from __future__ import division
from itertools import islice, tee
import headset
import time
import urllib2
import numpy as np
import msvcrt
imprintSham=False
current_milli_time = lambda: int(round(time.time() * 1000))
stimModes={"F4":0,"C4":1,"O2":2,"C3":3,"F3":4,"O1":5,"Reference electrode":6}
electrodeNames=["F3","C3","O1","F4","C4","O2"]
offsets={"F3":5,"C3":15,"O1":25,"F4":35,"C4":45,"O2":55}
nyquist=5
shamTimer=current_milli_time()
try:
from scipy import stats, special
from scipy.fftpack import rfft,rfftfreq
from scipy import stats, special
from scipy.signal import butter, lfilter, firwin
from math import sqrt
from scipy.fftpack import rfft,rfftfreq
except ImportError:
print("There seems to be a problem with the scipy installation. Please download and install scipy-stack.")
raw_input()
quit()
from random import *
try:
import easygui as eg
except ImportError:
print("There seems to be a problem with the EasyGui installation. Please download and install it.")
raw_input()
quit()
try:
import serial
except ImportError:
print("There seems to be a problem with the PySerial installation. Please download and install it.")
raw_input()
quit()
import math
import os
import subprocess
import thread
import time
def connectStim():
accepted=False
choice=""
while not accepted:
thePorts=headset.getPorts()
if len(thePorts) < 1:
eg.msgbox(title="No devices connected",msg="No devices were detected. Make sure the BrainKit stimulator is connected and powered on and try again")
portSelect="Cancel"
else:
print(str(thePorts))
portSelect=eg.buttonbox(title="Stimulator port", msg="Select the port to which the stimulator is connected. If you do not know the port, connected or unplug the stimultor and click refresh", choices=[thePorts, "Refresh"])
if portSelect and "Refresh" not in portSelect:
accepted=True
choice=portSelect
if "Cancel" not in portSelect:
try:
print(str(choice))
print("Attempting to connect to stimulator...")
headset.getConnection(choice[0][0])
return True
except Exception:
return False
def recordData(filename):
outFile=open(filename,'w')
started=time.time()*1000.0
lastAQ=started
updateTime=started
keepRunning=True
headset.startStim(300)
headset.flushData()
print("Data aquistion is running, press space to stop.")
samples=0
while msvcrt.kbhit():
msvcrt.getch()
while keepRunning:
samples=samples+1
if msvcrt.kbhit():
theKey=msvcrt.getch()
if " " in theKey:
keepRunning=False
print("Interrupt")
theData=headset.getData()
theData.append("\t0") #for compatibility with old version data files that used this as a trigger code
theData.append((time.time()*1000.0)-started) #Time since start
theData.append((time.time()*1000.0)-lastAQ) #Time since last sample
srate=1000/((time.time()*1000.0)-(lastAQ+1))
if (time.time()*1000.0)-updateTime > 2000:
if (srate < 10):
print("SAMPLE RATE TOO LOW, REDUCE PROCESSING LOAD")
print("Effective sample rate:"+str(srate)+" Hz")
updateTime=time.time()*1000.0
lastAQ=time.time()*1000.0
for item in theData:
outFile.write(str(item)+"\t")
outFile.write("\n")
outFile.flush()
outFile.close()
headset.closeConnection()
def createProtocol(preselected_channels=False, preselected_powers=None):
electrodes=[]
powers=[]
outcomes=[]
anodeChoice=eg.multchoicebox(title="Select electrodes", msg="Select the locations that you want to recieve stimulation. You can set them as anodes or cathodes in the next step.", choices=['F4','C4','O2','C3','F3','O1'])
if anodeChoice:
for item in anodeChoice:
electrodes.append(stimModes[item])
choices=anodeChoice
choices.append("Ramp up/down duration (set to 0 for no ramping)")
choices.append("Stimulation duration (minutes)")
choices.append("Sham probability(set to 0 for no sham trials")
choices.append("Frequency (set to 0 for dc stimulation)")
powers=eg.multenterbox("Enter the power that should be used for each electrode. Positive values represent anodal stimulation, and negative values represent cathodal stimulation. You can also set the duration, ramping parameters, and sham probability of the protocol","Stimulation parameters",choices)
if powers:
exMode=eg.ynbox(title="Outcome measures",msg="Do you want to add outcome measures to this protocol?")
