IBL Library
IBL data structure
Installation
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Contribution Statement
API Reference
IBL Library
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Index
Index
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
A
acorr() (in module brainbox.singlecell.singlecell)
acronym (BrainRegions attribute)
add_default_handler() (in module oneibl.onelight)
add_repo() (in module oneibl.onelight)
add_uuid_string() (in module alf.io)
adjust_extremes_linear() (EphysAlignment method)
adjust_extremes_uniform() (EphysAlignment static method)
alf
module
alf.files
module
alf.folders
module
alf.io
module
alf_parts() (in module alf.files)
AlfBunch (class in alf.io)
ALFMultipleCollectionsFound
ALFMultipleObjectsFound
ALFObjectNotFound
AlignmentQC (class in ibllib.qc.alignment_qc)
AllenAtlas (class in ibllib.atlas.atlas)
alyx() (OneAlyx property)
AlyxClient (class in oneibl.webclient)
AlyxSubjectNotFound
amp_heatmap() (in module brainbox.plot.plot)
ancestors() (BrainRegions method)
append() (AlfBunch method)
(in module ibllib.io.jsonable)
(SessionDataInfo method)
apply_sync() (in module ibllib.ephys.sync_probes)
arrange_into_regions() (EphysAlignment static method)
as_dict() (in module ibllib.io.params)
as_globus_path() (in module ibllib.io.globus)
authenticate() (AlyxClient method)
average_drift() (in module brainbox.metrics.metrics)
B
BaseBpodTrialsExtractor (class in ibllib.io.extractors.base)
BaseExtractor (class in ibllib.io.extractors.base)
bc (BrainAtlas attribute)
behavior_exists() (in module ibllib.pipes.misc)
beta (Insertion attribute)
bin_spikes() (in module brainbox.processing.processing)
bin_spikes_trials() (in module brainbox.population.cca)
bincount2D() (in module brainbox.processing.processing)
bp() (in module ibllib.dsp.fourier)
bpod_fpga_sync() (in module ibllib.io.extractors.ephys_fpga)
bpod_trials (BaseBpodTrialsExtractor attribute)
BrainAtlas (class in ibllib.atlas.atlas)
brainbox
module
brainbox.atlas
module
brainbox.atlas.atlas
module
brainbox.behavior
module
brainbox.behavior.behavior
module
brainbox.behavior.pyschofit
module
brainbox.behavior.training
module
brainbox.behavior.wheel
module
brainbox.core
module
brainbox.core.core
module
brainbox.experimental
module
brainbox.experimental.experimental
module
brainbox.io
module
brainbox.io.io
module
brainbox.io.one
module
brainbox.io.parquet
module
brainbox.lfp
module
brainbox.lfp.lfp
module
brainbox.metrics
module
brainbox.metrics.electrode_drift
module
brainbox.metrics.metrics
module
brainbox.modeling
module
brainbox.modeling.dataset
module
brainbox.modeling.fitting_method
module
brainbox.modeling.parameter
module
brainbox.plot
module
brainbox.plot.plot
module
brainbox.population
module
brainbox.population.cca
module
brainbox.population.population
module
brainbox.processing
module
brainbox.processing.processing
module
brainbox.quality
module
brainbox.quality.lfp_qc
module
brainbox.quality.permutation_test
module
brainbox.quality.quality
module
brainbox.simulation
module
brainbox.simulation.simulation
module
brainbox.singlecell
module
brainbox.singlecell.singlecell
module
brainbox.spike_features
module
brainbox.spike_features.spike_features
module
brainbox.task
module
brainbox.task.passive
module
brainbox.task.task
module
brainbox.tests
module
brainbox.tests.test_behavior
module
brainbox.tests.test_brainbox_io
module
brainbox.tests.test_cca
module
brainbox.tests.test_core
module
brainbox.tests.test_io
module
brainbox.tests.test_metrics
module
brainbox.tests.test_plot
module
brainbox.tests.test_population
module
brainbox.tests.test_processing
module
brainbox.tests.test_singlecell
module
brainbox.tests.test_task
module
BrainCoordinates (class in ibllib.atlas.atlas)
BrainRegions (class in ibllib.atlas.atlas)
Bunch (class in brainbox.core.core)
(class in oneibl.onelight)
butter_filter() (in module brainbox.lfp.lfp)
C
calculate_peths() (in module brainbox.singlecell.singlecell)
CameraTimestamps (class in ibllib.io.extractors.ephys_fpga)
(class in ibllib.io.extractors.training_trials)
cart2sph() (in module ibllib.atlas.atlas)
ccf2xyz() (AllenAtlas method)
check_audio_pre_trial() (in module ibllib.qc.task_metrics)
check_correct_trial_event_sequence() (in module ibllib.qc.task_metrics)
check_create_raw_session_flag() (in module ibllib.pipes.misc)
check_detected_wheel_moves() (in module ibllib.qc.task_metrics)
check_dimensions() (AlfBunch property)
(in module alf.io)
check_error_trial_event_sequence() (in module ibllib.qc.task_metrics)
check_errorCue_delays() (in module ibllib.qc.task_metrics)
check_goCue_delays() (in module ibllib.qc.task_metrics)
check_iti_delays() (in module ibllib.qc.task_metrics)
check_n_trial_events() (in module ibllib.qc.task_metrics)
check_negative_feedback_stimOff_delays() (in module ibllib.qc.task_metrics)
check_positive_feedback_stimOff_delays() (in module ibllib.qc.task_metrics)
check_response_feedback_delays() (in module ibllib.qc.task_metrics)
check_response_stimFreeze_delays() (in module ibllib.qc.task_metrics)
check_reward_volume_set() (in module ibllib.qc.task_metrics)
check_reward_volumes() (in module ibllib.qc.task_metrics)
check_stimFreeze_delays() (in module ibllib.qc.task_metrics)
check_stimOff_delays() (in module ibllib.qc.task_metrics)
check_stimOff_itiIn_delays() (in module ibllib.qc.task_metrics)
check_stimOn_delays() (in module ibllib.qc.task_metrics)
check_stimOn_goCue_delays() (in module ibllib.qc.task_metrics)
check_stimulus_move_before_goCue() (in module ibllib.qc.task_metrics)
check_transfer() (in module ibllib.pipes.misc)
check_trial_length() (in module ibllib.qc.task_metrics)
check_wheel_freeze_during_quiescence() (in module ibllib.qc.task_metrics)
check_wheel_integrity() (in module ibllib.qc.task_metrics)
check_wheel_move_before_feedback() (in module ibllib.qc.task_metrics)
check_wheel_move_during_closed_loop() (in module ibllib.qc.task_metrics)
check_wheel_move_during_closed_loop_bpod() (in module ibllib.qc.task_metrics)
Choice (class in ibllib.io.extractors.training_trials)
clean_publish() (FigshareUploader method)
cli_ask_default() (in module ibllib.pipes.misc)
cli_ask_options() (in module ibllib.pipes.misc)
