/usr/share/pyshared/neo/io/elanio.py is in python-neo 0.2.0-1.
This file is owned by root:root, with mode 0o644.
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"""
Class for reading/writing data from Elan.
Elan is software for studying time-frequency maps of EEG data.
Elan is developed in Lyon, France, at INSERM U821
An Elan dataset is separated into 3 files :
- .eeg raw data file
- .eeg.ent hearder file
- .eeg.pos event file
Depend on:
Supported : Read and Write
Author: sgarcia
"""
from .baseio import BaseIO
from ..core import *
from .tools import create_many_to_one_relationship
import numpy as np
from numpy import dtype, zeros, fromstring, empty, log, fromfile
import quantities as pq
import os
import datetime
import re
class VersionError(Exception):
def __init__(self, value):
self.value = value
def __str__(self):
return repr(self.value)
class ElanIO(BaseIO):
"""
Classe for reading/writing data from Elan.
Usage:
>>> from neo import io
>>> r = io.ElanIO( filename = 'File_elan_1.eeg')
>>> seg = r.read_segment(lazy = False, cascade = True,)
>>> print seg.analogsignals # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
[<AnalogSignal(array([ 89.21203613, 88.83666992, 87.21008301, ..., 64.56298828,
67.94128418, 68.44177246], dtype=float32) * pA, [0.0 s, 101.5808 s], sampling rate: 10000.0 Hz)>]
>>> print seg.spiketrains # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
[]
>>> print seg.eventarrays # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
[]
"""
is_readable = True
is_writable = False
supported_objects = [Segment, AnalogSignal, EventArray]
readable_objects = [Segment]
writeable_objects = [ ]
has_header = False
is_streameable = False
read_params = { Segment : [ ] }
write_params = { Segment : [ ] }
name = None
extensions = ['eeg']
mode = 'file'
def __init__(self , filename = None) :
"""
This class read/write a elan based file.
**Arguments**
filename : the filename to read or write
"""
BaseIO.__init__(self)
self.filename = filename
def read_segment(self, lazy = False, cascade = True):
## Read header file
f = open(self.filename+'.ent' , 'rU')
#version
version = f.readline()
if version[:2] != 'V2' and version[:2] != 'V3':
# raise('read only V2 .eeg.ent files')
raise VersionError('Read only V2 or V3 .eeg.ent files. %s given' %
version[:2])
return
#info
info1 = f.readline()[:-1]
info2 = f.readline()[:-1]
# strange 2 line for datetime
#line1
l = f.readline()
r1 = re.findall('(\d+)-(\d+)-(\d+) (\d+):(\d+):(\d+)',l)
r2 = re.findall('(\d+):(\d+):(\d+)',l)
r3 = re.findall('(\d+)-(\d+)-(\d+)',l)
YY, MM, DD, hh, mm, ss = (None, )*6
if len(r1) != 0 :
DD , MM, YY, hh ,mm ,ss = r1[0]
elif len(r2) != 0 :
hh ,mm ,ss = r2[0]
elif len(r3) != 0:
DD , MM, YY= r3[0]
#line2
l = f.readline()
r1 = re.findall('(\d+)-(\d+)-(\d+) (\d+):(\d+):(\d+)',l)
r2 = re.findall('(\d+):(\d+):(\d+)',l)
r3 = re.findall('(\d+)-(\d+)-(\d+)',l)
