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diff --git a/_modules/brainbox/atlas.html b/_modules/brainbox/atlas.html
index c4b90887..039bb745 100644
--- a/_modules/brainbox/atlas.html
+++ b/_modules/brainbox/atlas.html
@@ -56,7 +56,7 @@
diff --git a/_modules/brainbox/behavior/dlc.html b/_modules/brainbox/behavior/dlc.html
index 144ae723..3488b70d 100644
--- a/_modules/brainbox/behavior/dlc.html
+++ b/_modules/brainbox/behavior/dlc.html
@@ -56,7 +56,7 @@
diff --git a/_modules/brainbox/behavior/training.html b/_modules/brainbox/behavior/training.html
index e7fe1153..10108007 100644
--- a/_modules/brainbox/behavior/training.html
+++ b/_modules/brainbox/behavior/training.html
@@ -56,7 +56,7 @@
block_idx = trials.probabilityLeft == block
contrasts, n_contrasts = np.unique(signed_contrast[block_idx], return_counts=True)
- reaction_time = np.vectorize(lambda x: np.nanmedian((trials[stim_off_type] - trials[stim_on_type])
- [(x == signed_contrast) & block_idx]))(contrasts)
+ reaction_time = np.vectorize(
+ lambda x: np.nanmedian((trials[stim_off_type] - trials[stim_on_type])[(x == signed_contrast) & block_idx]),
+ otypes=[float]
+ )(contrasts)
+
if compute_ci:
ci = np.full((contrasts.size, 2), np.nan)
for i, x in enumerate(contrasts):
diff --git a/_modules/brainbox/behavior/wheel.html b/_modules/brainbox/behavior/wheel.html
index 34dd6349..3ca48053 100644
--- a/_modules/brainbox/behavior/wheel.html
+++ b/_modules/brainbox/behavior/wheel.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/brainbox/core.html b/_modules/brainbox/core.html
index eaa4bf2b..d95a9a10 100644
--- a/_modules/brainbox/core.html
+++ b/_modules/brainbox/core.html
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Data Release - Behavior
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Data Release - Reproducible Ephys Paper
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Information and troubleshooting
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index 52017421..a22d551d 100644
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Information and troubleshooting
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index c2c3b333..a166bd31 100644
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Information and troubleshooting
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index d4d76552..ca968632 100644
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Information and troubleshooting
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index 2feeddc6..9092b866 100644
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Information and troubleshooting
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index 49dbdb15..43d5b663 100644
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Information and troubleshooting
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index e314c95c..3e0ab142 100644
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Information and troubleshooting
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index 500d82a8..6e0fc401 100644
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Information and troubleshooting
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index 5ce9f956..c59d57a8 100644
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Information and troubleshooting
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index 210ced0b..a957af49 100644
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index f20e0612..5fdaf4d6 100644
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Information and troubleshooting
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index 052ace80..dc548073 100644
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Information and troubleshooting
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index 0b8bd307..01adfc69 100644
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Information and troubleshooting
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index dfa5ea66..36832d4c 100644
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Information and troubleshooting
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Information and troubleshooting
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Information and troubleshooting
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index 8030ab8c..66c35c95 100644
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Information and troubleshooting
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Information and troubleshooting
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index 60572f17..d0dc6ded 100644
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Information and troubleshooting
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Information and troubleshooting
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index 217ef824..8251601b 100644
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Information and troubleshooting
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Information and troubleshooting
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Information and troubleshooting
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index 356ad53c..6f612316 100644
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Information and troubleshooting
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index 926e1e64..8b945169 100644
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Information and troubleshooting
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Information and troubleshooting
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index 0bf0ccaa..2cac552c 100644
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index c608f2cf..7bc3ca7c 100644
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Information and troubleshooting
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index 381980c7..2036a79c 100644
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Information and troubleshooting
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Information and troubleshooting
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index 4c879848..df495ad6 100644
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Information and troubleshooting