cm_to_deg() (in module brainbox.behavior.wheel)
cm_to_rad() (in module brainbox.behavior.wheel)
coherence() (in module brainbox.lfp.lfp)
color_cycle() (in module ibllib.plots)
compress() (in module ibllib.io.ffmpeg)
compress_file() (Reader method)
compute() (AlignmentQC method)
(HabituationQC method)
(ONEQC method)
(TaskQC method)
compute_alignment_status() (AlignmentQC method)
compute_bias_info() (in module brainbox.behavior.training)
compute_median_reaction_time() (in module brainbox.behavior.training)
compute_n_trials() (in module brainbox.behavior.training)
compute_performance_easy() (in module brainbox.behavior.training)
compute_psychometric() (in module brainbox.behavior.training)
compute_session_status() (TaskQC method)
compute_similarity_matrix() (AlignmentQC method)
compute_training_info() (in module brainbox.behavior.training)
concatenate_trials() (in module brainbox.behavior.training)
config_dir() (in module oneibl.onelight)
config_file() (in module oneibl.onelight)
confirm_ephys_remote_folder() (in module ibllib.pipes.misc)
confirm_video_remote_folder() (in module ibllib.pipes.misc)
connect() (FtpUploader method)
contamination() (in module brainbox.metrics.metrics)
contamination_alt() (in module brainbox.metrics.metrics)
ContrastLR (class in ibllib.io.extractors.biased_trials)
(class in ibllib.io.extractors.training_trials)
convert_pgts() (in module ibllib.time)
convolve() (in module ibllib.dsp.fourier)
copy() (Bunch method)
,
[1]
(TimeSeries method)
copy_wiring_files() (in module ibllib.pipes.misc)
coverage() (in module ibllib.pipes.histology)
cpu (EphysAudio attribute)
(EphysDLC attribute)
(EphysPulses attribute)
(RawEphysQC attribute)
(Task attribute)
(TrainingAudio attribute)
(TrainingDLC attribute)
create_alyx_probe_insertions() (in module ibllib.pipes.misc)
create_alyx_tasks() (Pipeline method)
create_audio_flags() (in module ibllib.io.flags)
create_channel_dict() (in module ibllib.pipes.histology)
create_compress_video_flags() (in module ibllib.io.flags)
create_create_flags() (in module ibllib.io.flags)
create_custom_ephys_wirings() (in module ibllib.pipes.misc)
create_dataset() (FTPPatcher method)
(Patcher method)
create_dlc_flags() (in module ibllib.io.flags)
create_ephys_flags() (in module ibllib.pipes.misc)
create_ephys_transfer_done_flag() (in module ibllib.pipes.misc)
create_ephyspc_params() (in module ibllib.pipes.misc)
create_extract_flags() (in module ibllib.io.flags)
create_flags() (in module ibllib.io.flags)
create_other_flags() (in module ibllib.io.flags)
create_register_flags() (in module ibllib.io.flags)
create_session() (RegistrationClient method)
create_sessions() (RegistrationClient method)
create_trajectory_dict() (in module ibllib.pipes.histology)
create_transfer_flags() (in module ibllib.io.flags)
create_video_transfer_done_flag() (in module ibllib.pipes.misc)
create_videopc_params() (in module ibllib.pipes.misc)
criteria (TaskQC attribute)
criterion_1a() (in module brainbox.behavior.training)
criterion_1b() (in module brainbox.behavior.training)
criterion_delay() (in module brainbox.behavior.training)
criterion_ephys() (in module brainbox.behavior.training)
csv_as_list() (in module ibllib.io.ascii)
D
data (SessionDataInfo attribute)
dataframe() (in module alf.io)
DataSet (class in brainbox.modeling.dataset)
dataset_id (SessionDataInfo attribute)
dataset_record_to_url() (in module oneibl.webclient)
dataset_type (SessionDataInfo attribute)
date2isostr() (in module ibllib.time)
decode() (in module brainbox.population.population)
decompress_file() (Reader method)
default() (in module oneibl.params)
default_config() (in module oneibl.onelight)
default_download_dir() (in module oneibl.onelight)
default_path (BaseExtractor attribute)
delete() (AlyxClient method)
delete_dataset() (Patcher method)
delete_empty_folders() (in module ibllib.io.misc)
delete_flags() (in module ibllib.io.flags)
delete_session_datasets() (Patcher method)
dense_layout() (in module ibllib.ephys.neuropixel)
Density (class in ibllib.plots)
dephas() (in module ibllib.dsp.fourier)
depth (Insertion attribute)
depth() (in module brainbox.spike_features.spike_features)
descendants() (BrainRegions method)
detect_missing_histology_tracks() (in module ibllib.pipes.histology)
dft() (in module ibllib.dsp.fourier)
dft2() (in module ibllib.dsp.fourier)
differentiate_units() (in module brainbox.task.task)
display_status() (in module brainbox.behavior.training)
download_dataset() (OneAlyx method)
download_datasets() (OneAlyx method)
download_dir() (in module oneibl.onelight)
download_file() (in module oneibl.onelight)
download_raw_partial() (OneAlyx method)
download_taskqc_raw_data() (in module ibllib.qc.oneutils)
driftmap() (in module brainbox.plot.plot)
driftmap_color() (in module brainbox.plot.plot)
dxyz() (BrainCoordinates property)
E
eid (SessionDataInfo attribute)
eid2path() (in module ibllib.misc.exp_ref)
eid2ref() (in module ibllib.misc.exp_ref)
eid_from_path() (OneAbstract method)
(OneAlyx method)
entry() (Insertion property)
EphysAlignment (class in ibllib.pipes.ephys_alignment)
EphysAudio (class in ibllib.pipes.ephys_preprocessing)
EphysCellsQc (class in ibllib.pipes.ephys_preprocessing)
EphysDLC (class in ibllib.pipes.ephys_preprocessing)
EphysExtractionPipeline (class in ibllib.pipes.ephys_preprocessing)
EphysMtscomp (class in ibllib.pipes.ephys_preprocessing)
EphysPulses (class in ibllib.pipes.ephys_preprocessing)
EphysTrials (class in ibllib.pipes.ephys_preprocessing)
EphysVideoCompress (class in ibllib.pipes.ephys_preprocessing)
eq() (in module ibllib.misc.version)
erf_psycho() (in module brainbox.behavior.pyschofit)
erf_psycho_2gammas() (in module brainbox.behavior.pyschofit)
ErrorCueTriggerTimes (class in ibllib.io.extractors.training_trials)
estimate_drift() (in module brainbox.metrics.electrode_drift)
eval_x() (Trajectory method)
eval_y() (Trajectory method)
eval_z() (Trajectory method)
excise_flag_file() (in module ibllib.io.flags)
execute() (in module ibllib.pipes.scan_fix_passive_files)
exists() (in module alf.io)
exit_points() (Trajectory method)
explanation (ALFMultipleCollectionsFound attribute)
(ALFMultipleObjectsFound attribute)
(ALFObjectNotFound attribute)
