def _getdata(pathname):
try:
fd = open(pathname, 'rb')
except:
if whazup:
print 'open failed ', pathname
return []
rp = rawlist.rawparams(fd) # get num chans and scales
dta = []
for ch in range(rp[0]):
ans = rawlist.rawreadvalues(fd, ch)
if ans[0] == None:
if whazup:
print 'error', ans[1]
fd.close()
return [] # some error
dta.append(ans)
fd.close()
return dta
def _getdata(pathname):
fd = open(pathname, 'rb')
rp = rawlist.rawparams(fd) # get num chans and scales
dta = []
TC = 0.5
part = 1 / (TC * 256)
most = 1 - part
for ch in range(rp[0]):
ans = rawlist.rawreadvalues(fd, ch)
if ans[0] == None:
##print 'error',ans[1]
return [] # some error
vdata = []
if 0:
intg = ans[0]
for sample in ans:
intg = intg * most + abs(sample) * 3.14159 * part
vdata.append(intg)
dta.append(vdata)
else:
dta.append(ans)
fd.close()
##print len(dta),rp
return dta
def smdumpfile(fname, fmtcheck=0):
# get # channels of raw
svals = []
try:
fd = open(fname, 'rb')
except:
return None, None
# make sure new format
hasextradata = 0
subset = rawlist.rawheaderfield(fd, 'SUBSET')
if subset > 1:
hasextradata = subset
if fmtcheck:
if hasextradata == 0:
fd.close()
return None, None
delta = 0
if hasextradata >= 3:
delta = 1
fstr = rawlist.rawheaderfield(fd, 'FORMATSTRING')
maxchan = 0
for c in fstr:
if c == 'C':
maxchan += 1
# get data list for each channel
datalist = []
for ch in range(maxchan):
dta = rawlist.rawreadvalues(fd, ch)
if dta[0] == None:
break
datalist.append(dta)
# get filtered data
filtlist = []
if hasextradata:
for ch in range(14 + delta):
dta = rawlist.rawreadamplvalues(fd, ch)
if dta == []:
break
filtlist.append(dta)
# get reward list
rwddict = _rawrewards(fd)
datecode = rawlist.rawheaderfield(fd, 'DATECODE')
timecode = rawlist.rawheaderfield(fd, 'TIMECODE')
dt = mx.DateTime.DateTimeFromAbsDateTime(int(datecode), int(timecode))
datetime = (dt.year, dt.month, dt.day, dt.hour, dt.minute, int(dt.second))
threshdict = None
if hasextradata:
pos = rawlist.rawheaderfield(fd, 'SUMMARYOFFSET')
if pos:
threshdict = _getthresh(fd, pos)
fd.close()
if len(datalist) == 0:
return None, None
fmftext = None
for frm in range(len(datalist[0])):
data = []
for dta in datalist:
try:
data.append(dta[frm])
except:
data.append(0.0)
filt = []
if hasextradata:
for flst in filtlist:
try:
filt.append(flst[frm])
except:
filt.append(0.0)
events = rwddict.get(frm, ())
other = ''
rwd = 0
if len(events):
for t, reason, x in events:
if reason.find('REWARD') >= 0:
rwd = 1
#for testing
if len(other):
other = other + ','
other = other + reason
else:
if len(other):
other = other + ','
other = other + reason
if not fmftext:
fmftext = 'Time'
fmf = '%.4f'
for i in range(len(data)):
fmftext = fmftext + ',Chan%s' % 'ABCD'[i]
fmf = fmf + ",%.3f"
fmftext = fmftext + ',Reward'
fmf = fmf + ',%d'
if hasextradata:
delta = 0
if hasextradata >= 3:
delta = 1
for i in range(len(filt) - delta):
fmftext = fmftext + ',%d' % i
fmf = fmf + ',%.2f'
if delta:
fmftext = fmftext + ',OT'
fmf = fmf + ',%x'
filt[-1] = 100 * filt[-1]
fmftext = fmftext + ',other'
fmf = fmf + ',"%s"'
if threshdict:
tx = threshdict.keys()
tx.sort()
thr = threshdict[tx[0]]
for i in range(len(thr)):
fmf = fmf + ',%.3f'
