulus timestamps in seconds with th emonitor delay
added
delta: int
Difference between the length of timestamps
and the number of frames reported in the stimulus
pickle file, i.e.
len(timestamps) - len(pkl_file['items']['behavior']['intervalsms']
"""
if self._clipped_stim_ts_delta is None:
(self._clipped_stim_timestamp_values, self._clipped_stim_ts_delta
) = self._get_clipped_stim_timestamps()
return (self._clipped_stim_timestamp_values,
self._clipped_stim_ts_delta)
def _get_monitor_delay(self):
timestamps, delta = self.clipped_stim_timestamps
photodiode_key = self._keys["photodiode"]
delay = calculate_monitor_delay(self.dataset, timestamps,
photodiode_key)
return delay
@property
def monitor_delay(self):
"""
The monitor delay (in seconds) associated with the session
"""
if self._monitor_delay is None:
self._monitor_delay = self._get_monitor_delay()
return self._monitor_delay
@property
def corrected_stim_timestamps(self):
"""
The stimulus timestamps corrected for monitor delay
Returns
-------
timestamps: np.ndarray
An array of stimulus timestamps in seconds with th emonitor delay
added
delta: int
Difference between the length of timestamps and
the number of frames reported in the stimulus
pickle file, i.e.
len(timestamps) - len(pkl_file['items']['behavior']['intervalsms']
delay: float
The monitor delay in seconds
"""
timestamps, delta = self.clipped_stim_timestamps
delay = self.monitor_delay
return timestamps + delay, delta, delay
@property
def behavior_video_timestamps(self):
key = self._keys["behavior_camera"]
return self.dataset.get_falling_edges(key, units="seconds")
@property
def corrected_behavior_video_timestamps(self):
return corrected_video_timestamps("Behavior video",
self.behavior_video_timestamps,
self.behavior_data_length)
@property
def eye_video_timestamps(self):
key = self._keys["eye_camera"]
return self.dataset.get_falling_edges(key, units="seconds")
@property
def corrected_eye_video_timestamps(self):
return corrected_video_timestamps("Eye video",
self.eye_video_timestamps,
self.eye_data_length)
class OphysTimeAligner(object):
def __init__(self,
sync_file,
scanner=None,
dff_file=None,
stimulus_pkl=None,
eye_video=None,
behavior_video=None,
long_stim_threshold=LONG_STIM_THRESHOLD):
self.scanner = scanner if scanner is not None else "SCIVIVO"
self._dataset = Dataset(sync_file)
self._keys = get_keys(self._dataset)
self.long_stim_threshold = long_stim_threshold
if dff_file is not None:
self.ophys_data_length = get_ophys_data_length(dff_file)
else:
self.ophys_data_length = None
if stimulus_pkl is not None:
self.stim_data_length = get_stim_data_length(stimulus_pkl)
else:
self.stim_data_length = None
if eye_video is not None:
self.eye_data_length = get_video_length(eye_video)
else:
self.eye_data_length = None
if behavior_video is not None:
self.behavior_data_length = get_video_length(behavior_video)
else:
self.behavior_data_length = None
@property
def dataset(self):
return self._dataset
@property
def ophys_timestamps(self):
"""Get the timestamps for the ophys data."""
ophys_key = self._keys["2p"]
if self.scanner == "SCIVIVO":
# Scientifica data looks different than Nikon.
# http://confluence.corp.alleninstitute.org/display/IT/Ophys+Time+Sync
times = self.dataset.get_rising_edges(ophys_key, units="seconds")
elif self.scanner == "NIKONA1RMP":
# Nikon has a signal that indicates when it started writing to disk
acquiring_key = self._keys["acquiring"]
acquisition_start = self._dataset.get_rising_edges(
acquiring_key, units="seconds")[0]
ophys_times = self._dataset.get_falling_edges(ophys_key,
units="seconds")
times = ophys_times[ophys_times >= acquisition_start]
else:
raise ValueError("Invalid scanner: {}".format(self.scanner))
return times
@property
def corrected_ophys_timestamps(self):
times = self.ophys_timestamps
delta = 0
if self.ophys_data_length is not None:
if len(times) < self.ophys_data_length:
raise ValueError(
"Got too few timestamps ({}) for ophys data length "
"({})".format(len(times), self.ophys_data_length))
elif len(times) > self.ophys_data_length:
logging.info(
"Ophys data of length %s has timestamps of "
"length %s, truncating timestamps", self.ophys_data_length,
len(times))
delta = len(times) - self.ophys_data_length
times = times[:-delta]
else:
logging.info("No data length provided for ophys stream")
return times, delta
@property
def stim_timestamps(self):
stim_key = self._keys["stimulus"]
return self.dataset.get_falling_edges(stim_key, units="seconds")
@property
def corrected_stim_timestamps(self):
timestamps = self.stim_timestamps
delta = 0
if self.stim_data_length is not None and \
self.stim_data_length < len(timestamps):
stim_key = self._keys["stimulus"]
rising = self.dataset.get_rising_edges(stim_key, units="seconds")
