def new_eve(eve, epochs, eve_dir, rej_dir):
print 'Running %s' % eve
eve_d = readTable(eve)
rej_types = ('blink',) # , 'grad', 'mag', 'eeg'
type_rep = {'blink':'1000'}
print 'epochs.keys listed in condCodes:',epochs.keys()
k = filter(lambda y: y in eve, epochs.keys()) #given your eve file name, see if it contains any paradigm names
paradigmKey = max(k, key=len) #In case your filename contained more than one paradigm name, pick the longest one (to avoid substring problems)
print 'using epoch key:', paradigmKey
new_eve = eve_d[:]
for type in rej_types:
#get type from all_rej
bname = op.basename(eve)
base, _, _ = bname.rpartition('Mod.eve')
search = op.join(rej_dir, '%s-Filtered_raw_%s.txt' % (base,type))
#print 'Search:', search
rej = glob(search)
#print rej
if len(rej) < 1:
raise Exception('No rej of this type found!')
print epochs[paradigmKey] ##print this line if you want to see what time samples are being used
bad_dict = reject(type, epochs[paradigmKey], new_eve, readTable(rej[0]))
#print bad_dict
for code, r in bad_dict.items():
f = lambda x:[x[0], x[1], x[2], str(int(type_rep[type])+int(code))] if x[3] == code and int(x[0]) in r else x
new_eve[:] = map(f, new_eve)
pass
new_fname = op.join(eve_dir, '%s%s.eve' % (op.basename(eve).rpartition('.eve')[0], 'Rej'))
print("Writing new eve to %s" % new_fname)
writeTable(new_fname, new_eve)
print
def new_eve(eve):
print 'Starting with %s' % eve
eve_d = readTable(eve)
rej_types = ('veog', 'heog') # , 'grad', 'mag', 'eeg'
k = filter(lambda y: y in eve, epochs.keys())[0]
new_eve = eve_d[:]
for type in rej_types:
#get type from all_rej
bname = op.basename(eve)
base, _, _ = bname.rpartition('Mod.eve')
search = op.join(temp_d, '%s_raw_%s.txt' % (base, type))
rej = glob(search)
if len(rej) < 1:
raise Exception('No rej of this type found!')
bad_dict = reject(type, epochs[k], new_eve, readTable(rej[0]))
for code, r in bad_dict.items():
f = lambda x: [
x[0], x[1], x[2],
str(int(type_rep[type]) + int(code))
] if x[3] == code and int(x[0]) in r else x
new_eve[:] = map(f, new_eve)
pass
new_fname = op.join(
eve_dir, '%s%s.eve' % (op.basename(eve).rpartition('.eve')[0], 'Rej'))
print("Writing new eve to %s" % new_fname)
writeTable(new_fname, new_eve)
def equalizeTriggers(subjID):
os.chdir("/cluster/kuperberg/SemPrMM/MEG/data/"+subjID)
expList = ['ATLLoc','MaskedMM','BaleenLP','BaleenHP','AXCPT']
runDict = { 'ATLLoc':[''],'MaskedMM':['Run1','Run2'],'BaleenLP':['Run1','Run2','Run3','Run4'],'BaleenHP':['Run1','Run2','Run3','Run4'],'AXCPT':['Run1','Run2']}
codeGroupDict = { 'AXCPT':['AXCPT_prime','AXCPT_target']}
codeDict = { 'AXCPT_prime':['5','6'],'AXCPT_target':['1','2','3']}
minDict = {}
if subjID == 'ya3':
runDict['AXCPT']=['Run1']
if (subjID == 'ya1' or subjID == 'ya2' or subjID == 'ya4' or subjID == 'ya7' or subjID == 'ya8' or subjID == 'ya16'):
runDict['AXCPT']=''
#########################
##EQUALIZE TRIGGER COUNTS###
print '----equalize triggers'
for exp in expList:
for codeGroup in codeGroupDict[exp]:
evMin = 9999
for code in codeDict[codeGroup]:
print int(code)-1
aveName = '/cluster/kuperberg/SemPrMM/MEG/data/%s/ave_projon/%s_%s_All-ave.fif' % (subjID, subjID, exp)
print aveName
evoked = fiff.Evoked(aveName,setno=int(code)-1) #needs revision
print evoked.nave
if int(evoked.nave) < evMin:
evMin = int(evoked.nave)
minDict[codeGroup] = evMin
print codeGroup, evMin, minDict[codeGroup]
for run in runDict[exp]:
inFile = 'eve/' + subjID + '_'+exp+run+'Mod.eve'
outFile = 'eve/' + subjID + '_' + exp + run + 'Mod-testeq.eve' #when finalized, this should probably be ModRejEq.eve, and later scripts changed
print inFile
if os.path.exists(inFile):
data = readInput.readTable(inFile)
firstRow = data[0]
firstSample = firstRow[0]
firstTime = firstRow[1]
flag = ''
for row in data:
trigger = row[3]
time = row[1]
writeOutput.writeTable(outFile,data)
def roistats2R(subj_gp, exp):
tableLength=0
dataTable=lineTemp=line=Con=dataLine=[]
allData=[]
Contrasts = []
subj = []
hem = ['lh', 'rh']
roiName = []
inFile = "/cluster/kuperberg/SemPrMM/MRI/results/roi_fsfast/roi_summary/" + subj_gp +"_" + exp +"FullTable.txt"
dataTable = readInput.readTable(inFile)
tableLength = len(dataTable)
##parse the data to figure out number of contrasts, rois, and subjects
for i in range(1, tableLength): #skip the header row
lineTemp = dataTable[i]
Con = dataTable[0]
if len(lineTemp)<6:
roiName.append(str(lineTemp[2]))
elif len(lineTemp)>4:
subj.append(lineTemp[0])
subj_num = (len(subj)/len(roiName))
##Get out the contrasts
numContrasts = (len(Con)-1)/2 ##figure out how many contrasts there are
for c in range(numContrasts):
conIndex = c*2+1
[Con[conIndex],x] = str.split(str(Con[conIndex]), '_')
Contrasts.append(Con[conIndex])
## print Contrasts
i = 0
for i in range(1, tableLength): #skip the header row
line = dataTable[i]
curr_subj = line[0]
if len(line) < 4: ##This is the beginning of a new label block so update current label
curr_label = line[2]
## print curr_label
if len(line) > 4:
for c in range(numContrasts):
for m in [0, 1]:
curr_contrast = str(Contrasts[c])
curr_hem = hem[m]
curr_signal = line[c*2+1+m] #for each contrast, this will find correct signal