(AlyxSubjectNotFound attribute)
(IblError attribute)
(Neuropixel3BSyncFrontsNonMatching attribute)
(SyncBpodFpgaException attribute)
(SyncBpodWheelException attribute)
export_to_alf() (in module ibllib.io.certification_protocol)
extract() (BaseBpodTrialsExtractor method)
(BaseExtractor method)
extract_all() (in module ibllib.io.extractors.biased_trials)
(in module ibllib.io.extractors.ephys_fpga)
(in module ibllib.io.extractors.habituation_trials)
(in module ibllib.io.extractors.training_trials)
(in module ibllib.io.extractors.training_wheel)
extract_behaviour_sync() (in module ibllib.io.extractors.ephys_fpga)
extract_camera_sync() (in module ibllib.io.extractors.ephys_fpga)
extract_data() (TaskQCExtractor method)
extract_first_movement_times() (in module ibllib.io.extractors.training_wheel)
extract_passive_periods() (in module ibllib.io.extractors.ephys_passive)
extract_replay_debug() (in module ibllib.io.extractors.ephys_passive)
extract_rfmapping() (in module ibllib.io.extractors.ephys_passive)
extract_rmsmap() (in module ibllib.ephys.ephysqc)
extract_sound() (in module ibllib.io.extractors.training_audio)
extract_stimulus_info_to_alf() (in module ibllib.io.certification_protocol)
extract_sync() (in module ibllib.io.extractors.ephys_fpga)
extract_task_replay() (in module ibllib.io.extractors.ephys_passive)
extract_training() (in module ibllib.pipes.training_preprocessing)
extract_waveforms() (in module brainbox.io.io)
extract_wheel_moves() (in module ibllib.io.extractors.training_wheel)
extract_wheel_sync() (in module ibllib.io.extractors.ephys_fpga)
F
falls() (in module ibllib.dsp.utils)
fcn_cosine() (in module ibllib.dsp.utils)
feat_vars() (in module brainbox.plot.plot)
feature2track() (EphysAlignment static method)
feature2track_lin() (EphysAlignment static method)
FeedbackTimes (class in ibllib.io.extractors.training_trials)
FeedbackType (class in ibllib.io.extractors.training_trials)
fexpand() (in module ibllib.dsp.fourier)
figshare_request() (in module oneibl.onelight)
FigshareOne (class in oneibl.onelight)
FigshareUploader (class in oneibl.onelight)
file_record_to_url() (in module oneibl.webclient)
file_size (SessionDataInfo attribute)
fill_dataframe() (TrialData method)
filter_by() (in module alf.files)
filter_units() (in module brainbox.processing.processing)
find_first_2d() (in module brainbox.io.parquet)
find_mouse_sessions() (in module alf.folders)
find_pairs() (in module ibllib.pipes.scan_fix_passive_files)
find_session_dirs() (in module oneibl.onelight)
find_session_files() (in module oneibl.onelight)
find_sessions() (in module alf.folders)
find_subject_folders() (in module alf.folders)
find_subject_names() (in module alf.folders)
firing_rate() (in module brainbox.plot.plot)
(in module brainbox.singlecell.singlecell)
firing_rate_coeff_var() (in module brainbox.metrics.metrics)
firing_rate_fano_factor() (in module brainbox.metrics.metrics)
firstlast() (WindowGenerator property)
fit() (FittingMethod method)
(MaximumLikelihoodEstimation method)
(Trajectory static method)
fit_cca() (in module brainbox.population.cca)
fit_phase() (in module ibllib.dsp.fourier)
FittingMethod (class in brainbox.modeling.fitting_method)
flatten() (in module ibllib.misc.flatten)
format_date_range() (in module ibllib.time)
format_download_dir() (in module oneibl.onelight)
FpgaTrials (class in ibllib.io.extractors.ephys_fpga)
freduce() (in module ibllib.dsp.fourier)
from_datasets() (SessionDataInfo static method)
from_dict() (in module ibllib.io.params)
(Insertion static method)
from_pandas() (SessionDataInfo static method)
from_session_details() (SessionDataInfo static method)
from_track() (Insertion static method)
fronts() (in module ibllib.dsp.utils)
fs() (Reader property)
fscale() (in module ibllib.dsp.fourier)
FTPPatcher (class in oneibl.patcher)
FtpUploader (class in oneibl.onelight)
G
ge() (in module ibllib.misc.version)
generate_spike_train() (in module brainbox.tests.test_metrics)
get() (AlyxClient method)
(BrainRegions method)
(in module oneibl.params)
get_bpodqc_metrics_frame() (in module ibllib.qc.task_metrics)
get_brain_entry() (Insertion static method)
get_brain_exit() (Insertion static method)
get_brain_locations() (EphysAlignment method)
get_brain_regions() (in module ibllib.pipes.histology)
get_cca_projection() (in module brainbox.population.cca)
get_channel_locations() (EphysAlignment method)
get_config() (in module oneibl.onelight)
get_contrast_reversal_stimulus() (in module ibllib.io.certification_protocol)
get_correlations() (in module brainbox.population.cca)
get_details() (OneAlyx method)
get_event_bin_indexes() (in module brainbox.population.cca)
get_expected_ttl_pulses() (in module ibllib.io.certification_protocol)
get_feedback_times_ge5() (FeedbackTimes static method)
get_feedback_times_lt5() (FeedbackTimes static method)
get_frame() (VideoStreamer method)
get_hardware_config() (in module ibllib.io.spikeglx)
get_histology_regions() (EphysAlignment static method)
get_ibl_sync_map() (in module ibllib.io.extractors.ephys_fpga)
get_iblscripts_folder() (in module ibllib.pipes.misc)
get_included_trials_ge5() (IncludedTrials static method)
get_included_trials_lt5() (IncludedTrials static method)
get_insertion_track() (EphysAlignment method)
get_lab_training_status() (in module brainbox.behavior.training)
get_labels() (BrainAtlas method)
get_micro_manipulator_data() (in module ibllib.pipes.histology)
get_nearest_boundary() (EphysAlignment static method)
get_neuropixel_version_from_files() (in module ibllib.io.spikeglx)
get_neuropixel_version_from_folder() (in module ibllib.io.spikeglx)
get_new_filename() (in module ibllib.pipes.misc)
get_on_off_times_and_positions() (in module brainbox.task.passive)
get_one() (in module oneibl.onelight)
get_perp_vector() (EphysAlignment method)
get_picked_tracks() (in module ibllib.pipes.histology)
get_port_events() (in module ibllib.io.raw_data_loaders)
get_repo() (in module oneibl.onelight)
get_rf_map_over_depth() (in module brainbox.task.passive)
get_rf_ttl_pulses() (in module ibllib.io.certification_protocol)
get_scale_factor() (EphysAlignment method)
get_session_extractor_type() (in module ibllib.io.extractors.base)