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index 0ad7ac86..edde7f1d 100644
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Information and troubleshooting
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index efddeb2b..d44a7097 100644
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Information and troubleshooting
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index 18094244..f0b8b698 100644
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Information and troubleshooting
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index b04580ce..a6d32b91 100644
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Information and troubleshooting
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index 4beaf326..f81668e3 100644
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Information and troubleshooting
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index f49bebb6..33cc3136 100644
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index c1394247..cb6a5154 100644
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Information and troubleshooting
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index 9c8ad925..efd5dad8 100644
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Information and troubleshooting
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index fcddf673..9d03ad87 100644
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Information and troubleshooting
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Information and troubleshooting
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Information and troubleshooting
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Information and troubleshooting
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Information and troubleshooting
diff --git a/_modules/ibllib/io/extractors/ephys_passive.html b/_modules/ibllib/io/extractors/ephys_passive.html
index 4a32dc2a..f2e87490 100644
--- a/_modules/ibllib/io/extractors/ephys_passive.html
+++ b/_modules/ibllib/io/extractors/ephys_passive.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/extractors/fibrephotometry.html b/_modules/ibllib/io/extractors/fibrephotometry.html
index c0f1910b..a8e545bc 100644
--- a/_modules/ibllib/io/extractors/fibrephotometry.html
+++ b/_modules/ibllib/io/extractors/fibrephotometry.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/extractors/habituation_trials.html b/_modules/ibllib/io/extractors/habituation_trials.html
index 002dccd5..ee7fed94 100644
--- a/_modules/ibllib/io/extractors/habituation_trials.html
+++ b/_modules/ibllib/io/extractors/habituation_trials.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/extractors/mesoscope.html b/_modules/ibllib/io/extractors/mesoscope.html
index 6700e758..07261d11 100644
--- a/_modules/ibllib/io/extractors/mesoscope.html
+++ b/_modules/ibllib/io/extractors/mesoscope.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
@@ -402,12 +402,22 @@
Source code for ibllib.io.extractors.mesoscope
out['valveOpen_times'] = assign_to_trial(valve_driver_ttls[:, 0])
# Stimulus times extracted based on trigger times
+ # When assigning events all start times must not be NaN so here we substitute freeze
+ # trigger times on nogo trials for stim on trigger times, then replace with NaN again
+ go_trials = np.where(out['choice'] != 0)[0]
+ lims = np.copy(out['stimOnTrigger_times'])
+ lims[go_trials] = out['stimFreezeTrigger_times'][go_trials]
out['stimFreeze_times'] = assign_to_trial(
self.frame2ttl['times'], 'last',
- starts=out['stimFreezeTrigger_times'], t_trial_end=out['stimOffTrigger_times'])
+ starts=lims, t_trial_end=out['stimOffTrigger_times'])
+ out['stimFreeze_times'][out['choice'] == 0] = np.nan
+
+ # Here we do the same but use stim off trigger times
+ lims = np.copy(out['stimOffTrigger_times'])
+ lims[go_trials] = out['stimFreezeTrigger_times'][go_trials]
out['stimOn_times'] = assign_to_trial(
self.frame2ttl['times'], 'first',
- starts=out['stimOnTrigger_times'], t_trial_end=out['stimFreezeTrigger_times'])
+ starts=out['stimOnTrigger_times'], t_trial_end=lims)
out['stimOff_times'] = assign_to_trial(
self.frame2ttl['times'], 'first',
starts=out['stimOffTrigger_times'], t_trial_end=out['intervals'][:, 1]
diff --git a/_modules/ibllib/io/extractors/opto_trials.html b/_modules/ibllib/io/extractors/opto_trials.html
index 4a82a8e4..4894bf3e 100644
--- a/_modules/ibllib/io/extractors/opto_trials.html
+++ b/_modules/ibllib/io/extractors/opto_trials.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/extractors/passive_plotting.html b/_modules/ibllib/io/extractors/passive_plotting.html
index 7009db6f..148f2059 100644
--- a/_modules/ibllib/io/extractors/passive_plotting.html
+++ b/_modules/ibllib/io/extractors/passive_plotting.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/extractors/signatures.html b/_modules/ibllib/io/extractors/signatures.html
index 9eb0a8d6..7f85236e 100644
--- a/_modules/ibllib/io/extractors/signatures.html
+++ b/_modules/ibllib/io/extractors/signatures.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/extractors/training_audio.html b/_modules/ibllib/io/extractors/training_audio.html
index a13dfa83..fffeb445 100644
--- a/_modules/ibllib/io/extractors/training_audio.html
+++ b/_modules/ibllib/io/extractors/training_audio.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/extractors/training_trials.html b/_modules/ibllib/io/extractors/training_trials.html
index 282b883e..dd1116c9 100644
--- a/_modules/ibllib/io/extractors/training_trials.html
+++ b/_modules/ibllib/io/extractors/training_trials.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
@@ -782,7 +782,8 @@
Source code for ibllib.io.extractors.training_trials
class
PhasePosQuiescence(BaseBpodTrialsExtractor):
-
"""Extracts stimulus phase, position and quiescence from Bpod data.
+
"""Extract stimulus phase, position and quiescence from Bpod data.
+
For extraction of pre-generated events, use the ProbaContrasts extractor instead.
"""
save_names = (None, None, '_ibl_trials.quiescencePeriod.npy')
@@ -795,6 +796,18 @@
Source code for ibllib.io.extractors.training_trials
return
phase, position, quiescence
+
class PauseDuration(BaseBpodTrialsExtractor):
+
"""Extract pause duration from raw trial data."""
