def fftgram(timeseries, stride, pad=False):
"""
calculates fourier-gram with automatic
50% overlapping hann windowing.
Parameters
----------
timeseries : gwpy TimeSeries
time series to take fftgram of
stride : `int`
number of seconds in single PSD
Returns
-------
fftgram : gwpy spectrogram
a fourier-gram
"""
fftlength = stride
dt = stride
df = 1. / fftlength
# number of values in a step
stride *= timeseries.sample_rate.value
# number of steps
nsteps = 2 * int(timeseries.size // stride) - 1
# only get positive frequencies
if pad:
nfreqs = int(fftlength * timeseries.sample_rate.value)
df = df / 2
f0 = df
else:
nfreqs = int(fftlength * timeseries.sample_rate.value) / 2
dtype = np.complex
# initialize the spectrogram
out = Spectrogram(np.zeros((nsteps, nfreqs), dtype=dtype),
name=timeseries.name, epoch=timeseries.epoch,
f0=df, df=df, dt=dt, copy=True,
unit=1 / u.Hz**0.5, dtype=dtype)
# stride through TimeSeries, recording FFTs as columns of Spectrogram
for step in range(nsteps):
# indexes for this step
idx = (stride / 2) * step
idx_end = idx + stride
stepseries = timeseries[idx:idx_end]
# zeropad, window, fft, shift zero to center, normalize
# window
stepseries = np.multiply(stepseries,
np.hanning(stepseries.value.size))
# take fft
if pad:
stepseries = TimeSeries(np.hstack((stepseries, np.zeros(stepseries.size))),
name=stepseries.name, x0=stepseries.x0,
dx=timeseries.dx)
tempfft = stepseries.fft(stepseries.size)
else:
tempfft = stepseries.fft(stepseries.size)
tempfft.override_unit(out.unit)
out[step] = tempfft[1:]
return out
def dump_calibrated_data(fname):
data = numpy.load(fname)
# Figure out the times covered by the file from the filename
# I should start using HDF5 so I can store metadata
temp = fname.split('.')[0]
temp = temp.split('-')
ifo = temp[0]
st, dur = int(temp[-2]), int(temp[-1])
et = st + dur
maxidx = len(data)
width = 45
weights = 1. - ((numpy.arange(-width, width) / float(width))**2)
# The VCO frequencies are integers so we could dither them
# to avoid quantization error if we wanted to be fancy
# but it seems to make no differece
if False:
from numpy.random import triangular
data[:, 1] += triangular(-1., 0., 1., size=len(data))
# Just fit the whole thing at once, to get a single coefficient
a, b = numpy.polyfit(data[:, 0], data[:, 1], 1)
print "%.1f %u" % (a, b)
# Slide through the data fitting PSL to IMC for data around each sample
coeffs = []
for idx in xrange(maxidx):
idx1 = max(0, idx - width)
idx2 = min(idx + width, maxidx)
coeffs.append(numpy.polyfit(data[idx1:idx2, 0], data[idx1:idx2, 1], 1,
w=weights[idx1 - idx + width:idx2 - idx + width]))
coeffs = numpy.array(coeffs)
times = numpy.arange(len(coeffs)) + 0.5
connection = datafind.GWDataFindHTTPConnection()
cache = connection.find_frame_urls(
ifo[0], '%s_R' % ifo, st, et, urltype='file')
imc = TimeSeries.read(cache, "%s:IMC-F_OUT_DQ" % ifo, st, et)
imc = imc[::16384 / 256]
print imc
samp_times = numpy.arange(len(imc)) / 256.
coeffs0 = numpy.interp(samp_times, times, coeffs[:, 0])
coeffs1 = numpy.interp(samp_times, times, coeffs[:, 1]) - 7.6e7
vco_interp = coeffs0 * imc.data + coeffs1
chan = "%s:IMC-VCO_PREDICTION" % (ifo,)
vco_data = TimeSeries(vco_interp, epoch=st,
sample_rate=imc.sample_rate.value,
name=chan, channel=chan)
vco_data.write("%s-vcoprediction-%u-%u.hdf" % (ifo, st, dur), format='hdf')
def noise_from_psd(length, sample_rate, psd, seed=0, name=None, unit=u.m):
""" Create noise with a given psd.
Return noise with a given psd. Note that if unique noise is desired
a unique seed should be provided.
Parameters
----------
length : int
The length of noise to generate in seconds.
sample_rate : float
the sample rate of the data
stride : int
Length of noise segments in seconds
psd : FrequencySeries
The noise weighting to color the noise.
seed : {0, int}
The seed to generate the noise.
Returns
--------
noise : TimeSeries
A TimeSeries containing gaussian noise colored by the given psd.
"""
if name is None:
name='noise'
length *=sample_rate
noise_ts = TimeSeries(np.zeros(length),
sample_rate=sample_rate, name=name, unit=unit)
randomness = lal.gsl_rng("ranlux", seed)
N = int (sample_rate / psd.df.value)
n = N/2+1
stride = N/2
if n > len(psd):
raise ValueError("PSD not compatible with requested delta_t")
psd = (psd[0:n]).to_lal()
psd.data.data[n-1] = 0
segment = TimeSeries(np.zeros(N), sample_rate=sample_rate).to_lal()
length_generated = 0
SimNoise(segment, 0, psd, randomness)
while (length_generated < length):
if (length_generated + stride) < length:
noise_ts.data[length_generated:length_generated+stride] = segment.data.data[0:stride]
else:
noise_ts.data[length_generated:length] = segment.data.data[0:length-length_generated]
length_generated += stride
SimNoise(segment,stride, psd, randomness)
return noise_ts
def refresh(self):
lines = [l for ax in self._fig.axes for l in ax.lines]
axes = cycle(self._fig.get_axes(self.AXES_CLASS.name))
params = self.params['draw']
for i, channel in enumerate(self.channels):
try:
line = lines[i]
except IndexError:
# haven't plotted this channel before
ax = next(axes)
label = (hasattr(channel, 'label') and channel.label or
channel.texname)
pparams = {}
for key in params:
try:
if params[key][i]:
pparams[key] = params[key][i]
except IndexError:
pass
ts = self.data[channel][0].copy()
for t2 in self.data[channel][1:]:
ts.append(t2, pad=self.buffer.pad, gap=self.buffer.gap)
l = ax.plot(ts, label=label, **pparams)
ax.legend()
else:
# TODO: remove .copy() as soon as copy=True is fixed in gwpy
ts = TimeSeries(line.get_ydata(), times=line.get_xdata(),
copy=True).copy()
for t2 in self.buffer.get((ts.span[1], self.epoch), channel,
fetch=False):
ts.append(t2, pad=self.buffer.pad, gap=self.buffer.gap)
line.set_xdata(ts.times.value)
line.set_ydata(ts.value)
# format figure
if 'ylim' not in self.params['refresh']:
for ax in self._fig.get_axes(self.AXES_CLASS.name):
ax.relim()
ax.autoscale_view(scalex=False)
self.logger.info('Figure data updated')
for ax in self._fig.get_axes(self.AXES_CLASS.name):
if float(self.epoch) > (self.gpsstart + self.duration):
ax.set_xlim(float(self.epoch - self.duration),
float(self.epoch))
else:
ax.set_xlim(float(self.gpsstart),
float(self.gpsstart) + self.duration)
ax.set_epoch(self.epoch)
self.set_params('refresh')
self._fig.refresh()
self.logger.debug('Figure refreshed')
def _next(self):
uchannels = self._unique_channel_names(self.channels)
new = TimeSeriesDict()
span = 0
epoch = 0
self.logger.debug('Waiting for next NDS2 packet...')
while span < self.interval:
try:
buffers = next(self.iterator)
except RuntimeError as e:
self.logger.error('RuntimeError caught: %s' % str(e))
self.restart()
break
for buff, c in zip(buffers, uchannels):
ts = TimeSeries.from_nds2_buffer(buff)
try:
new.append({c: ts}, gap=self.gap, pad=self.pad)
except ValueError as e:
if 'discontiguous' in str(e):
e.args = ('NDS connection dropped data between %d and '
'%d' % (epoch, ts.span[0]),)
raise
span = abs(new[c].span)
epoch = new[c].span[-1]
self.logger.debug('%ds data for %s received'
% (abs(ts.span), str(c)))
out = type(new)()
for chan in self.channels:
out[chan] = new[self._channel_basename(chan)].copy()
return out
def get_data(channel,start_time,length):
print 'Starting data transfer for channel: ' + str(channel)
connection = datafind.GWDataFindHTTPConnection()
cache = connection.find_frame_urls(ifo[0],ifo+'_R',start_time,start_time+length,urltype='file')
data = TimeSeries.read(cache,channel)
print "Got data for channel: " + str(channel)
return data
def _next(self):
uchannels = self._unique_channel_names(self.channels)
new = TimeSeriesDict()
span = 0
epoch = 0
att = 0
self.logger.debug('Waiting for next NDS2 packet...')
