# unless asked otherwise, revert the dynamic range factor
if not args.dyn_range_factor:
out_strain /= pycbc.DYN_RANGE_FAC
# Adding strain channel info
data = {}
det_channels = {}
logging.info("Adding strain channel named {} ...".format(args.channel_name))
det_channels[args.channel_name.split(':')[0]] = [args.channel_name]
data[args.channel_name.split(':')[0]] = [out_strain]
if args.other_channel_names:
for channel in args.other_channel_names:
logging.info("Reading channel {} ...".format(channel))
det = channel.split(':')[0]
det_channels[det].append(channel)
data[det].append(
frame.query_and_read_frame(args.frame_type, channel, start, stop))
logging.info("Writing frames, each of duration {} sec".format(step))
for d in data.keys():
for s in tqdm.trange(start, stop, step):
fname = os.path.join(
args.outdir,
filename.format(d, args.frame_type, s,
step if s + step < stop else stop - s))
frame.write_frame(fname, det_channels[d], [
ts.time_slice(s, s + step if s + step < stop else stop)
for ts in data[d]
])
def from_cli(opt, dyn_range_fac=1, precision='single'):
"""Parses the CLI options related to strain data reading and conditioning.
Parameters
----------
opt : object
Result of parsing the CLI with OptionParser, or any object with the
required attributes (gps-start-time, gps-end-time, strain-high-pass,
pad-data, sample-rate, (frame-cache or frame-files), channel-name,
fake-strain, fake-strain-seed, gating_file).
dyn_range_fac: {float, 1}, optional
A large constant to reduce the dynamic range of the strain.
Returns
-------
strain : TimeSeries
The time series containing the conditioned strain data.
"""
gating_info = {}
if opt.frame_cache or opt.frame_files or opt.frame_type:
if opt.frame_cache:
frame_source = opt.frame_cache
if opt.frame_files:
frame_source = opt.frame_files
logging.info("Reading Frames")
if opt.frame_type:
strain = query_and_read_frame(opt.frame_type, opt.channel_name,
start_time=opt.gps_start_time-opt.pad_data,
end_time=opt.gps_end_time+opt.pad_data)
else:
strain = read_frame(frame_source, opt.channel_name,
start_time=opt.gps_start_time-opt.pad_data,
end_time=opt.gps_end_time+opt.pad_data)
if opt.zpk_z and opt.zpk_p and opt.zpk_k:
logging.info("Highpass Filtering")
strain = highpass(strain, frequency=opt.strain_high_pass)
logging.info("Applying zpk filter")
z = numpy.array(opt.zpk_z)
p = numpy.array(opt.zpk_p)
k = float(opt.zpk_k)
strain = filter_zpk(strain.astype(numpy.float64), z, p, k)
if opt.normalize_strain:
logging.info("Dividing strain by constant")
l = opt.normalize_strain
strain = strain / l
if opt.injection_file:
logging.info("Applying injections")
injections = InjectionSet(opt.injection_file)
injections.apply(strain, opt.channel_name[0:2],
distance_scale=opt.injection_scale_factor)
if opt.sgburst_injection_file:
logging.info("Applying sine-Gaussian burst injections")
injections = SGBurstInjectionSet(opt.sgburst_injection_file)
injections.apply(strain, opt.channel_name[0:2],
distance_scale=opt.injection_scale_factor)
logging.info("Highpass Filtering")
strain = highpass(strain, frequency=opt.strain_high_pass)
if precision == 'single':
logging.info("Converting to float32")
