Index

Symbols

--animal sl-manage-migrate command line option sl-run-session command line option --animal_weight sl-run-session command line option --destination sl-manage-migrate command line option --duration_step sl-run-session-run-training command line option --experiment sl-run-session-experiment command line option --increase_threshold sl-run-session-run-training command line option --initial_duration sl-run-session-run-training command line option --initial_speed sl-run-session-run-training command line option --input_string sl-get-checksum command line option --maximum_delay sl-run-session-lick-training command line option --maximum_idle_time sl-run-session-run-training command line option --maximum_time sl-run-session-lick-training command line option sl-run-session-run-training command line option --maximum_volume sl-run-session-lick-training command line option sl-run-session-run-training command line option --minimum_delay sl-run-session-lick-training command line option --project sl-get-experiments command line option sl-run-session command line option --session-path sl-manage-delete command line option sl-manage-preprocess command line option --source sl-manage-migrate command line option --speed_step sl-run-session-run-training command line option --transport sl-get-mcp command line option sl-manage-mcp command line option --unconsumed_rewards sl-run-session-experiment command line option sl-run-session-lick-training command line option sl-run-session-run-training command line option --user sl-run-session command line option

-a sl-manage-migrate command line option sl-run-session command line option -d sl-manage-migrate command line option -ds sl-run-session-run-training command line option -e sl-run-session-experiment command line option -i sl-get-checksum command line option -id sl-run-session-run-training command line option -is sl-run-session-run-training command line option -it sl-run-session-run-training command line option -max sl-run-session-lick-training command line option -min sl-run-session-lick-training command line option -mit sl-run-session-run-training command line option -p sl-get-experiments command line option sl-run-session command line option -s sl-manage-migrate command line option -sp sl-manage-delete command line option sl-manage-preprocess command line option -ss sl-run-session-run-training command line option -t sl-get-mcp command line option sl-manage-mcp command line option sl-run-session-lick-training command line option sl-run-session-run-training command line option -u sl-run-session command line option -ur sl-run-session-experiment command line option sl-run-session-lick-training command line option sl-run-session-run-training command line option -v sl-run-session-lick-training command line option sl-run-session-run-training command line option -w sl-run-session command line option

_

_animal_id (sl_experiment.shared_components.SurgeryLog attribute) _animal_tab_id (sl_experiment.shared_components.WaterLog attribute) _animals (sl_experiment.shared_components.SurgeryLog attribute) (sl_experiment.shared_components.WaterLog attribute) _calculator (sl_experiment.mesoscope_vr.CRCCalculator attribute) _calibrate (sl_experiment.shared_components.ValveInterface attribute) _calibration_count (sl_experiment.shared_components.ValveInterface attribute) _check_state (sl_experiment.shared_components.EncoderInterface attribute) (sl_experiment.shared_components.LickInterface attribute) (sl_experiment.shared_components.TorqueInterface attribute) (sl_experiment.shared_components.TTLInterface attribute) _close (sl_experiment.shared_components.GasPuffValveInterface attribute) (sl_experiment.shared_components.ValveInterface attribute) _cm_per_pulse (sl_experiment.shared_components.EncoderInterface attribute) _configured_state (sl_experiment.shared_components.GasPuffValveInterface attribute) _configured_valve_state (sl_experiment.shared_components.ValveInterface attribute) _current_time (sl_experiment.shared_components.WaterLog attribute) _cycle_timer (sl_experiment.shared_components.ValveInterface attribute) _disengage (sl_experiment.shared_components.BrakeInterface attribute) _distance_tracker (sl_experiment.shared_components.EncoderInterface attribute) _enabled (sl_experiment.shared_components.BrakeInterface attribute) (sl_experiment.shared_components.ScreenInterface attribute) _engage (sl_experiment.shared_components.BrakeInterface attribute) _headers (sl_experiment.shared_components.SurgeryLog attribute) (sl_experiment.shared_components.WaterLog attribute) _lick_threshold (sl_experiment.shared_components.LickInterface attribute) _lick_tracker (sl_experiment.shared_components.LickInterface attribute) _maximum_brake_strength (sl_experiment.shared_components.BrakeInterface attribute) _minimum_brake_strength (sl_experiment.shared_components.BrakeInterface attribute) _monitoring (sl_experiment.shared_components.EncoderInterface attribute) (sl_experiment.shared_components.LickInterface attribute) (sl_experiment.shared_components.TorqueInterface attribute) (sl_experiment.shared_components.TTLInterface attribute)