if exMode:
outcomes=[]
selected=""
keepPrompting=True
while keepPrompting:
keepPrompting=False
prompt=eg.buttonbox(title="Select outcome measures",msg="Current outcome measures:\n"+selected,choices=["Add","Done"])
if prompt:
keepPrompting=True
if "Add" in prompt:
name=eg.enterbox(title="Outcome measure name",msg="Enter the name for this outcome measure. Enter NPHYS to use automatically collected neurophsyiological measurements")
if name:
details=eg.buttonbox(title="Logging options",msg="How do you want to collect data on this measure?",choices=['Before stimulation only','After stimulation only','Both before and after stimulation'])
name=name.replace("/","")
selected=selected+name+ " "+details.lower()+"\n"
if 'Before stimulation only' in details:
name=name+"/1"
elif 'After stimulation only' in details:
name=name+"/2"
else:
name=name+"/3"
outcomes.append(name)
else:
keepPrompting=False
pwrite=eg.filesavebox(title="Where do you want to save this protocol?",msg="Where do you want to save this protocol?")
if pwrite:
outFile=open(pwrite,'w')
outstring=""
outstring=outstring+("phaselength:60\n")
outstring=outstring+("duration:"+powers[len(powers)-3]+"\n")
outstring=outstring+("rampdur:"+powers[len(powers)-4]+"\n")
outstring=outstring+("sham:"+powers[len(powers)-2]+"\n")
outstring=outstring+("frequency:"+powers[len(powers)-1]+"\n")
outstring=outstring+("****\n")
for item in outcomes:
outstring=outstring+(item+"\n")
outstring=outstring+("****\n")
for item in range(0,len(choices)):
outstring=outstring+(choices[item]+":"+powers[item]+"\n")
outFile.write(outstring)
outFile.flush()
outFile.close()
def qmean(num):
return sqrt(float(sum(n*n for n in num))/float(len(num)))
def averageArray(theInput):
items=0
total=0
for item in theInput:
try:
total=total+float(item)
items=items+1
except Exception:
1+1
if (items > 0):
return total/float(items)
else:
return -1
def preprocess(lines):
dataOut=[]
tempFile=""
lastLine=""
deviation=0.0
lc=0
for line in lines:
skipThis=False
line=line.replace("\t\n","\n") #prevent error from converting \n to float when processing new format files
splitup=line.split("\t")
lastItem=len(splitup)
timestamp=float(splitup[lastItem-1].replace("\n",""))
diff=100-timestamp
deviation=deviation+diff
if (deviation > 50):
tempFile=tempFile+line+"\n"
deviation=deviation-timestamp
elif (deviation < -50):
#skipThis=True
#deviation=deviation+timestamp
1+1
if not skipThis :
tempFile=tempFile+line+"\n"
lines=tempFile.split("\n")
#now just pull out the data that we want
for line in lines:
splitup=line.split("\t")
if len(splitup) >= 10:
dataOut.append(splitup[0]+"\t"+splitup[1]+"\t"+splitup[2]+"\t"+splitup[3]+"\t"+splitup[4]+"\t"+splitup[5]+"\t"+splitup[7]+"\n")
return dataOut
def permCorrelation(data1,data2,permutations, teststat):
rs=[]
wtf1=data1
wtf2=data2
for perm in range(0,permutations):
temp1=[]
temp2=[]
buf1=wtf1
buf2=wtf2
while len(temp1) < len(buf1):
temp1.append(choice(buf1+buf2))
#temp1.append(buf1[0])
while len(temp2) < len(buf2):
temp2.append(choice(buf2+buf1))
#temp2.append(buf2[0])
slope, intercept, r_value, p_value, std_err =stats.linregress(temp1, temp2)
rs.append(r_value)
#print("Computed permutation "+str(perm)+" of "+str(permutations))
pval=float(0)
for item in rs:
if (abs(item) >= abs(teststat)):
pval=pval+1
pval=float(pval)/float(permutations)
return pval
def permttest(data1,data2,permutations, teststat):
rs=[]
wtf1=data1
wtf2=data2
