def ncs_check_timestamps(ncsfname):
"""
checks if records are equispaced
"""
f = NcsFile(ncsfname)
ts = f.read(0, f.num_recs, mode='timestamp')
ts = ts.astype(int)
err = np.diff(ts, 2).sum()
return err
def ncs_check_timestamps(ncsfname):
"""
checks if records are equispaced
"""
f = NcsFile(ncsfname)
ts = f.read(0, f.num_recs, mode='timestamp')
ts = ts.astype(int)
err = np.diff(ts, 2).sum()
return err
def main(fname):
fid = NcsFile(fname)
nrec = fid.num_recs
# out_size = (nrec + 1) * 512/Q
times = fid.read(0, fid.num_recs, mode='timestamp')
times = times.astype(float) / 1000
arr = expandts(times, 1e3 * fid.timestep, 16)
idx_err = np.diff(arr, 2).nonzero()[0]
print(idx_err.shape[0])
print(np.diff(arr, 2)[idx_err])
outfile = tables.open_file('times_16.h5', 'w')
outfile.create_array('/', 'times', arr)
outfile.close()
def main(fname):
fid = NcsFile(fname)
nrec = fid.num_recs
# out_size = (nrec + 1) * 512/Q
times = fid.read(0, fid.num_recs, mode='timestamp')
times = times.astype(float) / 1000
arr = expandts(times, 1e3 * fid.timestep, 16)
idx_err = np.diff(arr, 2).nonzero()[0]
print(idx_err.shape[0])
print(np.diff(arr, 2)[idx_err])
outfile = tables.open_file('times_16.h5', 'w')
outfile.create_array('/', 'times', arr)
outfile.close()
def downsampling(ncsfname, h5fname, Q=16, include_times=True):
"""
Main routine for downsampling
"""
ncsf = NcsFile(ncsfname)
chname = ncsf.header['AcqEntName']
h5f = initfile(h5fname, ncsf, Q, include_times)
nrec = ncsf.num_recs
ds_order = 8
ts = ncsf.timestep
if DEBUG:
print('{} has {} records'.format(ncsfname, nrec))
blocks = make_blocks(nrec, min(100000, nrec))
if Q > 1:
# design filter for lowpass filtering before downsampling
# use 80% of the Nyquist frequency as cutoff
b_down, a_down = scipy.signal.cheby1(ds_order, .05, 0.8/Q)
for start, stop in blocks:
print('Filtering {} {}-{}'.format(chname, start, stop))
data, ts = ncsf.read(start, stop, mode='both')
if include_times:
h5f.root.time.append(ts)
if Q > 1:
# Warning!
# scipy.signal.decimate uses lfilt,
# so the decimated signal has a phase shift
# for this reason, we use
ds_data = scipy.signal.filtfilt(b_down, a_down, data)[::Q]
else:
ds_data = data
h5f.root.data.rawdata.append(ds_data)
# if you would like to create other traces
# (e.g. filtered versions of the data), do it here
# by calling appropriate functions
h5f.flush()
h5f.close()
def downsampling(ncsfname, h5fname, Q=16, include_times=True):
"""
Main routine for downsampling
"""
ncsf = NcsFile(ncsfname)
chname = ncsf.header['AcqEntName']
h5f = initfile(h5fname, ncsf, Q, include_times)
nrec = ncsf.num_recs
ds_order = 8
ts = ncsf.timestep
if DEBUG:
print('{} has {} records'.format(ncsfname, nrec))
blocks = make_blocks(nrec, min(100000, nrec))
if Q > 1:
# design filter for lowpass filtering before downsampling
# use 80% of the Nyquist frequency as cutoff
b_down, a_down = scipy.signal.cheby1(ds_order, .05, 0.8 / Q)
for start, stop in blocks:
print('Filtering {} {}-{}'.format(chname, start, stop))
data, ts = ncsf.read(start, stop, mode='both')
if include_times:
h5f.root.time.append(ts)
if Q > 1:
# Warning!
# scipy.signal.decimate uses lfilt,
# so the decimated signal has a phase shift
# for this reason, we use
ds_data = scipy.signal.filtfilt(b_down, a_down, data)[::Q]
else:
ds_data = data
h5f.root.data.rawdata.append(ds_data)
# if you would like to create other traces
# (e.g. filtered versions of the data), do it here
# by calling appropriate functions
h5f.flush()
h5f.close()
def plot_spectrum(fname):
fid = NcsFile(fname)
rawdata = fid.read(0, 1000)
data = rawdata * (1e6 * fid.header['ADBitVolts'])
fs = 1/fid.timestep
my_filter = DefaultFilter(fid.timestep)
filt_data = my_filter.filter_extract(data)
[f, p] = sig.welch(data, fs, nperseg=32768)
[f_filt, p_filt] = sig.welch(filt_data, fs, nperseg=32768)
fig = mpl.figure()
plot = fig.add_subplot(1, 1, 1)
plot.plot(f, p, label='Unfiltered')
plot.plot(f_filt, p_filt, label='Filtered')
plot.set_yscale('log')
plot.legend()
plot.set_ylabel(r'$\mu\mathrm{V}^2/\mathrm{Hz}$')
plot.set_xlabel(r'$\mathrm{Hz}$')
def to_original():
ncsfiles = glob('*.ncs')
for nf in ncsfiles:
n = NcsFile(nf)
oldname = n.header['AcqEntName'] + '.ncs'
if os.path.exists(oldname):
print('Not renaming {} to {}, file exists'.format(nf, oldname))
else:
print('renaming {} to {}'.format(nf, oldname))
os.rename(nf, oldname)
def main(fnames):
"""
for each file in fnames, get entity name
write everything to a csv file
"""
fnames.sort()
out_data = list()
for name in fnames:
fid = NcsFile(name)
label = os.path.splitext(name)[0]
entity = fid.header['AcqEntName']
out_data.append((label, entity))
with open(FNAME_OUT, 'w') as fid:
csv_writer = csv.writer(fid, delimiter=';')
csv_writer.writerows(out_data)
# -*- coding: utf-8 -*-
# JN 2014-10-21
# script creates a clinRecConv.py from ncs files
import os
import numpy as np
from combinato import NcsFile
from matplotlib.dates import date2num
if __name__ == "__main__":
if os.path.exists('clinRecConv.py'):
print('File exists, doing nothing')
else:
fid = NcsFile('CSC1.ncs')
d = fid.header['opened']
n = date2num(d)
ts = fid.read(0, 1, 'timestep')
np.save('clinRecConv', np.array((ts, d)))
data = nf.read(start, stop, mode='data')
data = data.reshape(-1, fs)
block[i::ns, :] = data
edffile.write(block)
if __name__ == "__main__":
""" missing:
outfilename
"""
from argparse import ArgumentParser
parser = ArgumentParser()
parser.add_argument('--out')
parser.add_argument('--patid')
parser.add_argument('--comment', default='')
args = parser.parse_args()
chs = get_channel_list(os.getcwd())
ncsfiles = []
for ch in chs:
ncsfiles.append(NcsFile(ch))
h1, h2 = create_edf_header(ncsfiles, args.patid, args.comment)
f = open(args.out, 'w')
f.write(h1)
f.write(h2)
write_data(ncsfiles, f)
f.close()
with open(fname, 'r') as fid:
lines = [line.strip() for line in fid.readlines()]
for line in lines:
if line[0] == '#':
continue
fields = line.split()
if fields[0] == target:
dtime, micro = fields[2].split('.')
dstr = fields[1] + ' ' + dtime
dfmt = '%Y-%m-%d %H:%M:%S'
start_date = datetime.datetime.strptime(dstr, dfmt)
start_date += datetime.timedelta(microseconds=int(micro))
break
ts_start_nlx = float(fields[3]) / 1000
return ts_start_nlx, start_date
if __name__ == "__main__":
"""
a small test case
"""
from combinato import NcsFile
import sys
Q = 16
ncsfname = sys.argv[1]
fid = NcsFile(ncsfname)
h5f = initfile('out.h5', fid, Q)
print(h5f)