## print c*2+1+m
dataLine = [curr_subj, curr_contrast, curr_label, curr_hem, curr_signal]
allData.append(dataLine)
dataLine = []
outFile = "/cluster/kuperberg/SemPrMM/MRI/results/roi_fsfast/R/" + subj_gp +"_" + exp + "_" + "roiTable.txt"
writeOutput.writeTable(outFile, allData)
def rej_rej2eve_projon(subjID):
filePrefix = '/cluster/kuperberg/SemPrMM/MEG/data/' + subjID
##expList = ['ATLLoc','MaskedMM','BaleenLP','BaleenHP','AXCPT']
expList = ['BaleenHP']
runDict = {
'ATLLoc': [''],
'MaskedMM': ['Run1', 'Run2'],
'BaleenLP': ['Run1', 'Run2', 'Run3', 'Run4'],
'BaleenHP': ['Run1', 'Run2', 'Run3', 'Run4'],
'AXCPT': ['Run1', 'Run2']
}
for exp in expList:
print exp
for run in runDict[exp]:
inFile1 = filePrefix + '/ave_projon/logs/ssp_avelogs/' + subjID + '_' + exp + run + '_ecgeog1-ave.log'
inFile2 = filePrefix + '/eve/' + subjID + '_' + exp + run + 'ModRej.eve'
outFile = filePrefix + '/eve/' + subjID + '_' + exp + run + 'ModRej4projoff.eve'
## print inFile1
## print inFile2
## print('Step1 done')
if os.path.exists(outFile):
os.remove(outFile)
if os.path.exists(inFile1) and os.path.exists(inFile2):
data1 = readInput.readTable(inFile1)
rowsin1 = len(data1)
data2 = readInput.readTable(inFile2)
rowsin2 = len(data2)
firstLine = data2[0]
firstTimept = int((firstLine[0]))
## print(firstTimept)
timept1 = timept2 = []
for i in range(0, len(data1)):
lineTemp1 = data1[i]
if len(lineTemp1) > 10:
timept1.append((lineTemp1[0]))
print(timept1)
for i in range(0, len(data2)):
lineTemp2 = data2[i]
timeN = int(lineTemp2[0])
timept2 = str(timeN - firstTimept)
if str(timept2) in timept1:
lineTemp2[3] = 4000 + int(lineTemp2[3])
writeOutput.writeTable(outFile, data2)
def rej_rej2eve_projon(subjID):
filePrefix = '/cluster/kuperberg/SemPrMM/MEG/data/'+subjID
##expList = ['ATLLoc','MaskedMM','BaleenLP','BaleenHP','AXCPT']
expList = ['BaleenHP']
runDict = {'ATLLoc':[''],'MaskedMM':['Run1','Run2'],'BaleenLP':['Run1','Run2','Run3','Run4'],'BaleenHP':['Run1','Run2','Run3','Run4'], 'AXCPT':['Run1','Run2']}
for exp in expList:
print exp
for run in runDict[exp]:
inFile1 = filePrefix + '/ave_projon/logs/ssp_avelogs/' + subjID + '_' + exp + run + '_ecgeog1-ave.log'
inFile2 = filePrefix + '/eve/' + subjID + '_' + exp + run + 'ModRej.eve'
outFile = filePrefix + '/eve/' + subjID + '_' + exp + run + 'ModRej4projoff.eve'
## print inFile1
## print inFile2
## print('Step1 done')
if os.path.exists(outFile):
os.remove(outFile)
if os.path.exists(inFile1) and os.path.exists(inFile2):
data1 = readInput.readTable(inFile1)
rowsin1 = len(data1)
data2 = readInput.readTable(inFile2)
rowsin2 = len(data2)
firstLine = data2[0]
firstTimept = int((firstLine[0]))
## print(firstTimept)
timept1=timept2=[]
for i in range (0, len(data1)):
lineTemp1 = data1[i]
if len(lineTemp1) > 10:
timept1.append((lineTemp1[0]))
print(timept1)
for i in range (0, len(data2)):
lineTemp2 = data2[i]
timeN = int(lineTemp2[0])
timept2= str(timeN - firstTimept)
if str(timept2) in timept1:
lineTemp2[3] = 4000 + int(lineTemp2[3])
writeOutput.writeTable(outFile,data2)
def binary_conversion(exp, subjID, paradigm):
maxCount = 16777215 #2^24-1, because we use 24 good triggers (162-187, excluding 176 and 177; could go to 188 but more than 2^24 screws MNE conversion)
filePath = '/Volumes/CUTTLEFISH/MEG_Experiments/'+exp+'/data/' #Lawrence added 'Experiments' 4.23.13
trigSeqDict = {1:162,2:163,3:164,4:165,5:166,6:167,7:168,8:169,9:170,10:171,11:172,12:173,13:174,14:175,15:178,16:179,17:180,18:181,19:182,20:183,21:184,22:185,23:186,24:187}
binaryDict = {maxCount-2**0:1,maxCount-2**1:2,maxCount-2**2:3,maxCount-2**3:4,maxCount-2**4:5,maxCount-2**5:6,maxCount-2**6:7,maxCount-2**7:8,maxCount-2**8:9,maxCount-2**9:10,maxCount-2**10:11,maxCount-2**11:12,maxCount-2**12:13,maxCount-2**13:14,maxCount-2**14:15,maxCount-2**15:16,maxCount-2**16:17,maxCount-2**17:18,maxCount-2**18:19,maxCount-2**19:20,maxCount-2**20:21,maxCount-2**21:22,maxCount-2**22:23,maxCount-2**23:24}
count = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
#print binaryDict
inFile = filePath + subjID + '/eve/' + subjID + '_' + paradigm + '.eve'
outFile = filePath + subjID + '/eve/' + subjID + '_' + paradigm + 'Mod.eve'
eveData = readInput.readTable(inFile)
for row in eveData:
#print row
if (not row[3] == str(maxCount)) and (not row[3] == '0'):
#print row
code = binaryDict[int(row[3])]
#print trigSeqDict[code]
count[code-1] = count[code-1]+1
row[3] = trigSeqDict[code]
row[2] = 0
for row in eveData:
if row[3] == str(maxCount):
#print 'catch'
eveData.remove(row)
writeOutput.writeTable(outFile,eveData)
print count
i=0
for item in count:
i = i+1
print "trigger_"+str(i)+" = "+str(item)
def new_eve(eve):
print 'Starting with %s' % eve
eve_d = readTable(eve)
rej_types = ('veog', 'heog') # , 'grad', 'mag', 'eeg'
k = filter(lambda y: y in eve, epochs.keys())[0]
new_eve = eve_d[:]
for type in rej_types:
#get type from all_rej
bname = op.basename(eve)
base, _, _ = bname.rpartition('Mod.eve')
search = op.join(temp_d, '%s_raw_%s.txt' % (base,type))
rej = glob(search)
if len(rej) < 1:
raise Exception('No rej of this type found!')
