def read_frame(frame, channel, st=None, et=None, cfac=1.589459e-9): """ reads ligo frames Parameters ---------- frame : `str` filepath to a frame channel : `str` channel in the frame to load st : `int`, date string, optional optional start time. defaults to beginning of frame et : `int ,date string, optional optional end time. defaults to end of frame Returns ------- TS : `Trace` time series trace """ if st is not None and et is not None: d1 = cfac * Trace.read(frame, channel, st, et).detrend() d2 = TimeSeries.read(frame, channel, st, et, format='lalframe') else: d1 = cfac * Trace.read(frame, channel).detrend() d2 = TimeSeries.read(frame, channel, format='lalframe') d1 = Trace(d1.value) d1.__dict__ = d2.copy_metadata() d1.location = d1.get_location() return d1
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
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 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: imc = TimeSeries.fetch(chan2_pat % ifo, st, st + 1) pslvco = TimeSeries.fetch(chan1_pat % ifo, st, et + 1) 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_array2d(start,end,axis='X',prefix='./data',**kwargs): ''' ''' nproc = kwargs.pop('nproc',4) bandpass = kwargs.pop('bandpass',None) blrms = kwargs.pop('blrms',None) fftlen = kwargs.pop('fftlen',2**8) overlap = fftlen/2 # check existance of the spectrogram data fname_hdf5 = fname_hdf5_asd(start,end,prefix,axis) if os.path.exists(fname_hdf5): specgram = Spectrogram.read(fname_hdf5) if blrms: timeseries = specgram.crop_frequencies(blrms[0],blrms[1]).sum(axis=1) return timeseries return specgram # If spectrogram dose not exist, calculate it from timeseries data. try: fname = fname_gwf(start,end,prefix='./data') chname = get_seis_chname(start,end,axis=axis) # check existance of the timeseries data if os.path.exists(fname): data = TimeSeries.read(fname,chname,nproc=nproc) else: # when timeseries data dose not exist fnamelist = existedfilelist(start,end) chname = get_seis_chname(start,end) datadict = TimeSeriesDict.read(fnamelist,chname,nproc=nproc) datadict = datadict.resample(32) datadict = datadict.crop(start,end) chname = get_seis_chname(start,end,axis=axis) datadict.write(fname,format='gwf.lalframe') data = TimeSeries.read(fname,chname,nproc=nproc) # If data broken, raise Error. if data.value.shape[0] != 131072: log.debug(data.value.shape) log.debug('####### {0} {1}'.format(start,end)) raise ValueError('data broken') except: log.debug(traceback.format_exc()) raise ValueError('!!!') # if data broken, raise Error. if data.value.shape[0] != 131072: # (131072 = 2**17 = 2**12[sec] * 2**5[Hz] ) log.debug(data.value.shape) log.debug('!!!!!!!! {0} {1}'.format(start,end)) raise ValueError('data broken') # calculate from timeseries data specgram = data.spectrogram2(fftlength=fftlen,overlap=overlap,nproc=nproc) specgram.write(fname_hdf5,format='hdf5',overwrite=True) return specgram
def channeling_read(out_channels: List[str], **kwargs) -> TimeSeriesDict: out = TimeSeriesDict() for channel in out_channels: for prefix in search_dirs: for in_channel in in_channels: try: # lock the target file h5file, _ = path2h5file(get_path( f'{in_channel} {generation_start}', 'hdf5', prefix=prefix), mode='r') # read off the dataset out[channel] = TimeSeries.read(h5file, channel, **kwargs) except (FileNotFoundError, KeyError, OSError): # file not found / hdf5 can't open file (OSError), channel not in file (KeyError) continue break else: continue break else: # tried all search dirs but didn't find it. Attempt to download. raise FileNotFoundError(f'CANNOT FIND {channel}!!') # out[channel] = TimeSeries.get(channel, **kwargs) # slow. return out
def test_ascii_read(self): fp = self.test_ascii_write(delete=False) try: ts = TimeSeries.read(fp) finally: if os.path.isfile(fp): os.remove(fp)
def check_idq(cache, channel, start, end): """Looks for iDQ frame and reads them. Parameters ---------- cache : :class:`glue.lal.Cache` Cache from which to check. channel : str which idq channel (pglitch) start, end: int or float GPS start and end times desired. Returns ------- tuple Tuple mapping iDQ channel to its maximum P(glitch). Example ------- >>> check_idq(cache, 'H1:IDQ-PGLITCH-OVL-100-1000', 1216496260, 1216496262) ('H1:IDQ-PGLITCH-OVL-100-1000', 0.87) """ if cache: try: idq_prob = TimeSeries.read(cache, channel, start=start, end=end) return (channel, float(idq_prob.max())) except RuntimeError: log.exception('Failed to read from low-latency iDQ frame files') # FIXME: figure out how to get access to low-latency frames outside # of the cluster. Until we figure that out, actual I/O errors have # to be non-fatal. return (channel, None)
