First version of the fNIRS experiment using the serial port (A triggers - blocks, B triggers - stimuli)

fNIRS_experiment_alpha.py

#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
This experiment was created using PsychoPy2 Experiment Builder (v1.83.04), February 07, 2017, at 16:33
If you publish work using this script please cite the relevant PsychoPy publications
  Peirce, JW (2007) PsychoPy - Psychophysics software in Python. Journal of Neuroscience Methods, 162(1-2), 8-13.
  Peirce, JW (2009) Generating stimuli for neuroscience using PsychoPy. Frontiers in Neuroinformatics, 2:10. doi: 10.3389/neuro.11.010.2008
"""

from __future__ import division  # so that 1/3=0.333 instead of 1/3=0
from psychopy import locale_setup, visual, core, data, event, logging, sound, gui
from psychopy.constants import *  # things like STARTED, FINISHED
import numpy as np  # whole numpy lib is available, prepend 'np.'
from numpy import sin, cos, tan, log, log10, pi, average, sqrt, std, deg2rad, rad2deg, linspace, asarray
from numpy.random import random, randint, normal, shuffle
import os  # handy system and path functions
import sys # to get file system encoding
import serial

# set the serial port
port = serial.Serial('COM1', 9600, timeout=0)

# Ensure that relative paths start from the same directory as this script
_thisDir = os.path.dirname(os.path.abspath(__file__)).decode(sys.getfilesystemencoding())
os.chdir(_thisDir)

# Store info about the experiment session
expName = 'fNIRS_experiment'  # from the Builder filename that created this script
expInfo = {'participant':'', 'session':'001'}
dlg = gui.DlgFromDict(dictionary=expInfo, title=expName)
if dlg.OK == False: core.quit()  # user pressed cancel
expInfo['date'] = data.getDateStr()  # add a simple timestamp
expInfo['expName'] = expName

# Data file name stem = absolute path + name; later add .psyexp, .csv, .log, etc
filename = _thisDir + os.sep + 'data/%s_%s_%s' %(expInfo['participant'], expName, expInfo['date'])

# An ExperimentHandler isn't essential but helps with data saving
thisExp = data.ExperimentHandler(name=expName, version='',
    extraInfo=expInfo, runtimeInfo=None,
    originPath=u'E:\\Experiments\\Test\\fNIRS_experiment.psyexp',
    savePickle=True, saveWideText=True,
    dataFileName=filename)
#save a log file for detail verbose info
logFile = logging.LogFile(filename+'.log', level=logging.EXP)
logging.console.setLevel(logging.WARNING)  # this outputs to the screen, not a file

endExpNow = False  # flag for 'escape' or other condition => quit the exp

# Start Code - component code to be run before the window creation

# Setup the Window
win = visual.Window(size=(2048, 1152), fullscr=True, screen=0, allowGUI=False, allowStencil=False,
    monitor='testMonitor', color=[0,0,0], colorSpace='rgb',
    blendMode='avg', useFBO=True,
    )
# store frame rate of monitor if we can measure it successfully
expInfo['frameRate']=win.getActualFrameRate()
if expInfo['frameRate']!=None:
    frameDur = 1.0/round(expInfo['frameRate'])
else:
    frameDur = 1.0/60.0 # couldn't get a reliable measure so guess

# Initialize components for Routine "trial"
trialClock = core.Clock()
ISI = core.StaticPeriod(win=win, screenHz=expInfo['frameRate'], name='ISI')
introduction = visual.TextStim(win=win, ori=0, name='introduction',
    text='Welcome to the experiment.',    font='Arial',
    pos=[0, 0], height=0.1, wrapWidth=None,
    color='white', colorSpace='rgb', opacity=1,
    depth=-1.0)

# Initialize components for Routine "sound_2"
sound_2Clock = core.Clock()
a_sound = sound.Sound('example.wav', secs=-1)
a_sound.setVolume(1)
ISI_2 = core.StaticPeriod(win=win, screenHz=expInfo['frameRate'], name='ISI_2')

# Initialize components for Routine "end"
endClock = core.Clock()
the_end = visual.TextStim(win=win, ori=0, name='the_end',
    text='THE END. Press SPACE to finish.',    font='Arial',
    pos=[0, 0], height=0.1, wrapWidth=None,
    color='white', colorSpace='rgb', opacity=1,
    depth=0.0)

# Create some handy timers
globalClock = core.Clock()  # to track the time since experiment started
routineTimer = core.CountdownTimer()  # to track time remaining of each (non-slip) routine 