bad_dict = reject(type, epochs[k], new_eve, readTable(rej[0]))
for code, r in bad_dict.items():
f = lambda x:[x[0], x[1], x[2], str(int(type_rep[type])+int(code))] if x[3] == code and int(x[0]) in r else x
new_eve[:] = map(f, new_eve)
pass
new_fname = op.join(eve_dir, '%s%s.eve' % (op.basename(eve).rpartition('.eve')[0], 'Rej'))
print("Writing new eve to %s" % new_fname)
writeTable(new_fname, new_eve)
def fixTriggersAllUnrelated(subjID):
os.chdir("/cluster/kuperberg/SemPrMM/MEG/data/" + subjID)
expList = ['BaleenLP', 'BaleenHP']
runDict = {
'BaleenLP': ['Run1', 'Run2', 'Run3', 'Run4'],
'BaleenHP': ['Run1', 'Run2', 'Run3', 'Run4']
}
###############################################
#BALEEN Change all codes to Unrelated
for exp in expList:
for run in runDict[exp]:
inFile = 'eve/' + subjID + '_' + exp + run + 'ModRej.eve'
outFile = 'eve/' + subjID + '_' + exp + run + 'ModRejAllU.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
rowCount = 0
flag2 = 0
for row in data:
trigger = row[3]
#BaleenLP
if trigger == '2':
row[3] = '4'
#BaleenHP
if trigger == '7':
row[3] = '9'
rowCount += 1
writeOutput.writeTable(outFile, data)
def fixTriggersAllUnrelated(subjID):
os.chdir("/cluster/kuperberg/SemPrMM/MEG/data/"+subjID)
expList = ['BaleenLP','BaleenHP']
runDict = {'BaleenLP':['Run1','Run2','Run3','Run4'],'BaleenHP':['Run1','Run2','Run3','Run4']}
###############################################
#BALEEN Change all codes to Unrelated
for exp in expList:
for run in runDict[exp]:
inFile = 'eve/'+subjID+'_'+exp+run+'ModRej.eve'
outFile = 'eve/'+subjID+'_'+exp+run+'ModRejAllU.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
rowCount = 0
flag2 = 0
for row in data:
trigger = row[3]
#BaleenLP
if trigger == '2':
row[3] = '4'
#BaleenHP
if trigger == '7':
row[3] = '9'
rowCount +=1
writeOutput.writeTable(outFile, data)
##You should only check samples 100ms from beginning/end of file, to have the full window
samples2Check = range(winSizeSamp,len(times)-winSizeSamp)
for currSample in samples2Check:
preWinMean = np.mean( blink_data_rms[currSample-winSizeSamp : currSample] )
postWinMean = np.mean( blink_data_rms[currSample : currSample+winSizeSamp] )
stepTest = postWinMean - preWinMean
if stepTest > thresh or stepTest < -thresh:
badSample = currSample
badSampleList.append([badSample,3]) #The 3 should be deprecated once we fully shift to this script
##Write out text file containing rejected samples
writeOutput.writeTable(outfile_fname, badSampleList)
print
print 'Artifact rejection complete'
print
##Run rej_blink2eve.py which applies the rejected samples to marking rejected epochs in eve file
import rej_blink2eve
rej_blink2eve.main(args.exp, args.subjID, args.par)
##Make a plot of the RMS
cm = plt.get_cmap('cool') # this chooses the colors to use for data lines
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(times[0:50000],blink_data_rms[0:50000],linewidth=2)
#label = 'S_temporal_sup-'+hem #label = 'G_pariet_inf-Angular-'+hem #values, times, vertices = mne.label_time_courses(label_fname, stc_fname) #vtv = [mne.label_time_courses(label_fname, stc_fname) for stc_fname in stcs_fname] valuesAll = [] for stc_fname in stcs_fname: values, times, vertices = mne.label_time_courses(label_fname, stc_fname) values = np.mean(values,0) values = values[sample1:sample2] values = np.mean(values,0) #print values valuesAll.append(values) valuesHem.append(valuesAll) print "mean",np.mean(valuesAll) outTable = [] for x in range(len(stcs_fname)): temp = [] temp.append(valuesHem[0][x]) temp.append(valuesHem[1][x]) temp.append(valuesHem[0][x]-valuesHem[1][x]) outTable.append(temp) outFile = '/cluster/kuperberg/SemPrMM/MEG/results/source_space/hem_measures/ya.n'+str(len(stcs_fname))+'.'+args.protocol+'_c'+args.set+'_'+args.label+str(int(args.t1))+'-'+str(int(args.t2))+'.txt' writeOutput.writeTable(outFile, outTable)
def equalizeTriggers(subjID):
os.chdir("/cluster/kuperberg/SemPrMM/MEG/data/" + subjID)
expList = ['ATLLoc', 'MaskedMM', 'BaleenLP', 'BaleenHP', 'AXCPT']
runDict = {
'ATLLoc': [''],
'MaskedMM': ['Run1', 'Run2'],
'BaleenLP': ['Run1', 'Run2', 'Run3', 'Run4'],
'BaleenHP': ['Run1', 'Run2', 'Run3', 'Run4'],
'AXCPT': ['Run1', 'Run2']
