Index

A

acorr() (in module brainbox.singlecell) acronym (BrainRegions attribute) adc_shifts() (in module ibllib.ephys.neuropixel) add_default_handler() (in module oneibl.onelight) add_lines() (DefaultPlot method) (in module brainbox.plot_base) 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.tests module alf.tests.test_alf_files module alf.tests.test_alf_folders module alf.tests.test_alf_io module alf_parts() (in module alf.files) AlfBunch (class in alf.io)

ALFMultipleCollectionsFound ALFMultipleObjectsFound ALFObjectNotFound align_all_trials() (MotionAlignment method) align_motion() (MotionAlignment method) align_with_audio() (in module ibllib.io.extractors.camera) 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) ancestors() (BrainRegions method) append() (AlfBunch method) (in module ibllib.io.jsonable) (SessionDataInfo method) apply_sync() (in module ibllib.ephys.sync_probes) arrange_channels2banks() (in module brainbox.plot_base) arrange_into_regions() (EphysAlignment static method) as_dict() (in module ibllib.io.params) as_globus_path() (in module ibllib.io.globus) assert_eq() (TestVersionTags method) assert_g() (TestVersionTags method) assert_l() (TestVersionTags method) assert_read_glx() (TestsSpikeGLX_Meta method) assert_valid_label() (in module ibllib.io.video) attribute_times() (in module ibllib.io.extractors.camera) authenticate() (AlyxClient method) average_drift() (in module brainbox.metrics.single_units)

B

BaseBpodTrialsExtractor (class in ibllib.io.extractors.base) BaseExtractor (class in ibllib.io.extractors.base) bbox (DlcQC attribute) bc (BrainAtlas attribute) behavior_exists() (in module ibllib.pipes.misc) beta (Insertion attribute) between_sorted() (in module brainbox.numerical) bin_spikes() (in module brainbox.processing) bin_spikes_trials() (in module brainbox.population.cca) bincount2D() (in module brainbox.processing) bp() (in module ibllib.dsp.fourier) bpod_trials (BaseBpodTrialsExtractor attribute) BrainAtlas (class in ibllib.atlas.atlas) brainbox module brainbox.atlas module brainbox.behavior module brainbox.behavior.pyschofit module brainbox.behavior.training module brainbox.behavior.wheel module brainbox.core module brainbox.ephys_plots module brainbox.experimental module brainbox.io module brainbox.io.one module brainbox.io.parquet module brainbox.io.spikeglx module brainbox.lfp module brainbox.metrics module brainbox.metrics.electrode_drift module brainbox.metrics.single_units module brainbox.modeling module brainbox.modeling.dataset module brainbox.modeling.fitting_method module brainbox.modeling.parameter module brainbox.numerical module brainbox.plot module brainbox.plot_base module

brainbox.population module brainbox.population.cca module brainbox.population.decode module brainbox.processing module brainbox.quality module brainbox.quality.lfp_qc module brainbox.quality.permutation_test module brainbox.singlecell module brainbox.spike_features module brainbox.task module brainbox.task.closed_loop module brainbox.task.passive module brainbox.tests module brainbox.tests.test_behavior module brainbox.tests.test_cca module brainbox.tests.test_core module brainbox.tests.test_io module brainbox.tests.test_metrics module brainbox.tests.test_numerical module brainbox.tests.test_passive module brainbox.tests.test_plot_base module brainbox.tests.test_population module brainbox.tests.test_processing module brainbox.tests.test_singlecell module brainbox.tests.test_task module brainbox.tests.test_video module brainbox.video module BrainCoordinates (class in ibllib.atlas.atlas) BrainRegions (class in ibllib.atlas.regions) Bunch (class in brainbox.core) (class in oneibl.onelight) butter_filter() (in module brainbox.lfp)

C

calculate_peths() (in module brainbox.singlecell) CameraQC (class in ibllib.qc.camera) CameraTimestampsBpod (class in ibllib.io.extractors.camera) CameraTimestampsFPGA (class in ibllib.io.extractors.camera) cart2sph() (in module ibllib.atlas.atlas) ccf2xyz() (AllenAtlas method) check_audio_pre_trial() (in module ibllib.qc.task_metrics) check_brightness() (CameraQC method) check_camera_times() (CameraQC method) 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_dropped_frames() (CameraQC method) check_error_trial_event_sequence() (in module ibllib.qc.task_metrics) check_errorCue_delays() (in module ibllib.qc.task_metrics) check_file_headers() (CameraQC method) check_focus() (CameraQC method) check_framerate() (CameraQC method) check_goCue_delays() (in module ibllib.qc.task_metrics) check_iti_delays() (in module ibllib.qc.task_metrics) check_lick_detection() (DlcQC method) check_mean_in_bbox() (DlcQC method) check_n_trial_events() (in module ibllib.qc.task_metrics) check_negative_feedback_stimOff_delays() (in module ibllib.qc.task_metrics) check_pin_state() (CameraQC method) check_position() (CameraQC method) check_positive_feedback_stimOff_delays() (in module ibllib.qc.task_metrics) check_pupil_blocked() (DlcQC method) check_resolution() (CameraQC method) 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_time_trace_length_match() (DlcQC method) check_timestamps() (CameraQC method) check_trace_all_nan() (DlcQC method) check_transfer() (in module ibllib.pipes.misc) check_trial_length() (in module ibllib.qc.task_metrics) check_wheel_alignment() (CameraQC method) 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) classify() (in module brainbox.population.decode) 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) code_to_outcome() (QC static method) coherence() (in module brainbox.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_cluster_average() (in module brainbox.processing) compute_labels() (in module brainbox.metrics.single_units) 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.single_units) contamination_alt() (in module brainbox.metrics.single_units) ContrastLR (class in ibllib.io.extractors.biased_trials) (class in ibllib.io.extractors.training_trials) convert2dict() (DefaultPlot method) 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) (EphysPassive 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) 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_fake_alf_folder_dlc_data() (in module ibllib.tests.fixtures.utils) create_fake_complete_ephys_session() (in module ibllib.tests.fixtures.utils) create_fake_ephys_recording_bad_passive_transfer_sessions() (in module ibllib.tests.fixtures.utils) create_fake_raw_behavior_data_folder() (in module ibllib.tests.fixtures.utils) create_fake_raw_ephys_data_folder() (in module ibllib.tests.fixtures.utils) create_fake_raw_video_data_folder() (in module ibllib.tests.fixtures.utils) create_fake_session_folder() (in module ibllib.tests.fixtures.utils) 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) data_for_keys() (in module ibllib.qc.camera) 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) datasets_from_type() (OneAlyx method) date2isostr() (in module ibllib.time) decode() (in module brainbox.population.decode) 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) DefaultPlot (class in brainbox.plot_base) delete() (AlyxClient method) delete_empty_folders() (in module ibllib.io.misc) delete_flags() (in module ibllib.io.flags) 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) 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.closed_loop) display_status() (in module brainbox.behavior.training) DlcQC (class in ibllib.qc.dlc) download_dataset() (OneAlyx method) download_datasets() (OneAlyx method) download_dir() (in module oneibl.onelight) download_file() (AlyxClient method) (in module oneibl.onelight) download_raw_partial() (OneAlyx method) driftmap() (in module brainbox.plot) driftmap_color() (in module brainbox.plot) dstypes (CameraQC attribute) (DlcQC attribute) dstypes_fpga (CameraQC attribute) 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) EphysPassive (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) extent() (BrainAtlas method) extract() (BaseBpodTrialsExtractor method) (BaseExtractor method) extract_all() (in module ibllib.io.extractors.biased_trials) (in module ibllib.io.extractors.bpod_trials) (in module ibllib.io.extractors.camera) (in module ibllib.io.extractors.ephys_fpga) (in module ibllib.io.extractors.habituation_trials) (in module ibllib.io.extractors.opto_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.camera) 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_waveforms() (in module brainbox.io.spikeglx) 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) 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) find_face() (CameraQC method) find_first_2d() (in module brainbox.numerical) find_mouse_sessions() (in module alf.folders) find_nearest() (in module ibllib.io.extractors.video_motion) 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) (in module brainbox.singlecell)