for perm in range(0,permutations):
temp1=[]
temp2=[]
buf1=wtf1
buf2=wtf2
while len(temp1) < len(buf1):
temp1.append(choice(buf1+buf2))
#temp1.append(buf1[0])
while len(temp2) < len(buf2):
temp2.append(choice(buf2+buf1))
#temp2.append(buf2[0])
tval,pval=stats.ttest_rel(temp1,temp2)
rs.append(tval)
#print("Computed permutation "+str(perm)+" of "+str(permutations))
pval=float(0)
for item in rs:
if (abs(item) >= abs(teststat)):
pval=pval+1
pval=float(pval)/float(permutations)
return pval
def getPhysData(filename, winLength,thresh,mode): #get neurophys measures from a file
thefilter=firwin(251, 0.05, pass_zero=False,nyq=nyquist)
closedset=[]
openset=[]
elecOut=[]
try:
print(filename)
print(os.getcwd())
theFile=open(filename,'r')
fileLines=theFile.readlines()
theFile.close()
#step one:prprocessing and timing error correction
lines=preprocess(fileLines)
#step two:filter
ave1=0
ave2=0
ave3=0
ave4=0
ave5=0
ave6=0
samples=0
sticky=0;
#raw_input()
el1=[]
el2=[]
el3=[]
el4=[]
el5=[]
el6=[]
for line in lines:
splitup=line.split("\t")
average=(float(splitup[0])+float(splitup[1])+float(splitup[2])+float(splitup[3])+float(splitup[4])+float(splitup[5]))/6
el1.append(float(splitup[0])-average)
el2.append(float(splitup[1])-average)
el3.append(float(splitup[2])-average)
el4.append(float(splitup[3])-average)
el5.append(float(splitup[4])-average)
el6.append(float(splitup[5])-average)
el1=lfilter(thefilter,1.0,el1).tolist()
el2=lfilter(thefilter,1.0,el2).tolist()
el3=lfilter(thefilter,1.0,el3).tolist()
el4=lfilter(thefilter,1.0,el4).tolist()
el5=lfilter(thefilter,1.0,el5).tolist()
el6=lfilter(thefilter,1.0,el6).tolist()
#step 3:epoch and reject bad epochs
epochHolder=[]
linenum=0
numtaken=0
while len(el1) > 0:
# print(str(len(el1)))
epoch=[]
keepRunning=True
while len(epoch) < (winLength*10) and keepRunning:
try:
line=lines[numtaken]
if numtaken >=260:
epoch.append([el1.pop(0), el2.pop(0), el3.pop(0), el4.pop(0), el5.pop(0), el6.pop(0), int(line.split("\t")[6])])
else:
foo=([el1.pop(0), el2.pop(0), el3.pop(0), el4.pop(0), el5.pop(0), el6.pop(0), int(line.split("\t")[6])])
numtaken=numtaken+1
except IndexError:
keepRunning=False
keepEpoch=True
for thing in epoch:
startType=epoch[0][6]
if (thing[6] != startType):
keepEpoch=False
if keepEpoch or True:
epochHolder.append(epoch)
#for epoch in epochHolder[5:]:
print("*****")
for epochnum in range(1,len(epochHolder)):
epoch=epochHolder[epochnum];
#raw_input()
lastEpoch=epochHolder[epochnum-1];
badEpoch=False
for electrode in [0,1,2,3,4,5]:
thistrode=[]
for timepoint in lastEpoch:
thistrode.append(timepoint[electrode])
ave=averageArray(thistrode)
newtrode=[]
for timepoint in epoch:
thistrode=timepoint[electrode]
if abs(thistrode-ave) > thresh:
badEpoch=True
#print(str(len(epoch[1])))
if not badEpoch:
closedset.append(epoch)
for electrode in [0,1,2,3,4,5]:
closedout=0
closedlog=[]
openout=0;
conout=0
for epoch in closedset:
ts=[]
for point in epoch:
ts.append(point[electrode])
ave=averageArray(ts)
newts=[]
for point in ts:
newts.append(point-ave)
ts=newts
if "sessions" in mode:
closedout=closedout+qmean(ts)
else:
closedlog.append(qmean(ts))
if "sessions" in mode:
closedout=closedout/len(closedset)
elecOut.append(closedout)
else:
elecOut.append(closedlog)
except Exception:
eg.msgbox("Error loading data file:"+filename)
return elecOut
lastPacket={}
runDisplayThread=True
print("Brainkit 1.0 by Nathan Whitmore")
try:
print("Checking for critical updates...")
