def loadBiosig(fname):
"""Loads biosig compatible datasets.
Parameters
----------
fname : path to dataset
Returns
-------
data : dataset as a numpy matrix
sample_rate : dataset sample rate
Examples
--------
>>> data_path = "/PATH/TO/PATH/dataset.gdf"
>>> EEGdata = loadBiosig(data_path)
"""
# Loads GDF competition data
HDR = biosig.constructHDR(0, 0)
HDR = biosig.sopen(fname, 'r', HDR)
sample_rate = HDR.SampleRate
data = biosig.sread(0, HDR.NRec, HDR)
biosig.sclose(HDR)
biosig.destructHDR(HDR)
return data, sample_rate
def load_biosig(fname):
"""Loads biosig compatible datasets.
Parameters
----------
fname : path to dataset
Returns
-------
data : dataset as a numpy matrix
sample_rate : dataset sample rate
Examples
--------
>>> data_path = "/PATH/TO/PATH/dataset.gdf"
>>> EEGdata = loadBiosig(data_path)
"""
# Loads GDF competition data
HDR = biosig.constructHDR(0, 0)
HDR = biosig.sopen(fname, 'r', HDR)
sample_rate = HDR.SampleRate
data = biosig.sread(0, HDR.NRec, HDR)
biosig.sclose(HDR)
biosig.destructHDR(HDR)
return data, sample_rate
def edfreadin(filename):
hdr = biosig.sopen(filename, 'r', None)
n = hdr.NS
eegs = {}
v = biosig.sread(0, hdr.NRec * hdr.SPR, hdr)
for i in range(n):
k = hdr.CHANNEL[i].Label.split('\x00')[0]
if k in channels:
eegs[k] = v[i].astype('float32')
return eegs
def read_data(f_name):
t1 = time.time()
HDR = biosig.sopen(f_name, 'r')
print("Read header of %s in %f s\n" % (f_name, time.time() - t1))
t1 = time.time()
data = biosig.sread(HDR, HDR.NRec, 0)
print("Read data of %s in %f s\n" % (f_name, time.time() - t1))
biosig.sclose(HDR)
return HDR, data
def load(fname):
HDR = biosig.constructHDR(0, 0)
HDR = biosig.sopen(fname, "r", HDR)
# turn off all channels
# for i in range(HDR.NS):
# HDR.CHANNEL[i].OnOff = 0
# turn on specific channels
# HDR.CHANNEL[0].OnOff = 1
# HDR.CHANNEL[1].OnOff = 1
# HDR.CHANNEL[HDR.NS-1].OnOff = 1
data = biosig.sread(0, HDR.NRec, HDR)
biosig.sclose(HDR)
biosig.destructHDR(HDR)
return data
def load(fname):
HDR = biosig.constructHDR(0, 0)
HDR = biosig.sopen(fname, "r", HDR)
# turn off all channels
# for i in range(HDR.NS):
# HDR.CHANNEL[i].OnOff = 0
# turn on specific channels
# HDR.CHANNEL[0].OnOff = 1
# HDR.CHANNEL[1].OnOff = 1
# HDR.CHANNEL[HDR.NS-1].OnOff = 1
data = biosig.sread(0, HDR.NRec, HDR)
biosig.sclose(HDR)
biosig.destructHDR(HDR)
return data
def __init__(self, filename):
self.__filename = filename
#self.__hypdata = None
#self.__artdata = None
#self.__data = None
self.__channels = []
self.__epoch = None
self.__HDR = None
#self.__has_read_data = False
if not os.path.isfile(self.__filename):
raise IOError('file ' + self.__filename + ' cannot be opened!')
self.__HDR = biosig.constructHDR(0, 0)
self.__HDR = biosig.sopen(self.__filename, "r", self.__HDR)
self.__Fs = np.zeros(self.__HDR.NS)
for i in range(self.__HDR.NS):
self.__Fs[i] = self.__HDR.CHANNEL[i].SPR
channel = self.__HDR.CHANNEL[i].Label
nullpos = channel.find('\x00')
if nullpos != -1:
channel = channel[:nullpos]
self.__channels.append(channel)
self.__HDR.CHANNEL[i].OnOff = 0
def _load_biosig(filename):
import biosig
hdr = biosig.constructHDR(0, 0)
hdr = biosig.sopen(filename, 'r', hdr)
