def _getthresh(fd, pos):
fobj = sumfile.get_sum_file_fd(fd, baseposition=pos)
evd = sumcalc.make_all_events(fobj)
td = {}
tkt = evd.keys()
tkt.sort()
##print len(tkt)
for t in tkt:
evl = evd[t]
thr = None
for ev in evl:
if ev.type == sumfile.SUM_THRESH:
thr = ev.eThresh
if thr:
td[t * 256] = thr
return td
def _getthresh(pathname, fobj=None):
if not fobj:
try:
fobj = sumfile.get_sum_file(pathname[:-4] + '.sum')
except:
return None
evd = sumcalc.make_all_events(fobj)
td = {}
tkt = evd.keys()
tkt.sort()
##print len(tkt)
lastthr = 0.0
for t in tkt:
evl = evd[t]
thr = None
for ev in evl:
if ev.type == sumfile.SUM_THRESH and ev.newevent:
thr = ev.eThresh
#print thr
break
if thr:
td[t] = thr
thrdict = {}
tdk = td.keys()
tdk.sort()
pos = 0
for i, k in enumerate(tdk):
thr = td[k]
while pos < k:
thrdict[pos] = thr
pos += 1
thrdict[pos] = thr
pos += 1
while pos <= fobj.number_seconds:
thrdict[pos] = thr
pos += 1
return thrdict
def csv_dump_out(fo, fobj, rpt=0):
"dump one file"
rslt = []
if len(fobj.zscore):
has_zscore = 1
else:
has_zscore = 0
# dump header for csv file
if fo == None:
rslt = []
row = ''
for t in headers:
row = row + '"%s",' % t
for t in headn:
for i in range(fobj.number_streams):
v = '"%s-%d",' % (t, i)
row = row + v
if fobj.has_total_in_percent:
if t == '%over':
row = row + '"%total",' # there is one extra value - total %
if t == 'Ampl':
row = row + '"Scored",'
for i in range(fobj.number_streams):
for t in headf:
v = '"%s-%d",' % (t, i)
row = row + v
if len(fobj.periph):
row = row + '"Periph",'
has_periph = fobj.periph[0]
else:
has_periph = None
for i in range(fobj.number_lowpass):
if i == fobj.number_lowpass - 1:
last = ' '
else:
last = ','
v = '"%s-%c"%c' % (headc[0], chr(ord('A') + i), last)
row = row + v
if has_zscore:
endpt = 7
if fobj.zscore_kind:
endpt = 3
for i in range(endpt):
for f in range(8):
row = row + ',"%s %s"' % (ztitle[i], zfreq[f])
if fobj.zscore_kind == 0:
for i in range(7, 9):
for f in range(10):
row = row + ',"%s %d"' % (ztitle[i], f)
for i in range(fobj.number_streams):
row = row + ',EndAmpl-%d' % i
max_seconds = fobj.number_seconds
if max_seconds == 0:
return []
rslt.append(row)
# get timed event list
evdict = sumcalc.make_all_events(fobj)
## for sec in range(0,max_seconds):
## e=evdict.get(sec,None)
## if e:
## for ex in e:
## print sec,ex.eThresh,ex.ePeriod
# for every second, dump a row
numlow = fobj.number_lowpass
numtot = fobj.number_streams
prevperiod = 0
eMode = ''
eRDirs = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
eFreq = [(0.0, 0.0), (0.0, 0.0), (0.0, 0.0), (0.0, 0.0), (0.0, 0.0),
(0.0, 0.0), (0.0, 0.0), (0.0, 0.0), (0.0, 0.0), (0.0, 0.0),
(0.0, 0.0), (0.0, 0.0), (0.0, 0.0), (0.0, 0.0), (0.0, 0.0),
(0.0, 0.0), (0.0, 0.0), (0.0, 0.0)]
eSites = ['', '', '', '']
eThresh = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
eScale = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
ePeriod = 0
eMarkdata = ''
eMarklast = ''
eEyes = ''
pgame = ''
eoec = update_eyes(fobj)
eyes = 0
for sec in range(0, max_seconds):
if eoec.has_key(sec):
eyes = eoec[sec]
if not evdict.has_key(sec):
continue
row = ''
mxdt = mx.DateTime.DateTimeFromAbsDateTime(fobj.datecode,
float(fobj.timecode + sec))