get_session_path() (in module alf.io)
(in module ibllib.io.certification_protocol)
get_sessions() (in module brainbox.behavior.training)
get_signed_contrast() (in module brainbox.behavior.training)
get_spacer_times() (in module ibllib.io.certification_protocol)
get_stim_aligned_activity() (in module brainbox.task.passive)
get_stim_num_from_name() (in module ibllib.io.certification_protocol)
get_stimOn_times_ge5() (StimOnTimes static method)
get_stimOn_times_lt5() (StimOnTimes static method)
get_subject_training_status() (in module brainbox.behavior.training)
get_svd_map() (in module brainbox.task.passive)
get_sync_map() (in module ibllib.io.spikeglx)
get_task_extractor_type() (in module ibllib.io.extractors.base)
get_task_stimulus() (in module ibllib.io.certification_protocol)
get_track_and_feature() (EphysAlignment method)
get_training_status() (in module brainbox.behavior.training)
get_trial_start_times() (in module ibllib.io.extractors.training_wheel)
get_units_bunch() (in module brainbox.processing.processing)
get_wheel_position() (in module ibllib.io.extractors.training_wheel)
getfile() (in module ibllib.io.params)
gflatten() (in module ibllib.misc.flatten)
glob_ephys_files() (in module ibllib.io.spikeglx)
GlobusPatcher (class in oneibl.patcher)
GoCueTimes (class in ibllib.io.extractors.training_trials)
GoCueTriggerTimes (class in ibllib.io.extractors.training_trials)
gpu (EphysDLC attribute)
(SpikeSorting_KS2_Matlab attribute)
(Task attribute)
(TrainingDLC attribute)
gt() (in module ibllib.misc.version)
H
HabituationQC (class in ibllib.qc.task_metrics)
HabituationTrials (class in ibllib.io.extractors.habituation_trials)
hash (SessionDataInfo attribute)
help() (OneAlyx method)
hp() (in module ibllib.dsp.fourier)
http_download_file() (in module oneibl.webclient)
http_download_file_list() (in module oneibl.webclient)
HttpOne (class in oneibl.onelight)
I
i2x() (BrainCoordinates method)
i2xyz() (BrainCoordinates method)
i2y() (BrainCoordinates method)
i2z() (BrainCoordinates method)
IblError
ibllib
module
ibllib() (in module ibllib.misc.version)
ibllib.atlas
module
ibllib.atlas.atlas
module
ibllib.dsp
module
ibllib.dsp.fourier
module
ibllib.dsp.savitzky_golay
module
ibllib.dsp.smooth
module
ibllib.dsp.utils
module
ibllib.ephys
module
ibllib.ephys.ephysqc
module
ibllib.ephys.neuropixel
module
ibllib.ephys.spikes
module
ibllib.ephys.sync_probes
module
ibllib.exceptions
module
ibllib.graphic
module
ibllib.io
module
ibllib.io.ascii
module
ibllib.io.certification_protocol
module
ibllib.io.extractors
module
ibllib.io.extractors.base
module
ibllib.io.extractors.biased_trials
module
ibllib.io.extractors.ephys_fpga
module
ibllib.io.extractors.ephys_passive
module
ibllib.io.extractors.habituation_trials
module
ibllib.io.extractors.passive_plotting
module
ibllib.io.extractors.training_audio
module
ibllib.io.extractors.training_trials
module
ibllib.io.extractors.training_wheel
module
ibllib.io.ffmpeg
module
ibllib.io.flags
module
ibllib.io.globus
module
ibllib.io.hashfile
module
ibllib.io.jsonable
module
ibllib.io.misc
module
ibllib.io.npy_header
module
ibllib.io.params
module
ibllib.io.raw_data_loaders
module
ibllib.io.spikeglx
module
ibllib.misc
module
ibllib.misc.exp_ref
module
ibllib.misc.flatten
module
ibllib.misc.misc
module
ibllib.misc.timing
module
ibllib.misc.version
module
ibllib.pipes
module
ibllib.pipes.ephys_alignment
module
ibllib.pipes.ephys_preprocessing
module
ibllib.pipes.histology
module
ibllib.pipes.local_server
module
ibllib.pipes.misc
module
ibllib.pipes.purge_rig_data
module
ibllib.pipes.remote_server
module
ibllib.pipes.scan_fix_passive_files
module
ibllib.pipes.tasks
module
ibllib.pipes.training_preprocessing
module
ibllib.pipes.transfer_rig_data
module
ibllib.plots
module
ibllib.qc
module
ibllib.qc.alignment_qc
module
ibllib.qc.base
module
ibllib.qc.oneqc_metrics
module
ibllib.qc.oneutils
module
ibllib.qc.qcplots
module
ibllib.qc.task_extractors
module
ibllib.qc.task_metrics
module
ibllib.time
module
iblrig_video_compression() (in module ibllib.io.ffmpeg)
id (BrainRegions attribute)
iflatten() (in module ibllib.misc.flatten)
IncludedTrials (class in ibllib.io.extractors.training_trials)
infer_wheel_units() (in module ibllib.io.extractors.training_wheel)
Insertion (class in ibllib.atlas.atlas)
interpolate_along_track() (in module ibllib.pipes.histology)
interpolate_position() (in module brainbox.behavior.wheel)
interpolate_rf_mapping_stimulus() (in module ibllib.io.certification_protocol)
intersect2d() (in module brainbox.core.core)
Intervals (class in ibllib.io.extractors.training_trials)
io_charge (EphysDLC attribute)
(EphysPulses attribute)
(RawEphysQC attribute)
(SpikeSorting_KS2_Matlab attribute)
(Task attribute)
(TrainingDLC attribute)
is_details_dict() (in module alf.io)
is_documented_by() (in module oneibl.onelight)
is_exp_ref() (in module ibllib.misc.exp_ref)
is_file_in_session_dir() (in module oneibl.onelight)
is_mtscomp() (Reader property)
is_session_dir() (in module oneibl.onelight)
is_session_path() (in module alf.io)
is_uuid() (in module alf.io)
is_uuid_string() (in module alf.io)
is_valid() (in module alf.files)
ismember() (in module brainbox.core.core)
ismember2d() (in module brainbox.core.core)
isostr2date() (in module ibllib.time)
iter_files() (FigshareUploader method)
ItiDuration (class in ibllib.io.extractors.training_trials)
ItiInTimes (class in ibllib.io.extractors.habituation_trials)
(class in ibllib.io.extractors.training_trials)
J
job_creator() (in module ibllib.pipes.local_server)
job_run_ks2() (in module ibllib.pipes.remote_server)
job_runner() (in module ibllib.pipes.local_server)
job_transfer_ks2() (in module ibllib.pipes.remote_server)
json_field_delete() (AlyxClient method)
json_field_remove_key() (AlyxClient method)
json_field_update() (AlyxClient method)
json_field_write() (AlyxClient method)
K
keywords() (OneAlyx static method)
ks2_to_alf() (in module ibllib.ephys.spikes)
L
label (EphysExtractionPipeline attribute)
(Insertion attribute)
(TrainingExtractionPipeline attribute)
last_movement_onset() (in module brainbox.behavior.wheel)
launch_transfers() (GlobusPatcher method)
lda_project() (in module brainbox.population.population)