fmftext = fmftext + ',Thrsh' + '%d' % i
currthresh = thr
svals.append(fmftext)
if 0:
line = '%.4f' % (frm / 256.0)
for i in range(len(data)):
line = line + ',%.3f' % data[i]
line = line + ',%d' % rwd
for i in range(len(filt)):
line = line + ',%.2f' % filt[i]
line = line + ',"%s"' % other
else:
dx = [
frm / 256.0,
]
dx.extend(data)
dx.append(rwd)
if len(filt):
dx.extend(filt)
dx.append(other)
if threshdict:
currthresh = threshdict.get(frm, currthresh)
dx.extend(currthresh)
try:
line = fmf % tuple(dx)
except:
print fmf
print dx
print fmftext
raise
svals.append(line)
return '\n'.join(svals), datetime
def compute_data(fobj,prt=0):
try:
fdraw=open(fobj.fname[:-3]+'raw','rb')
except:
return []
if prt:
print fobj.fname
rslt=csv_dump_out.csv_dump_out(None,fobj)
seg=[]
ampoffset=[0,0,0,0]
throffset=[0,0,0,0]
siteoffset=[0,0,0,0]
frq=rawlist.rawheaderfield(fdraw,'CLOCKRATE')
#cbxx=rawlist.rawcb('',rawfd=fdraw)
#eoec=_update_eyes(cbxx[0],frq)
if prt:
print len(rslt)
per=0
# figure out which columns have data I want period,eyes,ampl-0,ampl-1,thresh-0,thresh-1
eyes=''
for num,ln in enumerate(rslt):
fld=ln.split(',')
if not num:
numraw=fobj.number_lowpass
perslot=fld.index('"Period"')
eyeslot=fld.index('"Eyes"')
for i in range(numraw):
try:
x=fld.index('"Ampl-%d"'%i)
ampoffset[i]=x
except:
pass
try:
x=fld.index('"Thresh-%d"'%i)
throffset[i]=x
except:
pass
try:
x=fld.index('"Chan-%c"' % chr(ord('A')+i))
siteoffset[i]=x
except:
pass
continue
#find beg of per
#if eoec.has_key(int(fld[0])):
# eyes=eoec[int(fld[0])]
if int(fld[perslot]) == 0:
if per == 0:
##if prt:
## print 'not found first period ',num
continue # not found end of first period
if prt:
print 'found end of period ',per,num
#here to process previous period logic
p=fobj.per[per-1]
ssites=p.sitelist
for i in range(numraw):
for s in checksites:
look=s+'-a'
if fld[siteoffset[i]][1:-1].lower()[:4] == look:
# aha- this a a valid site
lnx=rslt[num-1].split(',')
seg.append((p.start,p.end,perstart,num-1,i,per,fld[eyeslot],fld[siteoffset[i]][1:-1]))
#if prt:
# print 'match ',fld[siteoffset[i]][1:-1],look,i,numraw,len(ssites)
##if prt:
## print 'no match ',ssites[j],look,i
else:
#if prt:
# print 'no match ',fld[siteoffset[i]][1:-1],fld[siteoffset[i]][1:-1].lower()[:4],look,i
pass
per=0
continue
if per== 0:
perstart=num
per=int(fld[perslot])
if prt:
print 'start of period ',per,num
# get here with possibles in seg
if prt:
print 'found possible ',len(seg)
ans=[]
for start,end,pstart,pend,ch,per,eyes,site in seg:
if prt:
print "s,e,ps,pe,ch,per",start,end,pstart,pend,ch,per
if end-start < 30:
if prt:
print ' less than 30 seconds'
continue # too short
for i in range(numraw):
if i != ch:
#if prt:
# print "not this chan"
continue
ans.append([start,end,pstart,pend,ch+100,per,eyes,site])
thrv=[]
amplv=[]
for k in range(pstart,pend):
fld=rslt[k].split(',')
thrv.append(fld[throffset[i]])
amplv.append(fld[ampoffset[i]])
beg=pstart
org=None
lstart=lend=0
poss=[]
while beg < pend:
if thrv[beg-pstart] > amplv[beg-pstart]:
if org:
if beg-org >= 30:
poss.append((beg-org,org,beg-1))
org=None
else:
if org == None:
org=beg
beg += 1
if org:
if pend-org >= 30:
poss.append((pend-org,org,pend))