if 0:
for q in range(len(evdict[sec])):
e = evdict[sec][q]
ePeriod = evdict[sec][0].ePeriod
if e.type == sumfile.SUM_FREQ:
eFreq = e.eFreq
elif e.type == sumfile.SUM_SITE:
eSites = e.eSites
elif e.type == sumfile.SUM_PERIOD:
ePeriod = e.ePeriod
elif e.type == sumfile.SUM_MARK:
if rpt:
print 'Mark', e.eMarks, eMarkdata
if eMarkdata == '':
eMarkdata = e.eMarks
else:
eMarkdata = eMarkdata + '/' + e.eMarks
elif e.type == sumfile.SUM_MODE:
eMode = e.eMode[0]
e.RDirs = e.eMode[1]
if e.RDirs[15] == 1:
eEyes = 'Open'
elif e.RDirs[15] == 2:
eEyes = 'Closed'
elif e.type == sumfile.SUM_THRESH:
eThresh = e.eThresh
#print sec,q,eThresh
elif e.type == sumfile.SUM_SCALE:
eScale = e.eScale
break
else:
e = evdict[sec][0]
if e.Freq:
eFreq = e.Freq
if e.Sites:
eSites = e.Sites
ePeriod = e.Period
if e.Mode:
eMode = e.Mode[0]
eRDirs = e.Mode[1]
else:
pass
if e.Thresh:
eThresh = e.Thresh
if e.Scale:
eScale = e.Scale
if e.Marks:
if eMarkdata == '':
eMarkdata = e.Marks[:]
else:
eMarkdata = eMarkdata + '/' + e.Marks[:]
## for ex in evdict[sec]:
## if ex.Marks:
## ##print 'MARK ',sec,ex.Marks
## if eMarkdata == '':
## eMarkdata=ex.Marks[:]
## else:
## eMarkdata=eMarkdata+'/'+ex.Marks[:]
Overpct = 0
if ePeriod == 0 and prevperiod:
endperiod = prevperiod
Overpct = e.overall_reward
else:
endperiod = 0
prevperiod = ePeriod
#deltatime,#raw,#total,period#,score,periodendflag,fbmode
##print sec,numlow,numtot,prevperiod,0,endperiod,eMode
if eMode == None:
eMode = ''
try:
over = fobj.pct[0].data[sec]
except:
over = [0]
deltascore = over[
0] % 100 # get the fractional part which is the delta score
row = row + '%d,%d,%d,%d,%d,%d,%d,"%s","%s"' % (
sec, numlow, numtot, prevperiod, deltascore, endperiod, Overpct,
eMode, ('', 'EOpen', 'EClosed')[eyes])
if eMarklast == eMarkdata:
eMarkdata = ''
else:
eMarklast = eMarkdata
#,marktype,markdata,fmtstring,date,time,
if fobj.gameid != pgame:
pgame = fobj.gameid
gm = pgame
else:
gm = ''
row = row + ',"%s","%s","%s","%s","%s",' % (
gm, eMarkdata, fobj.formatstring, fobj.datestring,
mx.DateTime.ISO.str(mxdt)[11:19])
eMarkdata = ''
hadscore = 0
#ampl0,ampl1,..., (# of streams total)
try:
amp = fobj.seg[0].data[sec]
except:
amp = [0 for i in range(numtot)]
for i in range(numtot):
row = row + '%6.2f,' % (abs(int(amp[i])) / 100.0)
if amp[i] < 0:
hadscore = 1 # remember that scoring occurred
row = row + '%d,' % hadscore
#%over0,%over1,..., (# of streams total)
mynum = numtot
if fobj.has_total_in_percent:
mynum += 1
for i in range(mynum):
if i >= len(over):
v = 0
else:
v = over[i]
row = row + '%d,' % (v / 100)
#thresh0,thresh1,..., (# of streams total)
thr = eThresh
for i in range(numtot):
try:
tval = float(abs(thr[i]))
except:
tval = 0.0
row = row + '%6.2f,' % (tval)
#average values
try:
movavg = fobj.avg[0].data[sec]
except:
movavg = [0 for i in range(numtot)]
for i in range(numtot):
row = row + '%6.2f,' % (abs(int(movavg[i])) / 100.0)
#rwdirs0,rsdirs1,..., (# of streams total)
rwd = eRDirs
if rwd == None:
rwd = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
for i in range(numtot):
row = row + '%d,' % (rwd[i], )
#frqlo0,frqhi0,...... (# of streams total times 2)
frql = eFreq
for i in range(numtot):
try:
fv = frql[i]
except:
fv = (0.0, 0.0)
row = row + '%6.3f,%6.3f,' % fv
if has_periph:
try:
pval = has_periph.data[sec][0]
pval = float(pval)
except:
pval = -10.0
row = row + '%6.3f,' % (pval / 10, )
#siteA,siteB,..., (# of raw streams)
sl = eSites
for i in range(numlow):
if i == numlow - 1:
last = ' '
else:
last = ','
if i >= len(sl):
site = ''
else:
site = sl[i]
row = row + '"%s"%c' % (site, last)
if has_zscore:
if sec < len(fobj.zscore[0].data):
dta = fobj.zscore[0].data[sec]
endpt = 7
if fobj.zscore_kind:
endpt = 3
for i in range(endpt):
for f in range(8):
row = row + ',%.2f' % (int(dta[8 * i + f]) / 100.0)
if fobj.zscore_kind == 0:
for i in range(7, 9):
for f in range(10):
if i > 7:
adjust = 2
else:
adjust = 0
row = row + ',%.2f' % (
int(dta[8 * i + adjust + f]) / 100.0)
if endperiod:
for i in range(fobj.number_streams):
row = row + ',%.2f' % fobj.per[endperiod - 1].ampl[i]
else:
for i in range(fobj.number_streams):
row = row + ','
rslt.append(row)
if fo:
fo.write('\n'.join(rslt))
fo.write('\n') # trailing newline
return rslt
def refilter(root, fn, edict=None, recompute=0):
if root:
bob = BusyBox.BusyBox(root, 'Busy processing raw data')
ans = rawlist.rawinfo(fn)
if ans[0] == None:
if root:
bob.destroy() # oops
return None # couldn't open
# must also insert the site and eyes open/close changes
cbxx = rawlist.rawcb(fn)
cbl = cbxx[0]
true_length = ans[0]
if len(cbl):
ans = _handle_other_events(ans, cbl)
# now figure out the periods
plist = _decode_evlist(ans)
fobj = sumfile.get_sum_file(fn[:-4] + '.sum')
evd = sumcalc.make_all_events(fobj)
get_freqset(edict)
dofilts.Load_Filter_File(edict)
dofilts.Load_Raw_File(fn)
d = {}
per = 1
for itm in plist:
# get the starting sample, and length
end = itm[1]
if end == 0:
end = true_length
begin = itm[0]
if recompute:
start = begin
else:
start = end - 30 * 256
if start < begin:
start = begin
if start < 0:
start = 0
length = (end - start) / 256.0
for chan in range(len(itm[2])):
# compute them
clamp = _getclamp(evd, chan, start, end)
move = dofilts.Get_Average_Value(chan,
freqlims,
start,
length,
trueaverage=1,
clamp=clamp,
useartifact=avalue)
if len(move) == 0:
continue
##print itm,chan,move
##print start,length,true
v = Value()
v.theta = move[0][0]
v.alpha = move[0][1]
v.beta = move[0][2]
v.hibeta = move[0][3]
v.values = move[0][:] # for newer method
v.period = per
v.site = itm[2]
v.eyes = itm[3]
v.rewards = itm[-1]
v.freqlims = freqlims
# following for debug only
v.tx = move[2]
v.secs = length
v.sums = move[3]
v.count = move[4]
d['%2d%02d' % (per, chan)] = v
if len(itm[2]) > 1:
d['%2dxx' % (per, )] = len(itm[2])
per += 1
if root:
bob.destroy()
dofilts.Unload_Filter_File()
return d
def get_annotation_list(summary):
''' Return list of annotations from summary file '''
global MAX_CHAN_LENGTH
annotations = [] # list of annotations
eventlist = sumcalc.make_all_events(
summary) # dict of all events keyed by time in seconds
time = -1
position = 0
period = 1
for event in summary.events:
### must use MAX_CAHN_LENGTH and it must get set to tru length
if event.start >= MAX_CHAN_LENGTH: # If reach end of data, cut off annotations
break
if time == event.start: # Get the correct position for the DataSegment in eventlist.