+
save_names = None
+
var_names = 'pause_duration'
+
+
def _extract(self, **kwargs):
+
# pausing logic added in version 8.9.0
+
ver = version.parse(self.settings.get('IBLRIG_VERSION') or '0')
+
default = 0. if ver < version.parse('8.9.0') else np.nan
+
return np.fromiter((t.get('pause_duration', default) for t in self.bpod_trials), dtype=float)
+
+
class TrialsTable(BaseBpodTrialsExtractor):
"""
Extracts the following into a table from Bpod raw data:
@@ -825,15 +838,15 @@
Source code for ibllib.io.extractors.training_trials
class
TrainingTrials(BaseBpodTrialsExtractor):
save_names = ('_ibl_trials.repNum.npy', '_ibl_trials.goCueTrigger_times.npy', '_ibl_trials.stimOnTrigger_times.npy', None,
None, None, None, '_ibl_trials.table.pqt', None, None, '_ibl_wheel.timestamps.npy', '_ibl_wheel.position.npy',
-
'_ibl_wheelMoves.intervals.npy', '_ibl_wheelMoves.peakAmplitude.npy', None, None, None, None, None)
+
'_ibl_wheelMoves.intervals.npy', '_ibl_wheelMoves.peakAmplitude.npy', None, None, None, None, None, None)
var_names = ('repNum', 'goCueTrigger_times', 'stimOnTrigger_times', 'itiIn_times', 'stimOffTrigger_times',
'stimFreezeTrigger_times', 'errorCueTrigger_times', 'table', 'stimOff_times', 'stimFreeze_times',
'wheel_timestamps', 'wheel_position', 'wheelMoves_intervals', 'wheelMoves_peakAmplitude',
-
'peakVelocity_times', 'is_final_movement', 'phase', 'position', 'quiescence')
+
'peakVelocity_times', 'is_final_movement', 'phase', 'position', 'quiescence', 'pause_duration')
def _extract(self) -> dict:
base = [RepNum, GoCueTriggerTimes, StimOnTriggerTimes, ItiInTimes, StimOffTriggerTimes, StimFreezeTriggerTimes,
-
ErrorCueTriggerTimes, TrialsTable, PhasePosQuiescence]
+
ErrorCueTriggerTimes, TrialsTable, PhasePosQuiescence, PauseDuration]
out, _ = run_extractor_classes(
base, session_path=self.session_path, bpod_trials=self.bpod_trials, settings=self.settings, save=False,
task_collection=self.task_collection)
diff --git a/_modules/ibllib/io/extractors/training_wheel.html b/_modules/ibllib/io/extractors/training_wheel.html
index 7efb7de6..31d16db6 100644
--- a/_modules/ibllib/io/extractors/training_wheel.html
+++ b/_modules/ibllib/io/extractors/training_wheel.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/extractors/video_motion.html b/_modules/ibllib/io/extractors/video_motion.html
index c1cb09a7..0566a3cf 100644
--- a/_modules/ibllib/io/extractors/video_motion.html
+++ b/_modules/ibllib/io/extractors/video_motion.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/extractors/widefield.html b/_modules/ibllib/io/extractors/widefield.html
index cd9c5a05..f3c4c89d 100644
--- a/_modules/ibllib/io/extractors/widefield.html
+++ b/_modules/ibllib/io/extractors/widefield.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/ffmpeg.html b/_modules/ibllib/io/ffmpeg.html
index 0371bfd0..9dce6576 100644
--- a/_modules/ibllib/io/ffmpeg.html
+++ b/_modules/ibllib/io/ffmpeg.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/flags.html b/_modules/ibllib/io/flags.html
index 01fc8d5d..e6316518 100644
--- a/_modules/ibllib/io/flags.html
+++ b/_modules/ibllib/io/flags.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/misc.html b/_modules/ibllib/io/misc.html
index bf3222bf..259dc5cf 100644
--- a/_modules/ibllib/io/misc.html
+++ b/_modules/ibllib/io/misc.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/npy_header.html b/_modules/ibllib/io/npy_header.html
index 6c6420ee..94b3d729 100644
--- a/_modules/ibllib/io/npy_header.html
+++ b/_modules/ibllib/io/npy_header.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/raw_daq_loaders.html b/_modules/ibllib/io/raw_daq_loaders.html
index 6b94a826..c68ae86f 100644
--- a/_modules/ibllib/io/raw_daq_loaders.html
+++ b/_modules/ibllib/io/raw_daq_loaders.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/raw_data_loaders.html b/_modules/ibllib/io/raw_data_loaders.html
index db83dc48..5e2601ee 100644
--- a/_modules/ibllib/io/raw_data_loaders.html
+++ b/_modules/ibllib/io/raw_data_loaders.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/session_params.html b/_modules/ibllib/io/session_params.html
index 1fa1a7f0..66b53799 100644
--- a/_modules/ibllib/io/session_params.html
+++ b/_modules/ibllib/io/session_params.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/io/video.html b/_modules/ibllib/io/video.html
