trial_lengths = np.zeros(n_trials, dtype=np.int32)
print "computing trial lengths..."
for filename in data_files:
channel, trial = get_channel(filename), get_trial(filename)
if channel == 1:
trial_lengths[trial] = os.path.getsize(filename) // 2
print "trial length %i: %d" % (trial, trial_lengths[trial])
trial_starts = np.append(0, np.cumsum(trial_lengths))
n_samples_total = trial_starts[-1]
if not dry_run:
Data_sc = np.memmap(datfilename,
shape=(n_samples_total, n_channels),
dtype=out_dtype,
mode="w+")
for filename in data_files:
if not dry_run: X_c = np.fromfile(filename, dtype=in_dtype)
channel, trial = get_channel(filename), get_trial(filename)
print "inserting data from %s" % filename
if not dry_run:
Data_sc[trial_starts[trial]:trial_starts[trial + 1], channel] = X_c
if not dry_run:
del Data_sc
xmlpath = switch_ext(datfilename, "xml")
print "writing %s" % xmlpath
write_xml(n_channels, 0, 0, 24000., xmlpath)
os.chdir(orig_dir)
plot(t[::10],out1,'r')
plot(t[::10],out2,'g')
legend(('original','noisy signal','1-way','2-way'))
print "Notice phase lag from 1-way (causal) filter"
hold(False)
show()
if __name__ == '__main__':
usage = """
Downsample your data. Default ratio is 16, so N_out = floor(N_in/16).
By default this script does a two-way filter (like filtfilt). To see why, try %prog -t
If output file is not specified, it will have extension eeg (foo.dat -> foo.eeg)
%prog your_dat_file.dat [output filename]
%prog -h displays help"""
parser = OptionParser(usage)
parser.add_option("-1",help="One-way filter.",action="store_false",default=True,dest="two_way")
parser.add_option("-r",help="Downsampling ratio",type=int,action="store",dest="ratio",default=RATIO)
parser.add_option("-t",help="Test 1-way and two-way filtering.",action="store_true",dest="test",default=False)
parser.add_option("--in-type",help="Datatype of input file. One of i2,i4,i8,f4,f8. Default i2 (16-bit integer).",action="store",dest="dt_in",default=DT_IN)
parser.add_option("--out-type",help="Datatype of output file. One of i2,i4,i8,f4,f8. Default i2 (16-bit integer).",action="store",dest="dt_out",default=DT_OUT)
(opts,args) = parser.parse_args()
if opts.test:
test_ds()
exit()
OUTNAME = args[1] if len(args) > 1 else switch_ext(args[0],"eeg")
DT_IN = opts.dt_in
DT_OUT = opts.dt_out
downsample(args[0],OUTNAME,two_way=opts.two_way,ratio=opts.ratio)
def filter_2way(b,a,in_memmap,out_memmap):
print "Forward filtering"
filter_1way(b,a,in_memmap,out_memmap)
print "Backward filtering"
filter_1way(b,a,out_memmap[::-1],out_memmap[::-1])
if __name__ == '__main__':
usage = """
Filter your data between f_hi and f_lo, measured in Hz (the frequencies you give will be compared with sample rate in xml file.)
Give either f_hi, f_lo, or both using --hi and --lo.
By default this script does a two-way filter (like filtfilt).