firing_rate_coeff_var() (in module brainbox.metrics.single_units) firing_rate_fano_factor() (in module brainbox.metrics.single_units) 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) frame_diff() (in module brainbox.video) frame_diffs() (in module brainbox.video) 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) fshift() (in module ibllib.dsp.fourier) FTPPatcher (class in oneibl.patcher) FtpUploader (class in oneibl.onelight)

G

ge() (in module ibllib.misc.version) generate_pseudo_blocks() (in module brainbox.task.closed_loop) generate_pseudo_session() (in module brainbox.task.closed_loop) generate_pseudo_stimuli() (in module brainbox.task.closed_loop) generate_spike_train() (in module brainbox.tests.test_metrics) get() (AlyxClient method) (BrainRegions method) (in module oneibl.params) get_active_wheel_period() (CameraQC static method) 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_diameter() (DlcQC 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_local_endpoint() (in module ibllib.io.globus) get_main_probe_sync() (in module ibllib.io.extractors.ephys_fpga) 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_pregenerated_events() (ProbaContrasts static method) 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_spike_counts_in_bins() (in module brainbox.population.decode) 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) get_video_frame() (in module ibllib.io.video) get_video_frames_preload() (in module ibllib.io.video) get_video_length() (in module ibllib.io.extractors.camera) get_video_meta() (in module ibllib.io.video) 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) globus_path_from_dataset() (in module oneibl.webclient) 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) groom_pin_state() (in module ibllib.io.extractors.camera) 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.atlas.regions 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.bpod_trials module ibllib.io.extractors.camera module ibllib.io.extractors.ephys_fpga module ibllib.io.extractors.ephys_passive module ibllib.io.extractors.habituation_trials module ibllib.io.extractors.opto_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.extractors.video_motion 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.io.video 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.camera module ibllib.qc.dlc module ibllib.qc.oneqc_metrics module ibllib.qc.qcplots module ibllib.qc.task_extractors module ibllib.qc.task_metrics module ibllib.tests module ibllib.tests.extractors module ibllib.tests.extractors.test_ephys_fpga module ibllib.tests.extractors.test_ephys_passive module ibllib.tests.extractors.test_ephys_trials module ibllib.tests.extractors.test_extractors module ibllib.tests.extractors.test_folders module ibllib.tests.fixtures module ibllib.tests.fixtures.utils module ibllib.tests.qc module ibllib.tests.qc.test_alignment_qc module ibllib.tests.qc.test_base_qc module ibllib.tests.qc.test_camera_qc module ibllib.tests.qc.test_dlc_qc module ibllib.tests.qc.test_oneqc_metrics module ibllib.tests.qc.test_task_metrics module ibllib.tests.test_atlas module ibllib.tests.test_dsp module ibllib.tests.test_ephys module ibllib.tests.test_histology module ibllib.tests.test_io module ibllib.tests.test_misc module ibllib.tests.test_pipes module ibllib.tests.test_tasks module ibllib.tests.test_time module ibllib.time module iblrig_video_compression() (in module ibllib.io.ffmpeg) id (BrainRegions attribute) iflatten() (in module ibllib.misc.flatten) image_crosscorr_plot() (in module brainbox.ephys_plots) image_fr_plot() (in module brainbox.ephys_plots) image_lfp_spectrum_plot() (in module brainbox.ephys_plots) image_rms_plot() (in module brainbox.ephys_plots) ImagePlot (class in brainbox.plot_base) imshow() (CameraQC static method) 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.numerical) Intervals (class in ibllib.io.extractors.training_trials) io_charge (EphysDLC attribute) (EphysPassive attribute) (EphysPulses attribute) (RawEphysQC attribute) (SpikeSorting_KS2_Matlab attribute) (Task attribute) (TrainingDLC attribute) ipeak (TestParabolicMax 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.numerical) ismember2d() (in module brainbox.numerical) isostr2date() (in module ibllib.time) iter_files() (FigshareUploader method) ItiDuration (class in ibllib.io.extractors.training_trials) ItiInTimes (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) ks2_to_tar() (in module ibllib.ephys.spikes)

L

label (EphysExtractionPipeline attribute) (Insertion attribute) (TrainingExtractionPipeline attribute) label_from_path() (in module ibllib.io.video) LaserBool (class in ibllib.io.extractors.opto_trials) last_movement_onset() (in module brainbox.behavior.wheel) launch_transfers() (GlobusPatcher method) launch_transfers_secondary() (GlobusPatcher method) lda_project() (in module brainbox.population.decode) le() (in module ibllib.misc.version) leaves() (BrainRegions method) level (BrainRegions attribute) (EphysAudio attribute) (EphysCellsQc attribute) (EphysDLC attribute) (EphysMtscomp attribute) (EphysPassive attribute) (EphysPulses attribute) (EphysTrials attribute) (EphysVideoCompress attribute) (RawEphysQC attribute) (SpikeSorting_KS2_Matlab attribute) (Task attribute) (Task02_error attribute) (Task10 attribute) (Task11 attribute) (TrainingAudio attribute) (TrainingDLC attribute) (TrainingTrials attribute) lim() (BrainCoordinates method) line_amp_plot() (in module brainbox.ephys_plots) line_fr_plot() (in module brainbox.ephys_plots) LinePlot (class in brainbox.plot_base) 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_camera_frame_count() (in module ibllib.io.raw_data_loaders) load_camera_gpio() (in module ibllib.io.raw_data_loaders) load_camera_ssv_times() (in module ibllib.io.raw_data_loaders) load_channel_locations() (in module brainbox.io.one) load_data() (AlignmentQC method) (CameraQC method) (DlcQC method) (in module ibllib.io.raw_data_loaders) (MotionAlignment method) (QC method) (TaskQC method)