position += 1 # We need this because there can be multiple DataSegment (events)
else: # for any specific time.
time = event.start #
position = 0 #
# We only care for events of type:
# FREQ, SITE, MODE, MARK, BEGIN, and END
if event.typename in TRIGGERS:
type = event.typename
time = event.start
temp_data = ''
temp_data2 = ''
if type == 'SITE ':
for site in event.sites:
temp_data += site + ','
temp_data = temp_data[:-1]
elif type == 'MODE ':
try:
temp_data = 'MODE ' + eventlist[time][position].Mode[0]
except:
# For old version 4.0.3h and before
temp_data = 'MODE ' + eventlist[time][position -
1].Mode[0]
try:
v = eventlist[time][position].Mode[1][15]
if v == 1:
temp_data2 = 'Open'
elif v == 2:
temp_data2 = 'Closed'
except:
pass
elif type == 'FREQ ':
temp_data = 'FREQ ' + combine_freq(
eventlist[time][position].Freq)
elif type == 'THRESH ':
temp_data = 'THRESH ' + combine_thresh(
eventlist[time][position].Thresh)
elif type == 'BEGIN':
temp_data = 'BEGIN ' + str(period)
elif type == 'MARK ':
if event.markdata == '0 Impedance check OFF':
continue
else:
temp_data = 'MARK ' + event.markdata
elif type == 'END':
temp_data = 'END ' + str(period)
period += 1
else:
return 0
annotations.append([time, temp_data, type])
if temp_data2 != '':
annotations.append([time, temp_data2, 'Eyes'])
temp_data2 = ''
return annotations
def ExportResult(root, edict, sumpath, header=0):
"export a single results csv file"
# read file using sumfile
fobj = sumfile.get_sum_file(sumpath, 1)
if not fobj:
return # some error reading summary file
if header == 0:
if os.environ.has_key('WANTRESULTSHEADER'):
header = 2
# determine first two protocol groups
evd = sumcalc.make_all_events(fobj)
if 0:
for pernum in range(len(fobj.per)):
per = fobj.per[pernum]
print pernum, per.start, per.end
site = ''
rmode = ''
rdir = ''
# this works by finding the 'time' of all changes in site, rmode, rdir
# after all have been set (ignore first 10 seconds....), a change means a new "protocol"
changelist = []
dt = 1
chkprint = 0
prevperiod = 0
change = 0
while 1:
if not evd.has_key(dt):
break
evl = evd[dt]
for ev in evl:
##print ev.__dict__
if ev.newevent:
if ev.Sites and ev.Sites != site:
##print 'site change',site,ev.Sites
site = ev.Sites
change = 1
if ev.Mode and (ev.Mode[0] != rmode or ev.Mode[1] != rdir):
if ev.Mode[0] != rmode:
##print 'fb change',rmode,ev.Mode[0]
rmode = ev.Mode[0]
change = change | 2
if ev.Mode[1] != rdir:
##print 'rdir change',rdir,ev.Mode[1]
rdir = ev.Mode[1]
change = change | 4
if chkprint:
print dt, change, ev.newevent, ev.Period, prevperiod
if change:
if ev.Period and prevperiod != ev.Period:
# save accumulated values
dome = 1
if len(changelist):
if changelist[-1][1] == site and changelist[-1][
2] == rmode and changelist[-1][3] == rdir:
dome = 0 # ignore same things
if dome:
changelist.append((dt, site, rmode, rdir, ev.Period))
if chkprint:
print 'append ', changelist[-1]