while span < self.interval:
try:
buffers = next(self.iterator)
except RuntimeError as e:
self.logger.error('RuntimeError caught: %s' % str(e))
if att < self.attempts:
att += 1
wait_time = att / 3 + 1
self.logger.warning(
'Attempting to reconnect to the nds server... %d/%d'
% (att, self.attempts))
self.logger.warning('Next attempt in minimum %d seconds' %
wait_time)
self.restart()
sleep(wait_time - tconvert('now') % wait_time)
continue
else:
self.logger.critical(
'Maximum number of attempts reached, exiting')
break
att = 0
for buff, c in zip(buffers, uchannels):
ts = TimeSeries.from_nds2_buffer(buff)
try:
new.append({c: ts}, gap=self.gap, pad=self.pad)
except ValueError as e:
if 'discontiguous' in str(e):
e.message = (
'NDS connection dropped data between %d and '
'%d, restarting building the buffer from %d ') \
% (epoch, ts.span[0], ts.span[0])
self.logger.warning(str(e))
new = TimeSeriesDict()
new[c] = ts.copy()
elif ('starts before' in str(e)) or \
('overlapping' in str(e)):
e.message = (
'Overlap between old data and new data in the '
'nds buffer, only the new data will be kept.')
self.logger.warning(str(e))
new = TimeSeriesDict()
new[c] = ts.copy()
else:
raise
span = abs(new[c].span)
epoch = new[c].span[-1]
self.logger.debug('%ds data for %s received'
% (abs(ts.span), str(c)))
out = type(new)()
for chan in self.channels:
out[chan] = new[self._channel_basename(chan)].copy()
return out
def psd():
h5path = os.path.join(os.path.dirname(__file__), 'data',
'HLV-HW100916-968654552-1.hdf')
try:
data = TimeSeries.read(h5path, 'L1:LDAS-STRAIN', format='hdf5')
except ImportError as e:
pytest.skip(str(e))
return data.psd(.4, overlap=.2, window=('kaiser', 24))
def test_add_timeseries(self):
a = TimeSeries([1, 2, 3, 4, 5], name='test name', epoch=0,
sample_rate=1)
# test simple add using 'name'
data.add_timeseries(a)
self.assertIn('test name', globalv.DATA)
self.assertEqual(globalv.DATA['test name'], [a])
# test add using key kwarg
data.add_timeseries(a, key='test key')
self.assertIn('test key', globalv.DATA)
self.assertEqual(globalv.DATA['test key'], [a])
# test add to existing key with coalesce
b = TimeSeries([6, 7, 8, 9, 10], name='test name 2', epoch=5,
sample_rate=1)
data.add_timeseries(b, key='test key', coalesce=True)
self.assertEqual(globalv.DATA['test key'],
[a.append(b, inplace=False)])
def calibrate_imc_pslvco(ifo, start_time, dur, cache=None):
st, et = start_time, start_time + dur
if cache:
pslvco = TimeSeries.read(cache, chan1_pat % ifo, start=st, end=et)
imc = TimeSeries.read(cache, chan2_pat % ifo, start=st, end=et)
else:
imc = TimeSeries.fetch(chan2_pat % ifo, st, et)
pslvco = TimeSeries.fetch(chan1_pat % ifo, st, et)
arr_psl = pslvco[8::16]
arr_imc = imc
tmp1 = (arr_imc[8192::16384])[:-1]
tmp2 = arr_psl[1:]
a, b = numpy.polyfit(tmp1, tmp2, 1)
return a, b
def test_save_loudest_tile_features():
# prepare input data
channel = GW.channels[0]
noise = TimeSeries(
numpy.random.normal(loc=1, scale=.5, size=16384 * 68),
sample_rate=16384, epoch=-34).zpk([], [0], 1)
glitch = TimeSeries(
signal.gausspulse(numpy.arange(-1, 1, 1./16384), bw=100),
sample_rate=16384, epoch=-1) * 1e-4
in_ = noise.inject(glitch)
_, _, _, qgram, _, _, _ = core.scan(
gps=0, channel=channel, xoft=in_, resample=4096, fftlength=8)
# test loudest tiles
channel.save_loudest_tile_features(qgram, correlate=glitch)
assert channel.Q == numpy.around(qgram.plane.q, 1)
assert channel.energy == numpy.around(qgram.peak['energy'], 1)
assert channel.snr == numpy.around(qgram.peak['snr'], 1)
assert channel.t == numpy.around(qgram.peak['time'], 3)
assert channel.f == numpy.around(qgram.peak['frequency'], 1)
assert channel.corr == numpy.around(glitch.max().value, 1)
assert channel.delay == 0.0
assert channel.stdev == glitch.std().value
def _read_data(channel, st, et, frames=False):
"""
get data, either from frames or from nds2
"""
ifo = channel.split(':')[0]
if frames:
# read from frames
connection = datafind.GWDataFindHTTPConnection()
print ifo[0]
if channel.split(':')[1] == 'GDS-CALIB_STRAIN':
cache = connection.find_frame_urls(ifo[0],ifo+'_HOFT_C00', st, et, urltype='file')
else:
cache = connection.find_frame_urls(ifo[0], ifo + '_C', st, et,urltype='file')
try:
data = TimeSeries.read(cache, channel, st, et)
except IndexError:
cache = connection.find_frame_urls(ifo[0], ifo+'_R', st, et, urltype='file')
data = TimeSeries.read(cache, channel, st, et)
else:
data = TimeSeries.fetch(channel, st, et)
return data
def generate_fast_vco(ifo, segment, frames=False, fit=True):
"""
Parameters:
-----------
ifo : start
interferometer, e.g. 'L1'
segment : array like
time segment. first entry start second entry end
frames : bool
read from frames or nds2
fit : bool
fit from imc-f (default)
or spline interpolation
Returns:
--------
vco_data : saves file 'L1:IMC-VCO_PREDICTION-st-dur.hdf'
"""
st = segment[0]
et = segment[1]
chan1_pat = '%s:SYS-TIMING_C_FO_A_PORT_11_SLAVE_CFC_FREQUENCY_5'
chan2_pat = '%s:IMC-F_OUT_DQ'
if frames:
connection = datafind.GWDataFindHTTPConnection()
cache = connection.find_frame_urls(
ifo[0], '%s_R' % ifo, st, et + 1, urltype='file')
if fit:
imc = TimeSeries.read(cache, chan2_pat % ifo, st, et)
else:
imc = TimeSeries.read(cache, chan2_pat % ifo, st, st + 1)
pslvco = TimeSeries.read(cache, chan1_pat % ifo, st, et + 1)
else:
if fit:
imc = TimeSeries.fetch(chan2_pat % ifo, st, et)
else:
print 'HI BEFORE LOADING IMC'
imc = TimeSeries.fetch(chan2_pat % ifo, st, st + 1)
print 'HI BEFORE LOADING PSL'
pslvco = TimeSeries.fetch(chan1_pat % ifo, st, et + 1)
print 'HI AFTER LOADING'
pslvco = pslvco[16 + 8::16]
if fit:
imc_srate = int(imc.sample_rate.value)
imc2 = imc[imc_srate / 2::imc_srate]
data = np.array((imc2.value, pslvco.value)).T
vco_interp = fit_with_imc(data, imc)
else:
vco_interp = interp_spline(pslvco)
chan = "%s:IMC-VCO_PREDICTION" % (ifo,)
vco_data = TimeSeries(vco_interp, epoch=st,
sample_rate=256,
name=chan, channel=chan)
return vco_data
def _get_vco_data(vco_file, times):
print('Finding mean values of %s' % channel)
s = times.size
amp = numpy.zeros(s)
vco = TimeSeries.from_hdf5(vco_file)
for i, t in enumerate(times):
t = t.seconds + t.nanoseconds / 1e9
idx1 = int(
(t - vco.times.value[0] - 0.01) * vco.sample_rate.value)
idx2 = int(
(t - vco.times.value[0] + 0.01) * vco.sample_rate.value)
temp = vco[idx1:idx2]
amp[i] = (temp.mean().value - 3e6) / 1.e3
print(' Processed trigger %d/%d' % (i + 1, s), end='\r')
print(' Processed trigger %d/%d' % (s, s))
return amp
def test_fetch(self):
try:
nds_buffer = mockutils.mock_nds2_buffer(
'X1:TEST', self.data, 1000000000, self.data.shape[0], 'm')
except ImportError as e:
self.skipTest(str(e))
nds_connection = mockutils.mock_nds2_connection([nds_buffer])
with mock.patch('nds2.connection') as mock_connection, \
mock.patch('nds2.buffer', nds_buffer):
mock_connection.return_value = nds_connection
# use verbose=True to hit more lines
ts = TimeSeries.fetch('X1:TEST', 1000000000, 1000000001,
verbose=True)
nptest.assert_array_equal(ts.value, self.data)
self.assertEqual(ts.sample_rate, self.data.shape[0] * units.Hz)
self.assertTupleEqual(ts.span, (1000000000, 1000000001))
self.assertEqual(ts.unit, units.meter)
x1500_ns = read_gif('X1500_TR240posNS', start, end, write=True)
x1500_ud = read_gif('X1500_TR240posUD', start, end, write=True)
strain = read_gif('CALC_STRAIN', start, end, write=True)
print('read')
x1500_ew.write(_gwf_fmt.format(sensor='x1500_ew'),
format='gwf.lalframe')
x1500_ns.write(_gwf_fmt.format(sensor='x1500_ns'),
format='gwf.lalframe')
x1500_ud.write(_gwf_fmt.format(sensor='x1500_ud'),
format='gwf.lalframe')
strain.write(gwf_fmt.format(sensor='strain'), format='gwf.lalframe')
print('wrote')
#exit()
else:
x1500_ew = TimeSeries.read(_gwf_fmt.format(sensor='x1500_ew'),
'X1500_TR240posEW',
format='gwf.lalframe')
x1500_ns = TimeSeries.read(_gwf_fmt.format(sensor='x1500_ns'),
'X1500_TR240posNS',
format='gwf.lalframe')
x1500_ud = TimeSeries.read(_gwf_fmt.format(sensor='x1500_ud'),
'X1500_TR240posUD',
format='gwf.lalframe')
strain = TimeSeries.read(gwf_fmt.format(sensor='strain'),
'CALC_STRAIN',
format='gwf.lalframe')
if True:
# rotate
x1500 = SeismoMeter(x1500_ew, x1500_ns, x1500_ud)
x1500.rotate(-30)
from gwpy.timeseries import TimeSeries
ifo = 'H1'
st_lst = [1160194829, 1160194829 + 16 * 60]
dur = 300
chan_lst = []
names = []
for pd in ['AS_A', 'AS_B', 'REFL_A', 'REFL_B']:
for quad in ['I', 'Q']:
for dof in ['PIT', 'YAW']:
chan_lst.append('ASC-%s_RF45_%s_%s_OUT_DQ' % (pd, quad, dof))
names.append(pd + '45' + quad + dof[0])
chan_lst.append('LSC-MOD_RF45_AM_CTRL_OUT_DQ')
names.append('RF45AM')
chan_lst.extend([
'LSC-DARM_IN1_DQ', 'LSC-POP_A_RF45_I_ERR_DQ', 'LSC-POP_A_RF45_Q_ERR_DQ',
'LSC-POP_A_RF9_I_ERR_DQ', 'LSC-POP_A_RF9_Q_ERR_DQ'
])
names.extend(['DARM', 'POP45I', 'POP45Q', 'POP9I', 'POP9Q'])
for st in st_lst:
for chan, name in zip(chan_lst, names):
data = TimeSeries.fetch('%s:%s' % (ifo, chan), st, st + dur)
data.write('%s-%s-%u-%u.hdf' % (ifo, name, st, dur))
start_time = end_time - duration
roll_off = 0.4 # smoothness in a tukey window, default is 0.4s
# This determines the time window used to fetch open data
psd_duration = 32 * duration
psd_start_time = start_time - psd_duration
psd_end_time = start_time
filter_freq = None # low pass filter frequency to cut signal content above
# Nyquist frequency. The condition is 2 * filter_freq >= sampling_frequency
ifo_list = bilby.gw.detector.InterferometerList([])
for det in interferometer_names:
logger.info("Downloading analysis data for ifo {}".format(det))
ifo = bilby.gw.detector.get_empty_interferometer(det)
data = TimeSeries.fetch_open_data(det, start_time, end_time)
ifo.set_strain_data_from_gwpy_timeseries(data)