}
codeGroupDict = {'AXCPT': ['AXCPT_prime', 'AXCPT_target']}
codeDict = {'AXCPT_prime': ['5', '6'], 'AXCPT_target': ['1', '2', '3']}
minDict = {}
if subjID == 'ya3':
runDict['AXCPT'] = ['Run1']
if (subjID == 'ya1' or subjID == 'ya2' or subjID == 'ya4'
or subjID == 'ya7' or subjID == 'ya8' or subjID == 'ya16'):
runDict['AXCPT'] = ''
#########################
##EQUALIZE TRIGGER COUNTS###
print '----equalize triggers'
for exp in expList:
for codeGroup in codeGroupDict[exp]:
evMin = 9999
for code in codeDict[codeGroup]:
print int(code) - 1
aveName = '/cluster/kuperberg/SemPrMM/MEG/data/%s/ave_projon/%s_%s_All-ave.fif' % (
subjID, subjID, exp)
print aveName
evoked = fiff.Evoked(aveName,
setno=int(code) - 1) #needs revision
print evoked.nave
if int(evoked.nave) < evMin:
evMin = int(evoked.nave)
minDict[codeGroup] = evMin
print codeGroup, evMin, minDict[codeGroup]
for run in runDict[exp]:
inFile = 'eve/' + subjID + '_' + exp + run + 'Mod.eve'
outFile = 'eve/' + subjID + '_' + exp + run + 'Mod-testeq.eve' #when finalized, this should probably be ModRejEq.eve, and later scripts changed
print inFile
if os.path.exists(inFile):
data = readInput.readTable(inFile)
firstRow = data[0]
firstSample = firstRow[0]
firstTime = firstRow[1]
flag = ''
for row in data:
trigger = row[3]
time = row[1]
writeOutput.writeTable(outFile, data)
def fixTriggers(subjID):
os.chdir("/cluster/kuperberg/SemPrMM/MEG/data/" + subjID)
expList = ['ATLLoc', 'MaskedMM', 'BaleenLP', 'BaleenHP', 'AXCPT']
runDict = {
'ATLLoc': [''],
'MaskedMM': ['Run1', 'Run2'],
'BaleenLP': ['Run1', 'Run2', 'Run3', 'Run4'],
'BaleenHP': ['Run1', 'Run2', 'Run3', 'Run4'],
'AXCPT': ['Run1', 'Run2']
}
if subjID == 'ya3':
runDict['AXCPT'] = ['Run1']
if (subjID == 'ya1' or subjID == 'ya2' or subjID == 'ya4'
or subjID == 'ya7' or subjID == 'ya8' or subjID == 'ya16'):
runDict['AXCPT'] = ''
print '----subject specific fixes'
#########################
##FIX RANDOM YA19 ERROR
##This is only case where original .eve files gets changed, because somehow incorrect trigger got sent on a single trial (how could this happen? spooky)
inFile = 'eve/ya19_BaleenLPRun2.eve'
outFile = 'eve/ya19_BaleenLPRun2.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
for row in data:
trigger = row[3]
time = row[1]
if (time == '162.257' and trigger == '2'):
print row
row[3] = 14
print row
writeOutput.writeTable(outFile, data)
###########################FIX RANDOM YA22 ERROR
##This is only case where original .eve files gets changed, because somehow incorrect trigger got sent on a single trial (how could this happen? spooky)
inFile = 'eve/ya22_BaleenHPRun3.eve'
outFile = 'eve/ya22_BaleenHPRun3.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
for row in data:
trigger = row[3]
time = row[1]
if (time == '71.100' and trigger == '6'):
print row
row[3] = 14
print row
writeOutput.writeTable(outFile, data)
#########################
##FIX RANDOM YA6 ERROR
##This is only case where original .eve files gets changed, because somehow incorrect trigger got sent on a single trial (how could this happen? spooky)
##NOt clear what this code was originally so changing to 600
inFile = 'eve/ya6_BaleenHPRun3.eve'
outFile = 'eve/ya6_BaleenHPRun3.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
for row in data:
trigger = row[3]
time = row[1]
if (time == '163.827' and trigger == '6'):
print row
row[3] = 600
print row
writeOutput.writeTable(outFile, data)
#########################
##FIX RANDOM YA16 MASKEDMM ERROR
##This is only case where original .eve files gets changed, because somehow incorrect trigger got sent on a single trial (how could this happen? spooky)
inFile = 'eve/ya16_MaskedMMRun1.eve'
outFile = 'eve/ya16_MaskedMMRun1.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
for row in data:
trigger = row[3]
time = row[1]
if (time == '232.349' and trigger == '2'):
print row
row[3] = 3
print row
writeOutput.writeTable(outFile, data)
##########################
##FIX UNKNOWN YA3 LPRUN3 ERROR
#Although no documentation to explain, vtsd logs and raw datafiles show run3 restarted after one minute (54 events), so responses to the stimuli that had already been shown should not be counted.