index 4e6715d5..5b9c976b 100644
--- a/_modules/ibllib/io/video.html
+++ b/_modules/ibllib/io/video.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/misc/misc.html b/_modules/ibllib/misc/misc.html
index ea3db3dc..1a1924ba 100644
--- a/_modules/ibllib/misc/misc.html
+++ b/_modules/ibllib/misc/misc.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/misc/qt.html b/_modules/ibllib/misc/qt.html
index 2fb33977..d6e9c482 100644
--- a/_modules/ibllib/misc/qt.html
+++ b/_modules/ibllib/misc/qt.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/oneibl/data_handlers.html b/_modules/ibllib/oneibl/data_handlers.html
index df0c1c8a..91ac727b 100644
--- a/_modules/ibllib/oneibl/data_handlers.html
+++ b/_modules/ibllib/oneibl/data_handlers.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/oneibl/patcher.html b/_modules/ibllib/oneibl/patcher.html
index a79097fb..dcf8e2c3 100644
--- a/_modules/ibllib/oneibl/patcher.html
+++ b/_modules/ibllib/oneibl/patcher.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/oneibl/registration.html b/_modules/ibllib/oneibl/registration.html
index 69c7bd42..13ab3917 100644
--- a/_modules/ibllib/oneibl/registration.html
+++ b/_modules/ibllib/oneibl/registration.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/oneibl/stream.html b/_modules/ibllib/oneibl/stream.html
index 3d54baef..5850dd46 100644
--- a/_modules/ibllib/oneibl/stream.html
+++ b/_modules/ibllib/oneibl/stream.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes.html b/_modules/ibllib/pipes.html
index d19d8588..fc538e9f 100644
--- a/_modules/ibllib/pipes.html
+++ b/_modules/ibllib/pipes.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/audio_tasks.html b/_modules/ibllib/pipes/audio_tasks.html
index b6adaec8..54724ad4 100644
--- a/_modules/ibllib/pipes/audio_tasks.html
+++ b/_modules/ibllib/pipes/audio_tasks.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/base_tasks.html b/_modules/ibllib/pipes/base_tasks.html
index 9c399761..df056622 100644
--- a/_modules/ibllib/pipes/base_tasks.html
+++ b/_modules/ibllib/pipes/base_tasks.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/behavior_tasks.html b/_modules/ibllib/pipes/behavior_tasks.html
index 87931b22..27f7f24a 100644
--- a/_modules/ibllib/pipes/behavior_tasks.html
+++ b/_modules/ibllib/pipes/behavior_tasks.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/dynamic_pipeline.html b/_modules/ibllib/pipes/dynamic_pipeline.html
index c9387aa1..4596f76e 100644
--- a/_modules/ibllib/pipes/dynamic_pipeline.html
+++ b/_modules/ibllib/pipes/dynamic_pipeline.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/ephys_alignment.html b/_modules/ibllib/pipes/ephys_alignment.html
index 528a372c..955f1ff4 100644
--- a/_modules/ibllib/pipes/ephys_alignment.html
+++ b/_modules/ibllib/pipes/ephys_alignment.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/ephys_preprocessing.html b/_modules/ibllib/pipes/ephys_preprocessing.html
index 1d491c08..6642c6c5 100644
--- a/_modules/ibllib/pipes/ephys_preprocessing.html
+++ b/_modules/ibllib/pipes/ephys_preprocessing.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/ephys_tasks.html b/_modules/ibllib/pipes/ephys_tasks.html
index 5b9ec034..80d2ebb8 100644
--- a/_modules/ibllib/pipes/ephys_tasks.html
+++ b/_modules/ibllib/pipes/ephys_tasks.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
@@ -764,7 +764,7 @@
Source code for ibllib.pipes.ephys_tasks
line = fid.readline()
version = re.search('version (.*), output', line)
version = version or re.search('version (.*)', line) # old versions have output, new have a version line
- version = re.sub('\\^[[0-9]+m', '', version.group(1)) # removes the coloring tags
+ version = re.sub(r'\^\[{2}[0-9]+m', '', version.group(1)) # removes the coloring tags
return version
def _run_iblsort(self, ap_file):
diff --git a/_modules/ibllib/pipes/histology.html b/_modules/ibllib/pipes/histology.html
index e7ed3424..694ef068 100644
--- a/_modules/ibllib/pipes/histology.html
+++ b/_modules/ibllib/pipes/histology.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/local_server.html b/_modules/ibllib/pipes/local_server.html
index 0362ebcd..66ab09d7 100644
--- a/_modules/ibllib/pipes/local_server.html
