def __init__(self, filename):
self.filename = filename
self.first, self.ext = os.path.splitext(filename)
if not self.ext:
# No extension: Assume this is a book number
from . import bookno
file_bookno = bookno.file_bookno(filename)
self.filename = dcache.find(rawfile_paths, file_bookno)
if self.filename:
self.first, self.ext = os.path.splitext(self.filename)
else:
raise Exception('Can\'t locate raw file for book number %s' %
filename)
self.addmethods = None
self.f = avg_q_file(self.filename)
self.fileformat = self.f.fileformat
self.epoched = False
if self.fileformat == 'freiburg':
from . import freiburg_setup
from .. import channelnames2channelpos
a = avg_q.avg_q()
nr_of_channels = a.get_description(self.f, 'nr_of_channels')
del a
self.setup = channelnames2channelpos.channelnames2channelpos(
freiburg_setup.sleep_channels(self.first, nr_of_channels))
elif self.fileformat == 'rec':
a = avg_q.avg_q()
comment, channelnames = a.get_description(
self.f, ('comment', 'channelnames'))
del a
if comment is not None and ('Somnoscreen' in comment
or 'Somnodcreen' in comment):
# Recording reference for Somnoscreen is Cz, makes no sense to analyze the channels like this
# M1 is the more common name but there are some recordings with A1 instead
channelnames = set(channelnames)
# Exclude NonEEGChannels from rereferencing and also channels containing a colon, since they
# should keep the indicated reference (eg 'C3:M2')
exclude_channelnames = channelnames.intersection(
avg_q.Channeltypes.NonEEGChannels).union(
[x for x in channelnames if ':' in x])
p, fname = os.path.split(self.first)
fname = fname.lower()
if fname in bad_channels:
channelnames = channelnames.difference(bad_channels[fname])
reference = channelnames.intersection(
set(['M1', 'M2', 'A1', 'A2']))
self.addmethods = '''
>add_zerochannel Cz 0 0 0
>set_channelposition =grid
>rereference -e %(exclude_channelnames)s %(reference)s
''' % {
'exclude_channelnames':
channel_list2arg(exclude_channelnames),
'reference': channel_list2arg(reference),
}
self.trigfile = None
def __init__(self,filename):
self.filename=filename
self.first,self.ext=os.path.splitext(filename)
if not self.ext:
# No extension: Assume this is a book number
from . import bookno
file_bookno=bookno.file_bookno(filename)
self.filename=None
self.filename=dcache.find(rawfile_paths,file_bookno)
if self.filename:
self.first,self.ext=os.path.splitext(self.filename)
else:
raise Exception('Can\'t locate raw file for book number %s' % filename)
self.addmethods=None
self.f=avg_q_file(self.filename)
self.fileformat=self.f.fileformat
if self.fileformat=='freiburg':
from . import freiburg_setup
from .. import channelnames2channelpos
a=avg_q.avg_q()
nr_of_channels=a.get_description(self.f,'nr_of_channels')
del a
self.setup=channelnames2channelpos.channelnames2channelpos(freiburg_setup.sleep_channels(self.first,nr_of_channels))
elif self.fileformat=='rec':
a=avg_q.avg_q()
comment,channelnames=a.get_description(self.f,('comment','channelnames'))
del a
if comment is not None and ('Somnoscreen' in comment or 'Somnodcreen' in comment):
# Recording reference for Somnoscreen is Cz, makes no sense to analyze the channels like this
# M1 is the more common name but there are some recordings with A1 instead
channelnames=set(channelnames)
# Exclude NonEEGChannels from rereferencing and also channels containing a colon, since they
# should keep the indicated reference (eg 'C3:M2')
exclude_channelnames=channelnames.intersection(avg_q.Channeltypes.NonEEGChannels).union([x for x in channelnames if ':' in x])
p,fname=os.path.split(self.first)
fname=fname.lower()
if fname in bad_channels:
channelnames=channelnames.difference(bad_channels[fname])
reference=channelnames.intersection(set(['M1','M2','A1','A2']))
self.addmethods='''
>add_zerochannel Cz 0 0 0
>set_channelposition =grid
>rereference -e %(exclude_channelnames)s %(reference)s
''' % {
'exclude_channelnames': channel_list2arg(exclude_channelnames),
'reference': channel_list2arg(reference),
}
self.trigfile=None
#!/usr/bin/env python
# Set the path to the avg_q python installation here if you
# didn't add it to the global python path
import sys
sys.path.append("R:/avg_q/python")
import avg_q
# The avg_q_ui.exe binary will be found automatically in the directory
# above python/
a = avg_q.avg_q(avg_q='avg_q_ui')
import glob
# Iterate over all files with extension .edf
for infile in glob.glob('N:/*.edf'):
# avg_q.Epochsource normally takes an avg_q_file() descriptor as first
# argument but for convenience also a file name with type inferred
# from the extension
# Read a single 2-s epoch from the start of the file
epochsource = avg_q.Epochsource(infile,
'1s',
'1s',
continuous=True,
epochs=1)
script = avg_q.Script(a)
script.add_Epochsource(epochsource)
script.add_transform('''
query -N sfreq stdout
query -N nr_of_points stdout
posplot''')
#!/usr/bin/env python
# Set the path to the avg_q python installation here if you
# didn't add it to the global python path
import sys
sys.path.append("R:/avg_q/python")
import avg_q
# The avg_q_ui.exe binary will be found automatically in the directory
# above python/
a=avg_q.avg_q(avg_q='avg_q_ui')
import glob
# Iterate over all files with extension .edf
for infile in glob.glob('N:/*.edf'):
# avg_q.Epochsource normally takes an avg_q_file() descriptor as first
# argument but for convenience also a file name with type inferred
# from the extension
# Read a single 2-s epoch from the start of the file
epochsource=avg_q.Epochsource(infile,'1s','1s',continuous=True,epochs=1)
script=avg_q.Script(a)
script.add_Epochsource(epochsource)
script.add_transform('''
query -N sfreq stdout
query -N nr_of_points stdout
posplot''')
# avg_q.Script() sets the collect method to null_sink automatically
script.run()
a.close()