versionID=urllib2.urlopen("http://montageexplorer.appspot.com/brainkitversion").read()
splitup=versionID.split("\n")
if float(splitup[1]) > 1.0:
print(splitup[2])
eg.msgbox(splitup[2])
except Exception:
print("Could not connect to server")
while True:
choices=["(1) Create protocol manually","(2) Create protocol from experiment","(3) Run protocol","(4) Record data","(5) Run stimulator self tests"]
userChoice=eg.choicebox("Welcome to BrainKit. Select an option to continue",title="BrainKit 1.0",choices=choices)
if "1" in userChoice:
createProtocol()
if "2" in userChoice: #create protocol from experiment
eFileName=eg.fileopenbox(title="Select the experiment file that you want to open")
filepath=""
splitup=eFileName.split("\\")
for item in range(0,len(splitup)-1):
filepath=filepath+splitup[item]+"\\"
os.chdir(filepath) #set working directory so that we can load the data files
eFile=open(eFileName,'r')
efLines=eFile.readlines()
exType=eg.buttonbox(title="Select experiment type",msg="What type of experiment is this?",choices=["Correlation experiment","Paired test experiment"])
if ("Correlation" in exType): # Correlating an IV with neurophys data
header=efLines[0]
splitHead=header.split("\t")[1:]
iv=eg.choicebox(title="Select behavioral variable",msg="Select which column designates the behavioral or cognitive variable of interest for this experiment",choices=splitHead)
if iv:
dv=[]
ivnum=-1
for item in range(0,len(splitHead)):
if iv in splitHead[item]:
ivnum=item
## #dv.append(item)
## for item in range(1,len(splitHead)):
## dv.append(splitHead[item])
setup=eg.multenterbox(title="Analysis settings",msg="Choose the settings you want for this analysis.",fields=["Critical p:","Use Bonferroni correction for multiple comparisons?(y/n)","Permutations per variable","Epoch size(seconds)","Artifact rejection threshold"],values=["0.05","n","10000","10","0.5"])
allSession=[]
for item in efLines[1:]:
print("Loading session "+str(item))
session=[]
splitup=item.split("\t")
#get the neurophys data
if True:
physdata=getPhysData(splitup[0],float(setup[3]),float(setup[4]),("sessions"))
print(str(physdata))
## for index in range(0,len(dv)):
## session.append(splitup[index])
session.append(splitup[ivnum+1])
for index in range(0,len(physdata)):
session.append(physdata[index])
allSession.append(session)
elif "epoch" in setup[5]: #Mode to come, epoch-level analysis of data
physdata=getPhysData(splitup[0],float(setup[3]),float(setup[4]),("sessions"))
for epoch in physdata:
session=[splitup[ivnum+1]];
for index in range(0,len(epoch)):
session.append(epoch[index])
allSession.append(session)
numItems=len(allSession[0])
## print(str(allSession))
## print(str(numItems))
## print(str(allSession[0]))
## print(str(dv))
## raw_input()
significant=[]
pvals=[]
rvals=[]
for item in range(1,6):
print("Computing variable "+str(item))
thisVar=[]
condition=[]
for line in allSession:
thisVar.append(line[item])
condition.append(float(line[0]))
slope, intercept, r_value, p_value, std_err =stats.linregress(thisVar, condition)
significance= permCorrelation(thisVar,condition,int(setup[2]), r_value)
if ("y" in setup[1]):
critical=float(setup[0])/numItems
else:
critical=float(setup[0])
if (significance <= critical):
significant.append(item)
pvals.append(significance)
rvals.append(r_value)
if len(significant) > 0:
choices=[]
headers=efLines[0].split("\t")
for itemnum in range(0,len(significant)):
item=int(significant[itemnum]-1)
dataline=(headers[ivnum+1]).upper()+"x"+electrodeNames[item].upper()+" r:"+str(rvals[itemnum])+" p:"+str(pvals[itemnum])
choices.append(str(itemnum+1)+"."+dataline)
acceptable=False
select=[]
while not acceptable:
sigselect=eg.multchoicebox(msg="The following significant correlations were found. Select which ones you want to use to design the protocol",title="Select significant correlations",choices=choices)
if sigselect:
acceptable=True
for thing in sigselect:
index=int(thing.split(".")[0])
select.append(significant[index-1])
createProtocol(preselected_channels=select)
else:
eg.msgbox("No correlations were significant at the chosen threshold")
else: #pre=post test
header=efLines[0]
m1ind=-1
m2ind=-1
splitHead=header.split("\t")
m1=eg.choicebox(title="Select measurement 1",msg="Select which column contains data files corresponding to measurement 1",choices=splitHead)
if m1:
for item in range(0,len(splitHead)):
if m1 in splitHead[item]:
m1ind=item
m2=eg.choicebox(title="Select measurement 2",msg="Select which column contains data files corresponding to measurement 2",choices=splitHead)
if m2:
for item in range(0,len(splitHead)):
if m2 in splitHead[item]:
m2ind=item
setup=eg.multenterbox(title="Analysis settings",msg="Choose the settings you want for this analysis.",fields=["Critical p:","Use Bonferroni correction for multiple comparisons?(y/n)","Permutations per variable","Epoch size(seconds)","Artifact rejection threshold"],values=["0.05","n","10000","10","0.5"])
cond1=[]
cond2=[]
for item in efLines[1:]:
print("Loading session "+str(item))
session1=[]
session2=[]
splitup=item.split("\t")
#get the neurophys data
if True:
physdata1=getPhysData(splitup[m1ind],float(setup[3]),float(setup[4]),("sessions"))
print(str(physdata1))
for index in range(0,len(physdata1)):
session1.append(physdata1[index])
cond1.append(session1)
physdata2=getPhysData(splitup[m2ind],float(setup[3]),float(setup[4]),("sessions"))
for index in range(0,len(physdata2)):
session2.append(physdata2[index])
cond2.append(session2)
elif "epoch" in setup[5]: #to come lather: epoch-level analysis
physdata1=getPhysData(splitup[m1ind],float(setup[3]),float(setup[4]),(setup[5]))
physdata2=getPhysData(splitup[m2ind],float(setup[3]),float(setup[4]),(setup[5]))
for item in physdata1:
session1=[]
for index in range(0,len(item)):
session1.append(item[index])
cond1.append(session1)
for item in physdata2:
session2=[]
for index in range(0,len(item)):
session2.append(item[index])
cond2.append(session2)
significant=[]
pvals=[]
meandiff=[]
rvals=[]
for item in range(1,6):
print("Computing variable "+str(item))
m1=[]
m2=[]
for line in range(0,len(cond1)):
m1.append(cond1[line][item])
m2.append(cond2[line][item])
print(str(m1))
print(str(m2))
tval,pval=stats.ttest_rel(m1,m2)
significance= permttest(m1,m2,int(setup[2]), tval)
if ("y" in setup[1]):
critical=float(setup[0])/numItems
else:
critical=float(setup[0])
if (significance <= critical):
significant.append(item)
pvals.append(significance)
rvals.append(tval)
if len(significant) > 0:
choices=[]
headers=efLines[0].split("\t")
for itemnum in range(0,len(significant)):
item=int(significant[itemnum]-1)
dataline=(electrodeNames[item].upper()+" t:"+str(rvals[itemnum])+" p:"+str(pvals[itemnum]))
choices.append(str(itemnum+1)+"."+dataline)
acceptable=False
select=[]
while not acceptable:
sigselect=eg.multchoicebox(msg="The following significant correlations were found. Select which ones you want to use to design the protocol",title="Select significant correlations",choices=choices)
if sigselect:
acceptable=True
for thing in sigselect:
index=int(thing.split(".")[0])
select.append(significant[index-1])
createProtocol(preselected_channels=select)
else:
eg.msgbox("No correlations were significant at the chosen threshold")
if "3" in userChoice: #run protocol
totalCurrent=0
intensityError=False
errors=""
fatalError=False
eList=""
fileName=""
pFileName=eg.fileopenbox(title="Select the protocol that you want to run")
if pFileName:
filepath=""
splitup=pFileName.split("\\")
for item in range(0,len(splitup)-1):
filepath=filepath+splitup[item]+"\\"
os.chdir(filepath) #set working directory so that we can load the data files
pFile=open(pFileName,'r')
fileName=splitup[len(splitup)-1]
pData=pFile.read()
pFile.close()
protosplit=pData.split("****")
protodict={}
for line in protosplit[0].split("\n"):
try:
argpair=line.split(":")
protodict[argpair[0]]=argpair[1]