else:
if len(poss) == 0:
poss.append((pend-pstart,pstart,pend))
#now find longest segment
if prt:
print poss
beg=0
for l,s,e in poss:
if l > beg:
lstart=s
lend=e
beg=l
# now have start end
if beg:
ans.append([start,end,lstart,lend,ch,per,eyes,site])
if prt:
print 'longest ',ch,per,start,end,lstart,lend
# if not found, good sample
# now do the fft stuff
if prt:
print 'found valid ',len(ans),' chans=',numraw
final=[]
dtaa=[]
for i in range(numraw):
dta=rawlist.rawreadvalues(fdraw,i)
dtaa.append(dta)
fdraw.close()
extfft.initfft(frq)
prevch=None
prevper=0
grp=[]
for start,end,valid,pend,ch,per,eyes,site in ans:
if prt:
print ch,valid,pend,per,site
if (ch%100) != prevch or prevper != per:
if prevch == None:
prevch = ch%100
prevper=per
else:
final.append((prevch%100,site,prevper,eyes[1:-1],grp))
grp=[]
prevch = ch%100
prevper=per
dta=dtaa[ch% 100]
#get the raw file
span=pend-valid
if ch < 100:
if span > 60:
span=60
b=pend-span-10*frq
if b < start:
b=start
sumr=[0 for x in range(640)]
cntr=0
for d in range((b+1)*frq,pend*frq,frq):
x=extfft.compute_fft_array(dta[d-frq*10:d],frq*10,640)
# take last 60 or less seconds of data and
# compute FFT in 0.1 Hz bins and average the bins
#
for i in range(640):
sumr[i] += x[i]
cntr += 1
biggie=0
if cntr:
for i in range(640):
sumr[i] = sumr[i]/cntr
if sumr[i] > biggie:
biggie=sumr[i]
else:
if prt:
print 'no fft samples!',b+1,pend
sumr.append(biggie)
grp.append(sumr)
if grp != []:
final.append((ch%100,site,per,eyes[1:-1],grp))
extfft.clean()
# i s i, s 65*f
if prt:
for item in final:
print item[0],item[1],item[2],len(item[4]),item[4][0][-1],
if len(item[4]) > 1:
print item[4][1][-1],
else:
print 'None',
print
return final # array of (chan,site, per,eyes,64 bins of average+max)
def raw_export(dest, rawfile, why=0, hidename=0, justname=0, exporttree=None):
rawFD = open(rawfile, 'rb') # open RAW file for reading
rawfile_info = rawlist.rawinfo(rawfile, why=why)
rate = rawfile_info[1]
if why > 1:
print dest, rawfile
# get base name for use with GetClientFile
basename = "\\".join(os.path.normpath(rawfile).split("\\")[:-2])
client = clients.GetClientFile(basename)
if why > 1:
print basename, client
# get patient identification, date and time from raw file
datetime = rawlist.rawdate(rawfile)
try:
pid = client['client.xguid']
except:
# for old version 4.0.3h and before
pid = client['client.fullname']
patient = client['client.clientid']
fullname = client['client.fullname']
# get annotations
annotations = []
initial_site = []
sumfilepath = os.path.splitext(rawfile)[0] + ".SUM"
tstart = []
fake = 0
if os.path.exists(sumfilepath):
summary = sumfile.get_sum_file(sumfilepath, 0, 0)
if summary:
annotations = get_annotation_list(summary)
if why > 3:
print 'summary:', annotations
else:
annotations = fake_raw_annot(rawfile)
fake = 1
if why > 3:
print 'fake sum', annotations
else:
##isa=[]
annotations = fake_raw_annot(rawfile, why=why)
fake = 1
if why > 3:
print 'faked', annotations
##initial_site.extend( _expand_rawsites(rawfile_info) )
##tstart.append(0)
temp_annot = []
start_site = ''
site_list = []
TIME = 0
TEXT = 1
TYPE = 2
# Break up annotations according to site change
stime = 0