le() (in module ibllib.misc.version)
leaves() (BrainRegions method)
level (BrainRegions attribute)
(EphysAudio attribute)
(EphysCellsQc attribute)
(EphysDLC attribute)
(EphysMtscomp attribute)
(EphysPulses attribute)
(EphysTrials attribute)
(EphysVideoCompress attribute)
(RawEphysQC attribute)
(SpikeSorting_KS2_Matlab attribute)
(Task attribute)
(TrainingAudio attribute)
(TrainingDLC attribute)
(TrainingTrials attribute)
lim() (BrainCoordinates method)
list() (HttpOne method)
(ONE method)
(OneAbstract method)
(OneAlyx method)
(OneOffline method)
Listable() (in module oneibl.one)
load() (Bunch static method)
(in module brainbox.io.parquet)
(OneAbstract method)
(OneAlyx method)
(OneOffline method)
load_ambient_sensor() (in module ibllib.io.raw_data_loaders)
load_array() (in module oneibl.onelight)
load_bpod() (in module ibllib.io.raw_data_loaders)
load_bpod_fronts() (in module ibllib.io.raw_data_loaders)
load_channel_locations() (in module brainbox.io.one)
load_data() (AlignmentQC method)
(in module ibllib.io.raw_data_loaders)
(QC method)
(TaskQC method)
load_dataset() (HttpOne method)
(ONE method)
(OneAlyx method)
load_dstype_qc_metrics() (ONEQC method)
load_encoder_events() (in module ibllib.io.raw_data_loaders)
load_encoder_positions() (in module ibllib.io.raw_data_loaders)
load_encoder_trial_info() (in module ibllib.io.raw_data_loaders)
load_ephys_session() (in module brainbox.io.one)
load_ephyspc_params() (in module ibllib.pipes.misc)
load_file_content() (in module alf.io)
load_lfp() (in module brainbox.io.one)
load_mic() (in module ibllib.io.raw_data_loaders)
load_nDatasetTypes() (ONEQC method)
load_object() (HttpOne method)
(in module alf.io)
(ONE method)
(OneAlyx method)
load_params_dict() (in module ibllib.pipes.misc)
load_raw_data() (TaskQCExtractor method)
load_rf_mapping_stimulus() (in module ibllib.io.certification_protocol)
load_session_metadata() (in module ibllib.io.certification_protocol)
load_settings() (in module ibllib.io.raw_data_loaders)
load_settings_file() (in module ibllib.pipes.scan_fix_passive_files)
load_spike_sorting() (in module brainbox.io.one)
load_spike_sorting_with_channel() (in module brainbox.io.one)
load_stim_position_screen() (in module ibllib.io.raw_data_loaders)
load_track_csv() (in module ibllib.pipes.histology)
load_trials_df() (in module brainbox.io.one)
load_ttl_pulses() (in module ibllib.io.certification_protocol)
load_videopc_params() (in module ibllib.pipes.misc)
load_wheel_reaction_times() (in module brainbox.io.one)
local_path (SessionDataInfo attribute)
LocalOne (class in oneibl.onelight)
log (Task attribute)
logger_config() (in module ibllib.misc.misc)
login() (in module ibllib.graphic)
(in module ibllib.io.globus)
login_auto() (in module ibllib.io.globus)
lp() (in module ibllib.dsp.fourier)
(in module ibllib.dsp.smooth)
lt() (in module ibllib.misc.version)
M
main() (in module ibllib.pipes.transfer_rig_data)
make_graph() (Pipeline method)
make_http_root_file() (in module oneibl.onelight)
MaximumLikelihoodEstimation (class in brainbox.modeling.fitting_method)
md5() (in module ibllib.io.hashfile)
merge_clusters_channels() (in module brainbox.io.one)
mgrid() (BrainCoordinates property)
mindist() (Trajectory method)
missed_spikes_est() (in module brainbox.metrics.metrics)
(in module brainbox.plot.plot)
mktree() (FTPPatcher method)
mle_fit_psycho() (in module brainbox.behavior.pyschofit)
module
alf
alf.files
alf.folders
alf.io
brainbox
brainbox.atlas
brainbox.atlas.atlas
brainbox.behavior
brainbox.behavior.behavior
brainbox.behavior.pyschofit
brainbox.behavior.training
brainbox.behavior.wheel
brainbox.core
brainbox.core.core
brainbox.experimental
brainbox.experimental.experimental
brainbox.io
brainbox.io.io
brainbox.io.one
brainbox.io.parquet
brainbox.lfp
brainbox.lfp.lfp
brainbox.metrics
brainbox.metrics.electrode_drift
brainbox.metrics.metrics
brainbox.modeling
brainbox.modeling.dataset
brainbox.modeling.fitting_method
brainbox.modeling.parameter
brainbox.plot
brainbox.plot.plot
brainbox.population
brainbox.population.cca
brainbox.population.population
brainbox.processing
brainbox.processing.processing
brainbox.quality
brainbox.quality.lfp_qc
brainbox.quality.permutation_test
brainbox.quality.quality
brainbox.simulation
brainbox.simulation.simulation
brainbox.singlecell
brainbox.singlecell.singlecell
brainbox.spike_features
brainbox.spike_features.spike_features
brainbox.task
brainbox.task.passive
brainbox.task.task
brainbox.tests
brainbox.tests.test_behavior
brainbox.tests.test_brainbox_io
brainbox.tests.test_cca
brainbox.tests.test_core
brainbox.tests.test_io
brainbox.tests.test_metrics
brainbox.tests.test_plot
brainbox.tests.test_population
brainbox.tests.test_processing
brainbox.tests.test_singlecell
brainbox.tests.test_task
ibllib
ibllib.atlas
ibllib.atlas.atlas
ibllib.dsp
ibllib.dsp.fourier
ibllib.dsp.savitzky_golay
ibllib.dsp.smooth
ibllib.dsp.utils
ibllib.ephys
ibllib.ephys.ephysqc
ibllib.ephys.neuropixel
ibllib.ephys.spikes
ibllib.ephys.sync_probes
ibllib.exceptions
ibllib.graphic
ibllib.io
ibllib.io.ascii
ibllib.io.certification_protocol
ibllib.io.extractors
ibllib.io.extractors.base
ibllib.io.extractors.biased_trials
ibllib.io.extractors.ephys_fpga
ibllib.io.extractors.ephys_passive
ibllib.io.extractors.habituation_trials
ibllib.io.extractors.passive_plotting
ibllib.io.extractors.training_audio
ibllib.io.extractors.training_trials
ibllib.io.extractors.training_wheel
ibllib.io.ffmpeg
ibllib.io.flags
ibllib.io.globus
ibllib.io.hashfile
ibllib.io.jsonable
ibllib.io.misc
ibllib.io.npy_header
ibllib.io.params
ibllib.io.raw_data_loaders
ibllib.io.spikeglx
ibllib.misc
ibllib.misc.exp_ref
ibllib.misc.flatten
ibllib.misc.misc
ibllib.misc.timing
ibllib.misc.version
ibllib.pipes
ibllib.pipes.ephys_alignment
ibllib.pipes.ephys_preprocessing
ibllib.pipes.histology
ibllib.pipes.local_server
ibllib.pipes.misc
ibllib.pipes.purge_rig_data
ibllib.pipes.remote_server
ibllib.pipes.scan_fix_passive_files
ibllib.pipes.tasks
ibllib.pipes.training_preprocessing
ibllib.pipes.transfer_rig_data
ibllib.plots
ibllib.qc
ibllib.qc.alignment_qc
ibllib.qc.base
ibllib.qc.oneqc_metrics
ibllib.qc.oneutils
ibllib.qc.qcplots
ibllib.qc.task_extractors