+++ b/_modules/ibllib/pipes/local_server.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/mesoscope_tasks.html b/_modules/ibllib/pipes/mesoscope_tasks.html
index b8b8ac04..60c03d26 100644
--- a/_modules/ibllib/pipes/mesoscope_tasks.html
+++ b/_modules/ibllib/pipes/mesoscope_tasks.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/misc.html b/_modules/ibllib/pipes/misc.html
index f54c8c4c..95b9ac2b 100644
--- a/_modules/ibllib/pipes/misc.html
+++ b/_modules/ibllib/pipes/misc.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/photometry_tasks.html b/_modules/ibllib/pipes/photometry_tasks.html
index 4ef533df..d541d6b6 100644
--- a/_modules/ibllib/pipes/photometry_tasks.html
+++ b/_modules/ibllib/pipes/photometry_tasks.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/purge_rig_data.html b/_modules/ibllib/pipes/purge_rig_data.html
index d4b9ea39..f7eda7a4 100644
--- a/_modules/ibllib/pipes/purge_rig_data.html
+++ b/_modules/ibllib/pipes/purge_rig_data.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/remote_server.html b/_modules/ibllib/pipes/remote_server.html
index 2bf33c3e..8ea5f334 100644
--- a/_modules/ibllib/pipes/remote_server.html
+++ b/_modules/ibllib/pipes/remote_server.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/scan_fix_passive_files.html b/_modules/ibllib/pipes/scan_fix_passive_files.html
index e49e14b4..75846fd7 100644
--- a/_modules/ibllib/pipes/scan_fix_passive_files.html
+++ b/_modules/ibllib/pipes/scan_fix_passive_files.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/sdsc_tasks.html b/_modules/ibllib/pipes/sdsc_tasks.html
index 49bcdd87..a9b10f5b 100644
--- a/_modules/ibllib/pipes/sdsc_tasks.html
+++ b/_modules/ibllib/pipes/sdsc_tasks.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/sync_tasks.html b/_modules/ibllib/pipes/sync_tasks.html
index 2a128233..86f08628 100644
--- a/_modules/ibllib/pipes/sync_tasks.html
+++ b/_modules/ibllib/pipes/sync_tasks.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/tasks.html b/_modules/ibllib/pipes/tasks.html
index 3fec3e71..3b6080f0 100644
--- a/_modules/ibllib/pipes/tasks.html
+++ b/_modules/ibllib/pipes/tasks.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
@@ -591,11 +591,11 @@
Source code for ibllib.pipes.tasks
actual_files = list(Path(self.session_path).rglob(str(Path(*filter(None, reversed(expected_file[:2]))))))
# Account for revisions
if len(actual_files) == 0:
- collection = expected_file[1] + '/#*' if expected_file[1] != '' else expected_file[1] + '#*'
+ collection = '/'.join(filter(None, (expected_file[1], '#*'))) # append pound with wildcard
expected_revision = (expected_file[0], collection, expected_file[2])
actual_files = list(
- Path(self.session_path).rglob(str(Path(*filter(None, reversed(expected_revision[:2]))))))
-
+ Path(self.session_path).rglob(str(Path(*filter(None, reversed(expected_revision[:2])))))
+ )
if len(actual_files) == 0 and expected_file[2]:
everything_is_fine = False
if not silent:
diff --git a/_modules/ibllib/pipes/training_preprocessing.html b/_modules/ibllib/pipes/training_preprocessing.html
index 855d76d0..136886c8 100644
--- a/_modules/ibllib/pipes/training_preprocessing.html
+++ b/_modules/ibllib/pipes/training_preprocessing.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/training_status.html b/_modules/ibllib/pipes/training_status.html
index 95ee6ca4..2f7e8300 100644
--- a/_modules/ibllib/pipes/training_status.html
+++ b/_modules/ibllib/pipes/training_status.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/transfer_rig_data.html b/_modules/ibllib/pipes/transfer_rig_data.html
index f84f6c92..79801fbf 100644
--- a/_modules/ibllib/pipes/transfer_rig_data.html
+++ b/_modules/ibllib/pipes/transfer_rig_data.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/video_tasks.html b/_modules/ibllib/pipes/video_tasks.html
index 3b339686..7d226ffb 100644
--- a/_modules/ibllib/pipes/video_tasks.html
+++ b/_modules/ibllib/pipes/video_tasks.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/pipes/widefield_tasks.html b/_modules/ibllib/pipes/widefield_tasks.html
index 406ad86c..f4a4daaf 100644
--- a/_modules/ibllib/pipes/widefield_tasks.html
+++ b/_modules/ibllib/pipes/widefield_tasks.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/plots/figures.html b/_modules/ibllib/plots/figures.html
index 45287037..7a2d979e 100644