except Exception:
1+1
for line in protosplit[2].split("\n"):
try:
argpair=line.replace("\n","").replace("\r","").split(":")
protodict[argpair[0]]=argpair[1]
if argpair[0] in electrodeNames:
totalCurrent=totalCurrent+float(argpair[1])
try:
print(str(argpair[1]))
if abs(float(argpair[1])) > 5:
fatalError=True
errors=errors+"ERROR: A single regulated electrode cannot be set to sink or source more than 5 mA\n"
if abs(float(argpair[1])) > 2:
errors=errors+"SAFETY WARNING: Current level exceeds typical max (2 mA). Excessive current can cause skin burns and may interefere with blinding or have unanticipated effects on the brain\n"
if abs(float(argpair[1])) <= 0.1:
errors=errors+"WARNING: Minimum current is 0.1 mA. Electrodes with less current specified will not be activated.\n"
eList=eList+line+"\n"
except Exception:
fatalError=True
errors=errors+"ERROR: Invalid current value for "+argpair[0]+"\n"
except Exception:
1+1
#nowscan settings for errors
try:
durDecode=float(protodict.get("duration","nf"))
if (durDecode > 25):
errors=errors+"SAFETY WARNING: Duration exceeds typical max (20 minutes)\n"
except Exception:
fatalError=True
errors=errors+"ERROR: Duration not specified\n"
try:
float(protodict.get("rampdur","nf"))
except Exception:
fatalError=True
errors=errors+"ERROR: Ramping duration not specified\n"
try:
float(protodict.get("frequency","nf"))
except Exception:
fatalError=True
errors=errors+"ERROR: Stimulation frequency not specified\n"
try:
float(protodict.get("sham","nf"))
except Exception:
fatalError=True
errors=errors+"ERROR: Sham probability not specified\n"
if totalCurrent > 0:
errors=errors+"WARNING:Total current is not balanced. You will need to attach an electrode to pin #3 to absorb "+str(totalCurrent)+" mA of excess current\n"
if totalCurrent < 0:
errors=errors+"WARNING:Total current is not balanced. You will need to attach an electrode to pin #13 to absorb "+str(abs(totalCurrent))+" mA of excess current\n"
errorAbort=False
if len(errors) > 0:
if fatalError:
errorAbort=True
eg.msgbox(title="Critical protocol errors detected",msg="This protocol cannot be used because of errors. All errors and warnings are listed below.\n"+errors)
continueRun=eg.buttonbox(title="Protocol issues detected", msg="At least one warning or safety issue was detected in this protocol. Do you want to continue?\n All issues are listed below.\n"+errors, choices=["Yes", "No"])
if "No" in continueRun:
errorAbort=True
if not errorAbort:
print("Load protocl")
outcomeSummary=protosplit[1].replace("NPHYS","Neurophysiological measurements").replace("/1"," before session").replace("/2"," after session").replace("/3"," before and after session")
summary="DURATION:"+protodict.get("duration")+" minutes\nSHAM PROBABILITY:"+protodict.get("sham")+"%\nRAMPING DURATION:"+protodict.get("rampdur")+" seconds"+"\nFREQUENCY:"+protodict.get("frequency")+"\nPOWER LEVELS:\n"+eList+"OUTCOME MEASURES:\n"+outcomeSummary+"\n\nDo you want to run this protocol?"
runproto=eg.ynbox(title="Protocol summary",msg=summary)
if runproto:
presession=[]
postsession=[]
prename=""
postname=""
hasData=False
preData=[]
postData=[]
if randint(0,100) <= int(protodict.get("sham")):
sham=True
else:
sham=False
for item in protosplit[1].split("\n"):
if "/1" in item or "/3" in item and "NPHYS" not in item:
presession.append(item[:item.find("/")])
print(protosplit[1])
print(str(len(presession)))
if len(presession) > 0:
hasData=True
presession.append("Comments")
preData=eg.multenterbox("This protocol requires values for the following pre-session metrics","Outcome measures",presession)
if "NPHYS/1" in protosplit[1] or "NPHYS/3" in protosplit[1]:
hasdata=True
eg.msgbox("This protocol calls for neurophysiological data collection. Click OK to begin data collection.")
connectStim()
prename=fileName+"-presession-"+str(randint(0,9999))
recordData(prename)
if connectStim():
print("Programming the stimulator...")