prevperiod = ev.Period
change = 0
## # now we must remove extraneous changes (duplicate types during rest periods!!!)
## # to do this we keep only the LAST site/mode/dir during a rest period
## if not ev.Period:
## if len(changelist):
## print changelist
## if changelist[-1][4] < 1:
## if changelist[-1][4] == -1:
## nlist=(dt,site,rmode,rdir,ev.Period)
## else:
## nlist=(changelist[-1][0],site,rmode,rdir,ev.Period)
## if chkprint:
## print 'update ',len(changelist)-1,changelist[-1],nlist
## changelist[-1]=nlist
## elif dt > fobj.per[0].start:
## changelist.append((dt,site,rmode,rdir,ev.Period))
## if chkprint:
## print 'append ',changelist[-1]
##
## if len(changelist) == 0 and dt > fobj.per[0].start:
## # force in "starting" values
## changelist.append((dt,site,rmode,rdir,-1))
## if chkprint:
## print 'forced ',changelist[0]
dt += 1
if len(changelist) < 1:
return 0 # too few entries
pgroups = []
##print "changelist",changelist
if len(changelist) > 1:
for dta in range(len(changelist)):
dt, site, rmode, rdir, pnum = changelist[dta]
if dta == len(changelist) - 1:
endval = fobj.number_seconds
else:
endval = changelist[dta + 1][0] - 1
pgroups.append((dt, endval, site, rmode, rdir))
if len(pgroups) < 1:
pgroups.append(
(10, fobj.number_seconds, site, rmode, rdir)) # one long entry
##print
##print pgroups
# determine channels to use
clist = []
# if fobj.protocol == AT and fmt string == CCRRII, first R is actually the inhibit
isminimap = 1
numlowpass = 0
for i in range(len(fobj.formatstring)):
ch = fobj.formatstring[i]
if ch == 'C':
numlowpass += 1
continue
elif ch == 'M':
continue
elif ch == 'I':
isminimap = 0
if len(clist) == 0:
clist.append(i)
elif len(clist) == 2:
clist.append(i)
break # found 2nd inhibit
elif ch == 'R':
isminimap = 0
if fobj.formatstring == 'CCRRII':
clist.append(i)
else:
if len(clist) == 1:
clist.append(i)
if isminimap:
# not a valid session sum file (no inhibits/rewards to get values)
for i in range(len(fobj.formatstring)):
if fobj.formatstring[i] == 'M':
clist.append(i)
ngroups = len(pgroups)
#print 'minimap',len(clist)
else:
if len(clist) != 3:
return
# reorganize
ngroups = 2 # normal session format
hold = clist[1]
clist[1] = clist[0] # move 1st inhibit
clist[0] = hold # make reward first
# recompute sd for each group (handles start/top times by only using in-period values)
rvlist = []
abfmt = 1 # assume unknown format
for numg in range(ngroups):
try:
startt, endt, site, rmode, rdir = pgroups[numg]
except:
#print 'access nonexistant pgroup',numg
break
prt = 0
if prt:
print 'hunting', startt, endt, numg, ngroups, pgroups
pernum = sumcalc.compute_end_period(fobj, startt, endt, prt=prt)
if pernum == 0:
if prt:
print 'no pernum found', startt, endt, numg, pgroups[
numg], fobj.fname
return # this is an invalid case so DON'T export anything
##break # should never happen
continue
rawin = 0
per = fobj.per[pernum - 1]
if rmode == 'SingleB' or rmode == 'MonitorB':
rawin = 1
cmin = 0
if rmode == 'MonitorAB':
dobe = 2
cmin = 6
abfmt = 2
else:
dobe = 1
for siteinx in range(dobe):
rv = ResultValue()
rv.name = fobj.ucode
rv.date = fobj.datestring