if len(r1) != 0 :
DD , MM, YY, hh ,mm ,ss = r1[0]
elif len(r2) != 0 :
hh ,mm ,ss = r2[0]
elif len(r3) != 0:
DD , MM, YY= r3[0]
try:
fulldatetime = datetime.datetime(int(YY) , int(MM) , int(DD) , int(hh) , int(mm) , int(ss) )
except:
fulldatetime = None
seg = Segment( file_origin = os.path.basename(self.filename),
elan_version = version,
info1 = info1,
info2 = info2,
rec_datetime = fulldatetime,
)
if not cascade : return seg
l = f.readline()
l = f.readline()
l = f.readline()
# sampling rate sample
l = f.readline()
sampling_rate = 1./float(l) * pq.Hz
# nb channel
l = f.readline()
nbchannel = int(l)-2
#channel label
labels = [ ]
for c in range(nbchannel+2) :
labels.append(f.readline()[:-1])
# channel type
types = [ ]
for c in range(nbchannel+2) :
types.append(f.readline()[:-1])
# channel unit
units = [ ]
for c in range(nbchannel+2) :
units.append(f.readline()[:-1])
#print units
#range
min_physic = []
for c in range(nbchannel+2) :
min_physic.append( float(f.readline()) )
max_physic = []
for c in range(nbchannel+2) :
max_physic.append( float(f.readline()) )
min_logic = []
for c in range(nbchannel+2) :
min_logic.append( float(f.readline()) )
max_logic = []
for c in range(nbchannel+2) :
max_logic.append( float(f.readline()) )
#info filter
info_filter = []
for c in range(nbchannel+2) :
info_filter.append(f.readline()[:-1])
f.close()
#raw data
n = int(round(log(max_logic[0]-min_logic[0])/log(2))/8)
data = fromfile(self.filename,dtype = 'i'+str(n) )
data = data.byteswap().reshape( (data.size/(nbchannel+2) ,nbchannel+2) ).astype('f4')
for c in range(nbchannel) :
if lazy:
sig = [ ]
else:
sig = (data[:,c]-min_logic[c])/(max_logic[c]-min_logic[c])*\
(max_physic[c]-min_physic[c])+min_physic[c]
try:
unit = pq.Quantity(1, units[c] )
except:
unit = pq.Quantity(1, '' )
anaSig = AnalogSignal( sig * unit,
sampling_rate = sampling_rate,
t_start=0.*pq.s,
name = labels[c],
)
if lazy:
anaSig.lazy_shape = data.shape[0]
anaSig.annotate(channel_index = c)
anaSig.annotate(channel_name= labels[c])
seg.analogsignals.append( anaSig )
# triggers
f = open(self.filename+'.pos')
times =[ ]
labels = [ ]
reject_codes = [ ]
for l in f.readlines() :
r = re.findall(' *(\d+) *(\d+) *(\d+) *',l)
times.append( float(r[0][0])/sampling_rate.magnitude )
labels.append(str(r[0][1]) )
reject_codes.append( str(r[0][2]) )
if lazy:
times = [ ]*pq.S
labels = np.array([ ], dtype = 'S')
reject_codes = [ ]
else:
times = np.array(times) * pq.s
labels = np.array(labels)
reject_codes = np.array(reject_codes)
ea = EventArray( times = times,
labels = labels,
reject_codes = reject_codes,
)
if lazy:
ea.lazy_shape = len(times)
seg.eventarrays.append(ea)
f.close()
create_many_to_one_relationship(seg)
return seg
#~ def write_segment(self, segment, ):
#~ """
#~ Arguments:
#~ segment : the segment to write. Only analog signals and events will be written.