load_dataset() (HttpOne method) (ONE method) (OneAlyx method) load_dstype_qc_metrics() (ONEQC method) load_embedded_frame_data() (in module ibllib.io.raw_data_loaders) 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_fake_bpod_data() (TestHabituationQC static method) (TestTaskMetrics static method) load_fake_wheel_data() (TestTaskMetrics static method) 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_passive_rfmap() (in module brainbox.io.one) load_raw_data() (TaskQCExtractor method) load_reference_frames() (CameraQC static 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_video_data() (CameraQC method) 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) maxi (TestParabolicMax attribute) 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.single_units) (in module brainbox.plot) mktree() (FTPPatcher method) mle_fit_psycho() (in module brainbox.behavior.pyschofit) MockExtracor (class in ibllib.tests.extractors.test_extractors) module alf alf.files alf.folders alf.io alf.tests alf.tests.test_alf_files alf.tests.test_alf_folders alf.tests.test_alf_io brainbox brainbox.atlas brainbox.behavior brainbox.behavior.pyschofit brainbox.behavior.training brainbox.behavior.wheel brainbox.core brainbox.ephys_plots brainbox.experimental brainbox.io brainbox.io.one brainbox.io.parquet brainbox.io.spikeglx brainbox.lfp brainbox.metrics brainbox.metrics.electrode_drift brainbox.metrics.single_units brainbox.modeling brainbox.modeling.dataset brainbox.modeling.fitting_method brainbox.modeling.parameter brainbox.numerical brainbox.plot brainbox.plot_base brainbox.population brainbox.population.cca brainbox.population.decode brainbox.processing brainbox.quality brainbox.quality.lfp_qc brainbox.quality.permutation_test brainbox.singlecell brainbox.spike_features brainbox.task brainbox.task.closed_loop brainbox.task.passive brainbox.tests brainbox.tests.test_behavior brainbox.tests.test_cca brainbox.tests.test_core brainbox.tests.test_io brainbox.tests.test_metrics brainbox.tests.test_numerical brainbox.tests.test_passive brainbox.tests.test_plot_base brainbox.tests.test_population brainbox.tests.test_processing brainbox.tests.test_singlecell brainbox.tests.test_task brainbox.tests.test_video brainbox.video ibllib ibllib.atlas ibllib.atlas.atlas ibllib.atlas.regions 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.bpod_trials ibllib.io.extractors.camera ibllib.io.extractors.ephys_fpga ibllib.io.extractors.ephys_passive ibllib.io.extractors.habituation_trials ibllib.io.extractors.opto_trials ibllib.io.extractors.passive_plotting ibllib.io.extractors.training_audio ibllib.io.extractors.training_trials ibllib.io.extractors.training_wheel ibllib.io.extractors.video_motion 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.io.video 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.camera ibllib.qc.dlc ibllib.qc.oneqc_metrics ibllib.qc.qcplots ibllib.qc.task_extractors ibllib.qc.task_metrics ibllib.tests ibllib.tests.extractors ibllib.tests.extractors.test_ephys_fpga ibllib.tests.extractors.test_ephys_passive ibllib.tests.extractors.test_ephys_trials ibllib.tests.extractors.test_extractors ibllib.tests.extractors.test_folders ibllib.tests.fixtures ibllib.tests.fixtures.utils ibllib.tests.qc ibllib.tests.qc.test_alignment_qc ibllib.tests.qc.test_base_qc ibllib.tests.qc.test_camera_qc ibllib.tests.qc.test_dlc_qc ibllib.tests.qc.test_oneqc_metrics ibllib.tests.qc.test_task_metrics ibllib.tests.test_atlas ibllib.tests.test_dsp ibllib.tests.test_ephys ibllib.tests.test_histology ibllib.tests.test_io ibllib.tests.test_misc ibllib.tests.test_pipes ibllib.tests.test_tasks ibllib.tests.test_time ibllib.time oneibl oneibl.dataclass oneibl.one oneibl.onelight oneibl.params oneibl.patcher oneibl.registration oneibl.stream oneibl.tests oneibl.tests.test_alyxclient oneibl.tests.test_alyxrest oneibl.tests.test_dataclass oneibl.tests.test_one oneibl.tests.test_one2 oneibl.tests.test_one_tutorial oneibl.tests.test_oneutils oneibl.tests.test_params oneibl.tests.test_registration oneibl.webclient

motion_energy() (in module brainbox.video) MotionAlignment (class in ibllib.io.extractors.video_motion) 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.single_units) 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) one_path_from_dataset() (in module oneibl.webclient) 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.tests module

oneibl.tests.test_alyxclient module oneibl.tests.test_alyxrest module oneibl.tests.test_dataclass module oneibl.tests.test_one module oneibl.tests.test_one2 module oneibl.tests.test_one_tutorial module oneibl.tests.test_oneutils module oneibl.tests.test_params module oneibl.tests.test_registration module oneibl.webclient module OneOffline (class in oneibl.one) ONEQC (class in ibllib.qc.oneqc_metrics) outcome() (QC property) outputs (Task attribute) overall_outcome() (QC static method)

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) patch_datasets() (GlobusPatcher method) (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) 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_alignment() (MotionAlignment method) plot_atlas() (in module brainbox.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_image() (in module brainbox.plot_base) plot_line() (in module brainbox.plot_base) 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_probe() (in module brainbox.plot_base) plot_results() (in module ibllib.qc.qcplots) plot_rfmapping() (in module ibllib.io.extractors.passive_plotting) plot_scatter() (in module brainbox.plot_base) 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) populate_bad_folders() (TestPipesMisc method) populate_task_settings() (in module ibllib.tests.fixtures.utils) popup() (in module ibllib.graphic) post() (AlyxClient method) power_spectrum() (in module brainbox.lfp) pprint() (in module ibllib.misc.misc) preprocess() (in module brainbox.population.cca) pres_ratio() (in module brainbox.metrics.single_units) (in module brainbox.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) probe_lfp_spectrum_plot() (in module brainbox.ephys_plots) probe_rms_plot() (in module brainbox.ephys_plots) ProbePlot (class in brainbox.plot_base) probes_description() (in module ibllib.ephys.spikes) project() (Trajectory method) PsychofitTest (class in brainbox.tests.test_behavior) ptp_over_noise() (in module brainbox.metrics.single_units) 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.single_units)

