Source code for AutoHeadFix.AHF_Stimulator

#! /usr/bin/python
#-*-coding: utf-8 -*


from AHF_Rewarder import AHF_Rewarder
from AHF_Mouse import Mouse
import time
import json
import os
from time import time, localtime,timezone, sleep
from datetime import datetime

[docs]class AHF_Stimulator (object): """ Stimulator does all stimulation and reward during a head fix task All events and their timings in a head fix, including rewards, are controlled by a Stimulator. """
[docs] def __init__ (self, configDict, rewarder, textfp): """ The Stimulator class is inited with: a config dictionary of settings; the same rewarder object used to give entry rewards; and a file pointer to the log file """ self.rewarder = rewarder self.textfp = textfp self.mouse = None if configDict == None: config_from_user () else: self.configDict = configDict self.setup()
[docs] def setup (self): pass
[docs] def change_config (self, changesDict): """ Edits the configuration dictionary, adding or replacing with key/value pairs from changesDict paramater """ for key in sorted (changesDict.keys()): self.configDict.update({key : changesDict.get (key)})
[docs] def config_from_user (self): """ makes or edits the dictionary object that holds settings for this stimulator Gets info from user with the input function, which returns strings so your sublass methods will need to use int() or float() to convert values as appropriate """ if self.configDict is not None and len (self.configDict.keys()) > 0: for key in sorted (self.configDict.keys()): tempInput = input ('set ' + key + '(currently ' + str (self.configDict[key]) + ') to :') if tempInput != '': self.configDict[key] = tempInput else: print ('starting with a new empty dictionary...') self.configDict = {} while True: key = input ('Enter a new Key, or -1 to quit:') if key == '-1' or key == '': break else: value = input ('Enter a value for ' + key + ':') self.configDict.update({key : value})
[docs] def configStim (self, mouse): """ Called before running each head fix trial, stimulator decides what to do and configures itself You may wish to different things for different mice, and to store data about stim presentations in the mouse object returns: a short string representing stim configuration, used to generate movie file name :param mouse: the object representing the mouse that is currently head-fixed """ if 'stimCount' in mouse.stimResultsDict: mouse.stimResultsDict.update ({'stimCount' : mouse.stimResultsDict.get('stimCount') + 1}) else: mouse.stimResultsDict.update({'stimCount' : 1}) self.mouse = mouse return 'stim'
[docs] def run (self): """ Called at start of each head fix. Gives a reward, increments mouse's reward count, then waits 10 seconds """ self.rewarder.giveReward ('task') self.mouse.headFixRewards += 1 sleep (10)
[docs] def logFile (self): """ 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 """ event = 'stim' mStr = '{:013}'.format(self.mouse.tag) + '\t' outPutStr = mStr + datetime.fromtimestamp (int (time())).isoformat (' ') + '\t' + event print (outPutStr) if self.textfp != None: outPutStr = mStr + '{:.2f}'.format (time ()) + '\t' + event self.textfp.write(outPutStr + '\n') self.textfp.flush()
[docs] def nextDay (self, newFP): """ 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 """ self.textfp = newFP
[docs] def quitting (self): """ 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 """ pass
@staticmethod
[docs] def get_class(fileName): """ Imports a module from a fileName (stripped of the .py) and returns the class Assumes the class is named the same as the module """ module = __import__(fileName) return getattr(module, fileName)
@staticmethod
[docs] def get_stimulator_from_user (): """ Static method that trawls through current folder looking for stimulator class python files Allows user to choose from the list of files found. Files are recognized by names starting with 'AHF_Stimulator_' and ending with '.py' Raises: FileNotFoundError if no stimulator class files found """ iFile=0 files = '' for f in os.listdir('.'): if f.startswith ('AHF_Stimulator') and f.endswith ('.py'): if iFile > 0: files += ';' files += f iFile += 1 if iFile == 0: print ('Could not find an AHF_Stimulator_ file in the current or enclosing directory') raise FileNotFoundError else: if iFile == 1: print ('Stimulator file found: ' + stimFile) stimFile = files.split('.')[0] else: inputStr = '\nEnter a number from 0 to ' + str (iFile -1) + ' to Choose a Stimulator class:\n' ii=0 for file in files.split(';'): inputStr += str (ii) + ': ' + file + '\n' ii +=1 inputStr += ':' stimFileNum = -1 while stimFileNum < 0 or stimFileNum > (iFile -1): stimFileNum = int(input (inputStr)) stimFile = files.split(';')[stimFileNum] stimFile = stimFile.split('.')[0] return stimFile
@staticmethod
[docs] def dict_from_user (stimDict): """ static method that makes or edits a dictionary object that holds settings for a stimulator configure gets info from user with the input function, which returns strings so your sublass methods will need to use int() or float() to convert values as appropriate """ if stimDict is not None and len (stimDict.keys()) > 0: for key in sorted (stimDict.keys()): tempInput = input ('set ' + key + '(currently ' + str (stimDict[key]) + ') to :') if tempInput != '': stimDict[key] = tempInput else: print ('starting with a new empty dictionary...') stimDict = {} while True: key = input ('Enter a new Key, or -1 to quit:') if key == '-1' or key == '': break else: value = input ('Enter a value for ' + key + ':') stimDict.update({key : value}) return stimDict
if __name__ == '__main__': import RPi.GPIO as GPIO GPIO.setmode(GPIO.BCM) rewarder = AHF_Rewarder (30e-03, 24) rewarder.addToDict ('task', 50e-03) thisMouse = Mouse (2525, 0,0,0,0) stimFile = AHF_Stimulator.get_stimulator_from_user () stimDict = AHF_Stimulator.get_class (stimFile).dict_from_user({}) stimulator = AHF_Stimulator.get_class (stimFile)(stimDict, rewarder, None) print (stimulator.configStim (thisMouse)) stimulator.run () stimulator.logFile() stimulator.config_from_user() print (stimulator.configStim (thisMouse)) stimulator.run () stimulator.logFile() thisMouse.show() GPIO.cleanup ()