#~ """
#~ assert self.filename.endswith('.eeg')
#~ fid_ent = open(self.filename+'.ent' ,'wt')
#~ fid_eeg = open(self.filename ,'wt')
#~ fid_pos = open(self.filename+'.pos' ,'wt')
#~ seg = segment
#~ sampling_rate = seg._analogsignals[0].sampling_rate
#~ N = len(seg._analogsignals)
#~ #
#~ # header file
#~ #
#~ fid_ent.write('V2\n')
#~ fid_ent.write('OpenElectrophyImport\n')
#~ fid_ent.write('ELAN\n')
#~ t = datetime.datetime.now()
#~ fid_ent.write(t.strftime('%d-%m-%Y %H:%M:%S')+'\n')
#~ fid_ent.write(t.strftime('%d-%m-%Y %H:%M:%S')+'\n')
#~ fid_ent.write('-1\n')
#~ fid_ent.write('reserved\n')
#~ fid_ent.write('-1\n')
#~ fid_ent.write('%g\n' % (1./sampling_rate))
#~ fid_ent.write( '%d\n' % (N+2) )
#~ # channel label
#~ for i, anaSig in enumerate(seg.analogsignals) :
#~ try :
#~ fid_ent.write('%s.%d\n' % (anaSig.label, i+1 ))
#~ except :
#~ fid_ent.write('%s.%d\n' % ('nolabel', i+1 ))
#~ fid_ent.write('Num1\n')
#~ fid_ent.write('Num2\n')
#~ #channel type
#~ for i, anaSig in enumerate(seg.analogsignals) :
#~ fid_ent.write('Electrode\n')
#~ fid_ent.write( 'dateur echantillon\n')
#~ fid_ent.write( 'type evenement et byte info\n')
#~ #units
#~ for i, anaSig in enumerate(seg._analogsignals) :
#~ unit_txt = str(anaSig.units).split(' ')[1]
#~ fid_ent.write('%s\n' % unit_txt)
#~ fid_ent.write('sans\n')
#~ fid_ent.write('sans\n')
#~ #range and data
#~ list_range = []
#~ data = np.zeros( (seg._analogsignals[0].size , N+2) , 'i2')
#~ for i, anaSig in enumerate(seg._analogsignals) :
#~ # in elan file unit is supposed to be in microV to have a big range
#~ # so auto translate
#~ if anaSig.units == pq.V or anaSig.units == pq.mV:
#~ s = anaSig.rescale('uV').magnitude
#~ elif anaSig.units == pq.uV:
#~ s = anaSig.magnitude
#~ else:
#~ # automatic range in arbitrry unit
#~ s = anaSig.magnitude
#~ s*= 10**(int(np.log10(abs(s).max()))+1)
#~ list_range.append( int(abs(s).max()) +1 )
#~ s2 = s*65535/(2*list_range[i])
#~ data[:,i] = s2.astype('i2')
#~ for r in list_range :
#~ fid_ent.write('-%.0f\n'% r)
#~ fid_ent.write('-1\n')
#~ fid_ent.write('-1\n')
#~ for r in list_range :
#~ fid_ent.write('%.0f\n'% r)
#~ fid_ent.write('+1\n')
#~ fid_ent.write('+1\n')
#~ for i in range(N+2) :
#~ fid_ent.write('-32768\n')
#~ for i in range(N+2) :
#~ fid_ent.write('+32767\n')
#~ #info filter
#~ for i in range(N+2) :
#~ fid_ent.write('passe-haut ? Hz passe-bas ? Hz\n')
#~ fid_ent.write('sans\n')
#~ fid_ent.write('sans\n')
#~ for i in range(N+2) :
#~ fid_ent.write('1\n')
#~ for i in range(N+2) :
#~ fid_ent.write('reserved\n')
#~ # raw file .eeg
#~ if len(seg._eventarrays) == 1:
#~ ea = seg._eventarrays[0]
#~ trigs = (ea.times*sampling_rate).magnitude
#~ trigs = trigs.astype('i')
#~ trigs2 = trigs[ (trigs>0) & (trigs<data.shape[0]) ]
#~ data[trigs2,-1] = 1
#~ fid_eeg.write(data.byteswap().tostring())
#~ # pos file eeg.pos
#~ if len(seg._eventarrays) == 1:
#~ ea = seg._eventarray[0]
#~ if 'reject_codes' in ea.annotations and len(ea.reject_codes) == len(ea.times):
#~ rcs = ea.reject_codes
#~ else:
#~ rcs = np.array( [ '' ]*ea.times.size)
#~ if len(ea.labels) == len(ea.times):
#~ labels = ea.labels
#~ else:
#~ labels = np.array( [ '' ]*ea.times.size)
#~ for t, label, rc in zip(ea.times, labels, rcs):
#~ fid_pos.write('%d %s %s\n' % (trigs[i] , ev.label,0))
#~ fid_ent.close()
#~ fid_eeg.close()
#~ fid_pos.close()
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