#------Prepare to start Routine "trial"-------
port.write('ST\r') # hardcoded start command
t = 0
trialClock.reset()  # clock 
frameN = -1
routineTimer.add(3.000000)
# update component parameters for each repeat
# keep track of which components have finished
trialComponents = []
trialComponents.append(ISI)
trialComponents.append(introduction)
for thisComponent in trialComponents:
    if hasattr(thisComponent, 'status'):
        thisComponent.status = NOT_STARTED

#-------Start Routine "trial"-------
continueRoutine = True
while continueRoutine and routineTimer.getTime() > 0:
    # get current time
    t = trialClock.getTime()
    frameN = frameN + 1  # number of completed frames (so 0 is the first frame)
    # update/draw components on each frame
    
    # *introduction* updates
    if t >= 0.0 and introduction.status == NOT_STARTED:
        # keep track of start time/frame for later
        introduction.tStart = t  # underestimates by a little under one frame
        introduction.frameNStart = frameN  # exact frame index
        introduction.setAutoDraw(True)
    if introduction.status == STARTED and t >= (0.0 + (3.0-win.monitorFramePeriod*0.75)): #most of one frame period left
        introduction.setAutoDraw(False)
    # *ISI* period
    if t >= 0.0 and ISI.status == NOT_STARTED:
        # keep track of start time/frame for later
        ISI.tStart = t  # underestimates by a little under one frame
        ISI.frameNStart = frameN  # exact frame index
        ISI.start(0.5)
    elif ISI.status == STARTED: #one frame should pass before updating params and completing
        ISI.complete() #finish the static period
    
    # check if all components have finished
    if not continueRoutine:  # a component has requested a forced-end of Routine
        break
    continueRoutine = False  # will revert to True if at least one component still running
    for thisComponent in trialComponents:
        if hasattr(thisComponent, "status") and thisComponent.status != FINISHED:
            continueRoutine = True
            break  # at least one component has not yet finished
    
    # check for quit (the Esc key)
    if endExpNow or event.getKeys(keyList=["escape"]):
        core.quit()
    
    # refresh the screen
    if continueRoutine:  # don't flip if this routine is over or we'll get a blank screen
        win.flip()

#-------Ending Routine "trial"-------
for thisComponent in trialComponents:
    if hasattr(thisComponent, "setAutoDraw"):
        thisComponent.setAutoDraw(False)

# set up handler to look after randomisation of conditions etc
trials = data.TrialHandler(nReps=10, method='sequential', 
    extraInfo=expInfo, originPath=-1,
    trialList=[None],
    seed=None, name='trials')
thisExp.addLoop(trials)  # add the loop to the experiment
thisTrial = trials.trialList[0]  # so we can initialise stimuli with some values
# abbreviate parameter names if possible (e.g. rgb=thisTrial.rgb)
if thisTrial != None:
    for paramName in thisTrial.keys():
        exec(paramName + '= thisTrial.' + paramName)

# start the sound block
port.write('A \r')
from time import sleep
sleep(0.2)
port.write('A \r')

for thisTrial in trials:
    currentLoop = trials
    # abbreviate parameter names if possible (e.g. rgb = thisTrial.rgb)
    if thisTrial != None:
        for paramName in thisTrial.keys():
            exec(paramName + '= thisTrial.' + paramName)
    
    #------Prepare to start Routine "sound_2"-------
    t = 0
    sound_2Clock.reset()  # clock 
    frameN = -1
    # update component parameters for each repeat
    # keep track of which components have finished
    sound_2Components = []
    sound_2Components.append(a_sound)
    sound_2Components.append(ISI_2)
    for thisComponent in sound_2Components:
        if hasattr(thisComponent, 'status'):
            thisComponent.status = NOT_STARTED
    
    #-------Start Routine "sound_2"-------
    # port.write('A \r') # shows A each time sound is played
    port.write('B \r')
    continueRoutine = True
    while continueRoutine:
        # get current time
        t = sound_2Clock.getTime()
        frameN = frameN + 1  # number of completed frames (so 0 is the first frame)
        # update/draw components on each frame
        # start/stop a_sound
        if t >= 0.0 and a_sound.status == NOT_STARTED:
            # keep track of start time/frame for later
            a_sound.tStart = t  # underestimates by a little under one frame
            a_sound.frameNStart = frameN  # exact frame index
            
            a_sound.play()  # start the sound (it finishes automatically)
        # *ISI_2* period
        if t >= 0.0 and ISI_2.status == NOT_STARTED:
            # keep track of start time/frame for later
            ISI_2.tStart = t  # underestimates by a little under one frame
            ISI_2.frameNStart = frameN  # exact frame index
            ISI_2.start(1.0)
        elif ISI_2.status == STARTED: #one frame should pass before updating params and completing
            ISI_2.complete() #finish the static period
        