ibllib.qc.task_metrics
ibllib.time
oneibl
oneibl.dataclass
oneibl.one
oneibl.onelight
oneibl.params
oneibl.patcher
oneibl.registration
oneibl.stream
oneibl.webclient
move_ephys_files() (in module ibllib.pipes.misc)
move_rename_pairs() (in module ibllib.pipes.scan_fix_passive_files)
movements() (in module brainbox.behavior.wheel)
multi_input() (in module ibllib.graphic)
multiple_spike_trains() (in module brainbox.tests.test_metrics)
N
name (BrainRegions attribute)
name() (Pipeline property)
(Task property)
nc() (Reader property)
NeedlesAtlas() (in module ibllib.atlas.atlas)
neg_likelihood() (in module brainbox.behavior.pyschofit)
Neuropixel3BSyncFrontsNonMatching
next_num_folder() (in module alf.folders)
noise_cutoff() (in module brainbox.metrics.metrics)
np2str() (in module brainbox.io.parquet)
np2uuid() (in module brainbox.io.parquet)
ns() (Reader property)
ns_optim_fft() (in module ibllib.dsp.fourier)
numinput() (in module ibllib.graphic)
nxyz() (BrainCoordinates property)
O
on_key_press() (Density method)
(Traces method)
ONE (class in oneibl.onelight)
one (Pipeline attribute)
(Task attribute)
ONE() (in module oneibl.one)
OneAbstract (class in oneibl.one)
OneAlyx (class in oneibl.one)
oneibl
module
oneibl.dataclass
module
oneibl.one
module
oneibl.onelight
module
oneibl.params
module
oneibl.patcher
module
oneibl.registration
module
oneibl.stream
module
oneibl.webclient
module
OneOffline (class in oneibl.one)
ONEQC (class in ibllib.qc.oneqc_metrics)
outputs (Task attribute)
P
parabolic_max() (in module ibllib.dsp.utils)
Parameter (class in brainbox.modeling.parameter)
parent (BrainRegions attribute)
parse_id() (in module oneibl.one)
PassiveChoiceWorld (class in ibllib.io.extractors.ephys_passive)
patch() (AlyxClient method)
patch_dataset() (Patcher method)
Patcher (class in oneibl.patcher)
path2ref() (in module ibllib.misc.exp_ref)
path_from_eid() (OneAbstract method)
(OneAlyx method)
peri_event_time_histogram() (in module brainbox.plot.plot)
permut_test() (in module brainbox.quality.permutation_test)
phi (Insertion attribute)
phy_model_from_ks2_path() (in module ibllib.ephys.ephysqc)
Pipeline (class in ibllib.pipes.tasks)
plot() (MaximumLikelihoodEstimation method)
plot2d_all() (in module ibllib.pipes.histology)
plot3d_all() (in module ibllib.pipes.histology)
plot_atlas() (in module brainbox.atlas.atlas)
plot_audio_times() (in module ibllib.io.extractors.passive_plotting)
plot_correlations() (in module brainbox.population.cca)
plot_cslice() (BrainAtlas method)
plot_gabor_times() (in module ibllib.io.extractors.passive_plotting)
plot_hslice() (BrainAtlas method)
plot_pairwise_correlations() (in module brainbox.population.cca)
plot_pairwise_correlations_mult() (in module brainbox.population.cca)
plot_passive_periods() (in module ibllib.io.extractors.passive_plotting)
plot_permut_test() (in module brainbox.quality.permutation_test)
plot_results() (in module ibllib.qc.qcplots)
plot_rfmapping() (in module ibllib.io.extractors.passive_plotting)
plot_sslice() (BrainAtlas method)
plot_stims_times() (in module ibllib.io.extractors.passive_plotting)
plot_sync_channels() (in module ibllib.io.extractors.passive_plotting)
plot_tilted_slice() (BrainAtlas method)
plot_top() (BrainAtlas method)
plot_valve_times() (in module ibllib.io.extractors.passive_plotting)
point (Trajectory attribute)
popup() (in module ibllib.graphic)
post() (AlyxClient method)
power_spectrum() (in module brainbox.lfp.lfp)
pprint() (in module ibllib.misc.misc)
preprocess() (in module brainbox.population.cca)
pres_ratio() (in module brainbox.metrics.metrics)
(in module brainbox.plot.plot)
print_progress() (in module ibllib.misc.misc)
(WindowGenerator method)
priority (EphysAudio attribute)
(EphysCellsQc attribute)
(EphysMtscomp attribute)
(EphysPulses attribute)
(EphysTrials attribute)
(EphysVideoCompress attribute)
(RawEphysQC attribute)
(SpikeSorting_KS2_Matlab attribute)
(Task attribute)
(TrainingAudio attribute)
(TrainingRegisterRaw attribute)
(TrainingTrials attribute)
ProbabilityLeft (class in ibllib.io.extractors.training_trials)
ProbaContrasts (class in ibllib.io.extractors.ephys_fpga)
probes_description() (in module ibllib.ephys.spikes)
project() (Trajectory method)
PsychofitTest (class in brainbox.tests.test_behavior)
ptp_over_noise() (in module brainbox.metrics.metrics)
purge_local_data() (in module ibllib.pipes.purge_rig_data)
put() (AlyxClient method)
Q
QC (class in ibllib.qc.base)
qc_fpga_task() (in module ibllib.ephys.ephysqc)
quick_unit_metrics() (in module brainbox.metrics.metrics)
R
r2ix() (BrainCoordinates method)
r2iy() (BrainCoordinates method)
r2iz() (BrainCoordinates method)
ram (Task attribute)
raw_qc_session() (in module ibllib.ephys.ephysqc)
RawEphysQC (class in ibllib.pipes.ephys_preprocessing)
rc2xy() (in module ibllib.ephys.neuropixel)
read() (in module ibllib.io.jsonable)
(in module ibllib.io.npy_header)
(in module ibllib.io.params)
(in module ibllib.io.spikeglx)
(Reader method)
read_flag_file() (in module ibllib.io.flags)
read_meta_data() (in module ibllib.io.spikeglx)
read_root_file() (in module oneibl.onelight)
read_samples() (Reader method)
read_sync() (Reader method)
read_sync_analog() (Reader method)
read_sync_digital() (Reader method)
read_ts() (in module alf.io)
Reader (class in ibllib.io.spikeglx)
rec2col() (in module brainbox.io.parquet)
ref2dict() (in module ibllib.misc.exp_ref)
ref2dj() (in module ibllib.misc.exp_ref)
ref2eid() (in module ibllib.misc.exp_ref)
ref2path() (in module ibllib.misc.exp_ref)
regions_from_allen_csv() (in module ibllib.atlas.atlas)
register_aligned_track() (in module ibllib.pipes.histology)
register_dataset() (in module oneibl.registration)
(Patcher method)
register_datasets() (Task method)
register_session() (RegistrationClient method)
register_session_raw_data() (in module oneibl.registration)
register_sync() (RegistrationClient method)
register_track() (in module ibllib.pipes.histology)
register_track_files() (in module ibllib.pipes.histology)
RegistrationClient (class in oneibl.registration)
remove_empty_folders() (in module alf.folders)
remove_uuid_file() (in module alf.io)
remove_uuid_recursive() (in module alf.io)