_nonlinearity_exponent (sl_experiment.shared_components.ValveInterface attribute) _open (sl_experiment.shared_components.GasPuffValveInterface attribute) (sl_experiment.shared_components.ValveInterface attribute) _polling_frequency (sl_experiment.shared_components.EncoderInterface attribute) (sl_experiment.shared_components.LickInterface attribute) (sl_experiment.shared_components.TorqueInterface attribute) (sl_experiment.shared_components.TTLInterface attribute) _ppr (sl_experiment.shared_components.EncoderInterface attribute) _previous_duration (sl_experiment.shared_components.GasPuffValveInterface attribute) _previous_module_state (sl_experiment.shared_components.GasPuffValveInterface attribute) (sl_experiment.shared_components.ValveInterface attribute) _previous_pulse_duration (sl_experiment.shared_components.BrakeInterface attribute) _previous_readout_zero (sl_experiment.shared_components.LickInterface attribute) _previous_tone_duration (sl_experiment.shared_components.ValveInterface attribute) _previous_volume (sl_experiment.shared_components.ValveInterface attribute) _project_name (sl_experiment.shared_components.SurgeryLog attribute) _puff_tracker (sl_experiment.shared_components.GasPuffValveInterface attribute) _pulse (sl_experiment.shared_components.BrakeInterface attribute) (sl_experiment.shared_components.GasPuffValveInterface attribute) _pulse_tracker (sl_experiment.shared_components.TTLInterface attribute) _reset_encoder (sl_experiment.shared_components.EncoderInterface attribute) _reward (sl_experiment.shared_components.ValveInterface attribute) _scale_coefficient (sl_experiment.shared_components.ValveInterface attribute) _service (sl_experiment.shared_components.SurgeryLog attribute) (sl_experiment.shared_components.WaterLog attribute) _session_row_index (sl_experiment.shared_components.WaterLog attribute) _sheet_id (sl_experiment.shared_components.SurgeryLog attribute) (sl_experiment.shared_components.WaterLog attribute) _toggle (sl_experiment.shared_components.ScreenInterface attribute) _tone (sl_experiment.shared_components.ValveInterface attribute) _torque_per_adc_unit (sl_experiment.shared_components.TorqueInterface attribute) _unity_unit_per_pulse (sl_experiment.shared_components.EncoderInterface attribute) _valve_tracker (sl_experiment.shared_components.ValveInterface attribute) _wheel_diameter (sl_experiment.shared_components.EncoderInterface attribute)

A

absolute_position (sl_experiment.shared_components.EncoderInterface property)

axis_label (sl_experiment.mesoscope_vr.ZaberDeviceSettings attribute)

B

BrakeInterface (class in sl_experiment.shared_components)

C

calibrate_valve() (sl_experiment.shared_components.ValveInterface method) calibrating (sl_experiment.shared_components.ValveInterface property) checksum (sl_experiment.mesoscope_vr.ZaberDeviceSettings attribute)

checksum_valid (sl_experiment.mesoscope_vr.ZaberValidationResult attribute) cm_per_pulse (sl_experiment.shared_components.EncoderInterface property) CRCCalculator (class in sl_experiment.mesoscope_vr) current_position (sl_experiment.mesoscope_vr.ZaberDeviceSettings attribute)

D

deliver_puff() (sl_experiment.shared_components.GasPuffValveInterface method) deliver_reward() (sl_experiment.shared_components.ValveInterface method)

delivered_volume (sl_experiment.shared_components.ValveInterface property) device_label (sl_experiment.mesoscope_vr.ZaberDeviceSettings attribute) discover_zaber_devices() (in module sl_experiment.mesoscope_vr)