# Additional arguments you might need to pass to TimeSeries.fetch_open_data:
# - sample_rate = 4096, most data are stored by LOSC at this frequency
# there may be event-related data releases with a 16384Hz rate.
# - tag = 'CLN' for clean data; C00/C01 for raw data (different releases)
# note that for O2 events a "tag" is required to download the data.
# - channel = {'H1': 'H1:DCS-CALIB_STRAIN_C02',
# 'L1': 'L1:DCS-CALIB_STRAIN_C02',
# 'V1': 'V1:FAKE_h_16384Hz_4R'}}
# for some events can specify channels: source data stream for LOSC data.
logger.info("Downloading psd data for ifo {}".format(det))
psd_data = TimeSeries.fetch_open_data(det, psd_start_time, psd_end_time)
psd_alpha = 2 * roll_off / duration # shape parameter of tukey window
psd = psd_data.psd(fftlength=duration,
overlap=0,
import numpy
from numpy import testing as nptest
from gwpy.testing.compat import mock
from gwpy.timeseries import (TimeSeries, TimeSeriesDict)
from gwpy.segments import (Segment, DataQualityFlag)
from .. import datafind
__author__ = 'Alex Urban <*****@*****.**>'
# global test objects
HOFT = TimeSeries(numpy.random.normal(loc=1, scale=.5, size=16384 * 66),
sample_rate=16384,
epoch=0,
name='X1:TEST-STRAIN')
FLAG = DataQualityFlag(known=[(-33, 33)],
active=[(-33, 33)],
name='X1:TEST-FLAG:1')
# -- make sure data can be read -----------------------------------------------
@mock.patch('gwpy.segments.DataQualityFlag.query', return_value=FLAG)
def test_check_flag(segserver):
# attempt to query segments database for an analysis flag
flag = 'X1:TEST-FLAG:1'
assert datafind.check_flag(flag, gpstime=0, duration=64, pad=1) is True
assert datafind.check_flag(flag, gpstime=800, duration=64, pad=1) is False
def read_data_archive(sourcefile):
"""Read archived data from an HDF5 archive source.
Parameters
----------
sourcefile : `str`
path to source HDF5 file
"""
from h5py import File
with File(sourcefile, 'r') as h5file:
# read all time-series data
try:
group = h5file['timeseries']
except KeyError:
group = dict()
for dataset in group.itervalues():
ts = TimeSeries.read(dataset, format='hdf')
if (re.search('\.(rms|min|mean|max|n)\Z', ts.channel.name)
and ts.sample_rate.value == 1.0):
ts.channel.type = 's-trend'
elif re.search('\.(rms|min|mean|max|n)\Z', ts.channel.name):
ts.channel.type = 'm-trend'
ts.channel = get_channel(ts.channel)
try:
add_timeseries(ts, key=ts.channel.ndsname)
except ValueError:
if mode.get_mode() == mode.SUMMARY_MODE_DAY:
raise
warnings.warn('Caught ValueError in combining daily archives')
# get end time
globalv.DATA[ts.channel.ndsname].pop(-1)
t = globalv.DATA[ts.channel.ndsname][-1].span[-1]
add_timeseries(ts.crop(start=t), key=ts.channel.ndsname)
# read all state-vector data
try:
group = h5file['statevector']
except KeyError:
group = dict()
for dataset in group.itervalues():
sv = StateVector.read(dataset, format='hdf')
sv.channel = get_channel(sv.channel)
add_timeseries(sv, key=sv.channel.ndsname)
# read all spectrogram data
try:
group = h5file['spectrogram']
except KeyError:
group = dict()
for key, dataset in group.iteritems():
key = key.rsplit(',', 1)[0]
spec = Spectrogram.read(dataset, format='hdf')
spec.channel = get_channel(spec.channel)
add_spectrogram(spec, key=key)
try:
group = h5file['segments']
except KeyError:
group = dict()
for name, dataset in group.iteritems():
dqflag = DataQualityFlag.read(dataset, format='hdf')
globalv.SEGMENTS += {name: dqflag}
# Demodulation is useful when trying to examine steady sinusoidal
# signals we know to be contained within data. For instance,
# we can download some data from LOSC to look at trends of the
# amplitude and phase of LIGO Livingston's calibration line at 331.3 Hz:
from gwpy.timeseries import TimeSeries
data = TimeSeries.fetch_open_data('L1', 1131350417, 1131357617)
# We can demodulate the `TimeSeries` at 331.3 Hz with a stride of one
# minute:
amp, phase = data.demodulate(331.3, stride=60)
# We can then plot these trends to visualize fluctuations in the
# amplitude of the calibration line:
from gwpy.plot import Plot
plot = Plot(amp)
ax = plot.gca()
ax.set_ylabel('Strain Amplitude at 331.3 Hz')
plot.show()
def load_gw(t0, detector):
strain = TimeSeries.fetch_open_data(detector, t0-14, t0+14, cache=False)
return strain
from gwpy.timeseries import TimeSeries
data = TimeSeries.fetch_open_data('L1', start, end)
from gwpy.timeseries import TimeSeries
h1 = TimeSeries.fetch_open_data('H1', 1187006834, 1187010930)
l1 = TimeSeries.fetch_open_data('L1', 1187006834, 1187010930)
def main():
# Parse commandline arguments
opts = parse_commandline()
###########################################################################
# Parse Ini File #
###########################################################################
# ---- Create configuration-file-parser object and read parameters file.
cp = ConfigParser.ConfigParser()
cp.read(opts.inifile)
