def snap_print(root=None, fname=None, pname=None, edict=None, prt=0):
"display/print one file, return 1 if destroy selected, -1 if error"
if not os.path.exists(fname):
return -1
dta = snap_read(fname, 0, prt)
if not dta:
return -1
name = dta['name']
if edict:
cl = clients.GetClientFile(edict['PROGRAMPATH'] + '/CLIENTS/' +
dta['code'])
if cl:
name = clients.HIPAA(cl, edict['SETTINGS'].get('HipTitle', 'All'))
container = _win_common(root, 'Display/print snapshots', fname, prt)
fr = container.fr
Label(fr,
text=name + ' ' + dta['time'] + ' (' + dta['sessiontime'] + ')',
font=('Tahoma', 16),
background='white').pack(side=TOP)
create_graphics(fr, dta)
return _win_work(container, _printme, pname, fname, prt)
def autoexport(root, edict, fsum, fraw, proto, prt=0):
if len(fsum) == 0:
if prt:
print 'no summary files found'
return
# get root filename(s)
fx = os.path.basename(fsum[0])
cname = fx[:-10]
cd = clients.GetClientFile(edict['DATAPATH'] + '\\' + cname)
if not cd:
if prt:
print 'no client file'
return
flst = []
# make list
for f in fsum:
rootname = os.path.basename(f)
flst.append((0, 1, 0, edict['DATAPATH'] + '\\' + cname + '\\' + proto +
'\\' + rootname))
if int(edict['SETTINGS']['ConsultRaw']):
for f in fraw:
rootname = os.path.basename(f)
flst.append((0, 1, 0, edict['DATAPATH'] + '\\' + cname + '\\' +
proto + '\\' + rootname))
# export
ans, path = _consultexport(root, edict, flst, cd, prt)
return ans
def getname(filename, edict):
"gets just the nameinfo from file"
dta = snap_read(filename, 1)
if dta:
name = dta['name']
if edict:
cl = clients.GetClientFile(edict['PROGRAMPATH'] + '/CLIENTS/' +
dta['code'])
if cl:
name = clients.HIPAA(cl,
edict['SETTINGS'].get('HipSelect', 'All'))
nm = name + ' ' + dta['time']
return nm
return None
def raw2edf(rawfile, destination_dir, debug=0):
''' Convert RAW file to EDF '''
global SAMPLING_RATE
global MAX_CHAN_LENGTH
rawFD = open(rawfile, 'rb') # open RAW file for reading
rawfile_info = rawlist.rawinfo(rawfile)
rawfile_subset = rawlist.rawheaderfield(rawFD, 'SUBSET')
rawfile_formatstring = rawlist.rawheaderfield(rawFD, 'FORMATSTRING')
# get base name for use with GetClientFile
basename = "\\".join(rawfile.split("\\")[:-2])
client = clients.GetClientFile(basename)
# get patient identification, date and time from raw file
datetime = rawlist.rawdate(rawfile)
if debug > 1:
print 'debugging'
try:
pid = client['client.xguid']
except:
# for old version 4.0.3h and before
pid = client['client.fullname']
patient = client['client.clientid']
rec_date = datetime[8:10] + '-' + MONTHS[int(datetime[5:7]) -
1] + '-' + datetime[0:4]
startdate = datetime[8:10] + '.' + datetime[5:7] + '.' + datetime[2:4]
starttime = datetime[11:13] + '.' + datetime[14:16] + '.00'
# Combine directory for edf file and name of files that's going to be created
rsplit = os.path.split(rawfile)
rdir = os.path.split(rsplit[0])
actname = rsplit[1].split('.')
output_file = destination_dir + '\\' + actname[0] + rdir[1][
0] # add E,B,A for category
c_scales = rawlist.rawparams(rawFD)[1:] # list of channel scales
c_channels = [] # list of channel data
peripheral = [] # peripheral data
# there will be up to 3 scales (2 for channel a and b, 1 for peripheral)
c_channels.append(rawlist.rawread(rawFD, CHAN_A)[0])
c_channels.append(rawlist.rawread(rawFD, CHAN_B)[0])
if rawfile_formatstring[2] == 'C':
# must be 4 chan
if debug > 1:
print 'aha- 4 channels'
c_channels.append(rawlist.rawread(rawFD, CHAN_C)[0])
c_channels.append(rawlist.rawread(rawFD, CHAN_D)[0])
####!!!!
# check for peripheral data (NOT INCORPORATED INTO EDF FILE YET)
#if len(c_scales) > 2:
# try:
# peripheral.append( rawlist.rawread(rawFD, PERIPH)[0] )
# except:
# pass
# set 1) Sampling Rate, 2) Max channel length
SAMPLING_RATE = rawfile_info[1]
MAX_CHAN_LENGTH = ((len(max(c_channels)) / 2) / 256)
if debug > 1:
print SAMPLING_RATE, MAX_CHAN_LENGTH
# get annotations
annotations = []
initial_site = []
initial_site.append(rawfile_info[len(rawfile_info) - 1][1:])
numchannels = 0
if rawfile_subset >= 2:
#sumfilepath = rawfile.split(".")[0] + ".SUM"
#if os.path.exists(sumfilepath):
# summary = sumfile.get_sum_file(sumfilepath, 0, 0)
# if summary:
# annotations = get_annotation_list(summary)
# numchannels=summary.number_streams
#if numchannels == 0:
# # do it the hard way
# while numchannels < 16:
# dta=rawlist.readrawamplvalues(fd,numchannels,countonly=1)
# if len(dta):
# numchannels += 1
# else:
# break
for astr in range(len(rawfile_formatstring)):
dta = rawlist.rawreadampl(rawFD, numchannels, prt=0)
if len(dta):
c_channels.append(dta[0][:])
if debug > 1:
print 'achan ', len(c_channels[-1]), numchannels
c_scales.append(0.01)
numchannels += 1
startinfo = (pid, patient, rec_date, startdate, starttime, initial_site,
numchannels, rawfile_formatstring)
rawevents, ans = rawlist.rawcb(rawfile)
if ans == 0:
# now merge in the desired raw event data
annotations = merge_rawsum(rawevents, annotations)
#if numchannels:
# for ch in range(numchannels):
# c_scales.append(0.0)
if debug > 1:
print 'write2file', len(c_channels)
for i in range(len(c_channels)):
print i, len(c_channels[i])
write2file(startinfo, c_channels, c_scales, annotations, output_file,
debug)
rawFD.close()
return 1
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