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.regions) register_aligned_track() (in module ibllib.pipes.histology) register_dataset() (in module oneibl.registration) (Patcher method) register_datasets() (Patcher method) (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)

regress() (in module brainbox.population.decode) 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.closed_loop) 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.closed_loop) roc_single_event() (in module brainbox.task.closed_loop) roi (MotionAlignment attribute) rolling_window() (in module ibllib.dsp.smooth) run() (AlignmentQC method) (CameraQC method) (DlcQC method) (Pipeline method) (QC method) (Task method) (TaskQC method) run_all_qc() (in module ibllib.qc.camera) (in module ibllib.qc.dlc) 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) (CameraTimestampsBpod attribute) (Choice attribute) (ContrastLR attribute), [1] (FeedbackTimes attribute) (FeedbackType attribute) (FpgaTrials attribute) (GoCueTimes attribute) (GoCueTriggerTimes attribute) (IncludedTrials attribute) (Intervals attribute) (ItiDuration attribute) (LaserBool attribute) (MockExtracor attribute) (PassiveChoiceWorld attribute) (ProbabilityLeft attribute) (ProbaContrasts attribute) (RepNum attribute) (ResponseTimes attribute) (RewardVolume attribute) (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) scatter_amp_depth_fr_plot() (in module brainbox.ephys_plots) scatter_raster_plot() (in module brainbox.ephys_plots) scatter_xyc_plot() (in module brainbox.plot_base) ScatterPlot (class in brainbox.plot_base) sdsc_globus_path_from_dataset() (in module oneibl.webclient) sdsc_path_from_dataset() (in module oneibl.webclient) 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_clim() (DefaultPlot method) set_color() (ScatterPlot method) set_config() (in module oneibl.onelight) set_download_dir() (ONE method) set_figshare_url() (in module oneibl.onelight) (ONE method) set_labels() (DefaultPlot method) set_line_color() (ScatterPlot method) set_line_style() (ScatterPlot method) set_line_width() (ScatterPlot method) set_local_dir() (ONE method) set_marker_size() (ScatterPlot method) set_marker_type() (ScatterPlot method) set_offset() (ImagePlot method) (ProbePlot method) set_opacity() (ScatterPlot method) set_repo() (in module oneibl.onelight) set_roi() (MotionAlignment static method) set_scale() (ImagePlot method) (ProbePlot method) set_xlim() (DefaultPlot method) set_ylim() (DefaultPlot method) set_zlim() (DefaultPlot method) settings (BaseBpodTrialsExtractor attribute) setup() (in module ibllib.io.globus) (in module oneibl.params) (OneAlyx static method) setUp() (PsychofitTest method) (Task method) (TestAlignmentQcExisting method) (TestAlignmentQcManual method) (TestArrangeChannels2Bank method) (TestBaseExtractorSavingMethods method) (TestCameraQC method) (TestDlcQC method) (TestDownloadHTTP method) (TestEphysBehaviorExtraction method) (TestExtractedWheelUnits method) (TestExtractTrialData method) (TestFolders method) (TestHabituationQC method) (TestHistology method) (TestIblChannelMaps method) (TestIO_ALF method) (TestJsonFieldMethods method) (TestList method) (TestLoad method) (TestOneOffline method) (TestONEParams method) (TestONEQCMetrics method) (TestPipelineAlyx method) (TestPipesMisc method) (TestPlotBase method) (TestPopulation method) (TestQC method) (TestRegistration method) (TestsAlf method) (TestsAlfPartsFilters method), [1], [2] (TestScanFixPassiveFiles method) (TestScatterXYC method) (TestSearch method) (TestsEphysAlignment method) (TestsEphysReconstruction method) (TestsFolderStructure method) (TestsGlobus method) (TestsHardwareParameters method) (TestSingletonPattern method) (TestsMisc method) (TestsParams method) (TestsPassiveExtractor method) (TestSpikeGLX_glob_ephys method) (TestsRawDataLoaders method) (TestsSpikeGLX_compress method) (TestsSpikeGLX_Meta method) (TestSyncExtraction method) (TestTask method) (TestTaskMetrics method) (TestTraining method) (TestUtils method) (TestVideo method), [1] (TestWheel method) (TestWheelExtraction method) (TestWheelLoaders method) (TestWheelMovesExtraction method)

setup_alyx_params() (in module oneibl.params) setup_silent() (in module oneibl.params) setUpClass() (TestAlignmentQcExisting class method) (TestAlignmentQcManual class method) (TestAtlasSlicesConversion class method) (TestBrainRegions class method) (TestCameraQC class method) (TestDlcQC class method) (TestIO_ALF class method) (TestTracingQc class method) (TestUploadToFlatIron method) (TestVideo class method) sha1() (in module ibllib.io.hashfile) shape() (Reader property) shuffle_analysis() (in module brainbox.population.cca) sigtest_linshift() (in module brainbox.population.decode) sigtest_pseudosessions() (in module brainbox.population.decode) slice() (BrainAtlas method) (WindowGenerator property) slice_array() (WindowGenerator method) slidingRP_viol() (in module brainbox.metrics.single_units) smooth_demo() (in module ibllib.dsp.smooth) SomePipeline (class in ibllib.tests.test_tasks) spectrum() (in module ibllib.plots) sph2cart() (in module ibllib.atlas.atlas) spike_sorting_metrics() (in module brainbox.metrics.single_units) 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) StimFreezeTriggerTimes (class in ibllib.io.extractors.training_trials) StimOffTriggerTimes (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) (in module ibllib.ephys.sync_probes) sync_gen() (TestSyncExtraction method) 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_timestamps() (in module ibllib.dsp.utils) sync_trials_robust() (in module ibllib.io.raw_data_loaders) SyncBpodFpgaException SyncBpodWheelException