headset.startStim(200) #make sure we're in stimulation mode
#decide whether this trial is a sham and send it
#if randint(0,100) <= int(protodict.get("sham")):
if sham:
headset.startStim(550)
#send the stimulation duration
headset.startStim(float(protodict.get("duration"))+600)
#send the ramping duration
headset.startStim(float(protodict.get("rampdur"))+400)
#If this is AC mode, send the frequency
if float(protodict.get("frequency","0")) >0:
headset.startStim(1000+float(protodict.get("frequency","0")))
#now go through all the electrodes nd set their values using the offset table
for line in eList.split("\n"):
if len(line) > 1:
splitup=line.replace("\n","").split(":")
#print(splitup[0])
#print(str(float(offsets[splitup[0]])+float(splitup[1])))
headset.startStim(float(offsets[splitup[0]])+float(splitup[1]))
#Send start command
headset.startStim(800)
print("Starting stimulation, press c to toggle current display or space to end")
headset.flushData()
keepRunning=True
displayCurrent=False
while keepRunning:
if msvcrt.kbhit():
thechar=msvcrt.getch()
if " " in thechar:
keepRunning=False
if "c" in thechar:
if displayCurrent:
displayCurrent=False
else:
displayCurrent=True
theCurrent=headset.getData()
if "SHUTDOWN" in str(theCurrent):
print("Stimulator initiated shutdown.")
keepRunning=False
if displayCurrent:
print(str(theCurrent))
print("Stimulator ramping down...")
headset.startStim(900)
headset.closeConnection()
print("Connection closed")
eg.msgbox("Press the reset button on the stimulator, then click OK")
print("Waiting for the stimulator to come back online...")
time.sleep(10)
postsession=[]
for item in protosplit[1].split("\n"):
if "/2" in item or "/3" in item and "NPHYS" not in item:
postsession.append(item[:item.find("/")])
print(str(postsession))
if len(postsession) > 0:
hasData=True
postsession.append("Comments")
postData=eg.multenterbox("This protocol requires values for the following post-session metrics","Outcome measures",postsession)
if "NPHYS/2" in protosplit[1] or "NPHYS/3" in protosplit[1]:
hasdata=True
eg.msgbox("This protocol calls for neurophysiological data collection. Click OK to begin data collection.")
connectStim()
postname=fileName+"-postsession-"+str(randint(0,9999))
recordData(postname)
#now string things together to make the log file
header=""
data=""
if len(prename) >0:
header=header+"prestim-nphys-file\t"
data=data+prename+"\t"
if len(postname) > 0:
header=header+"poststim-nphys-file\t"
data=data+postname+"\t"
header=header+"sham\t"
if sham:
data=data+"1\t"
else:
data=data+"0\t"
for index in range(0,len(presession)):
header=header+"presession-"+presession[index]+"\t"
data=data+preData[index]+"\t"
for index in range(0,len(postsession)):
header=header+"postsession-"+postsession[index]+"\t"
data=data+postData[index]+"\t"
alreadyWritten=False
dataSoFar=""
try:
expFile=open("log-"+fileName,'r')
dataSoFar=expFile.read()
if len(dataSoFar) > 1:
alreadyWritten=True
else:
alreadyWritten=False
expFile.close()
except Exception:
alreadyWritten=False
print(str(alreadyWritten))
print(str(header))
outFile=open("log-"+fileName,'w')
if not alreadyWritten:
outFile.write(header+"\n")
else:
outFile.write(dataSoFar)
outFile.write(data+"\n")
outFile.flush()
outFile.close()
else:
eg.msgbox("Could not connect stimulator.")
if "4" in userChoice:
accepted=False
choice=""
while not accepted:
thePorts=headset.getPorts()
if len(thePorts) < 1:
eg.msgbox(title="No devices connected",msg="No devices were detected. Make sure the BrainKit stimulator is connected and powered on and try again")
portSelect="Cancel"
else:
print(str(thePorts))
portSelect=eg.buttonbox(title="Stimulator port", msg="Select the port to which the stimulator is connected. If you do not know the port, connected or unplug the stimultor and click refresh", choices=[thePorts, "Refresh"])
if portSelect and "Refresh" not in portSelect:
accepted=True
choice=portSelect
if "Cancel" not in portSelect:
try:
print(str(choice))
print("Attempting to connect to stimulator...")