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 get_timeseries(chname,**kwargs): start = kwargs.pop('start',None) end = kwargs.pop('end',None) nds = kwargs.pop('nds',None) fname = to_gwffname(chname,**kwargs) if os.path.exists(fname): print('{0} exist.',format(fname)) print('Skip fetch from nds {0}'.format(fname)) data = TimeSeries.read(fname,chname,start,end, format='gwf.lalframe', verbose=True, pad=np.nan) return data elif nds and not os.path.exists(fname): print('{0} dose not exist.',format(fname)) data = TimeSeries.fetch(chname, start, end, verbose=True, host='10.68.10.121', port=8088, pad=np.nan, verify=True,type=1,dtype=np.float32) data.write(fname,format='gwf.lalframe') print('wrote data in '+fname) return data else: print(nds) print(os.path.exists(fname)) print(fname) raise ValueError('! Must use nds or load files') exit()
def generate_gauss_ifo_data(ifoparams, generalparams): # generate gaussian data asd1 = MagSpectrum.read(ifoparams['gw_noise_asd']) if asd1.f0.value != 0: raise ValueError('Initial frequency of supplied ASDs must be zero') # get psd psd1 = MagSpectrum(asd1.value**2, df=asd1.df, f0=asd1.f0, name=ifoparams['name'] + ':gauss_data') fname = (generalparams['output_prefix'] + '/' + 'gaussian_frames/' + '%s-GAUSSIAN-DATA-%d-DAYS.gwf') ndays = float(generalparams['ndays']) # generate gaussian noise print('Generating noise for %s:' % ifoparams['name']) print('Writing it to ' + fname % (ifoparams['name'], float(ndays))) print('============================') ts1 = psd1.generate_gaussian_timeseries(float(ndays) * 86400, float( generalparams['sample_rate']), name=psd1.name) ts1.write(str(fname % (ifoparams['name'], ndays))) # , overwrite=True) ts1_read = TimeSeries.read(str(fname % (ifoparams['name'], ndays)), ifoparams['name'] + ':gauss_data') plot = ts1.asd(10).plot() ax = plot.gca() ax.plot(asd1) ax.plot(ts1_read.asd(10)) plot.savefig('gauss_data_plot_test') print('>>>>>>> DONE GENERATING GAUSSIAN NOISE')
def main(centerTime,duration,frameTypes,channelNames,detectors,rightascension,declination,FFTlength,sampleFrequency): #----- Start and stop time for this event. startTime = centerTime - duration / 2; stopTime = centerTime + duration / 2; # zip frameTypes and detectors, and channel names and detectors frameType = dict(zip(detectors,frameTypes)) channelName = dict(zip(detectors,channelNames)) data = dict() white_data = dict() # Read in the data for iDet in detectors: connection = datafind.GWDataFindHTTPConnection() cache = connection.find_frame_urls(iDet.strip('1'), frameType[iDet], startTime, stopTime, urltype='file') data[iDet] = TimeSeries.read(cache,channelName[iDet], format='gwf',start=startTime,end=stopTime) for (iDet,iSeries) in data.iteritems(): # resample data if iSeries.sample_rate.decompose().value != sampleFrequency: iSeries = iSeries.resample(sampleFrequency) asd = iSeries.asd(FFTlength, FFTlength/2., method='median-mean') # Apply ASD to the data to whiten it whitened = iSeries.whiten(FFTlength, FFTlength/2., asd=asd) white_data[iDet] = whitened.fft()
def main_compare_gif_gotic2(): start = tconvert('Oct 15 2018 00:00:00') end = tconvert('Oct 21 2018 00:00:00') # gif data pfx = '/Users/miyo/Dropbox/KagraData/gif/' segments = GifData.findfiles(start, end, 'CALC_STRAIN', prefix=pfx) allfiles = [path for files in segments for path in files] strain = TimeSeries.read(source=allfiles, name='CALC_STRAIN', format='gif', pad=numpy.nan, nproc=2) strain = strain.detrend('linear') # gotic data source = '201805010000_201811010000.gotic' gifx = KagraGoticStrain.read(source, start=start, end=end).x gifx = gifx.detrend('linear') gifx = gifx * 0.9 # plot plot = Plot(gifx, strain, xscale='auto-gps') plot.legend() plot.subplots_adjust(right=.86) plot.savefig('result.png') plot.close()