# ---- Read needed variables from [parameters] and [channels] sections.
alwaysPlotFlag = cp.getint('parameters', 'alwaysPlotFlag')
sampleFrequency = cp.getint('parameters', 'sampleFrequency')
blockTime = cp.getint('parameters', 'blockTime')
searchFrequencyRange = json.loads(
cp.get('parameters', 'searchFrequencyRange'))
searchQRange = json.loads(cp.get('parameters', 'searchQRange'))
searchMaximumEnergyLoss = cp.getfloat('parameters',
'searchMaximumEnergyLoss')
searchWindowDuration = cp.getfloat('parameters', 'searchWindowDuration')
whiteNoiseFalseRate = cp.getfloat('parameters', 'whiteNoiseFalseRate')
plotTimeRanges = json.loads(cp.get('parameters', 'plotTimeRanges'))
plotFrequencyRange = json.loads(cp.get('parameters', 'plotFrequencyRange'))
plotNormalizedERange = json.loads(
cp.get('parameters', 'plotNormalizedERange'))
frameCacheFile = cp.get('channels', 'frameCacheFile')
frameTypes = cp.get('channels', 'frameType').split(',')
channelNames = cp.get('channels', 'channelName').split(',')
detectorName = channelNames[0].split(':')[0]
det = detectorName.split('1')[0]
###########################################################################
# create output directory #
###########################################################################
# if outputDirectory not specified, make one based on center time
if opts.outDir is None:
outDir = './scans'
else:
outDir = opts.outDir + '/'
outDir += '/'
# report status
if not os.path.isdir(outDir):
if opts.verbose:
print('creating event directory')
os.makedirs(outDir)
if opts.verbose:
print('outputDirectory: {0}'.format(outDir))
########################################################################
# Determine if this is a normal omega scan or a Gravityspy #
# omega scan with unique ID. If Gravity spy then additional #
# files and what not must be generated #
########################################################################
IDstring = "{0:.2f}".format(opts.eventTime)
###########################################################################
# Process Channel Data #
###########################################################################
# find closest sample time to event time
centerTime = np.floor(opts.eventTime) + np.round(
(opts.eventTime - np.floor(opts.eventTime)) *
sampleFrequency) / sampleFrequency
# determine segment start and stop times
startTime = round(centerTime - blockTime / 2)
stopTime = startTime + blockTime
# This is for ordering the output page by SNR
loudestEnergyAll = []
channelNameAll = []
peakFreqAll = []
mostSignQAll = []
for channelName in channelNames:
if 'STRAIN' in channelName:
frameType = frameTypes[0]
else:
frameType = frameTypes[1]
# Read in the data
if opts.NSDF:
data = TimeSeries.fetch(channelName, startTime, stopTime)
else:
connection = datafind.GWDataFindHTTPConnection()
cache = connection.find_frame_urls(det,
frameType,
startTime,
stopTime,
urltype='file')
data = TimeSeries.read(cache,
channelName,
format='gwf',
start=startTime,
end=stopTime)
# resample data
if data.sample_rate.decompose().value != sampleFrequency:
data = data.resample(sampleFrequency)
# Cropping the results before interpolation to save on time and memory
# perform the q-transform
try:
specsgrams = []
for iTimeWindow in plotTimeRanges:
durForPlot = iTimeWindow / 2
try:
outseg = Segment(centerTime - durForPlot,
centerTime + durForPlot)
qScan = data.q_transform(qrange=(4, 64),
frange=(10, 2048),
gps=centerTime,
search=0.5,
tres=0.002,
fres=0.5,
outseg=outseg,
whiten=True)
qValue = qScan.q
qScan = qScan.crop(centerTime - iTimeWindow / 2,
centerTime + iTimeWindow / 2)
except:
outseg = Segment(centerTime - 2 * durForPlot,
centerTime + 2 * durForPlot)
qScan = data.q_transform(qrange=(4, 64),
frange=(10, 2048),
gps=centerTime,
search=0.5,
tres=0.002,
fres=0.5,
outseg=outseg,
whiten=True)
qValue = qScan.q
qScan = qScan.crop(centerTime - iTimeWindow / 2,
centerTime + iTimeWindow / 2)
specsgrams.append(qScan)
loudestEnergyAll.append(qScan.max().value)
peakFreqAll.append(qScan.yindex[np.where(
qScan.value == qScan.max().value)[1]].value[0])
mostSignQAll.append(qValue)
channelNameAll.append(channelName)
except:
print('bad channel {0}: skipping qScan'.format(channelName))
continue
if opts.make_webpage:
# Set some plotting params
myfontsize = 15
mylabelfontsize = 20
myColor = 'k'
if detectorName == 'H1':
title = "Hanford"
elif detectorName == 'L1':
title = "Livingston"
else:
title = "VIRGO"
if 1161907217 < startTime < 1164499217:
title = title + ' - ER10'
elif startTime > 1164499217:
title = title + ' - O2a'
elif 1126400000 < startTime < 1137250000:
title = title + ' - O1'
else:
raise ValueError("Time outside science or engineering run\
or more likely code not updated to reflect\
new science run")
# Create one image containing all spectogram grams
superFig = Plot(figsize=(27, 6))
superFig.add_subplot(141, projection='timeseries')
superFig.add_subplot(142, projection='timeseries')
superFig.add_subplot(143, projection='timeseries')
superFig.add_subplot(144, projection='timeseries')
iN = 0
for iAx, spec in zip(superFig.axes, specsgrams):
iAx.plot(spec)
iAx.set_yscale('log', basey=2)
iAx.set_xscale('linear')
xticks = np.linspace(spec.xindex.min().value,
spec.xindex.max().value, 5)
xticklabels = []
dur = float(plotTimeRanges[iN])
[
xticklabels.append(str(i))
for i in np.linspace(-dur / 2, dur / 2, 5)
]
iAx.set_xticks(xticks)
iAx.set_xticklabels(xticklabels)
iAx.set_xlabel('Time (s)',
labelpad=0.1,
fontsize=mylabelfontsize,
color=myColor)
iAx.set_ylim(10, 2048)
iAx.yaxis.set_major_formatter(ScalarFormatter())
iAx.ticklabel_format(axis='y', style='plain')
iN = iN + 1
superFig.add_colorbar(ax=iAx,
cmap='viridis',
label='Normalized energy',
clim=plotNormalizedERange,
pad="3%",
width="5%")
superFig.suptitle(title,
fontsize=mylabelfontsize,
color=myColor,
x=0.51)
superFig.save(outDir + channelName.replace(':', '-') + '_' +
IDstring + '_spectrogram_' + '.png')
if opts.make_webpage:
channelNameAll = [i.replace(':', '-') for i in channelNameAll]
loudestEnergyAll = [str(i) for i in loudestEnergyAll]
peakFreqAll = [str(i) for i in peakFreqAll]
mostSignQAll = [str(i) for i in mostSignQAll]
# Zip SNR with channelName
loudestEnergyAll = dict(zip(channelNameAll, loudestEnergyAll))
peakFreqAll = dict(zip(channelNameAll, peakFreqAll))
mostSignQAll = dict(zip(channelNameAll, mostSignQAll))
plots = glob.glob(outDir + '*.png'.format(channelName))
plots = [i.split('/')[-1] for i in plots]
channelPlots = dict(zip(channelNameAll, plots))
f1 = open(outDir + 'index.html', 'w')
env = Environment(loader=FileSystemLoader('../'))
template = env.get_template('webpage/omegatemplate.html')
print >> f1, template.render(channelNames=channelNameAll,
SNR=loudestEnergyAll,
Q=mostSignQAll,
FREQ=peakFreqAll,
ID=IDstring,
plots=channelPlots)
f1.close()
for channelName in channelNameAll:
f2 = open(outDir + '%s.html' % channelName, 'w')
template = env.get_template('webpage/channeltemplate.html'.format(
opts.pathToHTML))
# List plots for given channel
print >> f2, template.render(channelNames=channelNameAll,
thisChannel=channelName,
plots=channelPlots)
f2.close()
would happen if a binary black hole merger signal occured at or near
the time of a glitch. In LIGO data analysis, this procedure is referred
to as an _injection_.
In the example below, we will create a stream of random, white Gaussian
noise, then inject a simulation of GW150914 into it at a known time.
"""
__author__ = "Alex Urban <*****@*****.**>"
__currentmodule__ = 'gwpy.timeseries'
# First, we prepare one second of Gaussian noise:
from numpy import random
from gwpy.timeseries import TimeSeries
noise = TimeSeries(random.normal(scale=.1, size=16384), sample_rate=16384)
# Then we can download a simulation of the GW150914 signal from LOSC:
from astropy.utils.data import get_readable_fileobj
source = 'https://losc.ligo.org/s/events/GW150914/P150914/'
url = '%s/fig2-unfiltered-waveform-H.txt' % source
with get_readable_fileobj(url) as f:
signal = TimeSeries.read(f, format='txt')
signal.t0 = .5 # make sure this intersects with noise time samples
# Note, since this simulation cuts off before a certain time, it is
# important to taper its ends to zero to avoid ringing artifacts.
# We can accomplish this using the
# :meth:`~gwpy.timeseries.TimeSeries.taper` method.
It is used to measure the 'Gaussianity' of those data, where a value of 1
indicates Gaussian behaviour, less than 1 indicates coherent variations,
and greater than 1 indicates incoherent variation.
It is a useful measure of the quality of the strain data being generated
and recorded at a LIGO site.
"""
__author__ = "Duncan Macleod <*****@*****.**>"
__currentmodule__ = 'gwpy.frequencyseries'
# To demonstate this, we can load some data from the LIGO Livingston
# intereferometer around the time of the GW151226 gravitational wave detection:
from gwpy.timeseries import TimeSeries
gwdata = TimeSeries.fetch_open_data('L1',
'Dec 26 2015 03:37',
'Dec 26 2015 03:47',
verbose=True)
# Next, we can calculate a Rayleigh statistic `FrequencySeries` using the
# :meth:`~gwpy.timeseries.TimeSeries.rayleigh_spectrum` method of the
# `~gwpy.timeseries.TimeSeries` with a 2-second FFT and 1-second overlap (50%):
rayleigh = gwdata.rayleigh_spectrum(2, 1)
# For easy comparison, we can calculate the spectral sensitivity ASD of the
# strain data and plot both on the same figure:
from gwpy.plot import Plot
plot = Plot(gwdata.asd(2, 1),
rayleigh,
geometry=(2, 1),
def make_q_scans(event_time, **kwargs):
"""Classify triggers in this table
Parameters:
----------
Returns
-------
"""
# Parse Keyword Arguments
config = kwargs.pop('config', GravitySpyConfigFile())
timeseries = kwargs.pop('timeseries', None)
source = kwargs.pop('source', None)
channel_name = kwargs.pop('channel_name', None)
frametype = kwargs.pop('frametype', None)
verbose = kwargs.pop('verbose', False)
if verbose:
logger = log.Logger('Gravity Spy: Making Q Scans')
if (timeseries is None) and (channel_name is None):
raise ValueError("If not directly passing a timeseries, then "
"the user must pass channel_name")
###########################################################################
# Parse Ini File #
###########################################################################
sample_frequency = config.sample_frequency
block_time = config.block_time
search_frequency_range = config.search_frequency_range
search_q_range = config.search_q_range
plot_time_ranges = config.plot_time_ranges
plot_normalized_energy_range = config.plot_normalized_energy_range
if verbose:
logger.info("""
You have chosen the following parameters
Sample Frequency : {0}
Block Time : {1}
Frequency Range : {2}
Q Range : {3}
Spectrogram Colorbar Range: {4}
""".format(sample_frequency, block_time,
search_frequency_range, search_q_range,
plot_time_ranges, plot_normalized_energy_range))
# find closest sample time to event time
center_time = (
numpy.floor(event_time) +
numpy.round((event_time - numpy.floor(event_time)) *
sample_frequency) / sample_frequency
)
# determine segment start and stop times
start_time = round(center_time - block_time / 2)
stop_time = start_time + block_time
# Read in the data
if timeseries:
data = timeseries.crop(start_time, stop_time, verbose=verbose)
elif source:
if verbose:
logger.info('Reading Data From Source ...')