rename_data() (TaskQCExtractor static method)
rename_ephys_files() (in module ibllib.pipes.misc)
rename_files_compatibility() (in module oneibl.registration)
rename_session() (in module ibllib.pipes.misc)
RepNum (class in ibllib.io.extractors.training_trials)
repo_dir() (in module oneibl.onelight)
report_health() (in module ibllib.pipes.local_server)
repository() (in module oneibl.onelight)
rerun() (Pipeline method)
(Task method)
rerun_failed() (Pipeline method)
resolve_manual() (AlignmentQC method)
ResponseTimes (class in ibllib.io.extractors.training_trials)
responsive_units() (in module brainbox.task.task)
rest() (AlyxClient method)
RewardVolume (class in ibllib.io.extractors.training_trials)
rgb (BrainRegions attribute)
rises() (in module ibllib.dsp.utils)
rms() (in module ibllib.dsp.utils)
rmsmap() (in module ibllib.ephys.ephysqc)
roc_between_two_events() (in module brainbox.task.task)
roc_single_event() (in module brainbox.task.task)
rolling_window() (in module ibllib.dsp.smooth)
run() (AlignmentQC method)
(Pipeline method)
(QC method)
(Task method)
(TaskQC method)
run_alyx_task() (in module ibllib.pipes.tasks)
run_extractor_classes() (in module ibllib.io.extractors.base)
S
samples_to_cm() (in module brainbox.behavior.wheel)
save() (Bunch method)
(in module brainbox.io.parquet)
save_bool() (in module ibllib.io.raw_data_loaders)
save_metadata() (in module alf.io)
save_names (BaseExtractor attribute)
(CameraTimestamps attribute)
,
[1]
(Choice attribute)
(ContrastLR attribute)
,
[1]
(ErrorCueTriggerTimes attribute)
(FeedbackTimes attribute)
(FeedbackType attribute)
(FpgaTrials attribute)
(GoCueTimes attribute)
(GoCueTriggerTimes attribute)
(IncludedTrials attribute)
(Intervals attribute)
(ItiDuration attribute)
(ItiInTimes attribute)
,
[1]
(PassiveChoiceWorld attribute)
(ProbabilityLeft attribute)
(ProbaContrasts attribute)
(RepNum attribute)
(ResponseTimes attribute)
(RewardVolume attribute)
(StimCenterTimes attribute)
(StimCenterTriggerTimes attribute)
(StimFreezeTriggerTimes attribute)
(StimOffTriggerTimes attribute)
,
[1]
(StimOnOffFreezeTimes attribute)
(StimOnTimes attribute)
(StimOnTriggerTimes attribute)
(TrialType attribute)
(Wheel attribute)
save_object_npy() (in module alf.io)
savitzky_golay() (in module ibllib.dsp.savitzky_golay)
scale_histology_regions() (EphysAlignment method)
search() (HttpOne method)
(in module alf.folders)
(ONE method)
(OneAbstract method)
(OneAlyx method)
(OneOffline method)
search_terms() (ONE method)
(OneAlyx static method)
session_name() (in module alf.folders)
session_path (BaseExtractor attribute)
session_path() (in module alf.folders)
SessionDataInfo (class in oneibl.dataclass)
set_config() (in module oneibl.onelight)
set_download_dir() (ONE method)
set_figshare_url() (in module oneibl.onelight)
(ONE method)
set_local_dir() (ONE method)
set_repo() (in module oneibl.onelight)
settings (BaseBpodTrialsExtractor attribute)
setup() (in module ibllib.io.globus)
(in module oneibl.params)
(OneAlyx static method)
setUp() (PsychofitTest method)
(Task method)
(TestIO_ALF method)
(TestTask method)
(TestTraining method)
(TestWheel method)
setup_alyx_params() (in module oneibl.params)
setup_silent() (in module oneibl.params)
sha1() (in module ibllib.io.hashfile)
shape() (Reader property)
shift() (in module ibllib.dsp.fourier)
shuffle_analysis() (in module brainbox.population.cca)
slice() (BrainAtlas method)
(WindowGenerator property)
slice_array() (WindowGenerator method)
slidingRP_viol() (in module brainbox.metrics.metrics)
smooth_demo() (in module ibllib.dsp.smooth)
spectrum() (in module ibllib.plots)
sph2cart() (in module ibllib.atlas.atlas)
spike_sorting_metrics() (in module brainbox.metrics.metrics)
spike_sorting_metrics_ks2() (in module ibllib.ephys.ephysqc)
SpikeSorting_KS2_Matlab (class in ibllib.pipes.ephys_preprocessing)
split_by_area() (in module brainbox.population.cca)
split_sync() (in module ibllib.io.spikeglx)
split_timepoints() (in module brainbox.population.cca)
split_trials() (in module brainbox.population.cca)
squares() (in module ibllib.plots)
SSHPatcher (class in oneibl.patcher)
StimCenterTimes (class in ibllib.io.extractors.habituation_trials)
StimCenterTriggerTimes (class in ibllib.io.extractors.habituation_trials)
StimFreezeTriggerTimes (class in ibllib.io.extractors.training_trials)
StimOffTriggerTimes (class in ibllib.io.extractors.habituation_trials)
(class in ibllib.io.extractors.training_trials)
StimOnOffFreezeTimes (class in ibllib.io.extractors.training_trials)
StimOnTimes (class in ibllib.io.extractors.training_trials)
StimOnTriggerTimes (class in ibllib.io.extractors.training_trials)
str2np() (in module brainbox.io.parquet)
strinput() (in module ibllib.graphic)
structarr() (in module ibllib.misc.misc)
subjects_data_folder() (in module alf.folders)
sync() (in module brainbox.processing.processing)
(in module ibllib.ephys.sync_probes)
sync_probe_front_times() (in module ibllib.ephys.sync_probes)
sync_rotary_encoder() (in module ibllib.io.extractors.training_wheel)
sync_spike_sorting() (in module ibllib.ephys.spikes)
sync_trials_robust() (in module ibllib.io.raw_data_loaders)
SyncBpodFpgaException
SyncBpodWheelException
T
Task (class in ibllib.pipes.tasks)
TaskQC (class in ibllib.qc.task_metrics)
TaskQCExtractor (class in ibllib.qc.task_extractors)
tasks (Pipeline attribute)
tasks_runner() (in module ibllib.pipes.local_server)
tearDown() (PsychofitTest method)
(Task method)
(TestIO_ALF method)
test_acorr_0() (TestPopulation method)
test_acorr_1() (TestPopulation method)
test_amp_heatmap() (in module brainbox.tests.test_plot)
test_bincount_2d() (TestProcessing method)
test_bunch_io() (TestBunch method)
test_clusters_metrics() (in module brainbox.tests.test_metrics)
test_concatenate_and_computations() (TestTraining method)
test_derivative() (TestWheel method)
test_differentiate_units() (TestTask method)
test_direction_changes() (TestWheel method)
test_drift_estimate() (in module brainbox.tests.test_metrics)
test_erf_psycho() (PsychofitTest method)
test_erf_psycho_2gammas() (PsychofitTest method)
test_feat_cutoff() (in module brainbox.tests.test_plot)
test_feat_vars() (in module brainbox.tests.test_plot)