strain = (strain * dyn_range_fac).astype(float32)
if opt.gating_file is not None:
logging.info("Gating glitches")
gate_params = numpy.loadtxt(opt.gating_file)
if len(gate_params.shape) == 1:
gate_params = [gate_params]
strain = gate_data(strain, gate_params)
gating_info['file'] = \
[gp for gp in gate_params \
if (gp[0] + gp[1] + gp[2] >= strain.start_time) \
and (gp[0] - gp[1] - gp[2] <= strain.end_time)]
if opt.autogating_threshold is not None:
# the + 0 is for making a copy
glitch_times = detect_loud_glitches(
strain + 0., threshold=opt.autogating_threshold,
cluster_window=opt.autogating_cluster,
low_freq_cutoff=opt.strain_high_pass,
high_freq_cutoff=opt.sample_rate/2,
corrupted_time=opt.pad_data+opt.autogating_pad)
gate_params = [[gt, opt.autogating_width, opt.autogating_taper] \
for gt in glitch_times]
if len(glitch_times) > 0:
logging.info('Autogating at %s',
', '.join(['%.3f' % gt for gt in glitch_times]))
strain = gate_data(strain, gate_params)
gating_info['auto'] = gate_params
logging.info("Resampling data")
strain = resample_to_delta_t(strain, 1.0/opt.sample_rate, method='ldas')
logging.info("Highpass Filtering")
strain = highpass(strain, frequency=opt.strain_high_pass)
logging.info("Remove Padding")
start = opt.pad_data*opt.sample_rate
end = len(strain)-opt.sample_rate*opt.pad_data
strain = strain[start:end]
if opt.fake_strain:
logging.info("Generating Fake Strain")
duration = opt.gps_end_time - opt.gps_start_time
tlen = duration * opt.sample_rate
pdf = 1.0/128
plen = int(opt.sample_rate / pdf) / 2 + 1
logging.info("Making PSD for strain")
strain_psd = pycbc.psd.from_string(opt.fake_strain, plen, pdf,
opt.low_frequency_cutoff)
logging.info("Making colored noise")
strain = pycbc.noise.noise_from_psd(tlen, 1.0/opt.sample_rate,
strain_psd,
seed=opt.fake_strain_seed)
strain._epoch = lal.LIGOTimeGPS(opt.gps_start_time)
if opt.injection_file:
logging.info("Applying injections")
injections = InjectionSet(opt.injection_file)
injections.apply(strain, opt.channel_name[0:2],
distance_scale=opt.injection_scale_factor)
if opt.sgburst_injection_file:
logging.info("Applying sine-Gaussian burst injections")
injections = SGBurstInjectionSet(opt.sgburst_injection_file)
injections.apply(strain, opt.channel_name[0:2],
distance_scale=opt.injection_scale_factor)
if precision == 'single':
logging.info("Converting to float32")
strain = (dyn_range_fac * strain).astype(float32)
if opt.injection_file or opt.sgburst_injection_file:
strain.injections = injections
strain.gating_info = gating_info
return strain
def from_cli(opt, dyn_range_fac=1, precision='single'):
"""Parses the CLI options related to strain data reading and conditioning.
Parameters
----------
opt : object
Result of parsing the CLI with OptionParser, or any object with the
required attributes (gps-start-time, gps-end-time, strain-high-pass,
pad-data, sample-rate, (frame-cache or frame-files), channel-name,
fake-strain, fake-strain-seed, gating_file).
dyn_range_fac: {float, 1}, optional
A large constant to reduce the dynamic range of the strain.
Returns
-------
strain : TimeSeries
The time series containing the conditioned strain data.