def load_data(self, gps_start, gps_end, ifos, fs, channel='GATED'): """ return dict(ifo : gwStrain) """ #print(self._contents) gps_seg = TimeSegment(gps_start, gps_end) ret = dict() for ifo in ifos: channel_name = f'{ifo}_{channel}' if channel in channel_dict: channel_ifo = channel_dict[channel_name] else: channel_ifo = channel_name value = np.array([]) epoch = gps_start check_epoch = True for frame, timeseg, fname in self._iter_segment(ifo): seg = gps_seg.check_overlap(timeseg) if seg is None: continue if check_epoch: epoch = seg.start check_epoch = False data = TimeSeries.read(fname, channel_ifo) srate = data.sample_rate.value idx = seg.get_idx(timeseg.start, srate) data = data[idx] if fs != srate: data = resample(data, srate, fs) value = np.insert(value, len(value), data) ret[ifo] = gwStrain(value, epoch, ifo, fs, info=f'{ifo}_strain') return ret
def load_data_manual(gpsstart, gpsend, ifo, channel, fs=4096): # This method will reset self.value & self.epoch & self.duration filelist, glist = find_data_path(ifo, gpsstart, gpsend) if len(filelist) == 0: return CEV.PROCESS_FAIL argsrt = np.argsort(np.asarray(glist)) value = np.array([]) epoch = int(gpsstart) for idx in argsrt: fname = filelist[idx] data = TimeSeries.read(fname, channel) srate = data.sample_rate.value gf0, gf1 = parse_datafile(fname.name) if epoch < gf0: dataidx0 = 0 if len(value) == 0: epoch = gf0 else: dataidx0 = int((epoch - gf0) * srate) if gpsend > gf1: dataidx1 = data.size else: dataidx1 = int((gpsend - gf0) * srate) + 1 value = np.concatenate([value, data.value[dataidx0:dataidx1]]) ret = gwStrain(value, epoch, ifo, srate, info=f'{ifo}_strain') if fs != srate: return ret.resample(fs) return ret
def raw_to_bandpass(strain_file, t_event, detector, bp_lo, bp_hi): strain = TimeSeries.read(strain_file, format='hdf5.losc') center = int(tevent) strain = strain.crop(center - 16, center + 16) white_data = strain.whiten() white_data_bp = white_data.bandpass(bp_lo, bp_hi) return white_data_bp
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 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 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 psd(): h5path = os.path.join(os.path.dirname(__file__), 'data', 'HLV-GW100916-968654552-1.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 append(self, filename, duration): try: data = TimeSeries.read(filename, self._channel) self._value = np.concatenate([self._value, data]) except: data = np.zeros(self._fs * duration) self._value = np.concatenate([self._value, data]) self._broken_time += duration self._duration += duration
def Grab_Sfiles(start, end, run, channel, frame): """Return a list of Time Series pulled from files stored in this script's directory. Arguments: run -- String representing an observing run (ie O1, O2, O3a, etc). Otherwise as for Grab_Series(). Returns: As for Grab_Series().""" modesl = [] entries = os.listdir('Local_Data/{}/{}'.format(run, channel)) for ends in Seg_Split(start, end, frame): for entry in entries: file = 'Local_Data/{}/{}/{}'.format(run, channel, entry) series = TimeSeries.read(file, channel) if series.times[0].value<=ends[0]<series.times[-1].value: modes = TimeSeries.read(file, channel, ends[0], ends[-1], verbose=True) modesl.append(modes) break return modesl
def read_gif(chname, start, end, write=False): segments = GifData.findfiles(start, end, chname, prefix=pfx) allfiles = [path for files in segments for path in files] data = TimeSeries.read(source=allfiles, name=chname, format='gif', pad=np.nan, nproc=2) data.name = chname return data
def load_inject_condition(t_i, t_f, t_inj, inj_type, inj_params=None, local=False, Tc=16, To=2, fw=2048, window='tukey', detector='H', qtrans=False, qsplit=False, dT=2.0, hp=None, save=False, data_path=None): """Fucntion to load a chunk, inject a waveform and condition, created to enable parallelizing. """ if local: files = get_files(detector) try: data = TimeSeries.read(files, start=t_i, end=t_f, format='hdf5.losc') # load data locally except: return else: # load data from losc try: data = TimeSeries.fetch_open_data(detector + '1', *(t_i, t_f), sample_rate=fw, verbose=False, cache=True) except: return if np.isnan(data.value).any(): return wf_times = data.times.value if inj_type == 'ccsn': shift = int((t_inj - (wf_times[0] + Tc/2)) * fw) hp = np.roll(hp.value, shift) hp = TimeSeries(hp, t0=wf_times[0], dt=data.dt) try: hp = hp.taper() except: pass injected_data = data.inject(hp) else: injected_data = inject(data, t_inj, inj_type, inj_params) cond_data = condition_data(injected_data, To, fw, window, qtrans, qsplit, dT) x = [] times = [] for dat in cond_data: x.append(dat.values) times.append(dat.t0) x = np.asarray(x) times = np.asarray(times) idx = find_closest_index(t_inj, times) x = x[idx] times = times[idx] return x, times