data = TimeSeries.read(source=source, channel=channel_name,
start=start_time, end=stop_time, verbose=verbose)
else:
if verbose:
logger.info('Fetching Data...')
data = TimeSeries.get(channel_name, start_time, stop_time,
frametype=frametype, verbose=verbose).astype('float64')
# resample data
if verbose:
logger.info('Resampling Data...')
if data.sample_rate.decompose().value != sample_frequency:
data = data.resample(sample_frequency)
# Cropping the results before interpolation to save on time and memory
# perform the q-transform
if verbose:
logger.info('Processing Q Scans...')
specsgrams = []
for time_window in plot_time_ranges:
duration_for_plot = time_window/2
try:
outseg = Segment(center_time - duration_for_plot,
center_time + duration_for_plot)
q_scan = data.q_transform(qrange=tuple(search_q_range),
frange=tuple(search_frequency_range),
gps=center_time,
search=0.5, tres=0.002,
fres=0.5, outseg=outseg, whiten=True)
q_value = q_scan.q
q_scan = q_scan.crop(center_time-time_window/2,
center_time+time_window/2)
except:
outseg = Segment(center_time - 2*duration_for_plot,
center_time + 2*duration_for_plot)
q_scan = data.q_transform(qrange=tuple(search_q_range),
frange=tuple(search_frequency_range),
gps=center_time, search=0.5,
tres=0.002,
fres=0.5, outseg=outseg, whiten=True)
q_value = q_scan.q
q_scan = q_scan.crop(center_time-time_window/2,
center_time+time_window/2)
specsgrams.append(q_scan)
if verbose:
logger.info('The most significant q value is {0}'.format(q_value))
return specsgrams, q_value
# download a 128 second chunk of data (the whole data length will be used to generate the
# power spectral density to get a good average)
duration = 128 # number of seconds of data to download
gpsstart = 1187008884 # start time
gpsend = gpsstart + duration
samplerate = 16384
detector = "L1"
# fetch the open data from GWOSC
data = TimeSeries.fetch_open_data(
detector,
gpsstart,
gpsend,
sample_rate=samplerate,
format='hdf5',
host='https://www.gw-openscience.org',
verbose=False,
cache=True,
)
# convert the data to a PyCBC time series
pycbcdata = PyCBCTimeSeries(data.data, delta_t=(1 / data.sample_rate.value))
# high-pass filter the data to only include the frequencies we're interested in
lowcutoff = 1000
buffer = 50 # just allow a bit of a buffer at the edges
pycbcdata = pycbcdata.highpass_fir(lowcutoff - buffer,
8) # 8 is the "order" of the filter
# create the template bank
import gwpy
from gwosc.datasets import event_gps
gps = event_gps('GW150914')
print(gps)
segment = (int(gps) - 5, int(gps) + 5)
print(segment)
from gwpy.timeseries import TimeSeries
ldata = TimeSeries.fetch_open_data('L1', *segment, verbose=True)
print(ldata)
def read_frame(filename,
ifo,
readstrain=True,
strain_chan=None,
dq_chan=None,
inj_chan=None):
"""
Helper function to read frame files
"""
from gwpy.timeseries import TimeSeries
if ifo is None:
raise TypeError("""To read GWF data, ifo must be 'H1', 'H2', or 'L1'.
def loaddata(filename, ifo=None):""")
#-- Read strain channel
if strain_chan is None:
strain_chan = ifo + ':LOSC-STRAIN'
if readstrain:
try:
sd = TimeSeries.read(filename, strain_chan)
strain = sd.value
gpsStart = sd.t0.value
ts = sd.dt.value
except:
print("ERROR reading file {0} with strain channel {1}".format(
filename, strain_chan))
raise
else:
ts = 1
strain = 0
#-- Read DQ channel
if dq_chan is None:
dq_chan = ifo + ':LOSC-DQMASK'
try:
qd = TimeSeries.read(str(filename), str(dq_chan))
gpsStart = qd.t0.value
qmask = np.array(qd.value)
dq_ts = qd.dt.value
shortnameList_wbit = str(qd.unit).split()
shortnameList = [name.split(':')[1] for name in shortnameList_wbit]
except:
print("ERROR reading DQ channel '{0}' from file: {1}".format(
dq_chan, filename))
raise
#-- Read Injection channel
if inj_chan is None:
inj_chan = ifo + ':LOSC-INJMASK'
try:
injdata = TimeSeries.read(str(filename), str(inj_chan))
injmask = injdata.value
injnamelist_bit = str(injdata.unit).split()
injnamelist = [name.split(':')[1] for name in injnamelist_bit]
except:
print("ERROR reading injection channel '{0}' from file: {1}".format(
inj_chan, filename))
raise
return strain, gpsStart, ts, qmask, shortnameList, injmask, injnamelist
"""Tests for :mod:`gwdetchar.daq`
"""
import numpy
import pytest
from numpy.testing import assert_array_equal
from unittest import mock
from gwpy.timeseries import TimeSeries
from gwpy.segments import (Segment, SegmentList)
from gwpy.testing.utils import assert_segmentlist_equal
from .. import daq
OVERFLOW_SERIES = TimeSeries([0, 0, 0, 1, 1, 0, 0, 1, 0, 1], dx=.5)
CUMULATIVE_SERIES = TimeSeries([0, 0, 0, 1, 2, 2, 2, 3, 3, 4], dx=.5)
OVERFLOW_TIMES = numpy.array([1.5, 3.5, 4.5])
OVERFLOW_SEGMENTS = SegmentList([
Segment(1.5, 2.5),
Segment(3.5, 4),
Segment(4.5, 5),
])
CROSSING_TIMES = numpy.array([1.5, 2.5, 3.5, 4, 4.5])
CHANNELS = [
'X1:TEST-CHANNEL_1',
'X1:FEC-1_ADC_OVERFLOW_ACC_0_1',
'X1:FEC-1_ADC_OVERFLOW_ACC_0_2',
'X1:FEC-1_ADC_OVERFLOW_ACC_0_3',
'X1:FEC-1_ADC_OVERFLOW_ACC_0_4',
sec_per_t_unit = 60.0
else:
t_unit = 'seconds'
sec_per_t_unit = 1.0
for i in range(0, num_points):
times[i] = times[i] / sec_per_t_unit
# Collect range data in arrays
ranges = []
medians = []
stds = []
for i in range(0, len(channel_list)):
ranges.append([])
for j in range(0, num_points):
data = TimeSeries.read(frame_cache_list[i], "%s:%s" % (ifo, channel_list[i]), start = gps_start_time + j * stride, end = gps_start_time + j * stride + integration_time)
PSD = data.psd(8, 4, method = 'lal_median')
BNS_range = float(inspiral_range(PSD, fmin=10).value)
ranges[i].append(BNS_range)
medians.append(numpy.median(ranges[i]))
stds.append(numpy.std(ranges[i]))
# Make plots
colors = ["blue", "green", "limegreen", "red", "yellow", "purple", "pink"] # Hopefully the user will not want to plot more than 7 datasets on one plot.
plt.figure(figsize = (12, 8))
for i in range(0, len(channel_list)):
plt.gcf().subplots_adjust(bottom=0.15)
plt.plot(times, ranges[i], colors[i % 6], linewidth = 1.5, label = r'%s:%s [median = %0.1f Mpc, $\sigma$ = %0.1f Mpc]' % (ifo, channel_list[i].replace('_', '\_'), medians[i], stds[i]))
if options.make_title:
plt.title("%s binary neutron star inspiral range" % ifo)
plt.ylabel('Angle-averaged range [Mpc]')
plt.xlabel('Time [%s] from %s UTC' % (t_unit, time.strftime("%b %d %Y %H:%M:%S", time.gmtime(gps_start_time + 315964782))))
def frame_read(self, format=None):
ts = TimeSeries.read(self.framefile, 'L1:LDAS-STRAIN', format=format)
self.assertTrue(ts.epoch == Time(968654552, format='gps', scale='utc'))
self.assertTrue(ts.sample_rate == units.Quantity(16384, 'Hz'))
self.assertTrue(ts.unit == units.Unit('strain'))
potential gravitational-wave signals.
This algorithm was used to visualise the first ever gravitational-wave
detection GW150914, so we can reproduce `that result (bottom panel of figure 1)
<https://doi.org/10.1103/PhysRevLett.116.061102>`_ here.