"""
gating_info = {}
if opt.frame_cache or opt.frame_files or opt.frame_type:
if opt.frame_cache:
frame_source = opt.frame_cache
if opt.frame_files:
frame_source = opt.frame_files
logging.info("Reading Frames")
if opt.frame_type:
strain = query_and_read_frame(opt.frame_type, opt.channel_name,
start_time=opt.gps_start_time-opt.pad_data,
end_time=opt.gps_end_time+opt.pad_data)
else:
strain = read_frame(frame_source, opt.channel_name,
start_time=opt.gps_start_time-opt.pad_data,
end_time=opt.gps_end_time+opt.pad_data)
if opt.zpk_z and opt.zpk_p and opt.zpk_k:
logging.info("Highpass Filtering")
strain = highpass(strain, frequency=opt.strain_high_pass)
logging.info("Applying zpk filter")
z = numpy.array(opt.zpk_z)
p = numpy.array(opt.zpk_p)
k = float(opt.zpk_k)
strain = filter_zpk(strain.astype(numpy.float64), z, p, k)
if opt.normalize_strain:
logging.info("Dividing strain by constant")
l = opt.normalize_strain
strain = strain / l
if opt.injection_file:
logging.info("Applying injections")
injections = InjectionSet(opt.injection_file)
injections.apply(strain, opt.channel_name[0:2],
distance_scale=opt.injection_scale_factor)
if opt.sgburst_injection_file:
logging.info("Applying sine-Gaussian burst injections")
injections = SGBurstInjectionSet(opt.sgburst_injection_file)
injections.apply(strain, opt.channel_name[0:2],
distance_scale=opt.injection_scale_factor)
logging.info("Highpass Filtering")
strain = highpass(strain, frequency=opt.strain_high_pass)
if precision == 'single':
logging.info("Converting to float32")
strain = (strain * dyn_range_fac).astype(pycbc.types.float32)
if opt.gating_file is not None:
logging.info("Gating glitches")
gate_params = numpy.loadtxt(opt.gating_file)
if len(gate_params.shape) == 1:
gate_params = [gate_params]
strain = gate_data(strain, gate_params)
gating_info['file'] = \
[gp for gp in gate_params \
if (gp[0] + gp[1] + gp[2] >= strain.start_time) \
and (gp[0] - gp[1] - gp[2] <= strain.end_time)]
if opt.autogating_threshold is not None:
# the + 0 is for making a copy
glitch_times = detect_loud_glitches(
strain + 0., threshold=opt.autogating_threshold,
cluster_window=opt.autogating_cluster,
low_freq_cutoff=opt.strain_high_pass,
high_freq_cutoff=opt.sample_rate/2,
corrupt_time=opt.pad_data+opt.autogating_pad)
gate_params = [[gt, opt.autogating_width, opt.autogating_taper] \
for gt in glitch_times]
if len(glitch_times) > 0:
logging.info('Autogating at %s',
', '.join(['%.3f' % gt for gt in glitch_times]))
strain = gate_data(strain, gate_params)
gating_info['auto'] = gate_params
logging.info("Resampling data")
strain = resample_to_delta_t(strain, 1.0/opt.sample_rate, method='ldas')
logging.info("Highpass Filtering")
strain = highpass(strain, frequency=opt.strain_high_pass)
logging.info("Remove Padding")
start = opt.pad_data*opt.sample_rate
end = len(strain)-opt.sample_rate*opt.pad_data
strain = strain[start:end]
if opt.fake_strain:
logging.info("Generating Fake Strain")
duration = opt.gps_end_time - opt.gps_start_time
tlen = duration * opt.sample_rate
pdf = 1.0/128
plen = int(opt.sample_rate / pdf) / 2 + 1
logging.info("Making PSD for strain")
strain_psd = pycbc.psd.from_string(opt.fake_strain, plen, pdf,
opt.low_frequency_cutoff)
logging.info("Making colored noise")
strain = pycbc.noise.noise_from_psd(tlen, 1.0/opt.sample_rate,
strain_psd,
seed=opt.fake_strain_seed)
strain._epoch = lal.LIGOTimeGPS(opt.gps_start_time)
if opt.injection_file:
logging.info("Applying injections")
injections = InjectionSet(opt.injection_file)
injections.apply(strain, opt.channel_name[0:2],
distance_scale=opt.injection_scale_factor)
if opt.sgburst_injection_file:
logging.info("Applying sine-Gaussian burst injections")
injections = SGBurstInjectionSet(opt.sgburst_injection_file)
injections.apply(strain, opt.channel_name[0:2],
distance_scale=opt.injection_scale_factor)
if precision == 'single':
logging.info("Converting to float32")
strain = (dyn_range_fac * strain).astype(pycbc.types.float32)
if opt.injection_file or opt.sgburst_injection_file:
strain.injections = injections
if opt.taper_data:
logging.info("Tapering data")
# Use auto-gating stuff for this, a one-sided gate is a taper
pd_taper_window = opt.taper_data
gate_params = [(strain.start_time, 0., pd_taper_window)]
gate_params.append( (strain.end_time, 0.,
pd_taper_window) )
gate_data(strain, gate_params)
strain.gating_info = gating_info
return strain
def from_cli(opt, dyn_range_fac=1, precision='single'):
"""Parses the CLI options related to strain data reading and conditioning.