T

Task (class in ibllib.pipes.tasks) Task00 (class in ibllib.tests.test_tasks) Task01_void (class in ibllib.tests.test_tasks) Task02_error (class in ibllib.tests.test_tasks) Task10 (class in ibllib.tests.test_tasks) Task11 (class in ibllib.tests.test_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) (TestBaseExtractorSavingMethods method) (TestCameraQC method) (TestDlcQC method) (TestExtractTrialData method) (TestFolders method) (TestIO_ALF method) (TestJsonFieldMethods method) (TestOneOffline method) (TestONEParams method) (TestPipelineAlyx method) (TestPipesMisc method) (TestRegistration method) (TestsAlf method) (TestsAlfPartsFilters method), [1], [2] (TestScanFixPassiveFiles method) (TestsFolderStructure method) (TestsMisc method) (TestsParams method) (TestsPassiveExtractor method) (TestSpikeGLX_glob_ephys method) (TestsRawDataLoaders method) (TestsSpikeGLX_compress method) tearDownClass() (TestAlignmentQcExisting class method) (TestAlignmentQcManual class method) (TestCameraQC class method) (TestTracingQc class method) (TestUploadToFlatIron class method) test_01_no_alignments() (TestAlignmentQcExisting method) test_01_normal_computation() (TestAlignmentQcManual method) test_02_manual_resolution_latest() (TestAlignmentQcManual method) test_02_one_alignment() (TestAlignmentQcExisting method) test_03_alignments_disagree() (TestAlignmentQcExisting method) test_03_manual_resolution_not_latest() (TestAlignmentQcManual method) test_04_alignments_agree() (TestAlignmentQcExisting method) test_05_not_latest_alignments_agree() (TestAlignmentQcExisting method) test_1d() (TestParabolicMax method) test_2d() (TestParabolicMax method) test__get_current_par() (TestONEParams method) test__isdatetime() (TestFolders method) test__set_eid_or_path() (TestQC method) test_acorr_0() (TestPopulation method) test_acorr_1() (TestPopulation method) test_add_uuid() (TestUUID_Files method) test_align_to_trial() (TestEphysSyncExtraction method) test_allen_ba() (TestAtlasSlicesConversion method) test_ancestors_descendants() (TestBrainRegions method) test_append() (TestSearch method) test_append_empty() (TestSearch method) test_append_list() (TestAlfBunch method) test_append_numpy() (TestAlfBunch method) test_as_globus_path() (TestsGlobus method) test_assert_valid_label() (TestVideo method) test_attribute_times() (TestCameraExtractors method) test_behavior_exists() (TestPipesMisc method) test_between_sorted_multiple_times() (TestBetweeenSorted method) test_between_sorted_single_time() (TestBetweeenSorted method) test_bincount_2d() (TestProcessing method) test_bpod_trace_extraction() (TestEphysSyncExtraction method) test_brain_coordinates() (TestsCoordinatesSimples method) test_bunch_io() (TestBunch method) test_ccf_xyz() (TestAtlasSlicesConversion method) test_channel_locations() (TestsEphysReconstruction method) test_channels() (Tests_REST method) test_check_audio_pre_trial() (TestTaskMetrics method) test_check_brightness() (TestCameraQC method) test_check_camera_times() (TestCameraQC method) test_check_correct_trial_event_sequence() (TestTaskMetrics method) test_check_create_raw_session_flag() (TestPipesMisc method) test_check_detected_wheel_moves() (TestTaskMetrics method) test_check_dimensions() (TestsAlf method) test_check_dropped_frames() (TestCameraQC method) test_check_ephys_file() (TestsSpikeGLX_Meta method) test_check_error_trial_event_sequence() (TestTaskMetrics method) test_check_errorCue_delays() (TestTaskMetrics method) test_check_file_headers() (TestCameraQC method) test_check_focus() (TestCameraQC method) test_check_frame_frequency() (TestTaskMetrics method) test_check_frame_updates() (TestTaskMetrics method) test_check_framerate() (TestCameraQC method) test_check_goCue_delays() (TestTaskMetrics method) test_check_iti_delays() (TestTaskMetrics method) test_check_lick_detection() (TestDlcQC method) test_check_mean_in_bbox() (TestDlcQC method) test_check_n_trial_events() (TestTaskMetrics method) test_check_negative_feedback_stimOff_delays() (TestTaskMetrics method) test_check_pin_state() (TestCameraQC method) test_check_position() (TestCameraQC method) test_check_positive_feedback_stimOff_delays() (TestTaskMetrics method) test_check_pupil_blocked() (TestDlcQC method) test_check_resolution() (TestCameraQC method) test_check_response_feedback_delays() (TestTaskMetrics method) test_check_response_stimFreeze_delays() (TestTaskMetrics method) test_check_reward_volume_set() (TestTaskMetrics method) test_check_reward_volumes() (TestTaskMetrics method) test_check_stimFreeze_delays() (TestTaskMetrics method) test_check_stimOff_delays() (TestTaskMetrics method) test_check_stimOff_itiIn_delays() (TestTaskMetrics method) test_check_stimOn_delays() (TestTaskMetrics method) test_check_stimOn_goCue_delays() (TestTaskMetrics method) test_check_stimulus_move_before_goCue() (TestTaskMetrics method) test_check_time_trace_length_match() (TestDlcQC method) test_check_timestamps() (TestCameraQC method) test_check_trace_all_nan() (TestDlcQC method) test_check_transfer() (TestPipesMisc method) test_check_trial_length() (TestTaskMetrics method) test_check_wheel_freeze_during_quiescence() (TestTaskMetrics method) test_check_wheel_integrity() (TestTaskMetrics method) test_check_wheel_move_before_feedback() (TestTaskMetrics method) test_check_wheel_move_during_closed_loop() (TestTaskMetrics method) test_classify() (TestPopulation method) test_clusters_metrics() (in module brainbox.tests.test_metrics) test_code_to_outcome() (TestQC method) test_compare_version_tags() (TestVersionTags method) test_compress() (TestsSpikeGLX_compress method) test_compute() (TestHabituationQC method) test_compute_cluster_averag() (TestProcessing method) test_concatenate_and_computations() (TestTraining method) test_create_alyx_probe_insertions() (TestPipesMisc method) test_create_ephys_flags() (TestPipesMisc method) test_create_ephys_transfer_done_flag() (TestPipesMisc method) test_create_video_transfer_done_flag() (TestPipesMisc method) test_creation() (TestProbeInsertion method) test_data_content() (TestUploadToFlatIron method) test_datasets_from_type() (TestMisc method) test_date2isostr() (TestUtils method) test_default() (TestPlotBase method) test_default_values() (TestsHardwareParameters method) test_delete_empty_folders() (TestsMisc method) test_derivative() (TestWheel method) test_dft() (TestFFT method) test_differentiate_units() (TestTask method) test_direction_changes() (TestWheel method) test_download_datasets() (TestDownloadHTTP method) test_download_datasets_with_api() (TestDownloadHTTP method) test_download_hash() (TestLoad method) test_drift_estimate() (in module brainbox.tests.test_metrics) test_dsets_2_path() (TestAlyx2Path method) test_dsp_cosine_func() (TestDspMisc method) test_eid_from_path() (TestUtils method) test_encoder_events_corrupt() (TestWheelLoaders method) test_encoder_positions_clock_errors() (TestExtractTrialData method) test_encoder_positions_clock_reset() (TestExtractTrialData method) test_encoder_positions_corrupts() (TestWheelLoaders method) test_ensure_data() (TestCameraQC method) (TestDlcQC method) test_erf_psycho() (PsychofitTest method) test_erf_psycho_2gammas() (PsychofitTest method) test_error_cases() (TestParabolicMax method) test_eval_trajectory() (TestTrajectory method) test_exists() (TestsAlf method) test_exit_volume() (TestTrajectory method) test_extended_qc() (TestQC method) test_extract_all() (TestExtractTrialData method) test_extract_first_movement_times() (TestWheelMovesExtraction method) test_extract_wheel_moves() (TestExtractedWheelUnits method) (TestWheelMovesExtraction method) test_fexpand() (TestFFT method) test_filename_parser() (TestHistology method) test_filter_by() (TestsAlfPartsFilters method) test_filter_lp_hp() (TestFFT method) test_find_pairs() (TestScanFixPassiveFiles method) test_firing_rate() (in module brainbox.tests.test_singlecell) test_firstlast_slices() (TestWindowGenerator method) test_fit_phase1d() (TestPhaseRegression method) test_fit_phase2d() (TestPhaseRegression method) test_flatten() (TestFlatten method) test_format_date_range() (TestUtils method) test_frame2ttl_flickers() (TestEphysFPGA_TTLsExtraction method) test_frame_diff() (TestVideo method) test_frame_diffs() (TestVideo method) test_freduce() (TestFFT method) test_fscale() (TestFFT method) test_generate_pseudo_blocks() (TestTask method) test_generate_pseudo_session() (TestTask method) test_generate_pseudo_stimuli() (TestTask method) test_generic_request() (TestDownloadHTTP method) test_get() (TestBrainRegions method) test_get_brain_exit_entry() (TestHistology method) test_get_channel_map() (TestsHardwareParameters method) test_get_choice() (TestExtractTrialData method) test_get_contrastLR() (TestExtractTrialData method) test_get_details() (TestUtils method) test_get_ephys_files() (TestsFolderStructure method) test_get_feedback_times_ge5() (TestExtractTrialData method) test_get_feedback_times_lt5() (TestExtractTrialData method) test_get_feedbackType() (TestExtractTrialData method) test_get_goCueOnset_times() (TestExtractTrialData method) test_get_goCueTrigger_times() (TestExtractTrialData method) test_get_included_trials() (TestExtractTrialData method) test_get_included_trials_ge5() (TestExtractTrialData method) test_get_included_trials_lt5() (TestExtractTrialData method) test_get_intervals() (TestExtractTrialData method) test_get_iti_duration() (TestExtractTrialData method) test_get_new_filename() (TestPipesMisc method) test_get_probabilityLeft() (TestEphysBehaviorExtraction method) (TestExtractTrialData method) test_get_repNum() (TestExtractTrialData method) test_get_response_times() (TestExtractTrialData method) test_get_rewardVolume() (TestExtractTrialData method) test_get_session_folder() (TestSessionFolder method) test_get_session_folder_regex() (TestSessionFolder method) test_get_spike_counts_in_bins() (TestPopulation method) test_get_stimOn_times_ge5() (TestExtractTrialData method) test_get_stimOn_times_lt5() (TestExtractTrialData method) test_get_stimOnTrigger_times() (TestExtractTrialData method) test_get_unit_bunches() (in module brainbox.tests.test_processing) test_get_wiring() (TestsHardwareParameters method) test_glob_ephys() (TestSpikeGLX_glob_ephys method) test_groom_pin_state() (TestCameraExtractors method) test_histology_get_brain_regions() (TestHistology method) test_histology_insertion_from_track() (TestHistology method) test_ibl_sync_maps() (TestIblChannelMaps method) test_image() (TestPlotBase method) test_impeccable_dataset() (TestFpgaTask method) test_imports() (TestFFT method) test_in_training() (TestTraining method) test_init_from_dict() (TestInsertion method) test_init_from_track() (TestInsertion method) test_interpolate_rf_mapping_stimulus() (TestsPassiveExtractor method) test_is_details_dict() (TestSessionFolder method) test_is_session_folder() (TestSessionFolder method) test_is_uuid() (TestSessionFolder method) test_is_uuid_string() (TestSessionFolder method) test_isdatetime() (TestSessionFolder method) test_ismember() (TestIsmember method) test_ismember2d() (TestIsmember method) test_ismember2d_uuids() (TestIsmember method) test_isostr2date() (TestUtils method) test_json_methods() (TestJsonFieldMethods method) test_label_from_path() (TestVideo method) test_layouts() (TestNeuropixel method) test_levels() (TestLoggingSystem method) test_line() (TestPlotBase method) test_linear_scaling() (TestsEphysAlignment method) test_list() (TestList method) test_list_pk_query() (Tests_REST method) test_load() (TestLoad method) test_load_all_data_available() (TestLoad method) test_load_camera_frame_count() (TestsRawDataLoaders method) test_load_camera_gpio() (TestsRawDataLoaders method) test_load_camera_ssv_times() (TestsRawDataLoaders method) test_load_embedded_frame_data() (TestsRawDataLoaders method) test_load_empty() (TestLoad method) test_load_encoder_events() (TestExtractTrialData method) test_load_encoder_positions() (TestExtractTrialData method) test_load_encoder_trial_info() (TestsRawDataLoaders method) test_load_ephys() (TestIO_ALF method) test_load_fileformats() (TestLoad method) test_load_from_uuid() (TestLoad method) test_load_multiple_sessions() (TestLoad method) test_load_object() (TestLoad method) (TestsAlf method) test_load_passive_stim_meta() (TestsPassiveExtractor method) test_load_uuid() (TestLoad method) test_login_auto() (TestsGlobus method) test_lookups() (TestAtlasSlicesConversion method) test_mappings_lateralized() (TestBrainRegions method) test_mappings_not_lateralized() (TestBrainRegions method) test_metadata_columns() (TestsAlf method) test_metadata_columns_UUID() (TestsAlf method) test_mle_fit_psycho() (PsychofitTest method)