headset.getConnection(choice[0][0])
print("Connected...")
savedata=eg.filesavebox(title="Select where to save the data file")
if savedata:
recordData(savedata)
except Exception:
eg.msgbox("Connection error")
if "5" in userChoice:
testSelect=eg.buttonbox(msg="Select the test that you want to run",title="Stimulator self test",choices=["Regulator test","Short/bridge test","Cancel"])
if testSelect and "Cancel" not in testSelect:
if "Regulator" in testSelect:
regFail=False
if connectStim():
eg.msgbox("Connect all 6 regulated outputs to each other, then click OK to continue")
print("Configuring the stimulator...")
gocommand=[6,16,26,36,46,56]
for command in range(0,len(gocommand)):
headset.startStim(2000)
headset.startStim(610)
headset.startStim(800)
print("Testing electrode "+electrodeNames[command])
headset.flushData()
for ncommand in [4, 14, 24, 34, 44, 54]:
headset.startStim(ncommand)
headset.startStim(gocommand[command])
time.sleep(5) #give it time to equilibrate
headset.flushData()
maxData=0
values=[]
for i in range(0,15):
theData=headset.getData()
#print(str(theData))
try:
if len(theData) >5:
thisData=theData[command]
if (thisData == 0):
regFail=True
print("CAUTION:The stimulator may have reset due to an electrical fault")
values.append(float(thisData))
except Exception: #some sort of decode failure
1+1
maxData=averageArray(values)
if (maxData >= 0.9 and maxData < 1.1):
print("Forward current test passed")
else:
print("***Forward current test failed! Mean current was "+str(maxData))
regFail=True
gocommand=[4,14,24,34,44,54]
maxData=0;
values=[]
for command in range(0,len(gocommand)):
headset.startStim(2000)
headset.startStim(610)
headset.startStim(800)
print("Testing electrode "+electrodeNames[command])
headset.flushData()
for ncommand in [6, 16, 26, 36, 46, 56]:
headset.startStim(ncommand)
headset.startStim(gocommand[command])
maxData=0
values=[]
time.sleep(5) #give it time to equilibrate
headset.flushData()
for i in range(0,15):
theData=headset.getData()
print(str(theData))
try:
if len(theData) > 5:
thisData=theData[command]
if (thisData == 0):
regFail=True
print("CAUTION:The stimulator may have reset due to an electrical fault")
values.append(float(thisData))
except Exception: #some sort of decode failure
1+1
maxData=abs(averageArray(values))
if (maxData >= 0.9 and maxData < 1.1):
print("Backward current test passed")
else:
print("***Backward current test failed! Mean current was "+str(maxData))
regFail=True
headset.closeConnection()
if regFail:
eg.msgbox("The regulator failed to generate the correct current on at least one electrode. Review the log to see details")
else:
eg.msgbox("Test complete. No issues detected.")
if "Short" in testSelect:
eg.msgbox("Disconnect the headset from your body, then click OK to continue.",title="Short/bridge test")
gocommand=[9,19,29,39,49,59]
gregFail=False
if connectStim():
for command in range(0,len(gocommand)):
headset.startStim(2000)
headset.startStim(610)
headset.startStim(800)
print("Testing electrode "+electrodeNames[command])
headset.flushData()
regFail=False
for ncommand in [4, 14, 24, 34, 44, 54]:
headset.startStim(ncommand)
headset.startStim(gocommand[command])
time.sleep(5) #give it time to equilibrate
headset.flushData()
maxData=0
values=[]
bridged=[]
for i in range(0,15):
theData=headset.getData()
try:
if len(theData) >5:
for elecNum in range(0,5):
if float(theData[elecNum]) > 0.1:
regFail=True
gregFail=True
#print(str(float(theData[elecNum])))
if electrodeNames[elecNum] not in bridged:
bridged.append(electrodeNames[elecNum])
except Exception: #some sort of decode failure
1+1
if regFail:
print("Electrode " +electrodeNames[command] +" may be shorted to electrodes:")
for item in bridged:
print(item)
else:
print("Electrode " +electrodeNames[command]+" does not appear to be shorted")
headset.closeConnection()
if gregFail:
eg.msgbox("One or more electrodes may be shorted. Check the console for more details")
else:
eg.msgbox("No shorted or bridged electrodes were detected.")