--- a/_modules/ibllib/plots/figures.html
+++ b/_modules/ibllib/plots/figures.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/plots/misc.html b/_modules/ibllib/plots/misc.html
index 7ccf0313..41380de4 100644
--- a/_modules/ibllib/plots/misc.html
+++ b/_modules/ibllib/plots/misc.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/plots/snapshot.html b/_modules/ibllib/plots/snapshot.html
index 78807fb6..64ee2026 100644
--- a/_modules/ibllib/plots/snapshot.html
+++ b/_modules/ibllib/plots/snapshot.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/qc/alignment_qc.html b/_modules/ibllib/qc/alignment_qc.html
index 3fcc64e7..f04304e3 100644
--- a/_modules/ibllib/qc/alignment_qc.html
+++ b/_modules/ibllib/qc/alignment_qc.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/qc/base.html b/_modules/ibllib/qc/base.html
index 1e3cd05b..b56a708a 100644
--- a/_modules/ibllib/qc/base.html
+++ b/_modules/ibllib/qc/base.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/qc/camera.html b/_modules/ibllib/qc/camera.html
index 5af41d41..8d0c1ac1 100644
--- a/_modules/ibllib/qc/camera.html
+++ b/_modules/ibllib/qc/camera.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/qc/critical_reasons.html b/_modules/ibllib/qc/critical_reasons.html
index f4233590..712708fe 100644
--- a/_modules/ibllib/qc/critical_reasons.html
+++ b/_modules/ibllib/qc/critical_reasons.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/qc/dlc.html b/_modules/ibllib/qc/dlc.html
index d1136651..1c8f5292 100644
--- a/_modules/ibllib/qc/dlc.html
+++ b/_modules/ibllib/qc/dlc.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/qc/qcplots.html b/_modules/ibllib/qc/qcplots.html
index 5000dc8e..4f3ed5bc 100644
--- a/_modules/ibllib/qc/qcplots.html
+++ b/_modules/ibllib/qc/qcplots.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/qc/task_extractors.html b/_modules/ibllib/qc/task_extractors.html
index 1356fe6d..4acfa1e2 100644
--- a/_modules/ibllib/qc/task_extractors.html
+++ b/_modules/ibllib/qc/task_extractors.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/qc/task_metrics.html b/_modules/ibllib/qc/task_metrics.html
index a78aeb41..5299e37e 100644
--- a/_modules/ibllib/qc/task_metrics.html
+++ b/_modules/ibllib/qc/task_metrics.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
@@ -841,12 +841,12 @@
Source code for ibllib.qc.task_metrics
[docs]
-
def check_iti_delays(data, **_):
+
def check_iti_delays(data, subtract_pauses=False, **_):
"""
Check the open-loop grey screen period is approximately 1 second.
Check that the period of grey screen between stim off and the start of the next trial is
-
1s +/- 10%.
+
1s +/- 10%. If the trial was paused during this time, the check will account for that
Metric:
M = stimOff (n) - trialStart (n+1) - 1.
@@ -857,16 +857,30 @@
Source code for ibllib.qc.task_metrics
Units:
seconds [s]
- :param data: dict of trial data with keys ('stimOff_times', 'intervals')
+ Parameters
+ ----------
+ data : dict
+ Trial data with keys ('stimOff_times', 'intervals', 'pause_duration').
+ subtract_pauses: bool
+ If True, account for experimenter-initiated pauses between trials; if False, trials where
+ the experimenter paused the task may fail this check.
+
+ Returns
+ -------
+ numpy.array
+ An array of metric values to threshold.
+ numpy.array
+ An array of boolean values, 1 per trial, where True means trial passes QC threshold.
"""
# Initialize array the length of completed trials
ITI = 1.
metric = np.full(data['intervals'].shape[0], np.nan)
passed = metric.copy()
+ pauses = (data['pause_duration'] if subtract_pauses else np.zeros_like(metric))[:-1]
# Get the difference between stim off and the start of the next trial
# Missing data are set to Inf, except for the last trial which is a NaN
metric[:-1] = \
- np.nan_to_num(data['intervals'][1:, 0] - data['stimOff_times'][:-1] - ITI, nan=np.inf)
+ np.nan_to_num(data['intervals'][1:, 0] - data['stimOff_times'][:-1] - ITI - pauses, nan=np.inf)
passed[:-1] = np.abs(metric[:-1]) < (ITI / 10) # Last trial is not counted
assert data['intervals'].shape[0] == len(metric) == len(passed)
return metric, passed
@@ -1631,7 +1645,7 @@
Source code for ibllib.qc.task_metrics
Parameters
----------
data : dict
- Dict of trial data with keys ('goCue_times', 'intervals', 'choice').