E

EncoderInterface (class in sl_experiment.shared_components) errors (sl_experiment.mesoscope_vr.ZaberValidationResult attribute)

experiment_logic() (in module sl_experiment.mesoscope_vr) extract_animal_data() (sl_experiment.shared_components.SurgeryLog method)

G

GasPuffValveInterface (class in sl_experiment.shared_components) get_animal_project() (in module sl_experiment.shared_components) get_duration_from_volume() (sl_experiment.shared_components.ValveInterface method)

get_project_experiments() (in module sl_experiment.shared_components) get_version_data() (in module sl_experiment.shared_components) get_zaber_device_settings() (in module sl_experiment.mesoscope_vr) get_zaber_devices_info() (in module sl_experiment.mesoscope_vr)

I

initialize_local_assets() (sl_experiment.shared_components.EncoderInterface method) (sl_experiment.shared_components.GasPuffValveInterface method) (sl_experiment.shared_components.LickInterface method) (sl_experiment.shared_components.TTLInterface method) (sl_experiment.shared_components.ValveInterface method) initialize_remote_assets() (sl_experiment.shared_components.BrakeInterface method) (sl_experiment.shared_components.EncoderInterface method) (sl_experiment.shared_components.GasPuffValveInterface method) (sl_experiment.shared_components.LickInterface method) (sl_experiment.shared_components.ScreenInterface method) (sl_experiment.shared_components.TorqueInterface method) (sl_experiment.shared_components.TTLInterface method) (sl_experiment.shared_components.ValveInterface method)

is_valid (sl_experiment.mesoscope_vr.ZaberValidationResult attribute)

L

lick_count (sl_experiment.shared_components.LickInterface property) lick_threshold (sl_experiment.shared_components.LickInterface property) lick_training_logic() (in module sl_experiment.mesoscope_vr)

LickInterface (class in sl_experiment.shared_components) limit_max (sl_experiment.mesoscope_vr.ZaberDeviceSettings attribute) limit_min (sl_experiment.mesoscope_vr.ZaberDeviceSettings attribute)

M

maintenance_logic() (in module sl_experiment.mesoscope_vr) maintenance_position (sl_experiment.mesoscope_vr.ZaberDeviceSettings attribute) maximum_brake_strength (sl_experiment.shared_components.BrakeInterface property) migrate_animal_between_projects() (in module sl_experiment.mesoscope_vr) minimum_brake_strength (sl_experiment.shared_components.BrakeInterface property)

module sl_experiment.command_line_interfaces sl_experiment.mesoscope_vr sl_experiment.shared_components mount_position (sl_experiment.mesoscope_vr.ZaberDeviceSettings attribute)

N

nonlinearity_exponent (sl_experiment.shared_components.ValveInterface property)

P

park_position (sl_experiment.mesoscope_vr.ZaberDeviceSettings attribute) positions_valid (sl_experiment.mesoscope_vr.ZaberValidationResult attribute) preprocess_session_data() (in module sl_experiment.mesoscope_vr) process_received_data() (sl_experiment.shared_components.BrakeInterface method) (sl_experiment.shared_components.EncoderInterface method) (sl_experiment.shared_components.GasPuffValveInterface method) (sl_experiment.shared_components.LickInterface method) (sl_experiment.shared_components.ScreenInterface method) (sl_experiment.shared_components.TorqueInterface method) (sl_experiment.shared_components.TTLInterface method) (sl_experiment.shared_components.ValveInterface method)

puff_count (sl_experiment.shared_components.GasPuffValveInterface property) pulse_count (sl_experiment.shared_components.TTLInterface property) purge_session() (in module sl_experiment.mesoscope_vr)

R

reference_valve() (sl_experiment.shared_components.ValveInterface method) reset_distance_tracker() (sl_experiment.shared_components.EncoderInterface method)

reset_pulse_count() (sl_experiment.shared_components.TTLInterface method) run_training_logic() (in module sl_experiment.mesoscope_vr)