test_move_rename_pairs() (TestScanFixPassiveFiles method) test_movement_log() (TestWheelMovesExtraction method) test_movements() (TestWheel method) test_movements_FPGA() (TestWheel method) test_multiple_singletons() (TestSingletonPattern method) test_nech_optim() (TestFFT method) test_neg_likelihood() (PsychofitTest method) test_new_default_param() (TestsParams method) test_no_pad() (TestArrangeChannels2Bank method) test_no_scaling() (TestsEphysAlignment method) test_note_with_picture_upload() (Tests_REST method) test_npy_parts_and_file_filters() (TestsAlfPartsFilters method) test_nwindows_computation() (TestWindowGenerator method) test_offset() (TestsEphysAlignment method) test_one_offline() (TestOneOffline method) test_ONEQC() (TestONEQCMetrics method) test_ONEQC_lazy() (TestONEQCMetrics method) test_outcome_setter() (TestQC method) test_overall_outcome() (TestQC method) test_pad() (TestArrangeChannels2Bank method) test_paginated_request() (TestDownloadHTTP method) test_param_get_file() (TestsParams method) test_params() (TestsParams method) test_path_eid() (TestOneOffline method) test_path_from_eid() (TestUtils method) test_path_to_url() (TestMisc method) test_peths_synthetic() (TestPeths method) test_pipeline_alyx() (TestPipelineAlyx method) test_plotting() (TestBunch method) test_probe() (TestPlotBase method) test_probe_qc() (TestHistologyQc method) test_project_mindist() (TestTrajectory method) test_psychometric_insufficient_data() (TestTraining method) test_read_3A() (TestsSpikeGLX_Meta method) test_read_3B() (TestsSpikeGLX_Meta method) test_read_corrupt() (TestsSpikeGLX_Meta method) test_read_nidq() (TestsSpikeGLX_Meta method) test_read_slices() (TestsSpikeGLX_compress method) test_read_ts() (TestsAlf method) test_ready4delay() (TestTraining method) test_ready4ephys() (TestTraining method) test_ready4recording() (TestTraining method) test_rec2col() (TestParquet method) test_registration_datasets() (TestRegistration method) test_registration_session() (TestRegistration method) test_regress() (TestPopulation method) test_remove_empty_folders() (TestsAlfPartsFilters method) test_remove_uuid() (TestUUID_Files method) test_rename_and_move() (TestPipesMisc method) test_responsive_units() (TestTask method) test_rest_all_actions() (TestDownloadHTTP method) test_rest_endpoint_read_only() (TestDownloadHTTP method) test_rest_endpoint_write() (TestDownloadHTTP method) test_reverse_directions() (TestsCoordinatesSimples method) test_rf_map() (TestPassive method) test_RGB_conversion() (TestScatterXYC method) test_RGB_conversion_with_clim() (TestScatterXYC method) test_rises_falls() (TestWindowGenerator method) test_roc_between_two_events() (TestTask method) test_roc_single_event() (TestTask method) test_save_npy() (TestsAlf method) test_saving_method() (TestBaseExtractorSavingMethods method) test_scan_fix() (TestScanFixPassiveFiles method) test_scatter() (TestPlotBase method) test_search_simple() (TestSearch method) test_session_creation() (TestHistologyQc method) test_session_does_not_exist() (TestLoad method) test_session_path() (TestFolders method) test_setup() (TestONEParams method) test_setup_silent() (TestONEParams method) test_shift_1d() (TestShift method) test_shift_2d() (TestShift method) test_sigtest_linshift() (TestPopulation method) test_sigtest_pseudosessions() (TestPopulation method) test_simple_print() (TestPrintProgress method) test_size_outputs() (TestExtractTrialData method) test_slice() (TestAtlasSlicesConversion method) test_smooth_lp() (TestSmooth method) test_spectral_convolution() (TestFFT method) test_sph2cart_and_back() (TestsCoordinatesSimples method) test_stim_aligned() (TestPassive method) test_stimOn_extractor_values() (TestExtractTrialData method) test_stimOnOffFreeze_times() (TestExtractTrialData method) test_sync() (TestBunch method) (TestProcessing method) test_sync_3A() (TestSyncExtraction method) test_sync_3B() (TestSyncExtraction method) test_sync_bpod_bonsai_poor_quality_timestamps() (TestSyncWheelBpod method) test_sync_nidq() (TestSyncExtraction method) test_task_names_extractors() (TestExtractors2Tasks method) (TestRegistrationEndpoint method) test_timestamps_lin() (TestSyncTimestamps method) test_to_dataframe_scalars() (TestAlfBunch method) test_to_dataframe_vectors() (TestAlfBunch method) test_to_eid() (TestMisc method) test_traces_by_trial() (TestWheel method) test_tracing_exists() (TestTracingQc method) test_tracing_not_exists() (TestTracingQc method) test_trained_1a() (TestTraining method) test_trained_1b() (TestTraining method) test_training_to_bias() (TestTraining method) test_trajectory() (TestTrajectory method) test_tscale() (TestWindowGenerator method) test_ttl_bpod_gaelle_writes_protocols_but_guido_doesnt_read_them() (TestEphysFPGA_TTLsExtraction method) test_tutuoral_script() (TestOneTutorial method) test_uniform_scaling() (TestsEphysAlignment method) test_update() (TestQC method) test_upload_to_flatiron() (TestUploadToFlatIron method) test_url_from_eid() (TestVideo method) test_uuids_conversions() (TestParquet method) test_uuids_intersections() (TestParquet method) test_validate_date_range() (TestMisc method) test_water_restriction() (Tests_REST method) test_weibull() (PsychofitTest method) test_weibull50() (PsychofitTest method) test_wheel_folders() (TestExtractTrialData method) test_wheel_trace_from_sync() (TestEphysSyncExtraction method) test_window_simple() (TestWindowGenerator method) test_with_depth() (TestArrangeChannels2Bank method) test_without_RGB_conversion() (TestScatterXYC method) test_x1_decoding() (TestWheelExtraction method) test_x2_decoding() (TestWheelExtraction method) test_x4_decoding() (TestWheelExtraction method) test_xcorr_0() (TestPopulation method) test_xcorr_1() (TestPopulation method) test_xcorr_2() (TestPopulation method) TestAlfBunch (class in alf.tests.test_alf_io) TestAlignmentQcExisting (class in ibllib.tests.qc.test_alignment_qc) TestAlignmentQcManual (class in ibllib.tests.qc.test_alignment_qc) TestAlyx2Path (class in oneibl.tests.test_one2) testAppendFlagFile() (TestsRawDataLoaders method) TestArrangeChannels2Bank (class in brainbox.tests.test_plot_base) TestAtlasSlicesConversion (class in ibllib.tests.test_atlas) TestBaseExtractorSavingMethods (class