test_firing_rate() (in module brainbox.tests.test_plot)
(in module brainbox.tests.test_singlecell)
test_get_spike_counts_in_bins() (TestTask method)
test_get_unit_bunches() (in module brainbox.tests.test_processing)
test_in_training() (TestTraining method)
test_ismember() (TestIsmember method)
test_load_ephys() (TestIO_ALF method)
test_mle_fit_psycho() (PsychofitTest method)
test_movements() (TestWheel method)
test_movements_FPGA() (TestWheel method)
test_neg_likelihood() (PsychofitTest method)
test_peths_synthetic() (TestPeths method)
test_plotting() (TestBunch method)
test_psychometric_insufficient_data() (TestTraining method)
test_ready4delay() (TestTraining method)
test_ready4ephys() (TestTraining method)
test_ready4recording() (TestTraining method)
test_rec2col() (TestParquet method)
test_responsive_units() (TestTask method)
test_roc_between_two_events() (TestTask method)
test_roc_single_event() (TestTask method)
test_single_unit_wf_comp() (in module brainbox.tests.test_plot)
test_sync() (TestBunch method)
(TestProcessing method)
test_traces_by_trial() (TestWheel method)
test_trained_1a() (TestTraining method)
test_trained_1b() (TestTraining method)
test_training_to_bias() (TestTraining method)
test_uuids_conversions() (TestParquet method)
test_uuids_intersections() (TestParquet method)
test_weibull() (PsychofitTest method)
test_weibull50() (PsychofitTest method)
test_xcorr_0() (TestPopulation method)
test_xcorr_1() (TestPopulation method)
test_xcorr_2() (TestPopulation method)
TestBunch (class in brainbox.tests.test_cca)
(class in brainbox.tests.test_core)
TestIO_ALF (class in brainbox.tests.test_brainbox_io)
TestIsmember (class in brainbox.tests.test_core)
TestParquet (class in brainbox.tests.test_io)
TestPeths (class in brainbox.tests.test_singlecell)
TestPopulation (class in brainbox.tests.test_population)
(class in brainbox.tests.test_singlecell)
TestProcessing (class in brainbox.tests.test_processing)
TestTask (class in brainbox.tests.test_task)
TestTraining (class in brainbox.tests.test_behavior)
TestWheel (class in brainbox.tests.test_behavior)
theta (Insertion attribute)
tilted_slice() (BrainAtlas method)
time_elapsed_secs (Task attribute)
time_out_secs (Task attribute)
TimeSeries (class in brainbox.core.core)
timing() (in module ibllib.misc.timing)
tip() (Insertion property)
to_alf() (in module alf.files)
to_df() (AlfBunch method)
(Bunch method)
to_eid() (OneAlyx method)
Traces (class in ibllib.plots)
traces_by_trial() (in module brainbox.behavior.wheel)
track2feature() (EphysAlignment static method)
TrainingAudio (class in ibllib.pipes.training_preprocessing)
TrainingDLC (class in ibllib.pipes.training_preprocessing)
TrainingExtractionPipeline (class in ibllib.pipes.training_preprocessing)
TrainingRegisterRaw (class in ibllib.pipes.training_preprocessing)
TrainingTrials (class in ibllib.pipes.training_preprocessing)
TrainingVideoCompress (class in ibllib.pipes.training_preprocessing)
Trajectory (class in ibllib.atlas.atlas)
trajectory() (Insertion property)
transfer_folder() (in module ibllib.pipes.misc)
trial_times_to_times() (in module ibllib.io.raw_data_loaders)
TrialData (class in brainbox.modeling.dataset)
TrialType (class in ibllib.io.extractors.training_trials)
tscale() (WindowGenerator method)
type() (Reader property)
U
uncycle_pgts() (in module ibllib.time)
UniqueSingletons (class in oneibl.webclient)
unit_labels() (in module brainbox.metrics.metrics)
unit_stability() (in module brainbox.metrics.metrics)
update() (QC method)
update_experimenter_evaluation() (AlignmentQC method)
update_extended_qc() (QC method)
update_repo() (in module oneibl.onelight)
upload() (FtpUploader method)
upload_channels() (AlignmentQC method)
upload_dir() (FigshareUploader method)
url (SessionDataInfo attribute)
uuid2np() (in module brainbox.io.parquet)
V
validate_ttl_test() (in module ibllib.ephys.ephysqc)
var_name (TrialType attribute)
var_names (CameraTimestamps attribute)
,
[1]
(Choice attribute)
(ContrastLR attribute)
,
[1]
(ErrorCueTriggerTimes attribute)
(FeedbackTimes attribute)
(FeedbackType attribute)
(FpgaTrials attribute)
(GoCueTimes attribute)
(GoCueTriggerTimes attribute)
(HabituationTrials attribute)
(IncludedTrials attribute)
(Intervals attribute)
(ItiDuration attribute)
(ItiInTimes attribute)
,
[1]
(PassiveChoiceWorld attribute)
(ProbabilityLeft attribute)
(ProbaContrasts attribute)
(RepNum attribute)
(ResponseTimes attribute)
(RewardVolume attribute)
(StimCenterTimes attribute)
(StimCenterTriggerTimes attribute)
(StimFreezeTriggerTimes attribute)
(StimOffTriggerTimes attribute)
,
[1]
(StimOnOffFreezeTimes attribute)
(StimOnTimes attribute)
(StimOnTriggerTimes attribute)
(Wheel attribute)
vector (Trajectory attribute)
velocity_smoothed() (in module brainbox.behavior.wheel)
verify_hash() (Reader method)
version (Task attribute)
version() (Reader property)
version3A() (in module ibllib.ephys.sync_probes)
version3B() (in module ibllib.ephys.sync_probes)
vertical_lines() (in module ibllib.plots)
VideoStreamer (class in oneibl.stream)
W
walk() (in module oneibl.onelight)
weibull() (in module brainbox.behavior.pyschofit)
weibull50() (in module brainbox.behavior.pyschofit)
welchogram() (in module ibllib.io.extractors.training_audio)
wf_comp() (in module brainbox.plot.plot)
wf_similarity() (in module brainbox.metrics.metrics)
Wheel (class in ibllib.io.extractors.training_wheel)
wiggle() (in module ibllib.plots)
WindowGenerator (class in ibllib.dsp.utils)
within_ranges() (in module brainbox.behavior.wheel)
write() (in module ibllib.io.jsonable)
(in module ibllib.io.params)
write_flag_file() (in module ibllib.io.flags)
write_root_file() (in module oneibl.onelight)
X
x (Insertion attribute)
x2i() (BrainCoordinates method)
xcorr() (in module brainbox.population.population)
xlim() (BrainCoordinates property)
xscale() (BrainCoordinates property)
xyz() (Insertion property)
xyz2ccf() (AllenAtlas method)
xyz2i() (BrainCoordinates method)
Y
y (Insertion attribute)
y2i() (BrainCoordinates method)
ylim() (BrainCoordinates property)
yscale() (BrainCoordinates property)
Z
z (Insertion attribute)
z2i() (BrainCoordinates method)
zlim() (BrainCoordinates property)
zscale() (BrainCoordinates property)