S

scale_coefficient (sl_experiment.shared_components.ValveInterface property) ScreenInterface (class in sl_experiment.shared_components) send_pulse() (sl_experiment.shared_components.BrakeInterface method) set_monitoring_state() (sl_experiment.shared_components.EncoderInterface method) (sl_experiment.shared_components.LickInterface method) (sl_experiment.shared_components.TorqueInterface method) (sl_experiment.shared_components.TTLInterface method) set_parameters() (sl_experiment.shared_components.EncoderInterface method) (sl_experiment.shared_components.LickInterface method) (sl_experiment.shared_components.ScreenInterface method) (sl_experiment.shared_components.TorqueInterface method) (sl_experiment.shared_components.TTLInterface method) set_state() (sl_experiment.shared_components.BrakeInterface method) (sl_experiment.shared_components.GasPuffValveInterface method) (sl_experiment.shared_components.ScreenInterface method) (sl_experiment.shared_components.ValveInterface method) set_zaber_device_setting() (in module sl_experiment.mesoscope_vr) shutdown_flag (sl_experiment.mesoscope_vr.ZaberDeviceSettings attribute) simulate_reward() (sl_experiment.shared_components.ValveInterface method) sl-get-checksum command line option --input_string -i sl-get-experiments command line option --project -p sl-get-mcp command line option --transport -t sl-manage-delete command line option --session-path -sp sl-manage-mcp command line option --transport -t sl-manage-migrate command line option --animal --destination --source -a -d -s sl-manage-preprocess command line option --session-path -sp sl-run-session command line option --animal --animal_weight --project --user -a -p -u -w

sl-run-session-experiment command line option --experiment --unconsumed_rewards -e -ur sl-run-session-lick-training command line option --maximum_delay --maximum_time --maximum_volume --minimum_delay --unconsumed_rewards -max -min -t -ur -v sl-run-session-run-training command line option --duration_step --increase_threshold --initial_duration --initial_speed --maximum_idle_time --maximum_time --maximum_volume --speed_step --unconsumed_rewards -ds -id -is -it -mit -ss -t -ur -v sl_experiment.command_line_interfaces module sl_experiment.mesoscope_vr module sl_experiment.shared_components module state (sl_experiment.shared_components.ScreenInterface property) string_checksum() (sl_experiment.mesoscope_vr.CRCCalculator method) SurgeryLog (class in sl_experiment.shared_components)

T

terminate_remote_assets() (sl_experiment.shared_components.BrakeInterface method) (sl_experiment.shared_components.EncoderInterface method) (sl_experiment.shared_components.GasPuffValveInterface method) (sl_experiment.shared_components.LickInterface method) (sl_experiment.shared_components.ScreenInterface method) (sl_experiment.shared_components.TorqueInterface method) (sl_experiment.shared_components.TTLInterface method) (sl_experiment.shared_components.ValveInterface method)

torque_per_adc_unit (sl_experiment.shared_components.TorqueInterface property) TorqueInterface (class in sl_experiment.shared_components) traveled_distance (sl_experiment.shared_components.EncoderInterface property) TTLInterface (class in sl_experiment.shared_components)

U

unsafe_flag (sl_experiment.mesoscope_vr.ZaberDeviceSettings attribute)

update_surgery_quality() (sl_experiment.shared_components.SurgeryLog method) update_water_log() (sl_experiment.shared_components.WaterLog method)

V

validate_zaber_device_configuration() (in module sl_experiment.mesoscope_vr)

ValveInterface (class in sl_experiment.shared_components)

W

warnings (sl_experiment.mesoscope_vr.ZaberValidationResult attribute)

WaterLog (class in sl_experiment.shared_components) window_checking_logic() (in module sl_experiment.mesoscope_vr)

Z

ZaberDeviceSettings (class in sl_experiment.mesoscope_vr)

ZaberValidationResult (class in sl_experiment.mesoscope_vr)