multielectrode_grasp/code/python-neo/neo/io/elanio.py

# -*- coding: utf-8 -*-
"""
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

"""

import datetime
import os
import re

import numpy as np
import quantities as pq

from neo.io.baseio import BaseIO
from neo.core import Segment, AnalogSignal, Event


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.events   # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
        []



    """

    is_readable = True
    is_writable = False

    supported_objects = [Segment, AnalogSignal, Event]
    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])

        #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(np.log(max_logic[0] - min_logic[0]) / np.log(2)) / 8)
        data = np.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, '')

            ana_sig = AnalogSignal(
                sig * unit, sampling_rate=sampling_rate,
                t_start=0. * pq.s, name=labels[c], channel_index=c)
            if lazy:
                ana_sig.lazy_shape = data.shape[0]
            ana_sig.annotate(channel_name=labels[c])
            seg.analogsignals.append(ana_sig)

        # 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 = Event(times=times, labels=labels, reject_codes=reject_codes)
        if lazy:
            ea.lazy_shape = len(times)
        seg.events.append(ea)

        f.close()

        seg.create_many_to_one_relationship()
        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()