Parameters
----------
opt : object
Result of parsing the CLI with OptionParser, or any object with the
required attributes (gps-start-time, gps-end-time, strain-high-pass,
pad-data, sample-rate, (frame-cache or frame-files), channel-name,
fake-strain, fake-strain-seed, gating_file).
dyn_range_fac: {float, 1}, optional
A large constant to reduce the dynamic range of the strain.
Returns
-------
strain : TimeSeries
The time series containing the conditioned strain data.
"""
if opt.frame_cache or opt.frame_files or opt.frame_type:
if opt.frame_cache:
frame_source = opt.frame_cache
if opt.frame_files:
frame_source = opt.frame_files
logging.info("Reading Frames")
if opt.frame_type:
strain = query_and_read_frame(opt.frame_type, opt.channel_name,
start_time=opt.gps_start_time-opt.pad_data,
end_time=opt.gps_end_time+opt.pad_data)
else:
strain = read_frame(frame_source, opt.channel_name,
start_time=opt.gps_start_time-opt.pad_data,
end_time=opt.gps_end_time+opt.pad_data)
if opt.zpk_z and opt.zpk_p and opt.zpk_k:
logging.info("Highpass Filtering")
strain = highpass(strain, frequency=opt.strain_high_pass)
logging.info("Applying zpk filter")
z = numpy.array(opt.zpk_z)
p = numpy.array(opt.zpk_p)
k = float(opt.zpk_k)
strain = filter_zpk(strain.astype(numpy.float64), z, p, k)
if opt.normalize_strain:
logging.info("Dividing strain by constant")
l = opt.normalize_strain
strain = strain / l
if opt.injection_file:
logging.info("Applying injections")
injections = InjectionSet(opt.injection_file)
injections.apply(strain, opt.channel_name[0:2])
if opt.sgburst_injection_file:
logging.info("Applying sine-Gaussian burst injections")
injections = SGBurstInjectionSet(opt.sgburst_injection_file)
injections.apply(strain, opt.channel_name[0:2])
logging.info("Highpass Filtering")
strain = highpass(strain, frequency=opt.strain_high_pass)
if precision == 'single':
logging.info("Converting to float32")
strain = (strain * dyn_range_fac).astype(float32)
if opt.gating_file is not None:
logging.info("Gating glitches")
gate_params = numpy.loadtxt(opt.gating_file)
if len(gate_params.shape) == 1:
gate_params = [gate_params]
strain = gate_data(
strain, gate_params,
data_start_time=(opt.gps_start_time - opt.pad_data))
logging.info("Resampling data")
strain = resample_to_delta_t(strain, 1.0/opt.sample_rate, method='ldas')
logging.info("Highpass Filtering")
strain = highpass(strain, frequency=opt.strain_high_pass)
logging.info("Remove Padding")
start = opt.pad_data*opt.sample_rate
end = len(strain)-opt.sample_rate*opt.pad_data
strain = strain[start:end]
if opt.fake_strain:
logging.info("Generating Fake Strain")
duration = opt.gps_end_time - opt.gps_start_time
tlen = duration * opt.sample_rate
pdf = 1.0/128
plen = int(opt.sample_rate / pdf) / 2 + 1
logging.info("Making PSD for strain")
strain_psd = psd.from_string(opt.fake_strain, plen,
pdf, opt.low_frequency_cutoff)
logging.info("Making colored noise")
strain = pycbc.noise.noise_from_psd(tlen, 1.0/opt.sample_rate,
strain_psd,
seed=opt.fake_strain_seed)
strain._epoch = lal.LIGOTimeGPS(opt.gps_start_time)
if opt.injection_file:
logging.info("Applying injections")
injections = InjectionSet(opt.injection_file)
injections.apply(strain, opt.channel_name[0:2])
if opt.sgburst_injection_file:
logging.info("Applying sine-Gaussian burst injections")
injections = SGBurstInjectionSet(opt.sgburst_injection_file)
injections.apply(strain, opt.channel_name[0:2])
if precision == 'single':
logging.info("Converting to float32")
strain = (dyn_range_fac * strain).astype(float32)
if opt.injection_file:
strain.injections = injections
return strain