inFile = 'eve/ya3_BaleenLPRun3.eve'
outFile = 'eve/ya3_BaleenLPRun3.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
for i in range(1, 54):
row = data[i]
row[3] = int(row[3]) + 900
writeOutput.writeTable(outFile, data)
##########################
##FIX YA24 MASKEDMMRUN1 LOSS OF DISPLAY ERROR
#Scan log notes that MaskedMMRun1 was ended early because display got disconnected. This probably happened several seconds before presentation was ended. The last moment at which the subject responded was 316.707, so to be conservative we are removing triggers in the 16 subsequent seconds, in which the subject did not respond to several probe trials
inFile = 'eve/ya24_MaskedMMRun1.eve'
outFile = 'eve/ya24_MaskedMMRun1.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
for row in data:
trigger = row[3]
time = row[1]
if (float(time) > 316.707):
row[3] = int(row[3]) + 900
print row
writeOutput.writeTable(outFile, data)
#########################
##FIX TIMING IN ALL SCRIPTS###
print '----fix Timing'
for exp in expList:
for run in runDict[exp]:
inFile = 'eve/' + subjID + '_' + exp + run + '.eve'
outFile = 'eve/' + subjID + '_' + exp + run + 'Mod.eve'
print inFile
if os.path.exists(inFile):
data = readInput.readTable(inFile)
firstRow = data[0]
firstSample = firstRow[0]
firstTime = firstRow[1]
wordCount = 0 ##for ATLLoc
flag = ''
for row in data:
trigger = row[3]
time = row[1]
sampleRate = float(row[0]) / float(row[1])
trueSample = float(
row[0]
) + 19 ## compensate for the time lag between projector and trigger
trueTime = trueSample / sampleRate
row[0] = str(int(round(trueSample, 0)))
row[1] = str(round(trueTime, 3))
finalRow = row
##Undo the timing change for the first row in file because this row indicates the beginning of the scan, not a visual event, so it shouldn't be changed
firstRow[0] = firstSample
firstRow[1] = firstTime
###add extra trigger to get around MNE bug that ignores last row
extraRow = [
str(int(finalRow[0]) + 1),
str(round(float(finalRow[1]) + 1, 3)), '0', '99'
]
data.append(extraRow)
writeOutput.writeTable(outFile, data)
print '-----fix codes'
###############################
###CHANGE CODES IN ATLLOC
inFile = 'eve/' + subjID + '_ATLLocMod.eve'
outFile = 'eve/' + subjID + '_ATLLocMod.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
print inFile
wordCount = 0
flag = ''
for row in data:
trigger = row[3]
if trigger == '1' or trigger == '2' or trigger == '3':
flag = trigger
wordCount = 0
else:
wordCount += 1
if trigger == '4' and wordCount <= 9:
row[3] = trigger + flag
writeOutput.writeTable(outFile, data)
###############################################
#MASKEDMM
for x in runDict['MaskedMM']:
inFile = 'eve/' + subjID + '_MaskedMM' + x + 'Mod.eve'
outFile = 'eve/' + subjID + '_MaskedMM' + x + 'Mod.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
print inFile
########################
##Change trigger for incorrect button presses ('go' responses)
rowCount = 0
for row in data:
trigger = row[3]
if (trigger == '1' or trigger == '2' or trigger == '3'):
nextRow = data[rowCount + 1]
nextTrigger = nextRow[3]
#print 'hello', trigger, row, nextRow
if nextTrigger == '16' or nextTrigger == '32' or nextTrigger == '64' or nextTrigger == '128':
print "false positive: ", row, nextRow
row[3] = '500' + row[3]
rowCount += 1
###############################################
#BALEENLP
for x in runDict['BaleenLP']:
inFile = 'eve/' + subjID + '_BaleenLP' + x + 'Mod.eve'
outFile = 'eve/' + subjID + '_BaleenLP' + x + 'Mod.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
print inFile
rowCount = 0
for row in data:
trigger = row[3]
##This part fixes the coding for the probe primes. Originally the trigger 11 was sent for the target when the prime was a probe. This recodes the target as 111 and codes the prime itself as 11
if trigger == '11': ##change the target to '111'
row[3] = '1' + trigger
#print row
for i in [
1, 2, 3
]: ## look through the previous three events to try to find the prime
compRow = data[rowCount - i]
#print 'Comparison', compRow
compTrigger = compRow[3]
compSOA = float(row[1]) - float(compRow[1])
if compTrigger == '14' and (
compSOA > .580 and compSOA < .620
): ##check for a prime with correct SOA
compRow[3] = trigger
#print 'new ', compRow, row
break
rowCount += 1
########################
##Change trigger for incorrect button presses ('go' responses)
rowCount = 0
for row in data:
trigger = row[3]
if (trigger == '1' or trigger == '2' or trigger == '4'):
nextRow = data[rowCount + 1]
nextTrigger = nextRow[3]
#print row, nextRow
if nextTrigger == '16' or nextTrigger == '32' or nextTrigger == '64' or nextTrigger == '128':
print "false positive: ", row, nextRow
row[3] = '500' + row[3]
rowCount += 1
writeOutput.writeTable(outFile, data)
###############################################
#BALEENHP
for x in runDict['BaleenHP']:
inFile = 'eve/' + subjID + '_BaleenHP' + x + 'Mod.eve'
outFile = 'eve/' + subjID + '_BaleenHP' + x + 'Mod.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
print inFile
rowCount = 0
flag2 = 0
for row in data:
trigger = row[3]
if trigger == '12': ##change the target to '112'
row[3] = '1' + trigger
#print row
for i in [
1, 2, 3
]: ## look through the previous three events to try to find the prime
compRow = data[rowCount - i]
#print 'Comparison', compRow
compTrigger = compRow[3]
compSOA = float(row[1]) - float(compRow[1])
if compTrigger == '14' and (
compSOA > .580 and compSOA < .620
): ##check for a prime with correct SOA
compRow[3] = trigger
#print 'new ', compRow, row
break
##Flip half of the related filler triggers to '18' to get equal number of related and unrelated
if trigger == '8':
if flag2 == 1:
row[3] = '18'
flag2 = 0
elif flag2 == 0:
flag2 = 1
rowCount += 1
########################
##Change trigger for incorrect button presses ('go' responses)
rowCount = 0
for row in data:
trigger = row[3]
if (trigger == '6' or trigger == '7' or trigger == '8'
or trigger == '9' or trigger == '18'):
nextRow = data[rowCount + 1]
nextTrigger = nextRow[3]
