AHF_Stimulator

Much of the Task control is handled by this AHF_Stimulator. Refer to the modules below for task descriptions, and to ensure the correct task is being used for the cage.

AHF_Stimulator.AHF_Stimulator module

class AHF_Stimulator.AHF_Stimulator(taskP, settingsDictP)

Bases: AHF_Base.AHF_Base

Stimulator does all stimulation and reward during a head fix task. All events and their timings in a head fix, including camera control and rewards, are controlled by a Stimulator.

static config_user_get(starterDict={}): static method that querries user for settings, with default responses from starterDict, and returns starterDict with settings as edited by the user.

abstract quitting()

abstract run(level=0, resultsDict={}, settingsDict={}): Called at start of each head fix. Does whatever

startVideo()

stop()

stopVideo()

AHF_Stimulator.AHF_Stimulator_LEDs module

class AHF_Stimulator_LEDs.AHF_Stimulator_LEDs(taskP)

Bases: AHF_Stimulator_Rewards.AHF_Stimulator_Rewards

static about(): Returns a brief message describing your sub-class, used when asking user to pick a sub-class of this class

configStim(mouse)

config_subject_get(starterDict={})

Returns: dict – the default dictionary for individualized parameters

static config_user_get(): static method that querries user for settings, with default responses from starterDict, and returns starterDict with settings as edited by the user.

config_user_subject_get(starterDict={}): Prompts the user for individualized parameters, with default responses from starterDict, and returns starterDict with settings as edited by the user.

hardwareTest(): Tests functionality, gives user a chance to change settings. :Returns: bool – True if any settings have changed

logFile()

Called after each head fix, prints more detailed text to the log file, perhaps a line for each event

You may wish to use the same format as writeToLogFile function in __main__.py

Or you may wish to override with pass and log from the run method

logfile()

run(resultsDict={}, settingsDict={}): Called at start of each head fix. Does whatever

setup()

does hardware initialization with(possibly updated) info in self.settingsDict Run by __init__, or can be run separately after editing the settingsDict

Returns

code: bool whether setup completed without errors

AHF_Stimulator_LEDs.random() → x in the interval [0, 1).

AHF_Stimulator.AHF_Stimulator_Lever module

class AHF_Stimulator_Lever.AHF_Stimulator_Lever(taskP, settingsDictP)

Bases: AHF_Stimulator.AHF_Stimulator

AHF_Stimulator_Lever runs a lever task by calling ptLeverThread C-module code that records lever position and puts torque on the lever

LEVER_FREQ = 250

MAX_FORCE_ARRAY_SIZE = 125

static about(): Returns a brief message describing your sub-class, used when asking user to pick a sub-class of this class

config_subject_get(starterDict={})

Returns: dict – the default dictionary for individualized parameters

static config_user_get(starterDict={}): static method that querries user for settings, with default responses from starterDict, and returns starterDict with settings as edited by the user.

config_user_subject_get(starterDict={}): Prompts the user for individualized parameters, with default responses from starterDict, and returns starterDict with settings as edited by the user.

defaultConstForce = 0.3: constant force on lever at start of trial that mouse must pull against, as opposed to perturbForce set during a trial a 12 bit value, 0 to 4095

defaultDemoteRate = 0.25: training for goal position

defaultGoalCenter = 200

defaultGoalCueFreq = 0: frequency for goal cue - 0 means DC, i.e., turn ON and OFF

defaultGoalCuePin = 23: GPIO pin to use for a cue played when lever is in goal pos

defaultGoalEndWidth = 10

defaultGoalIncr = 5: training for holdTime

defaultGoalStartWidth = 100

defaultGoalTrainOn = 0

defaultGoalWidth = 100: Perturbation settings for starting a mouse. Force on lever is adjusted up or down relative to const force, and then left at new value, and lever must be kept in goal area

defaultHoldEndTime = 2

defaultHoldIncr = 0.1

defaultHoldStartTime = 0.1

defaultHoldTime = 0.2

defaultHoldTrainOn = False

defaultLeverIsReversed = False: False means lever position numbers start at 0 and get bigger when mouse pulls lever, True means numbers get smaller

defaultMotorDir = 0: If MOTOR_DIR_PIN = 0, 16 bit force output(0 - 4095) goes from full counterclockwise force to full clockwise force with midpoint(2048) being no force on lever. If MOTOR_DIR_PIN is non-zero, 0-4095 maps from no force to full force, and MOTOR_DIR_PIN is the GPIO pin that controls the direction of the force, clockwise or counter-clockwise.

defaultMotorEnable = 20: GPIO Pin to enable motor

defaultMotorIsReversed = False

defaultPerturbForceOffset = 0

defaultPerturbForceRandom = 400: Training settings

defaultPerturbPercent = 0.0

defaultPerturbRampDur = 0.25

defaultPerturbStartRandom = 0

defaultPerturbStartTime = 1

defaultPrePullTime = 0.25: this many seconds of time before the lever reaches goal position is saved in a circular buffer

defaultPromoteRate = 0.75

defaultRecordingTime = 4: maximum of seconds of lever position data that will be recorded per trial

defaultStartCueDur = 0.1: duration in seconds of start cue

defaultStartCueFreq = 0: frequency for start cue - 0 means DC, i.e., turn ON and OFF

defaultStartCuePin = 27: GPIO pin to use for a cue when mouse should start a trial, this can be a pulse(freq =0) or a train

defaultToGoalTime = 0.25

defaultTrainSize = 50

defaultTrialIsCued = False: True means trials will be started with the start cue; False means mouse starts pulling lever whenever he likes

defaultTrialTimeout = 0.5: time in seconds between end of one trial(ended for any reason) and start of the next trial. Lever is rezeroed here

hardwareTest(): Tests functionality, gives user a chance to change settings. :Returns: bool – True if any settings have changed

quitting()