in ibllib.tests.extractors.test_extractors) TestBetweeenSorted (class in brainbox.tests.test_numerical) TestBrainRegions (class in ibllib.tests.test_atlas) TestBunch (class in brainbox.tests.test_cca) (class in brainbox.tests.test_core) TestCameraExtractors (class in ibllib.tests.extractors.test_extractors) TestCameraQC (class in ibllib.tests.qc.test_camera_qc) TestDlcQC (class in ibllib.tests.qc.test_dlc_qc) TestDownloadHTTP (class in oneibl.tests.test_alyxclient) TestDspMisc (class in ibllib.tests.test_dsp) TestEphysBehaviorExtraction (class in ibllib.tests.extractors.test_ephys_trials) TestEphysFPGA_TTLsExtraction (class in ibllib.tests.extractors.test_ephys_fpga) TestEphysSyncExtraction (class in ibllib.tests.extractors.test_ephys_trials) TestExtractedWheelUnits (class in ibllib.tests.extractors.test_ephys_fpga) TestExtractors2Tasks (class in ibllib.tests.test_pipes) TestExtractTrialData (class in ibllib.tests.extractors.test_extractors) TestFFT (class in ibllib.tests.test_dsp) testFlagFileRead() (TestsRawDataLoaders method) TestFlatten (class in ibllib.tests.test_misc) TestFolders (class in ibllib.tests.extractors.test_folders) TestFpgaTask (class in ibllib.tests.test_ephys) testGetAnalogSyncIndex() (TestsSpikeGLX_Meta method) testGetRevisionAndType() (TestsSpikeGLX_Meta method) testGetSerialNumber() (TestsSpikeGLX_Meta method) TestHabituationQC (class in ibllib.tests.qc.test_task_metrics) TestHistology (class in ibllib.tests.test_histology) TestHistologyQc (class in ibllib.tests.qc.test_alignment_qc) TestIblChannelMaps (class in ibllib.tests.extractors.test_ephys_fpga) TestInsertion (class in ibllib.tests.test_atlas) TestIO_ALF (class in brainbox.tests.test_io) TestIsmember (class in brainbox.tests.test_numerical) TestJsonFieldMethods (class in oneibl.tests.test_alyxclient) TestList (class in oneibl.tests.test_one) TestLoad (class in oneibl.tests.test_one) TestLoggingSystem (class in ibllib.tests.test_misc) TestMisc (class in oneibl.tests.test_one) TestNeuropixel (class in ibllib.tests.test_ephys) TestOneOffline (class in oneibl.tests.test_one) TestONEParams (class in oneibl.tests.test_params) TestONEQCMetrics (class in ibllib.tests.qc.test_oneqc_metrics) TestOneTutorial (class in oneibl.tests.test_one_tutorial) TestParabolicMax (class in ibllib.tests.test_dsp) TestParquet (class in brainbox.tests.test_io) TestPassive (class in brainbox.tests.test_passive) TestPeths (class in brainbox.tests.test_singlecell) TestPhaseRegression (class in ibllib.tests.test_dsp) TestPipelineAlyx (class in ibllib.tests.test_tasks) TestPipesMisc (class in ibllib.tests.test_pipes) TestPlotBase (class in brainbox.tests.test_plot_base) TestPopulation (class in brainbox.tests.test_population) (class in brainbox.tests.test_singlecell) TestPrintProgress (class in ibllib.tests.test_misc) TestProbeInsertion (class in ibllib.tests.qc.test_alignment_qc) TestProcessing (class in brainbox.tests.test_processing) TestQC (class in ibllib.tests.qc.test_base_qc) testReadChannelGainAPLF() (TestsSpikeGLX_Meta method) testReadChannelGainNIDQ() (TestsSpikeGLX_Meta method) testReadChannelMap() (TestsSpikeGLX_Meta method) testReadWrite() (TestsJsonable method) TestRegistration (class in oneibl.tests.test_registration) TestRegistrationEndpoint (class in oneibl.tests.test_registration) tests_headers() (TestNeuropixel method) Tests_REST (class in oneibl.tests.test_alyxrest) TestsAlf (class in alf.tests.test_alf_io) TestsAlfPartsFilters (class in alf.tests.test_alf_files) (class in alf.tests.test_alf_folders) (class in alf.tests.test_alf_io) TestScanFixPassiveFiles (class in ibllib.tests.test_pipes) TestScatterXYC (class in brainbox.tests.test_plot_base) TestsCoordinatesSimples (class in ibllib.tests.test_atlas) TestSearch (class in oneibl.tests.test_dataclass) (class in oneibl.tests.test_one) TestsEphysAlignment (class in ibllib.tests.test_histology) TestsEphysReconstruction (class in ibllib.tests.test_histology) TestSessionFolder (class in alf.tests.test_alf_io) TestsFolderStructure (class in ibllib.tests.extractors.test_ephys_fpga) TestsGlobus (class in ibllib.tests.test_io) TestsHardwareParameters (class in ibllib.tests.test_io) TestShift (class in ibllib.tests.test_dsp) TestSingletonPattern (class in oneibl.tests.test_alyxclient) TestsJsonable (class in ibllib.tests.test_io) TestsMisc (class in ibllib.tests.test_io) TestSmooth (class in ibllib.tests.test_dsp) TestsParams (class in ibllib.tests.test_io) TestsPassiveExtractor (class in ibllib.tests.extractors.test_ephys_passive) TestSpikeGLX_glob_ephys (class in ibllib.tests.test_io) testSplitSyncTrace() (TestsSpikeGLX_Meta method) TestsRawDataLoaders (class in ibllib.tests.test_io) TestsSpikeGLX_compress (class in ibllib.tests.test_io) TestsSpikeGLX_Meta (class in ibllib.tests.test_io) TestSyncExtraction (class in ibllib.tests.extractors.test_ephys_fpga) TestSyncTimestamps (class in ibllib.tests.test_dsp) TestSyncWheelBpod (class in ibllib.tests.extractors.test_extractors) TestTask (class in brainbox.tests.test_task) TestTaskMetrics (class in ibllib.tests.qc.test_task_metrics) TestTracingQc (class in ibllib.tests.qc.test_alignment_qc) TestTraining (class in brainbox.tests.test_behavior) TestTrajectory (class in ibllib.tests.test_atlas) TestUploadToFlatIron (class in ibllib.tests.qc.test_alignment_qc) TestUtils (class in ibllib.tests.test_time) (class in oneibl.tests.test_oneutils) TestUUID_Files (class in alf.tests.test_alf_io) TestVersionTags (class in ibllib.tests.test_misc) TestVideo (class in brainbox.tests.test_video) (class in ibllib.tests.test_io) TestWheel (class in brainbox.tests.test_behavior) TestWheelExtraction (class in ibllib.tests.extractors.test_ephys_fpga) TestWheelLoaders (class in ibllib.tests.extractors.test_extractors) TestWheelMovesExtraction (class in ibllib.tests.extractors.test_ephys_fpga) TestWindowGenerator (class in ibllib.tests.test_dsp) theta (Insertion attribute) tilted_slice() (BrainAtlas method) time_elapsed_secs (Task attribute) time_out_secs (Task attribute) TimeSeries (class in brainbox.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) trace_header() (in module ibllib.ephys.neuropixel) 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() (CameraQC property) (Reader property)