#print row, nextRow
if nextTrigger == '16' or nextTrigger == '32' or nextTrigger == '64' or nextTrigger == '128':
print "false positive: ", row, nextRow
row[3] = '500' + row[3]
rowCount += 1
##########################################write it all out
writeOutput.writeTable(outFile, data)
#########################
###AXCPT
for x in runDict['AXCPT']:
x
inFile = 'eve/' + subjID + '_AXCPT' + x + 'Mod.eve'
outFile = 'eve/' + subjID + '_AXCPT' + x + 'Mod.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
print inFile
###############################################################
if subjID == 'ya6': ####Fix error in triggers for this subject
logFile = '../../vtsd_logs/ya6/AXCPT_ya6_List101_' + x + '.vtsd_log'
print logFile
logData = readInput.readTable(logFile)
firstPrimeRow = data[2]
firstPrimeTime = firstPrimeRow[1]
count = 0
##Fix timing due to error in trigger coding
for row in data:
trueTime = round(float(row[1]) - float(firstPrimeTime))
if row[3] == '8':
for logRow in logData:
logTime = round(float(logRow[5]) + 1)
if logTime == trueTime:
#print logRow[5], logTime, trueTime, row[3], logRow[9]
row[3] = logRow[9]
#print logRow
################################################################
rowCount = 0
flag3 = 0
for row in data:
trigger = row[3]
if len(data) > rowCount + 1:
nextRow = data[rowCount + 1]
nextTrigger = nextRow[3]
else:
break
#############################################
##change blinks triggered as 6 to 7s
if trigger == '6':
if nextTrigger == '7':
row[3] = '7'
## #################################################
## ##Flip 3/4 of the 'A' triggers to 15, to match number of As and Bs
## if trigger == '5':
## if flag3 == 3:
## flag3 = 0
## elif flag3 != 3:
## flag3 = flag3 + 1
## row[3] = '15'
##
###########################################
##change triggers for incorrect trials#####
##AX case
if trigger == '4':
if len(nextTrigger
) < 2: ###Test for response (16, 32, 64 or 128)
row[3] = '9' + trigger
print 'miss:', row
##BX, BY, AY case
if (trigger == '1' or trigger == '2' or trigger == '3'):
if len(nextTrigger
) > 1: ###Test for response (16, 32, 64 or 128)
row[3] = '9' + trigger
print 'false positive:', row
rowCount += 1
writeOutput.writeTable(outFile, data)
print protocolList[x] for label in labelList: for hem in hemList: stcs_fname = ['/cluster/kuperberg/SemPrMM/MEG/data/ya%s/ave_projon/stc/%s/ya%s_%s_c%sM-%s-%s.stc' % (s, protocolList[x], s, protocolList[x],condList[x],args.model,hem) for s in subjects] label_fname = data_path + '/label/%s-%s.label' % (label, hem) if os.access(label_fname, os.F_OK): print label, hem valuesAll = [] for stc_fname in stcs_fname: values, times, vertices = mne.label_time_courses(label_fname, stc_fname) values = np.mean(values,0) values = values[sample1:sample2] values = np.mean(values,0) valuesAll.append(values) ##Update output table count = 0 for s in subjects: data = valuesAll[count] row = [s, protocolList[x]+condList[x], label, hem, data] dataTable.append(row) count = count + 1 fileName = '/cluster/kuperberg/SemPrMM/MEG/results/source_space/R/'+args.prefix+'.MaskedMMAll.'+args.model+'.'+str(int(args.t1))+'-'+str(int(args.t2))+'.txt' writeOutput.writeTable(fileName, dataTable)
def fixTriggers(subjID):
os.chdir("/cluster/kuperberg/SemPrMM/MEG/data/"+subjID)
expList = ['ATLLoc','MaskedMM','BaleenLP','BaleenHP','AXCPT']
runDict = { 'ATLLoc':[''],'MaskedMM':['Run1','Run2'],'BaleenLP':['Run1','Run2','Run3','Run4'],'BaleenHP':['Run1','Run2','Run3','Run4'],'AXCPT':['Run1','Run2']}
if subjID == 'ya3':
runDict['AXCPT']=['Run1']
if (subjID == 'ya1' or subjID == 'ya2' or subjID == 'ya4' or subjID == 'ya7' or subjID == 'ya8' or subjID == 'ya16'):
runDict['AXCPT']=''
print '----subject specific fixes'
#########################
##FIX RANDOM YA19 ERROR
##This is only case where original .eve files gets changed, because somehow incorrect trigger got sent on a single trial (how could this happen? spooky)
inFile= 'eve/ya19_BaleenLPRun2.eve'
outFile = 'eve/ya19_BaleenLPRun2.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
for row in data:
trigger = row[3]
time = row[1]
if (time == '162.257' and trigger == '2'):
print row
row[3] = 14
print row
writeOutput.writeTable(outFile,data)
###########################FIX RANDOM YA22 ERROR
##This is only case where original .eve files gets changed, because somehow incorrect trigger got sent on a single trial (how could this happen? spooky)
inFile= 'eve/ya22_BaleenHPRun3.eve'
outFile = 'eve/ya22_BaleenHPRun3.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
for row in data:
trigger = row[3]
time = row[1]
if (time == '71.100' and trigger == '6'):
print row
row[3] = 14
print row
writeOutput.writeTable(outFile,data)
#########################
##FIX RANDOM YA6 ERROR
##This is only case where original .eve files gets changed, because somehow incorrect trigger got sent on a single trial (how could this happen? spooky)
##NOt clear what this code was originally so changing to 600
inFile= 'eve/ya6_BaleenHPRun3.eve'
outFile = 'eve/ya6_BaleenHPRun3.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
for row in data:
trigger = row[3]
time = row[1]
if (time == '163.827' and trigger == '6'):
print row
row[3] = 600
print row
writeOutput.writeTable(outFile,data)
#########################
##FIX RANDOM YA16 MASKEDMM ERROR
##This is only case where original .eve files gets changed, because somehow incorrect trigger got sent on a single trial (how could this happen? spooky)
inFile= 'eve/ya16_MaskedMMRun1.eve'
outFile = 'eve/ya16_MaskedMMRun1.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
for row in data:
trigger = row[3]
time = row[1]
if (time == '232.349' and trigger == '2'):
print row
row[3] = 3
print row
writeOutput.writeTable(outFile,data)
##########################
##FIX UNKNOWN YA3 LPRUN3 ERROR
#Although no documentation to explain, vtsd logs and raw datafiles show run3 restarted after one minute (54 events), so responses to the stimuli that had already been shown should not be counted.