Called before AutoHEadFix exits. Gives stimulator chance to do any needed cleanup

A stimulator may, e.g., open files and wish to close them before exiting, or use hardware that needs to be cleaned up

run(level=- 1, settingsDict={}, resultsDict={}): Called at start of each head fix. Does whatever

setdown(): oppposite of setup. Releases any hardware resouces. can be run before editing settings so GPIO pins can be reused, for example. This strategy should be used in hardwareTest method.

setup()

does hardware initialization with(possibly updated) info in self.settingsDict Run by __init__, or can be run separately after editing the settingsDict

Returns

code: bool whether setup completed without errors

AHF_Stimulator_Lever.random() → x in the interval [0, 1).

AHF_Stimulator.AHF_Stimulator_LickWithhold module

class AHF_Stimulator_LickWithhold.AHF_Stimulator_LickWithhold(taskP, settingsDictP)

Bases: AHF_Stimulator.AHF_Stimulator

AHF_Stimulator_LickWithhold gives mice rewards based on their “level”
within the program. These rewards are given based on the mouse’s response
to a defined stimulus. Levels are as follows:

Level 0: Mouse gets periodic rewards paired with a stimulus. No input
required from the mouse at this stage.
Level 1: Mouse gets periodic rewards, again paired with a stimulus. The
mouse must refrain from licking for a defined withhold time before another
reward is given. If they lick within the withhold time, a buzzer sounds.
Level 2: Mouse must lick after a given delay time from the stimulus, and
within a defined response time, in order to receive a reward. In brief,
this is the “GO” task.
Level 3: Mouse must differentiate between two stimuluses, either one pulse
for “GO” or two successive pulses for “NO-GO”. In either case, they must
wait for the delay time before responding, and then within the response
time decide to either lick or not lick. “NO-GO” trials can be rewarded
with water or not if desired.
For levels 2 and 3, the outcome of the task is recorded as follows:
“GO”:
-4: licked within delay time, failure
-2: did not lick, failure
+2: waited until response time to lick and then licked, success
“NO-GO”:
-3: licked within delay time, failure
-1: waited until response time to lick and then licked, failure
+1: did not lick, success

static about(): Returns a brief message describing your sub-class, used when asking user to pick a sub-class of this class

config_subject_get(starterDict={})

Returns: dict – the default dictionary for individualized parameters

static config_user_get(starterDict={}): static method that querries user for settings, with default responses from starterDict, and returns starterDict with settings as edited by the user.

config_user_subject_get(starterDict={}): Prompts the user for individualized parameters, with default responses from starterDict, and returns starterDict with settings as edited by the user.

delayTime_def = 0.5

discrimTask()

goLikelihood_def = 0.5

goTask(): A GO trial. Mouse must lick before getting a reward.

hardwareTest(): Tests functionality, gives user a chance to change settings. :Returns: bool – True if any settings have changed

lickWithholdTime_def = 1

lickWrongTimeout_def = 5

noGoTask()

quitting()

Called before AutoHEadFix exits. Gives stimulator chance to do any needed cleanup

A stimulator may, e.g., open files and wish to close them before exiting, or use hardware that needs to be cleaned up

responseTime_def = 2.5

rewardNoGo_def = True

rewardTask()

run(level=- 1, resultsDict={}, settingsDict={}, tag=0): Called at start of each head fix. Does whatever

setdown(): oppposite of setup. Releases any hardware resouces. can be run before editing settings so GPIO pins can be reused, for example. This strategy should be used in hardwareTest method.

setup()

does hardware initialization with(possibly updated) info in self.settingsDict Run by __init__, or can be run separately after editing the settingsDict

Returns

code: bool whether setup completed without errors

speakerDuty_def = 0.8

speakerFreq_def = 300

speakerOffForReward_def = 1.5

speakerPin_def = 25

withholdWait(endTime)

AHF_Stimulator_LickWithhold.random() → x in the interval [0, 1).

AHF_Stimulator.AHF_Stimulator_Rewards module

class AHF_Stimulator_Rewards.AHF_Stimulator_Rewards(taskP, settingsDictP)

Bases: AHF_Stimulator.AHF_Stimulator

static about(): Returns a brief message describing your sub-class, used when asking user to pick a sub-class of this class

config_subject_get(starterDict={})

Returns: dict – the default dictionary for individualized parameters

static config_user_get(starterDict={}): static method that querries user for settings, with default responses from starterDict, and returns starterDict with settings as edited by the user.

config_user_subject_get(starterDict={}): Prompts the user for individualized parameters, with default responses from starterDict, and returns starterDict with settings as edited by the user.

defaultInterval = 3

defaultRewards = 5

hardwareTest(): Tests functionality, gives user a chance to change settings. :Returns: bool – True if any settings have changed

nextDay(): Called when the next day starts. The stimulator is given the new log file pointer. Can do other things as needed :param newFP: the file pointer for the new day’s log file

quitting()

Called before AutoHEadFix exits. Gives stimulator chance to do any needed cleanup

A stimulator may, e.g., open files and wish to close them before exiting, or use hardware that needs to be cleaned up

run(level=0, resultsDict={}, settingsDict={}): Called at start of each head fix. Does whatever

setdown(): oppposite of setup. Releases any hardware resouces. can be run before editing settings so GPIO pins can be reused, for example. This strategy should be used in hardwareTest method.

setup()

does hardware initialization with(possibly updated) info in self.settingsDict Run by __init__, or can be run separately after editing the settingsDict

Returns

code: bool whether setup completed without errors