U

uncycle_pgts() (in module ibllib.time) UniqueSingletons (class in oneibl.webclient) unit_stability() (in module brainbox.metrics.single_units) 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) url_from_eid() (in module ibllib.io.video) url_from_path() (OneAlyx method) uuid2np() (in module brainbox.io.parquet)

V

validate_ttl_test() (in module ibllib.ephys.ephysqc) var_name (TrialType attribute) var_names (CameraTimestampsBpod attribute) (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) (LaserBool attribute) (MockExtracor attribute) (PassiveChoiceWorld attribute) (ProbabilityLeft attribute) (ProbaContrasts attribute) (RepNum attribute) (ResponseTimes attribute) (RewardVolume attribute) (StimFreezeTriggerTimes attribute) (StimOffTriggerTimes attribute) (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) (Task00 attribute) version() (Reader property) version3A() (in module ibllib.ephys.sync_probes) version3B() (in module ibllib.ephys.sync_probes) vertical_lines() (in module ibllib.plots) video_meta (CameraQC attribute) 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) wf_similarity() (in module brainbox.metrics.single_units) Wheel (class in ibllib.io.extractors.training_wheel) wheel_radius_cm (TestExtractedWheelUnits attribute)

wheelMoves_fixture() (in module ibllib.tests.extractors.test_extractors) wiggle() (in module ibllib.plots) WindowGenerator (class in ibllib.dsp.utils) within_ranges() (in module brainbox.numerical) 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) (TestParabolicMax attribute) x2i() (BrainCoordinates method) xcorr() (in module brainbox.population.decode)

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)