for annot in annotations:
if fake:
tt = annot[0]
if tt <= 256:
tt = 0
if start_site == '':
start_site = annot[1]
tstart.append(tt)
site_list.append([annot[1]])
stime = annot[tt]
else:
if stime == annot[0]:
site_list[-1].append(annot[1])
else:
start_site = annot[1]
site_list.append([annot[1]])
tstart.append(annot[0])
stime = annot[0]
else:
if annot[TYPE] == 'SITE ' and start_site == '':
start_site = annot[TEXT]
site_list.append([start_site])
tstart.append(0)
stime = 0
elif annot[TYPE] == 'SITE ':
if stime == annot[TIME]:
site_list[-1].append(annot[TEXT])
else:
if annot[TEXT] != start_site:
start_site = annot[TEXT]
site_list.append([start_site])
tstart.append(annot[TIME])
stime = annot[TIME]
#print site_list,tstart
# make up filename
if dest == None:
return # for debug
if exporttree:
# make sure Brainchild folder exists in dest (which is the exporttree name
bc = os.path.join(exporttree, 'Brainchild')
if not os.path.exists(bc):
os.mkdir(bc)
# make sure client folder exists in brainchild
bc2 = os.path.join(bc, patient)
if not os.path.exists(bc2):
os.mkdir(bc2)
# make sure protocol class existss in client folder
bcx = os.path.normpath(rawfile).split('\\')
bc3 = os.path.join(bc2, bcx[-2])
if not os.path.exists(bc3):
os.mkdir(bc3)
# dest dest to result
dest = bc3
else:
dest = os.path.normpath(dest)
bn = os.path.basename(rawfile)
fdate = bn[-10:-4]
if hidename:
if hidename > 1:
hname = clients.HIPAAstring(fullname, pid, 'First')
asterisk = hname.find('*')
if asterisk > 0:
hname = hname[:asterisk] # remove those trailing asterisks
vfname = hname.replace(' ', '_')
fout = os.path.join(dest, vfname + fdate)
else:
fout = os.path.join(dest, pid + fdate)
else:
fout = os.path.join(dest, patient + fdate)
# get data (so I know how long it is)
data = []
for i in range(4):
dta = rawlist.rawreadvalues(rawFD, i)
if dta[0] == None:
break
data.append(dta)
if why > 1:
print 'data read ', len(data), len(tstart)
# write the file
for seg in range(len(tstart)):
if seg + 1 == len(tstart):
# here for the last segment
seconds = len(data[0]) / rate - tstart[seg]
else:
seconds = tstart[seg + 1] - tstart[seg]
if why > 1:
print fout + segtable[seg]
destname = fout + segtable[seg] + '.txt'
fdo = open(destname, 'w')
if justname:
print >> fdo, 'Filename: %s' % os.path.basename(destname)
else:
print >> fdo, 'Filename: %s' % fout
print >> fdo, 'Number of seconds: %d' % seconds
print >> fdo, 'Sample Rate: %d' % rate
print >> fdo, 'Multiplier: 1'
fdo.write('Time')
sl = site_list[seg]
##print site_list
vinx, vsites = match_sites(sl)
if why > 1:
print vinx, vsites, sl, site_list
xcntr = 1
##print len(data),len(sl),sl
for isite in vsites:
fdo.write(',')
fdo.write(isite)
fdo.write('\n')
base = p = tstart[seg] * rate
endpt = p + seconds * rate
col = 0
cntr = 0
while p < endpt:
fdo.write(str(p - base))
while 1:
if vinx[col] >= 0:
fdo.write(',%.3f' % data[vinx[col]][p])
else:
fdo.write(',0')
col += 1
if col >= len(vinx):
break
col = 0
fdo.write('\n')
p += 1
cntr += 1
while (cntr % rate): # round up to next second
fdo.write(str(p - base))
for j in range(len(vinx)):
fd.write(',0')
fd.write('\n')
p += 1
cntr += 1
fdo.close()
rawFD.close()
return 0