+ Trial data with keys ('goCue_times', 'intervals', 'choice').
photodiode : dict
The fronts from Bpod's BNC1 input or FPGA frame2ttl channel.
diff --git a/_modules/ibllib/qc/task_qc_viewer/ViewEphysQC.html b/_modules/ibllib/qc/task_qc_viewer/ViewEphysQC.html
index 191134ec..82ada502 100644
--- a/_modules/ibllib/qc/task_qc_viewer/ViewEphysQC.html
+++ b/_modules/ibllib/qc/task_qc_viewer/ViewEphysQC.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/qc/task_qc_viewer/task_qc.html b/_modules/ibllib/qc/task_qc_viewer/task_qc.html
index 302d1528..b8ae5f09 100644
--- a/_modules/ibllib/qc/task_qc_viewer/task_qc.html
+++ b/_modules/ibllib/qc/task_qc_viewer/task_qc.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/tests/extractors/test_ephys_fpga.html b/_modules/ibllib/tests/extractors/test_ephys_fpga.html
index e9c27745..1daca54b 100644
--- a/_modules/ibllib/tests/extractors/test_ephys_fpga.html
+++ b/_modules/ibllib/tests/extractors/test_ephys_fpga.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/tests/extractors/test_ephys_passive.html b/_modules/ibllib/tests/extractors/test_ephys_passive.html
index ee39b633..7653fde0 100644
--- a/_modules/ibllib/tests/extractors/test_ephys_passive.html
+++ b/_modules/ibllib/tests/extractors/test_ephys_passive.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
diff --git a/_modules/ibllib/tests/extractors/test_extractors.html b/_modules/ibllib/tests/extractors/test_extractors.html
index 42d2dc5e..7974eddd 100644
--- a/_modules/ibllib/tests/extractors/test_extractors.html
+++ b/_modules/ibllib/tests/extractors/test_extractors.html
@@ -56,7 +56,7 @@
Publicly available IBL data
Data Release - Behavior
Data Release - Pilot Dataset
-
Data Release - Reproducible Ephys Paper
+
Data Release - Reproducible Ephys
Data Release - Brain Wide Map
Data Release - Spike sorting benchmark datasets
Information and troubleshooting
@@ -173,7 +173,7 @@
Source code for ibllib.tests.extractors.test_extractors
self.training_ge5['ntrials'] = len(raw.load_data(self.training_ge5['path']))
self.biased_ge5['ntrials'] = len(raw.load_data(self.biased_ge5['path']))
self.ephys['ntrials'] = len(raw.load_data(self.ephys['path']))
- # turn off logging for unit testing as we will purposedly go into warning/error cases
+ # turn off logging for unit testing as we will purposely go into warning/error cases
self.wheel_ge5_path = self.main_path / 'data' / 'wheel_ge5'
self.wheel_lt5_path = self.main_path / 'data' / 'wheel_lt5'
@@ -249,16 +249,16 @@
Source code for ibllib.tests.extractors.test_extractors
# TRAINING SESSIONS
pl = training_trials.ProbabilityLeft(
self.training_lt5['path']).extract()[0]
-
self.assertTrue(isinstance(pl, np.ndarray))
+
self.assertIsInstance(pl, np.ndarray)
# -- version >= 5.0.0
pl = training_trials.ProbabilityLeft(
self.training_ge5['path']).extract()[0]
-
self.assertTrue(isinstance(pl, np.ndarray))
+
self.assertIsInstance(pl, np.ndarray)
# BIASED SESSIONS
pl = biased_trials.ProbabilityLeft(
self.biased_lt5['path']).extract()[0]
-
self.assertTrue(isinstance(pl, np.ndarray))
+
self.assertIsInstance(pl, np.ndarray)
# Test if only probs that are in prob set
md = raw.load_settings(self.biased_lt5['path'])
if md:
@@ -268,7 +268,7 @@
Source code for ibllib.tests.extractors.test_extractors
# -- version >= 5.0.0
pl = biased_trials.ProbabilityLeft(
self.biased_ge5['path']).extract()[0]
-
self.assertTrue(isinstance(pl, np.ndarray))
+
self.assertIsInstance(pl, np.ndarray)
# Test if only probs that are in prob set
md = raw.load_settings(self.biased_ge5['path'])
probs = md['BLOCK_PROBABILITY_SET']
@@ -298,7 +298,7 @@
Source code for ibllib.tests.extractors.test_extractors
