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 read_channel(self, channel):
"""
to avoid SEGMENTATION FAULT all channels have to be read one by one
we set the OnOff option (this option turns reading of a channel on or off) of all channels 0
if we want to read the channel we set its OnOff option to 1 this means reading is on and we read the data
after we read the channel's data we must set it again to 0, or else we get segmentation fault
"""
#print "Debug: self.__channels=", self.__channels, " channel=", channel
self.__HDR.CHANNEL[self.__channels.index(channel)].OnOff = 1
channeldata = np.array(biosig.sread(0, self.__HDR.NRec, self.__HDR),
dtype=np.float32)[0]
self.__HDR.CHANNEL[self.__channels.index(channel)].OnOff = 0
return channeldata
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 _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();
#for k in range(HDR.EVENT.N): print k,TYP[k],POS[k],POS[k]/HDR.EVENT.SampleRate #,HDR.EVENT.CodeDesc[TYP[k]]
for k in range(HDR.NS):
# convert C to Python string: get rid of everything after \x00, then remove leading and trailing whitespace
str = HDR.CHANNEL[k].Label
HDR.CHANNEL[k].Label = str[0:str.find(chr(0))].strip()
str = HDR.CHANNEL[k].Transducer
HDR.CHANNEL[k].Transducer = str[0:str.find(chr(0))].strip()
print k, HDR.CHANNEL[k].OnOff == 0, '<', HDR.CHANNEL[
k].Label, '>,<', HDR.CHANNEL[k].Transducer, '>'
# 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)
print data.shape
#
# close file
biosig.sclose(HDR)
#
# release allocated memory
biosig.destructHDR(HDR)
#
#return data