        # check if all components have finished
        if not continueRoutine:  # a component has requested a forced-end of Routine
            break
        continueRoutine = False  # will revert to True if at least one component still running
        for thisComponent in sound_2Components:
            if hasattr(thisComponent, "status") and thisComponent.status != FINISHED:
                continueRoutine = True
                break  # at least one component has not yet finished
        
        # check for quit (the Esc key)
        if endExpNow or event.getKeys(keyList=["escape"]):
            core.quit()
        
        # refresh the screen
        if continueRoutine:  # don't flip if this routine is over or we'll get a blank screen
            win.flip()
    
    #-------Ending Routine "sound_2"-------
    for thisComponent in sound_2Components:
        if hasattr(thisComponent, "setAutoDraw"):
            thisComponent.setAutoDraw(False)
    port.write('B \r')
    a_sound.stop() #ensure sound has stopped at end of routine
    # the Routine "sound_2" was not non-slip safe, so reset the non-slip timer
    routineTimer.reset()
    thisExp.nextEntry()
    
# completed 10 repeats of 'trials'
port.write('A \r')
sleep(0.2)
port.write('A \r')

#------Prepare to start Routine "end"-------
t = 0
endClock.reset()  # clock 
frameN = -1
# update component parameters for each repeat
key_resp_2 = event.BuilderKeyResponse()  # create an object of type KeyResponse
key_resp_2.status = NOT_STARTED
# keep track of which components have finished
endComponents = []
endComponents.append(the_end)
endComponents.append(key_resp_2)
for thisComponent in endComponents:
    if hasattr(thisComponent, 'status'):
        thisComponent.status = NOT_STARTED

#-------Start Routine "end"-------
continueRoutine = True
while continueRoutine:
    # get current time
    t = endClock.getTime()
    frameN = frameN + 1  # number of completed frames (so 0 is the first frame)
    # update/draw components on each frame
    
    # *the_end* updates
    if t >= 0.0 and the_end.status == NOT_STARTED:
        # keep track of start time/frame for later
        the_end.tStart = t  # underestimates by a little under one frame
        the_end.frameNStart = frameN  # exact frame index
        the_end.setAutoDraw(True)
    if the_end.status == STARTED and t >= (0.0 + (1.0-win.monitorFramePeriod*0.75)): #most of one frame period left
        the_end.setAutoDraw(False)
    
    # *key_resp_2* updates
    if t >= 0.0 and key_resp_2.status == NOT_STARTED:
        # keep track of start time/frame for later
        key_resp_2.tStart = t  # underestimates by a little under one frame
        key_resp_2.frameNStart = frameN  # exact frame index
        key_resp_2.status = STARTED
        # keyboard checking is just starting
        win.callOnFlip(key_resp_2.clock.reset)  # t=0 on next screen flip
        event.clearEvents(eventType='keyboard')
    if key_resp_2.status == STARTED:
        theseKeys = event.getKeys(keyList=['space'])
        
        # check for quit:
        if "escape" in theseKeys:
            endExpNow = True
        if len(theseKeys) > 0:  # at least one key was pressed
            key_resp_2.keys = theseKeys[-1]  # just the last key pressed
            key_resp_2.rt = key_resp_2.clock.getTime()
            # a response ends the routine
            continueRoutine = False
    
    # check if all components have finished
    if not continueRoutine:  # a component has requested a forced-end of Routine
        break
    continueRoutine = False  # will revert to True if at least one component still running
    for thisComponent in endComponents:
        if hasattr(thisComponent, "status") and thisComponent.status != FINISHED:
            continueRoutine = True
            break  # at least one component has not yet finished
    
    # check for quit (the Esc key)
    if endExpNow or event.getKeys(keyList=["escape"]):
        core.quit()
    
    # refresh the screen
    if continueRoutine:  # don't flip if this routine is over or we'll get a blank screen
        win.flip()

#-------Ending Routine "end"-------
for thisComponent in endComponents:
    if hasattr(thisComponent, "setAutoDraw"):
        thisComponent.setAutoDraw(False)
# check responses
if key_resp_2.keys in ['', [], None]:  # No response was made
   key_resp_2.keys=None
# store data for thisExp (ExperimentHandler)
thisExp.addData('key_resp_2.keys',key_resp_2.keys)
if key_resp_2.keys != None:  # we had a response
    thisExp.addData('key_resp_2.rt', key_resp_2.rt)
thisExp.nextEntry()
# the Routine "end" was not non-slip safe, so reset the non-slip timer
routineTimer.reset()

port.write('ED\r') # hardcoded end command

# these shouldn't be strictly necessary (should auto-save)
thisExp.saveAsWideText(filename+'.csv')
thisExp.saveAsPickle(filename)
logging.flush()
# make sure everything is closed down
thisExp.abort() # or data files will save again on exit
win.close()
core.quit()