"""
__author__ = "Duncan Macleod <*****@*****.**>"
__currentmodule__ = 'gwpy.timeseries'
# First, we need to download the `TimeSeries` record for the H1 strain
# measurement from |GWOSC|_:
from gwpy.timeseries import TimeSeries
data = TimeSeries.fetch_open_data('H1', 1126259446, 1126259478)
# Next, we generate the `~TimeSeries.q_transform` of these data:
qspecgram = data.q_transform(outseg=(1126259462.2, 1126259462.5))
# .. note::
# We can save memory by focusing on a specific window around the
# interesting time. The ``outseg`` keyword argument returns a `Spectrogram`
# that is only as long as we need it to be.
# Now, we can plot the resulting `~gwpy.spectrogram.Spectrogram`:
plot = qspecgram.plot(figsize=[8, 4])
ax = plot.gca()
ax.set_xscale('seconds')
ax.set_yscale('log')
would happen if a binary black hole merger signal occured at or near
the time of a glitch. In LIGO data analysis, this procedure is referred
to as an _injection_.
In the example below, we will create a stream of random, white Gaussian
noise, then inject a simulation of GW150914 into it at a known time.
"""
__author__ = "Alex Urban <*****@*****.**>"
__currentmodule__ = 'gwpy.timeseries'
# First, we prepare one second of Gaussian noise:
from numpy import random
from gwpy.timeseries import TimeSeries
noise = TimeSeries(random.normal(scale=.1, size=16384), sample_rate=16384)
# Then we can download a simulation of the GW150914 signal from GWOSC:
from astropy.utils.data import get_readable_fileobj
url = ("https://www.gw-openscience.org/s/events/GW150914/P150914/"
"fig2-unfiltered-waveform-H.txt")
with get_readable_fileobj(url) as f:
signal = TimeSeries.read(f, format='txt')
signal.t0 = .5 # make sure this intersects with noise time samples
# Note, since this simulation cuts off before a certain time, it is
# important to taper its ends to zero to avoid ringing artifacts.
# We can accomplish this using the
# :meth:`~gwpy.timeseries.TimeSeries.taper` method.
"""Filtering a `TimeSeries` with a ZPK filter
Several data streams read from the LIGO detectors are whitened before being
recorded to prevent numerical errors when using single-precision data
storage.
In this example we read such `channel <gwpy.detector.Channel>` and undo the
whitening to show the physical content of these data.
"""
__author__ = "Duncan Macleod <*****@*****.**>"
__currentmodule__ = 'gwpy.timeseries'
# First, we import the `TimeSeries` and :meth:`~TimeSeries.get` the data:
from gwpy.timeseries import TimeSeries
white = TimeSeries.get('L1:OAF-CAL_DARM_DQ', 'March 2 2015 12:00',
'March 2 2015 12:30')
# Now, we can re-calibrate these data into displacement units by first applying
# a `highpass <TimeSeries.highpass>` filter to remove the low-frequency noise,
# and then applying our de-whitening filter in `ZPK <TimeSeries.zpk>` format
# with five zeros at 100 Hz and five poles at 1 Hz (giving an overall DC
# gain of 10 :sup:`-10`:
hp = white.highpass(4)
displacement = hp.zpk([100] * 5, [1] * 5, 1e-10)
# We can visualise the impact of the whitening by calculating the ASD
# `~gwpy.frequencyseries.FrequencySeries` before and after the filter,
whiteasd = white.asd(8, 4)
dispasd = displacement.asd(8, 4)
from gwpy.timeseries import TimeSeries
llo = TimeSeries.fetch('L1:LDAS-STRAIN,rds', 'August 1 2010', 'August 1 2010 00:10')
variance = llo.spectral_variance(10, fftlength=1, log=True, low=1e-24, high=1e-19, nbins=100)
plot = variance.plot(norm='log', vmin=0.5, vmax=100)
ax = plot.gca()
ax.grid()
ax.set_xlim(40, 4096)
ax.set_ylim(1e-24, 1e-19)
ax.set_xlabel('Frequency [Hz]')
ax.set_ylabel(r'GW ASD [strain/\rtHz]')
ax.set_title('LIGO Livingston Observatory sensitivity variance')
plot.save('variance.png')
#commonto!
format='gwf.lalframe',
nproc=nproc)
ixv1 = data['K1:PEM-SEIS_IXV_GND_X_OUT_DQ']
exv = data['K1:PEM-SEIS_EXV_GND_X_OUT_DQ']
gif = data['K1:GIF-X_STRAIN_OUT16'] * 3e3 * 1e6
ixv_press = data['K1:PEM-WEATHER_IXV_FIELD_PRES_OUT16']
diff13 = (ixv1 - exv) / np.sqrt(2)
comm13 = (ixv1 + exv) / np.sqrt(2)
if tplot and readgwf:
plot = data.plot()
plot.savefig('img_timeseries.png')
plot.close()
if True:
x500_press = TimeSeries.read('2019May03_6hours_x500_press.gwf',
'X500_BARO', start, end)
x500_press = x500_press
plot = x500_press.plot(ylabel='Pressure')
plot.savefig('img_x500_press.png')
plot.close()
# -----------------------------------------------
# Calc Coherence
# -----------------------------------------------
import matplotlib.pyplot as plt
if plot_coherence and readgwf:
print('Calc Coherence ')
coh13 = ixv1.coherence(exv, fftlength, fftlength * ovlp, window=window)
deg13 = ixv1.csd(exv, fftlength, fftlength / 2).angle().rad2deg()
coh1 = gif.coherence(ixv_press, fftlength, fftlength * ovlp, window=window)
deg1 = gif.csd(ixv_press, fftlength, fftlength / 2).angle().rad2deg()
from matplotlib.ticker import MultipleLocator, FormatStrFormatter
from gwpy.time import Time
from gwpy.timeseries import (TimeSeries, TimeSeriesDict)
print "Import Modules Success"
#Start-End Time
start = Time('2014-06-17 04:00:00', format='iso', scale='utc')
end = Time('2014-06-17 15:00:00', format='iso', scale='utc')
print start.iso, start.gps
print end.iso, end.gps
data = TimeSeries.fetch('L1:HPI-ETMY_BLND_IPS_Z_IN1_DQ.mean,m-trend', start, end, verbose=True)
plot_data = data.plot()
ax = plot_data.gca()
#plot_data.show()
ax.set_epoch(start.gps)
ax.set_xlim(start.gps, end.gps)
ax.set_ylabel('Amplitude[ ]')
ax.set_title(data.channel.texname)
#ax.set_ylim([20000,30000])
plot_data.save('L1-HPI-ETMY_BLND_IPS_Z_IN1_DQ_JUN14.png')
print "PLOT SAVED"
### Set the channel that witnesses fringes (to plot specgram for)
witness_base = "GDS-CALIB_STRAIN"
#witness_base = "LSC-MICH_IN1_DQ"
#witness_base = '%s:ASC-Y_TR_A_NSUM_OUT_DQ' % ifo
#witness_base = 'LSC-SRCL_IN1_DQ'
#witness_base = "LSC-REFL_A_RF9_Q_ERR_DQ"
#witness_base = "ASC-AS_A_RF45_Q_PIT_OUT_DQ"
#witness_base = "ASC-AS_B_RF36_Q_PIT_OUT_DQ"
#witness_base = "OMC-LSC_SERVO_OUT_DQ"
if plotspec==1:
witness_chan = ifo + ':' + witness_base
print witness_chan
# load timeseries for witness channel
witness=TimeSeries.fetch(witness_chan, start_time, start_time+dur, verbose=True)
if witness_base=="GDS-CALIB_STRAIN":
witness=witness.highpass(20,gpass=3) # highpass the witness data
elif witness_base=="ASC-AS_B_RF45_I_PIT_OUT_DQ" or witness_base=="ASC-AS_B_RF36_Q_PIT_OUT_DQ" or witness_base=="LSC-MICH_IN1_DQ" or witness_base=="ASC-AS_A_RF45_Q_PIT_OUT_DQ":
witness=witness.highpass(10,gpass=3) # highpass the witness data
# Calculate DARM spectrogram
secsPerFFT = .75 # Hz
overlap = 0.9 # fractional overlap
Fs = witness.sample_rate.value
NFFT = int(round(Fs*secsPerFFT))
noverlap = int(round(overlap*NFFT))
Pxx, freq, t, im = specgram(witness.value,NFFT=NFFT,Fs=witness.sample_rate.value,noverlap=noverlap,scale_by_freq='magnitude',detrend=mlab.detrend_linear,window=mlab.window_hanning)
### Known SUS displacement w/r/t sus frame channels (in microns)
position_chans = [\
'SUS-BS_M1_DAMP_L_IN1_DQ',\
from urllib2 import urlopen
from numpy import asarray
from gwpy.timeseries import TimeSeries
data = urlopen('http://www.ligo.org/science/GW100916/'
'L-strain_hp30-968654552-10.txt').read()
ts = TimeSeries(asarray(data.splitlines(), dtype=float),
epoch=968654552,
sample_rate=16384)
plot = ts.plot()
plot.set_ylabel('Gravitational-wave strain amplitude')
plot.set_title('LIGO Livingston Observatory data for GW100916')
plot.show()
def setUp(self):
self.ts = TimeSeries.read(TEST_HDF_FILE, 'H1:LDAS-STRAIN')
self.sg = self.ts.spectrogram2(0.5, 0.49)
self.mmm = [self.ts, self.ts * 0.9, self.ts*1.1]
def setUp(self):
self.ts = TimeSeries.read(TEST_HDF_FILE, 'H1:LDAS-STRAIN')
def getTimeSeries(self, arg_list):
"""Verify and interpret arguments to get all
TimeSeries objects defined"""
# retrieve channel data from NDS as a TimeSeries
for chans in arg_list.chan:
for chan in chans:
if chan not in self.chan_list:
self.chan_list.append(chan)
if len(self.chan_list) < self.min_timeseries:
raise ArgumentError('A minimum of %d channels must be ' +
'specified for this product' %
self.min_timeseries)
if len(arg_list.start) > 0:
for start_arg in arg_list.start:
if type(start_arg) is list:
for starts in start_arg:
if isinstance(starts, basestring):
starti = int(starts)
elif starts is list:
for start_str in starts:
starti = int(start_str)
# ignore duplicates (to make it easy for ldvw)
if starti not in self.start_list:
self.start_list.append(starti)
else:
self.start_list.append(int(start_arg))
else:
raise ArgumentError('No start times specified')
# Verify the number of datasets specified is valid for this plot
self.n_datasets = len(self.chan_list) * len(self.start_list)
if self.n_datasets < self.get_min_datasets():
raise ArgumentError('%d datasets are required for this ' +
'plot but only %d are supplied' %
(self.get_min_datasets(), self.n_datasets))
if self.n_datasets > self.get_max_datasets():
raise ArgumentError('A maximum of %d datasets allowed for ' +
'this plot but %d specified' %
(self.get_max_datasets(), self.n_datasets))
if arg_list.duration:
self.dur = int(arg_list.duration)
else:
self.dur = 10
verb = self.verbose > 1
# determine how we're supposed get our data
source = 'NDS2'
frame_cache = False
if arg_list.framecache:
source = 'frames'
frame_cache = arg_list.framecache
# set up filter parameters for all channels
highpass = 0
if arg_list.highpass:
highpass = float(arg_list.highpass)
self.filter += "highpass(%.1f) " % highpass
# Get the data from NDS or Frames
# time_groups is a list of timeseries index grouped by
# start time for coherence like plots
self.time_groups = []
for start in self.start_list:
time_group = []
for chan in self.chan_list:
if verb:
print 'Fetching %s %d, %d using %s' % \
(chan, start, self.dur, source)
if frame_cache:
data = TimeSeries.read(frame_cache, chan, start=start,
end=start+self.dur)
else:
data = TimeSeries.fetch(chan, start, start+self.dur,
verbose=verb)
if highpass > 0:
data = data.highpass(highpass)
self.timeseries.append(data)
time_group.append(len(self.timeseries)-1)
self.time_groups.append(time_group)
# report what we have if they asked for it
self.log(3, ('Channels: %s' % self.chan_list))
self.log(3, ('Start times: %s, duration' % self.start_list, self.dur))
self.log(3, ('Number of time series: %d' % len(self.timeseries)))
if len(self.timeseries) != self.n_datasets:
self.log(0, ('%d datasets requested but only %d transfered' %
(self.n_datasets, len(self.timeseries))))
if len(self.timeseries) > self.get_min_datasets():
self.log(0, 'Proceeding with the data that was transferred.')
else:
self.log(0, 'Not enough data for requested plot.')
from sys import exit
exit(2)
return
import h5py
from numpy import (random, testing as nptest)
from gwpy.table import EventTable
from gwpy.timeseries import (TimeSeries, StateVector)
from gwpy.spectrogram import Spectrogram
from gwpy.segments import (Segment, SegmentList)
from gwsumm import (archive, data, globalv, channels, triggers)
__author__ = 'Duncan Macleod <*****@*****.**>'
TEST_DATA = TimeSeries([1, 2, 3, 4, 5, 6, 7, 8, 9, 10], epoch=100,
unit='meter', sample_rate=1, channel='X1:TEST-CHANNEL',
name='TEST DATA')
TEST_DATA.channel = channels.get_channel(TEST_DATA.channel)
# -- utilities ----------------------------------------------------------------
def empty_globalv():
globalv.DATA = type(globalv.DATA)()
globalv.SPECTROGRAMS = type(globalv.SPECTROGRAMS)()
globalv.SEGMENTS = type(globalv.SEGMENTS)()
globalv.TRIGGERS = type(globalv.TRIGGERS)()
def create(data, **metadata):
SeriesClass = metadata.pop('series_class', TimeSeries)
# Demodulation is useful when trying to examine steady sinusoidal
# signals we know to be contained within data. For instance,
# we can download some data from LOSC to look at trends of the
# amplitude and phase of Livingston's calibration line at 331.3 Hz:
from gwpy.timeseries import TimeSeries
data = TimeSeries.fetch_open_data('L1', 1131350417, 1131357617)
# We can demodulate the `TimeSeries` at 331.3 Hz with a stride of once
# per minute:
amp, phase = data.demodulate(331.3, stride=60)
# We can then plot these trends to visualize changes in the amplitude
# and phase of the calibration line:
from gwpy.plotter import TimeSeriesPlot
plot = TimeSeriesPlot(amp, phase, sep=True)
plot.show()
# We can design an arbitrarily complicated filter using
# :mod:`gwpy.signal.filter_design`
from gwpy.signal import filter_design
bp = filter_design.bandpass(50, 250, 4096.)
notches = [filter_design.notch(f, 4096.) for f in (60, 120, 180)]
zpk = filter_design.concatenate_zpks(bp, *notches)
# And then can download some data from LOSC to apply it using
# `TimeSeries.filter`:
from gwpy.timeseries import TimeSeries
data = TimeSeries.fetch_open_data('H1', 1126259446, 1126259478)
filtered = data.filter(zpk, filtfilt=True)
# We can plot the original signal, and the filtered version, cutting
# off either end of the filtered data to remove filter-edge artefacts
from gwpy.plotter import TimeSeriesPlot
plot = TimeSeriesPlot(data, filtered[128:-128], sep=True)
plot.show()
help=
'GPS start time or datetime of analysis. Default: 5 minutes prior to current time'
)
parser.add_argument(
'--duration',
type=int,
default=60,
required=False,
help='Duration of of analysis in seconds. Default: 60 seconds')
args = parser.parse_args()
gpsend = args.gpsstart + args.duration
#Timeseries Data
TS = TimeSeries.fetch(channel, args.gpsstart, gpsend)
specgram = TS.spectrogram(2, fftlength=1, overlap=.5)**(1 / 2.)
normalised = specgram.ratio('median')
#Plot QSpectrogram
qspecgram = TS.q_transform(qrange=(4, 150),
frange=(10, 100),
outseg=(args.gpsstart, gpsend),
fres=.01)
plot = qspecgram.imshow(figsize=[8, 4])
cmap = cm.get_cmap('viridis')
ax = plot.gca()
ax.set_title('Q Transform')
ax.set_xscale('seconds')
ax.set_yscale('log')
ax.set_ylim(10, 100)
def osem_velocity(osem_data, pad_sec=64, new_sample_rate=None):
nyquist = osem_data.sample_rate.value / 2.
assert new_sample_rate >= 16
result = fir_helper(osem_data, [0., 0.04, 0.08, 7.2, nyquist],
[0., 1.e-4, 2. * pi * 0.08, 2. * pi * 7.2, 0.],
pad_sec=pad_sec,
new_sample_rate=new_sample_rate,
deriv=True)
return result
if __name__ == '__main__':
times = arange(1024 * 256, dtype=float32) / 256.
test = TimeSeries(
cos(2. * pi * 0.4 * times) + 2. * sin(2. * pi * 1. * times) -
cos(2. * pi * 3. * times) - 10. * sin(2. * pi * 10. * times),
sample_rate=256,
name='test')
dtest = TimeSeries(
2. * pi *
(-0.4 * sin(2. * pi * 0.4 * times) + 2. * cos(2. * pi * 1. * times) +
3. * sin(2. * pi * 3. * times)),
sample_rate=256,
name='deriv')
result1 = fir_helper(
test, [0., 0.01, 0.02, 0.4, 7., 8., 128.],
[0., 0., 2 * pi * 0.02, 2 * pi * 0.4, 2 * pi * 7., 1.e-4, 0.],
pad_sec=64)
result = fir_helper(
parts of the detector, closely monitoring mechanical subsystems and
environmental conditions. We can cross-correlate data from these sensors with
the primary gravitational wave data to look for evidence of terrestrial noise.
We demonstrate below a prominent 'whistle glitch' in the gravitational wave
channel, which is also witnessed by a photodiode in the Pre-Stabilized Laser
(PSL) chamber. This example uses data from the LIGO Livingston detector during
Advanced LIGO's second observing run.
"""
__author__ = "Alex Urban <*****@*****.**>"
__currentmodule__ = 'gwpy.timeseries'
# First, we import the `TimeSeries` and :meth:`~TimeSeries.get` the data:
from gwpy.timeseries import TimeSeries
hoft = TimeSeries.get('L1:GDS-CALIB_STRAIN', 1172489751, 1172489815)
aux = TimeSeries.get('L1:PSL-ISS_PDA_REL_OUT_DQ', 1172489751, 1172489815)
# Next, we should `~TimeSeries.whiten` the data to enhance the higher-frequency
# content and make a more faithful comparison between data streams.
whoft = hoft.whiten(8, 4)
waux = aux.whiten(8, 4)
# We can now cross-correlate these channels:
mfilter = waux.crop(1172489782.57, 1172489783.57)
snr = whoft.correlate(mfilter).abs()
# and plot the resulting normalised signal-to-noise ratio:
plot = snr.crop(1172489782.07, 1172489784.07).plot()
plot.axes[0].set_epoch(1172489783.07)
plot.axes[0].set_ylabel('Signal-to-noise ratio', fontsize=16)
def read_data_archive(sourcefile):
"""Read archived data from an HDF5 archive source
This method reads all found data into the data containers defined by
the `gwsumm.globalv` module, then returns nothing.