If output file is not specified, it will have extension fil (foo.dat -> foo.fil)
%prog your_dat_file.dat [output filename] [--hi=f_hi] [--lo=f_lo]
%prog -h displays help"""
parser = OptionParser(usage)
parser.add_option("-1",help="One-way filter.",action="store_false",default=True,dest="two_way")
parser.add_option("--hi",help="Top of passband (Hz)",type=float,action="store",dest="hi")
parser.add_option("--lo",help="Bottom of passband (Hz)",type=float,action="store",dest="lo")
parser.add_option("--in-type",help="Datatype of input file. One of i2,i4,i8,f4,f8. Default i2 (16-bit integer).",action="store",dest="dt_in",default=DT_IN)
parser.add_option("--out-type",help="Datatype of output file. One of i2,i4,i8,f4,f8. Default i2 (16-bit integer).",action="store",dest="dt_out",default=DT_OUT)
(opts,args) = parser.parse_args()
if opts.hi is None and opts.lo is None:
parser.error("must specify high pass freq or low pass freq with --hi or --lo")
OUTNAME = args[1] if len(args) > 1 else switch_ext(abspath(args[0]),"fil")
DT_IN = opts.dt_in
DT_OUT = opts.dt_out
filt(args[0],OUTNAME,two_way=opts.two_way,f_hi=opts.hi,f_lo=opts.lo)
type=int,
action="store",
dest="ratio",
default=RATIO)
parser.add_option("-t",
help="Test 1-way and two-way filtering.",
action="store_true",
dest="test",
default=False)
parser.add_option(
"--in-type",
help=
"Datatype of input file. One of i2,i4,i8,f4,f8. Default i2 (16-bit integer).",
action="store",
dest="dt_in",
default=DT_IN)
parser.add_option(
"--out-type",
help=
"Datatype of output file. One of i2,i4,i8,f4,f8. Default i2 (16-bit integer).",
action="store",
dest="dt_out",
default=DT_OUT)
(opts, args) = parser.parse_args()
if opts.test:
test_ds()
exit()
OUTNAME = args[1] if len(args) > 1 else switch_ext(args[0], "eeg")
DT_IN = opts.dt_in
DT_OUT = opts.dt_out
downsample(args[0], OUTNAME, two_way=opts.two_way, ratio=opts.ratio)
type=float,
action="store",
dest="hi")
parser.add_option("--lo",
help="Bottom of passband (Hz)",
type=float,
action="store",
dest="lo")
parser.add_option(
"--in-type",
help=
"Datatype of input file. One of i2,i4,i8,f4,f8. Default i2 (16-bit integer).",
action="store",
dest="dt_in",
default=DT_IN)
parser.add_option(
"--out-type",
help=
"Datatype of output file. One of i2,i4,i8,f4,f8. Default i2 (16-bit integer).",
action="store",
dest="dt_out",
default=DT_OUT)
(opts, args) = parser.parse_args()
if opts.hi is None and opts.lo is None:
parser.error(
"must specify high pass freq or low pass freq with --hi or --lo")
OUTNAME = args[1] if len(args) > 1 else switch_ext(abspath(args[0]), "fil")
DT_IN = opts.dt_in
DT_OUT = opts.dt_out
filt(args[0], OUTNAME, two_way=opts.two_way, f_hi=opts.hi, f_lo=opts.lo)
print "%i channels, %i trials"%(n_channels, n_trials)
trial_lengths = np.zeros(n_trials,dtype=np.int32)
print "computing trial lengths..."
for filename in data_files:
channel,trial = get_channel(filename),get_trial(filename)
if channel == 1:
trial_lengths[trial] = os.path.getsize(filename)//2
print "trial length %i: %d"%(trial,trial_lengths[trial])
trial_starts = np.append(0,np.cumsum(trial_lengths))
n_samples_total = trial_starts[-1]
if not dry_run: Data_sc = np.memmap(datfilename,shape=(n_samples_total,n_channels),dtype=out_dtype,mode="w+")
for filename in data_files:
if not dry_run: X_c = np.fromfile(filename,dtype=in_dtype)
channel,trial = get_channel(filename),get_trial(filename)
print "inserting data from %s"%filename
if not dry_run: Data_sc[trial_starts[trial]:trial_starts[trial+1],channel] = X_c
if not dry_run:
del Data_sc
xmlpath = switch_ext(datfilename,"xml")
print "writing %s"%xmlpath
write_xml(n_channels,0,0,24000.,xmlpath)
os.chdir(orig_dir)