# The logic here does not match the biosig API. But it is deliberately
# this way to work around a bug loading EDF files in python-biosig 1.3.
# TODO: revisit this code when I finally get python-biosig 1.6 to install.
channels = hdr.NS - 1
fs = hdr.SampleRate / channels
npoints = hdr.NRec * hdr.SPR / channels
ar = np.zeros((npoints, channels), dtype=np.float64)
channelnames = []
for i in range(channels):
label = hdr.CHANNEL[i].Label
if '\x00' in label:
label = label[:label.index('\x00')]
channelnames.append(label)
for j in range(hdr.NS):
hdr.CHANNEL[j].OnOff = int(j == i)
data = biosig.sread(0, hdr.NRec, hdr)
ar[:, i] = data.reshape((npoints, channels))[:, 0]
biosig.sclose(hdr)
biosig.destructHDR(hdr)
return Timeseries(ar, labels=[None, channelnames], fs=fs)
import pylab
import numpy
import biosig
HDR=biosig.sopen('/home/schloegl/data/test/gdf/sample.gdf','r',biosig.constructHDR(0,0));
#for i in range(HDR.NS):
# HDR.CHANNEL[i].OnOff = 0
#HDR.CHANNEL[0].OnOff = 1
data = biosig.sread(0, HDR.NRec, HDR)
biosig.sclose(HDR)
#biosig.destructHDR(HDR)
pylab.ion();
pylab.plot(numpy.transpose(data))
pylab.show();
import biosig
import numpy as S
import ctypes
import datetime
filename = '/scratch/schloegl/R/data/test/CFS/example_6channels.dat'
filename = '/home/as/data/test/CFS/example_6channels.dat'
filename = '/home/as/data/test/BDF/sample_bdf_plus_file.bdf'
filename = '/fs/home/schloegl/data/test/gdf/test.clemens.20121220.gdf'
print 'open file ', filename
HDR = biosig.constructHDR(0, 0)
HDR = biosig.sopen(filename, 'r', HDR)
HDR.Patient.Id
HDR.Patient.Sex
HDR.Patient.Handedness
HDR.Patient.DrugAbuse
HDR.Patient.Smoking
### convert from gdftime/matlab/octave datetime format to python datetime format
### for some unknown reason, the starting point is 366 days off.
d = datetime.timedelta(days=HDR.T0 * (2**-32) - 366)
m, s = divmod(d.seconds, 60)
h, m = divmod(m, 60)
starttime = datetime.datetime.combine(datetime.date.fromordinal(d.days),
datetime.time(h, m, s))
print "starting time:", starttime
# download and extract
# http://www.biosemi.com/download/BDFtestfiles.zip
# into /tmp/
# then run this demo
#
# on linux you can run instead
# make test
import biosig
import numpy as S
#def load(fname):
HDR = biosig.constructHDR(0, 0)
#HDR = biosig.sopen('/scratch/schloegl/R/data/test/HekaPatchMaster/AP100427b.dat' , 'r', HDR)
#HDR = biosig.sopen('/scratch/schloegl/R/data/test/HekaPatchMaster/AP100429a.dat' , 'r', HDR)
HDR = biosig.sopen('/scratch/schloegl/R/data/test/CFS/example_6channels.dat',
'r', HDR)
# show header information
biosig.hdr2ascii(HDR, 4)
# turn off all channels
# for i in range(HDR.NS):
# HDR.CHANNEL[i].OnOff = 0
# turn on specific channels
# HDR.CHANNEL[0].OnOff = 1
# HDR.CHANNEL[1].OnOff = 1
# HDR.CHANNEL[HDR.NS-1].OnOff = 1
# read data
data = biosig.sread(0, HDR.NRec, HDR)
#!/usr/bin/env python3
import pylab
import numpy
import biosig
HDR = biosig.sopen(
'/home/sweet/1-workdir/eeg001-2017/S01_ME/motorexecution_subject1_run1.gdf',
'r')
#for i in range(HDR.NS):
# HDR.CHANNEL[i].OnOff = 0
#HDR.CHANNEL[0].OnOff = 1
# data = biosig.sread(HDR, HDR.NRec, 0)
# biosig.sclose(HDR)
# # #biosig.destructHDR(HDR)
# pylab.ion()
# pylab.plot(numpy.transpose(data))
# pylab.show()
import biosig import numpy as S import ctypes import datetime filename = '/scratch/schloegl/R/data/test/CFS/example_6channels.dat' filename = '/home/as/data/test/CFS/example_6channels.dat' filename = '/home/as/data/test/BDF/sample_bdf_plus_file.bdf' filename = '/fs/home/schloegl/data/test/gdf/test.clemens.20121220.gdf' print 'open file ',filename HDR = biosig.constructHDR(0, 0) HDR = biosig.sopen(filename , 'r', HDR) HDR.Patient.Id HDR.Patient.Sex HDR.Patient.Handedness HDR.Patient.DrugAbuse HDR.Patient.Smoking ### convert from gdftime/matlab/octave datetime format to python datetime format ### for some unknown reason, the starting point is 366 days off. d = datetime.timedelta(days=HDR.T0*(2**-32)-366) m, s = divmod(d.seconds, 60) h, m = divmod(m, 60) starttime = datetime.datetime.combine(datetime.date.fromordinal(d.days), datetime.time(h,m,s)) print "starting time:",starttime
# download and extract
# http://www.biosemi.com/download/BDFtestfiles.zip
# into /tmp/
# then run this demo
#
# on linux you can run instead
# make test
import biosig
import numpy as S
#def load(fname):
HDR = biosig.constructHDR(0, 0)
#HDR = biosig.sopen('/scratch/schloegl/R/data/test/HekaPatchMaster/AP100427b.dat' , 'r', HDR)
#HDR = biosig.sopen('/scratch/schloegl/R/data/test/HekaPatchMaster/AP100429a.dat' , 'r', HDR)
HDR = biosig.sopen('/scratch/schloegl/R/data/test/CFS/example_6channels.dat' , 'r', HDR)
# show header information
biosig.hdr2ascii(HDR,4)
# turn off all channels
# for i in range(HDR.NS):
# HDR.CHANNEL[i].OnOff = 0
# turn on specific channels
# HDR.CHANNEL[0].OnOff = 1
# HDR.CHANNEL[1].OnOff = 1
# HDR.CHANNEL[HDR.NS-1].OnOff = 1
# read data