Parameters
----------
sourcefile : `str`
path to source HDF5 file
"""
from h5py import File
with File(sourcefile, 'r') as h5file:
# -- channels ---------------------------
try:
ctable = Table.read(h5file['channels'])
except KeyError: # no channels table written
pass
else:
for row in ctable:
chan = get_channel(row['name'])
for p in ctable.colnames[1:]:
if row[p]:
setattr(chan, p, row[p])
# -- timeseries -------------------------
for dataset in h5file.get('timeseries', {}).values():
ts = TimeSeries.read(dataset, format='hdf5')
if (re.search(r'\.(rms|min|mean|max|n)\Z', ts.channel.name)
and ts.sample_rate.value == 1.0):
ts.channel.type = 's-trend'
elif re.search(r'\.(rms|min|mean|max|n)\Z', ts.channel.name):
ts.channel.type = 'm-trend'
ts.channel = get_channel(ts.channel)
try:
add_timeseries(ts, key=ts.channel.ndsname)
except ValueError:
if mode.get_mode() != mode.Mode.day:
raise
warnings.warn('Caught ValueError in combining daily archives')
# get end time
globalv.DATA[ts.channel.ndsname].pop(-1)
t = globalv.DATA[ts.channel.ndsname][-1].span[-1]
add_timeseries(ts.crop(start=t), key=ts.channel.ndsname)
# -- statevector -- ---------------------
for dataset in h5file.get('statevector', {}).values():
sv = StateVector.read(dataset, format='hdf5')
sv.channel = get_channel(sv.channel)
add_timeseries(sv, key=sv.channel.ndsname)
# -- spectrogram ------------------------
for tag, add_ in zip(
['spectrogram', 'coherence-components'],
[add_spectrogram, add_coherence_component_spectrogram]):
for key, dataset in h5file.get(tag, {}).items():
key = key.rsplit(',', 1)[0]
spec = Spectrogram.read(dataset, format='hdf5')
spec.channel = get_channel(spec.channel)
add_(spec, key=key)
# -- segments ---------------------------
for name, dataset in h5file.get('segments', {}).items():
dqflag = DataQualityFlag.read(h5file,
path=dataset.name,
format='hdf5')
globalv.SEGMENTS += {name: dqflag}
# -- triggers ---------------------------
for dataset in h5file.get('triggers', {}).values():
load_table(dataset)
def setUp(self):
self.ts = TimeSeries.read(TEST_HDF_FILE, 'H1:LDAS-STRAIN')
self.asd = self.ts.asd(1)
self.mmm = [self.asd, self.asd*0.9, self.asd*1.1]
The LIGO Laboratory has publicly released the strain data around the time of
the GW150914 gravitational-wave detection; we can use these to calculate
and display the spectral sensitivity of each of the detectors at that time.
"""
__author__ = "Duncan Macleod <*****@*****.**>"
__currentmodule__ = 'gwpy.frequencyseries'
# In order to generate a `FrequencySeries` we need to import the
# `~gwpy.timeseries.TimeSeries` and use
# :meth:`~gwpy.timeseries.TimeSeries.fetch_open_data` to download the strain
# records:
from gwpy.timeseries import TimeSeries
lho = TimeSeries.fetch_open_data('H1', 1126259446, 1126259478)
llo = TimeSeries.fetch_open_data('L1', 1126259446, 1126259478)
# We can then call the :meth:`~gwpy.timeseries.TimeSeries.asd` method to
# calculated the amplitude spectral density for each
# `~gwpy.timeseries.TimeSeries`:
lhoasd = lho.asd(4, 2)
lloasd = llo.asd(4, 2)
# We can then :meth:`~FrequencySeries.plot` the spectra using the 'standard'
# colour scheme:
plot = lhoasd.plot(label='LIGO-Hanford', color='gwo:ligo-hanford')
ax = plot.gca()
ax.plot(lloasd, label='LIGO-Livingston', color='gwo:ligo-livingston')
ax.set_xlim(10, 2000)
from gwpy.timeseries import TimeSeries
white = TimeSeries.get(
'L1:OAF-CAL_DARM_DQ', 'March 2 2015 12:00', 'March 2 2015 12:30')
# load data
from gwpy.timeseries import TimeSeries
raw = TimeSeries.fetch_open_data('L1', 1126259446, 1126259478)
# calculate filtered timeseries, and Q-transform spectrogram
data = raw.bandpass(50, 300).notch(60)
qtrans = raw.q_transform()
# plot
from matplotlib import pyplot
plot, axes = pyplot.subplots(nrows=2, sharex=True, figsize=(8, 6))
tax, qax = axes
tax.plot(data.crop(1126259462, 1126259463), color='gwpy:ligo-livingston')
qax.imshow(qtrans.crop(1126259462, 1126259463))
tax.set_xlabel('')
tax.set_xscale('auto-gps')
tax.set_xlim(1126259462.2, 1126259462.5)
tax.set_ylabel('Strain amplitude')
qax.set_yscale('log')
qax.set_ylabel('Frequency [Hz]')
qax.colorbar(clim=(0, 35), label='Normalised energy')
from gwpy.timeseries import TimeSeries
gwdata = TimeSeries.fetch('H1:LDAS-STRAIN', 'September 16 2010 06:40',
'September 16 2010 06:50')
specgram = gwdata.spectrogram(20, fftlength=8, overlap=4) ** (1/2.)
plot = specgram.plot(norm='log', vmin=1e-23, vmax=1e-19)
ax = plot.gca()
ax.set_ylim(40, 4000)
ax.set_yscale('log')
plot.add_colorbar(label='Gravitational-wave strain [m/$\sqrt{\mathrm{Hz}}$]')
plot.show()
# Heterodyning can be useful in analysing quasi-monochromatic signals
# with a known phase evolution, such as continuous-wave signals
# from rapidly rotating neutron stars. These sources radiate at a
# frequency that slowly decreases over time, and is Doppler modulated
# due to the Earth's rotational and orbital motion.
# To see an example of heterodyning in action, we can simulate a signal
# whose phase evolution is described by the frequency and its first
# derivative with respect to time. We can download some O1 era
# LIGO-Livingston data from GWOSC, inject the simulated signal, and
# recover its amplitude.
from gwpy.timeseries import TimeSeries
data = TimeSeries.fetch_open_data('L1', 1131350417, 1131354017)
# We now need to set the signal parameters, generate the expected
# phase evolution, and create the signal:
import numpy
f0 = 123.456789 # signal frequency (Hz)
fdot = -9.87654321e-7 # signal frequency derivative (Hz/s)
fpeoch = 1131350417 # phase epoch
amp = 1.5e-22 # signal amplitude
phase0 = 0.4 # signal phase at the phase epoch
times = data.times.value - fepoch
phase = 2 * numpy.pi * (f0 * times + 0.5 * fdot * times**2)
signal = TimeSeries(amp * numpy.cos(phase + phase0),
sample_rate=data.sample_rate,
t0=data.t0)
data = data.inject(signal)
temp[len(temp)/2] = 1.
return TimeSeries(temp, epoch=data.epoch, sample_rate=data.sample_rate)
def step_like(data):
temp = zeros(len(data))
temp[len(temp)/2:] = 1.
return TimeSeries(temp, epoch=data.epoch, sample_rate=data.sample_rate)
if __name__ == '__main__':
import sys
if len(sys.argv) < 6:
print "Args: chan t_PSD dur_PSD seglen t_glitch"
exit()
chan = sys.argv[1]
t1_psd = int(sys.argv[2])
dur_psd = int(sys.argv[3])
seglen = int(sys.argv[4])
tt = float(sys.argv[5])
st = int(tt) - seglen/2
data_for_psd = TimeSeries.fetch(chan, t1_psd, t1_psd+dur_psd)
data = TimeSeries.fetch(chan, st, st+seglen)
invasd = build_whitener(data_for_psd, seglen, method='median-mean')
data = step_like(data)
temp = apply_whitening(data, invasd)
#plot = data.plot()
plot = temp.plot()
plot.show()
from .. import (config, core)
from matplotlib import use
use('agg') # noqa
# backend-dependent import
from .. import plot # noqa: E402
__author__ = 'Alex Urban <*****@*****.**>'
# global test objects
FFTLENGTH = 8
NOISE = TimeSeries(numpy.random.normal(loc=1, scale=.5, size=16384 * 68),
sample_rate=16384,
epoch=-34).zpk([], [0], 1)
GLITCH = TimeSeries(signal.gausspulse(numpy.arange(-1, 1, 1. / 16384), bw=100),
sample_rate=16384,
epoch=-1) * 1e-4
INPUT = NOISE.inject(GLITCH)
CONFIGURATION = {
'q-range': '3.3166,150',
'frequency-range': '4.0,Inf',
'plot-time-durations': '4',
'always-plot': 'True',
}
CHANNEL = config.OmegaChannel(channelname='L1:TEST-STRAIN',
section='test',
**CONFIGURATION)