inFile = 'eve/ya3_BaleenLPRun3.eve'
outFile = 'eve/ya3_BaleenLPRun3.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
for i in range(1,54):
row = data[i]
row[3] = int(row[3])+900
writeOutput.writeTable(outFile,data)
##########################
##FIX YA24 MASKEDMMRUN1 LOSS OF DISPLAY ERROR
#Scan log notes that MaskedMMRun1 was ended early because display got disconnected. This probably happened several seconds before presentation was ended. The last moment at which the subject responded was 316.707, so to be conservative we are removing triggers in the 16 subsequent seconds, in which the subject did not respond to several probe trials
inFile= 'eve/ya24_MaskedMMRun1.eve'
outFile = 'eve/ya24_MaskedMMRun1.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
for row in data:
trigger = row[3]
time = row[1]
if (float(time) > 316.707):
row[3] = int(row[3])+900
print row
writeOutput.writeTable(outFile,data)
#########################
##FIX TIMING IN ALL SCRIPTS###
print '----fix Timing'
for exp in expList:
for run in runDict[exp]:
inFile = 'eve/' + subjID + '_'+exp+run+'.eve'
outFile = 'eve/' + subjID + '_' + exp + run + 'Mod.eve'
print inFile
if os.path.exists(inFile):
data = readInput.readTable(inFile)
firstRow = data[0]
firstSample = firstRow[0]
firstTime = firstRow[1]
wordCount = 0 ##for ATLLoc
flag = ''
for row in data:
trigger = row[3]
time = row[1]
sampleRate = float(row[0])/float(row[1])
trueSample = float(row[0]) + 19 ## compensate for the time lag between projector and trigger
trueTime = trueSample/sampleRate
row[0] = str(int(round(trueSample,0)))
row[1] = str(round(trueTime,3))
finalRow = row
##Undo the timing change for the first row in file because this row indicates the beginning of the scan, not a visual event, so it shouldn't be changed
firstRow[0] = firstSample
firstRow[1] = firstTime
###add extra trigger to get around MNE bug that ignores last row
extraRow = [str(int(finalRow[0])+1),str(round(float(finalRow[1])+1,3)),'0','99']
data.append(extraRow)
writeOutput.writeTable(outFile,data)
print '-----fix codes'
###############################
###CHANGE CODES IN ATLLOC
inFile = 'eve/' + subjID + '_ATLLocMod.eve'
outFile = 'eve/' + subjID + '_ATLLocMod.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
print inFile
wordCount = 0
flag = ''
for row in data:
trigger = row[3]
if trigger == '1' or trigger == '2' or trigger == '3':
flag = trigger
wordCount = 0
else: wordCount +=1
if trigger == '4' and wordCount <= 9:
row[3] = trigger+flag
writeOutput.writeTable(outFile,data)
###############################################
#MASKEDMM
for x in runDict['MaskedMM']:
inFile = 'eve/'+subjID+'_MaskedMM'+x+'Mod.eve'
outFile = 'eve/'+subjID+'_MaskedMM'+x+'Mod.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
print inFile
########################
##Change trigger for incorrect button presses ('go' responses)
rowCount = 0
for row in data:
trigger = row[3]
if (trigger == '1' or trigger == '2' or trigger == '3'):
nextRow = data[rowCount+1]
nextTrigger = nextRow[3]
#print 'hello', trigger, row, nextRow
if nextTrigger == '16' or nextTrigger == '32' or nextTrigger == '64' or nextTrigger == '128':
print "false positive: ", row, nextRow
row[3] = '500' + row[3]
rowCount +=1
###############################################
#BALEENLP
for x in runDict['BaleenLP']:
inFile = 'eve/'+subjID+'_BaleenLP'+x+'Mod.eve'
outFile = 'eve/'+subjID+'_BaleenLP'+x+'Mod.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
print inFile
rowCount = 0
for row in data:
trigger = row[3]
##This part fixes the coding for the probe primes. Originally the trigger 11 was sent for the target when the prime was a probe. This recodes the target as 111 and codes the prime itself as 11
if trigger == '11': ##change the target to '111'
row[3] = '1'+trigger
#print row
for i in [1,2,3]: ## look through the previous three events to try to find the prime
compRow = data[rowCount-i]
#print 'Comparison', compRow
compTrigger = compRow[3]
compSOA = float(row[1])-float(compRow[1])
if compTrigger == '14' and ( compSOA > .580 and compSOA < .620 ): ##check for a prime with correct SOA
compRow[3] = trigger
#print 'new ', compRow, row
break
rowCount +=1
########################
##Change trigger for incorrect button presses ('go' responses)
rowCount = 0
for row in data:
trigger = row[3]
if (trigger == '1' or trigger == '2' or trigger == '4'):
nextRow = data[rowCount+1]
nextTrigger = nextRow[3]
#print row, nextRow
if nextTrigger == '16' or nextTrigger == '32' or nextTrigger == '64' or nextTrigger == '128':
print "false positive: ", row, nextRow
row[3] = '500' + row[3]
rowCount +=1
writeOutput.writeTable(outFile, data)
###############################################
#BALEENHP
for x in runDict['BaleenHP']:
inFile = 'eve/'+subjID+'_BaleenHP'+x+'Mod.eve'
outFile = 'eve/'+subjID+'_BaleenHP'+x+'Mod.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
print inFile
rowCount = 0
flag2 = 0
for row in data:
trigger = row[3]