# TRAINING SESSIONS
choice = training_trials.Choice(
session_path=self.training_lt5['path']).extract(save=False)[0]
-
self.assertTrue(isinstance(choice, np.ndarray))
+
self.assertIsInstance(choice, np.ndarray)
data = raw.load_data(self.training_lt5['path'])
trial_nogo = np.array(
[~np.isnan(t['behavior_data']['States timestamps']['no_go'][0][0])
@@ -308,7 +308,7 @@
Source code for ibllib.tests.extractors.test_extractors
# -- version >= 5.0.0
choice = training_trials.Choice(
session_path=self.training_ge5['path']).extract(save=False)[0]
-
self.assertTrue(isinstance(choice, np.ndarray))
+
self.assertIsInstance(choice, np.ndarray)
data = raw.load_data(self.training_ge5['path'])
trial_nogo = np.array(
[~np.isnan(t['behavior_data']['States timestamps']['no_go'][0][0])
@@ -319,7 +319,7 @@
Source code for ibllib.tests.extractors.test_extractors
# BIASED SESSIONS
choice = biased_trials.Choice(
session_path=self.biased_lt5['path']).extract(save=False)[0]
-
self.assertTrue(isinstance(choice, np.ndarray))
+
self.assertIsInstance(choice, np.ndarray)
data = raw.load_data(self.biased_lt5['path'])
trial_nogo = np.array(
[~np.isnan(t['behavior_data']['States timestamps']['no_go'][0][0])
@@ -329,7 +329,7 @@
Source code for ibllib.tests.extractors.test_extractors
# -- version >= 5.0.0
choice = biased_trials.Choice(
session_path=self.biased_ge5['path']).extract(save=False)[0]
-
self.assertTrue(isinstance(choice, np.ndarray))
+
self.assertIsInstance(choice, np.ndarray)
data = raw.load_data(self.biased_ge5['path'])
trial_nogo = np.array(
[~np.isnan(t['behavior_data']['States timestamps']['no_go'][0][0])
@@ -344,13 +344,13 @@
Source code for ibllib.tests.extractors.test_extractors
# TRAINING SESSIONS
rn = training_trials.RepNum(
self.training_lt5['path']).extract()[0]
- self.assertTrue(isinstance(rn, np.ndarray))
+ self.assertIsInstance(rn, np.ndarray)
expected = [0, 1, 2, 0]
np.testing.assert_array_equal(rn, expected)
# -- version >= 5.0.0
rn = training_trials.RepNum(
self.training_ge5['path']).extract()[0]
- self.assertTrue(isinstance(rn, np.ndarray))
+ self.assertIsInstance(rn, np.ndarray)
expected = [0, 0, 1, 2, 3, 0, 0, 0, 1, 2, 0, 1]
np.testing.assert_array_equal(rn, expected)
@@ -364,22 +364,22 @@
Source code for ibllib.tests.extractors.test_extractors
# TRAINING SESSIONS
rv = training_trials.RewardVolume(
self.training_lt5['path']).extract()[0]
- self.assertTrue(isinstance(rv, np.ndarray))
+ self.assertIsInstance(rv, np.ndarray)
# -- version >= 5.0.0
rv = training_trials.RewardVolume(
self.training_ge5['path']).extract()[0]
- self.assertTrue(isinstance(rv, np.ndarray))
+ self.assertIsInstance(rv, np.ndarray)
# BIASED SESSIONS
rv = biased_trials.RewardVolume(
self.biased_lt5['path']).extract()[0]
- self.assertTrue(isinstance(rv, np.ndarray))
+ self.assertIsInstance(rv, np.ndarray)
# Test if all non-zero rewards are of the same value
self.assertTrue(all(x == max(rv) for x in rv if x != 0))
# -- version >= 5.0.0
rv = biased_trials.RewardVolume(
self.biased_ge5['path']).extract()[0]
- self.assertTrue(isinstance(rv, np.ndarray))
+ self.assertIsInstance(rv, np.ndarray)
# Test if all non-zero rewards are of the same value
self.assertTrue(all(x == max(rv) for x in rv if x != 0))
@@ -390,12 +390,12 @@
Source code for ibllib.tests.extractors.test_extractors
# TRAINING SESSIONS
ft = training_trials.FeedbackTimes(
self.training_ge5['path']).extract()[0]
- self.assertTrue(isinstance(ft, np.ndarray))
+ self.assertIsInstance(ft, np.ndarray)
# BIASED SESSIONS
ft = biased_trials.FeedbackTimes(
self.biased_ge5['path']).extract()[0]
- self.assertTrue(isinstance(ft, np.ndarray))
+
self.assertIsInstance(ft, np.ndarray)
+
+
+