if siteinx == 0:
try:
rv.site = site[rawin]
except:
if rawin:
rv.site = 'Unk B'
else:
rv.site = 'Unk A'
else:
try:
rv.site = site[1]
except:
rv.site == 'Unk B'
if rdir == '' or rdir == None:
rdir = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
rv.mode = rmode + rdircodes[rdir[clist[0]]]
if isminimap:
if rmode == 'MonitorAB':
if siteinx:
# must process 1st 6 for site 0 and last 6 for site b
offset = 6
else:
offset = 0
count = 6
else:
offset = 0
count = 12
else:
offset = 0
count = len(clist)
v = 0
for i in range(offset, offset + count):
newfreq = per.freqtext[clist[i]]
if newfreq.find('.') >= 0:
# only have to fix fractional values
fx = newfreq.split('-')
if len(fx) == 2:
vlow = fx[0].rstrip('0')
vhigh = fx[1].rstrip('0')
newfreq = vlow + '-' + vhigh
rv.freq[v] = newfreq
sdx = sumcalc.compute_sd_group(fobj, startt, endt, clist[i])
# sd,count,sumval,startt,endt,variance,aval
if sdx[1] > 0: # if valid
rv.avg[v] = sdx[6]
rv.sd[v] = sdx[0]
rv.seconds = sdx[1] # seconds of actual period data
v += 1
rvlist.append(rv)
# output the settings
# filename is nameyymmdduu.csv in 'RESULTSPATH'
dtval = fobj.datestring[2:4] + fobj.datestring[5:7] + fobj.datestring[
8:10] + fobj.fname[-6:-4]
uniq = int(fobj.fname[-6:-4])
if isminimap:
destpath = edict[
'RESULTSPATH'] + '\\' + fobj.ucode + '_' + dtval + '_mmap%s.csv' % abfmt
else:
destpath = edict[
'RESULTSPATH'] + '\\' + fobj.ucode + '_' + dtval + '.csv'
fd = open(destpath, "w")
if isminimap:
if header:
fd.write('Name,date,unique,site')
for k in range(len(rvlist[0].freq)):
fd.write(',freq,avg,SD')
fd.write('\n')
#name,date,uniq,site,freq lo,freq hi,a,sd,freq lo,freq hi,a,sd ....
for rv in rvlist:
ln = '%s,%s,%d,%s' % (rv.name, rv.date, uniq, rv.site)
fd.write(ln)
for k in range(count):
lx = ',%s,%5.1f,%4.1f' % (rv.freq[k], rv.avg[k], rv.sd[k])
fd.write(lx)
fd.write('\n')
else:
while len(rvlist) < 2:
rvlist.append(ResultValue()) # just so we don't blow up
if header:
fd.write(
'"name",date,unique,A-site,A-Reward freq,A-top inhibit freq,A-2nd inhibit freq,A-seconds,A-reward mode'
)
fd.write(
',B-site,B-Reward freq,B-top inhibit freq,B-2nd inhibit freq,B-seconds,B-reward mode'
)
fd.write(
',A-reward avg,A-reward sd,A-top inhibit avg,A-top inhibit sd,A-2nd inhibit avg,A-2nd inhibit sd'
)
fd.write(
',B-reward avg,B-reward sd,B-top inhibit avg,B-top inhibit sd,B-2nd inhibit avg,B-2nd inhibit sd'
)
fd.write('\n')
ln = '%s,%s,%d,%s,%s,%s,%s,%4.1f,%s,' % (
rvlist[0].name, rvlist[0].date, uniq, rvlist[0].site,
rvlist[0].freq[0], rvlist[0].freq[1], rvlist[0].freq[2],
rvlist[0].seconds / 60.0, rvlist[0].mode)
fd.write(ln)
ln = '%s,%s,%s,%s,%4.1f,%s,' % (
rvlist[1].site, rvlist[1].freq[0], rvlist[1].freq[1],
rvlist[1].freq[2], rvlist[1].seconds / 60.0, rvlist[1].mode)
fd.write(ln)
ln = '%5.1f,%4.1f,%5.1f,%4.1f,%5.1f,%4.1f,' % (
rvlist[0].avg[0], rvlist[0].sd[0], rvlist[0].avg[1],
rvlist[0].sd[1], rvlist[0].avg[2], rvlist[0].sd[2])
fd.write(ln)
ln = '%5.1f,%4.1f,%5.1f,%4.1f,%5.1f,%4.1f\n' % (
rvlist[1].avg[0], rvlist[1].sd[0], rvlist[1].avg[1],
rvlist[1].sd[1], rvlist[1].avg[2], rvlist[1].sd[2])
fd.write(ln)
fd.close()