# Some versions of camstim caused a spike when the DAQ is first
# initialized. Remove it.
if rising[1] - rising[0] > self.long_stim_threshold:
logging.info("Initial DAQ spike detected from stimulus, "
"removing it")
timestamps = timestamps[1:]
delta = len(timestamps) - self.stim_data_length
if delta != 0:
logging.info(
"Stim data of length %s has timestamps of "
"length %s", self.stim_data_length, len(timestamps))
elif self.stim_data_length is None:
logging.info("No data length provided for stim stream")
photodiode_key = self._keys["photodiode"]
delay = monitor_delay(self.dataset, timestamps, photodiode_key)
return timestamps + delay, delta, delay
@property
def behavior_video_timestamps(self):
key = self._keys["behavior_camera"]
return self.dataset.get_falling_edges(key, units="seconds")
@property
def corrected_behavior_video_timestamps(self):
return corrected_video_timestamps("Behavior video",
self.behavior_video_timestamps,
self.behavior_data_length)
@property
def eye_video_timestamps(self):
key = self._keys["eye_camera"]
return self.dataset.get_falling_edges(key, units="seconds")
@property
def corrected_eye_video_timestamps(self):
return corrected_video_timestamps("Eye video",
self.eye_video_timestamps,
self.eye_data_length)
def get_sync_data(sync_path):
sync_dataset = SyncDataset(sync_path)
meta_data = sync_dataset.meta_data
sample_freq = meta_data['ni_daq']['counter_output_freq']
# use rising edge for Scientifica, falling edge for Nikon http://confluence.corp.alleninstitute.org/display/IT/Ophys+Time+Sync
# 2P vsyncs
vs2p_r = sync_dataset.get_rising_edges('2p_vsync')
vs2p_f = sync_dataset.get_falling_edges(
'2p_vsync'
) # new sync may be able to do units = 'sec', so conversion can be skipped
frames_2p = vs2p_r / sample_freq
vs2p_fsec = vs2p_f / sample_freq
stimulus_times_no_monitor_delay = sync_dataset.get_falling_edges(
'stim_vsync') / sample_freq
if 'lick_times' in meta_data['line_labels']:
lick_times = sync_dataset.get_rising_edges('lick_1') / sample_freq
elif 'lick_sensor' in meta_data['line_labels']:
lick_times = sync_dataset.get_rising_edges('lick_sensor') / sample_freq
else:
lick_times = None
if '2p_trigger' in meta_data['line_labels']:
trigger = sync_dataset.get_rising_edges('2p_trigger') / sample_freq
elif 'acq_trigger' in meta_data['line_labels']:
trigger = sync_dataset.get_rising_edges('acq_trigger') / sample_freq
if 'stim_photodiode' in meta_data['line_labels']:
a = sync_dataset.get_rising_edges('stim_photodiode') / sample_freq
b = sync_dataset.get_falling_edges('stim_photodiode') / sample_freq
stim_photodiode = sorted(list(a) + list(b))
elif 'photodiode' in meta_data['line_labels']:
a = sync_dataset.get_rising_edges('photodiode') / sample_freq
b = sync_dataset.get_falling_edges('photodiode') / sample_freq
stim_photodiode = sorted(list(a) + list(b))
if 'cam1_exposure' in meta_data['line_labels']:
eye_tracking = sync_dataset.get_rising_edges(
'cam1_exposure') / sample_freq
elif 'eye_tracking' in meta_data['line_labels']:
eye_tracking = sync_dataset.get_rising_edges(
'eye_tracking') / sample_freq
if 'cam2_exposure' in meta_data['line_labels']:
behavior_monitoring = sync_dataset.get_rising_edges(
'cam2_exposure') / sample_freq
elif 'behavior_monitoring' in meta_data['line_labels']:
behavior_monitoring = sync_dataset.get_rising_edges(
'behavior_monitoring') / sample_freq
sync_data = {
'ophys_frames': frames_2p,
'lick_times': lick_times,
'ophys_trigger': trigger,
'eye_tracking': eye_tracking,
'behavior_monitoring': behavior_monitoring,
'stim_photodiode': stim_photodiode,
'stimulus_times_no_delay': stimulus_times_no_monitor_delay,
}
return sync_data