if trigger == '12': ##change the target to '112'
row[3] = '1'+trigger
#print row
for i in [1,2,3]: ## look through the previous three events to try to find the prime
compRow = data[rowCount-i]
#print 'Comparison', compRow
compTrigger = compRow[3]
compSOA = float(row[1])-float(compRow[1])
if compTrigger == '14' and ( compSOA > .580 and compSOA < .620 ): ##check for a prime with correct SOA
compRow[3] = trigger
#print 'new ', compRow, row
break
##Flip half of the related filler triggers to '18' to get equal number of related and unrelated
if trigger == '8':
if flag2 == 1:
row[3] = '18'
flag2 = 0
elif flag2 == 0:
flag2 = 1
rowCount +=1
########################
##Change trigger for incorrect button presses ('go' responses)
rowCount = 0
for row in data:
trigger = row[3]
if (trigger == '6' or trigger == '7' or trigger == '8' or trigger == '9' or trigger == '18'):
nextRow = data[rowCount+1]
nextTrigger = nextRow[3]
#print row, nextRow
if nextTrigger == '16' or nextTrigger == '32' or nextTrigger == '64' or nextTrigger == '128':
print "false positive: ", row, nextRow
row[3] = '500' + row[3]
rowCount +=1
##########################################write it all out
writeOutput.writeTable(outFile, data)
#########################
###AXCPT
for x in runDict['AXCPT']:
x
inFile = 'eve/'+subjID+'_AXCPT'+x+'Mod.eve'
outFile = 'eve/'+subjID+'_AXCPT'+x+'Mod.eve'
if os.path.exists(inFile):
data = readInput.readTable(inFile)
print inFile
###############################################################
if subjID == 'ya6': ####Fix error in triggers for this subject
logFile = '../../vtsd_logs/ya6/AXCPT_ya6_List101_'+x+'.vtsd_log'
print logFile
logData = readInput.readTable(logFile)
firstPrimeRow = data[2]
firstPrimeTime = firstPrimeRow[1]
count = 0
##Fix timing due to error in trigger coding
for row in data:
trueTime = round(float(row[1]) - float(firstPrimeTime))
if row[3] == '8':
for logRow in logData:
logTime = round(float(logRow[5])+1)
if logTime == trueTime:
#print logRow[5], logTime, trueTime, row[3], logRow[9]
row[3] = logRow[9]
#print logRow
################################################################
rowCount = 0
flag3 = 0
for row in data:
trigger = row[3]
if len(data) > rowCount +1:
nextRow = data[rowCount+1]
nextTrigger = nextRow[3]
else:
break
#############################################
##change blinks triggered as 6 to 7s
if trigger == '6':
if nextTrigger == '7':
row[3] = '7'
## #################################################
## ##Flip 3/4 of the 'A' triggers to 15, to match number of As and Bs
## if trigger == '5':
## if flag3 == 3:
## flag3 = 0
## elif flag3 != 3:
## flag3 = flag3 + 1
## row[3] = '15'
##
###########################################
##change triggers for incorrect trials#####
##AX case
if trigger == '4':
if len(nextTrigger) < 2: ###Test for response (16, 32, 64 or 128)
row[3] = '9' + trigger
print 'miss:',row
##BX, BY, AY case
if (trigger == '1' or trigger == '2' or trigger == '3'):
if len(nextTrigger) > 1: ###Test for response (16, 32, 64 or 128)
row[3] = '9' + trigger
print 'false positive:',row
rowCount +=1
writeOutput.writeTable(outFile,data)
#values, times, vertices = mne.label_time_courses(label_fname, stc_fname)
#vtv = [mne.label_time_courses(label_fname, stc_fname) for stc_fname in stcs_fname]
valuesAll = []
for stc_fname in stcs_fname:
values, times, vertices = mne.label_time_courses(
label_fname, stc_fname)
values = np.mean(values, 0)
values = values[sample1:sample2]
values = np.mean(values, 0)
#print values
valuesAll.append(values)
valuesHem.append(valuesAll)
print "mean", np.mean(valuesAll)
outTable = []
for x in range(len(stcs_fname)):
temp = []
temp.append(valuesHem[0][x])
temp.append(valuesHem[1][x])
temp.append(valuesHem[0][x] - valuesHem[1][x])
outTable.append(temp)
outFile = '/cluster/kuperberg/SemPrMM/MEG/results/source_space/hem_measures/ya.n' + str(
len(stcs_fname
)) + '.' + args.protocol + '_c' + args.set + '_' + args.label + str(
int(args.t1)) + '-' + str(int(args.t2)) + '.txt'
writeOutput.writeTable(outFile, outTable)
'/cluster/kuperberg/SemPrMM/MEG/data/ya%s/ave_projon/stc/%s/ya%s_%s_c%sM-%s-%s.stc'
% (s, protocolList[x], s, protocolList[x], condList[x],
args.model, hem) for s in subjects
]
label_fname = data_path + '/label/%s-%s.label' % (label, hem)
if os.access(label_fname, os.F_OK):
print label, hem
valuesAll = []
for stc_fname in stcs_fname:
values, times, vertices = mne.label_time_courses(
label_fname, stc_fname)
values = np.mean(values, 0)
values = values[sample1:sample2]
values = np.mean(values, 0)
valuesAll.append(values)
##Update output table
count = 0
for s in subjects:
data = valuesAll[count]
row = [s, protocolList[x] + condList[x], label, hem, data]
dataTable.append(row)
count = count + 1
fileName = '/cluster/kuperberg/SemPrMM/MEG/results/source_space/R/' + args.prefix + '.Baleen_fillers' + args.model + '.' + str(
int(args.t1)) + '-' + str(int(args.t2)) + '.txt'
writeOutput.writeTable(fileName, dataTable)