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 get_open_strain_data( name, start_time, end_time, outdir, cache=False, buffer_time=0, **kwargs): """ A function which accesses the open strain data This uses `gwpy` to download the open data and then saves a cached copy for later use Parameters ========== name: str The name of the detector to get data for start_time, end_time: float The GPS time of the start and end of the data outdir: str The output directory to place data in cache: bool If true, cache the data buffer_time: float Time to add to the beginning and end of the segment. **kwargs: Passed to `gwpy.timeseries.TimeSeries.fetch_open_data` Returns ======= strain: gwpy.timeseries.TimeSeries The object containing the strain data. If the connection to the open-data server fails, this function returns `None`. """ from gwpy.timeseries import TimeSeries filename = '{}/{}_{}_{}.txt'.format(outdir, name, start_time, end_time) if buffer_time < 0: raise ValueError("buffer_time < 0") start_time = start_time - buffer_time end_time = end_time + buffer_time if os.path.isfile(filename) and cache: logger.info('Using cached data from {}'.format(filename)) strain = TimeSeries.read(filename) else: logger.info('Fetching open data from {} to {} with buffer time {}' .format(start_time, end_time, buffer_time)) try: strain = TimeSeries.fetch_open_data(name, start_time, end_time, **kwargs) logger.info('Saving cache of data to {}'.format(filename)) strain.write(filename) except Exception as e: logger.info("Unable to fetch open data, see debug for detailed info") logger.info("Call to gwpy.timeseries.TimeSeries.fetch_open_data returned {}" .format(e)) strain = None return strain
def make_omegascan(ifo, t0, durs): """Helper function to create a single omegascan image, with multiple durations. Parameters ---------- ifo : str 'H1', 'L1', or 'V1' t0 : int or float Central time of the omegascan. durs : list of floats/ints List of three durations which will be scanned symmetrically about t0. Example: [0.5, 2, 10] Returns ------- bytes or None bytes of png of the omegascan, or None if no omegascan created. """ # Explicitly use a non-interactive Matplotlib backend. plt.switch_backend('agg') # Collect data longest = max(durs) long_start, long_end = t0 - longest, t0 + longest cache = create_cache(ifo, long_start, long_end) strain_name = app.conf['strain_channel_names'][ifo] try: ts = TimeSeries.read(cache, strain_name, start=long_start, end=long_end).astype('float64') # Do q_transforms for the different durations qgrams = [ts.q_transform( frange=(20, 4096), gps=t0, outseg=(t0 - dur, t0 + dur), logf=True) for dur in durs] except (IndexError, FloatingPointError, ValueError): # data from cache can't be properly read, or data is weird fig = plt.figure() plt.axis("off") plt.text(0.1, 0.45, f"Failed to create {ifo} omegascan", fontsize=17) else: fig = Plot(*qgrams, figsize=(10 * len(durs), 5), geometry=(1, len(durs)), yscale='log', method='pcolormesh') for ax in fig.axes: fig.colorbar(ax=ax, label='Normalized energy', clim=(0, 30)) ax.set_epoch(t0) fig.suptitle(f'Omegascans of {strain_name} at {t0}', fontweight="bold") outfile = io.BytesIO() fig.savefig(outfile, format='png', dpi=300) return outfile.getvalue()
def test_hdf5_read(self): try: hdfout = self.test_hdf5_write(delete=False) except ImportError as e: raise unittest.SkipTest(str(e)) else: try: ts = TimeSeries.read(hdfout, 'TEST CASE') finally: if os.path.isfile(hdfout): os.remove(hdfout)
def set_from_csv(self, filename): """ Set the strain data from a csv file Parameters ========== filename: str The path to the file to read in """ from gwpy.timeseries import TimeSeries timeseries = TimeSeries.read(filename, format='csv') self.set_from_gwpy_timeseries(timeseries)
def generate_noise_from_file(cls, file_name, event_time, block_time, channel_names, sample_frequency, verbose=False): """Obtain data for either on source, off source, or injections. This uses the gwpy `TimeSeriesDict.get` method Parameters ---------- event_time : (`float) trigger time of event to be processing block_time : (`int`) length of data to be processed channel_names (`list`) : required data channels. sample_frequency (`int`): sample rate of the data desired verbose : `bool`, optional print verbose output about NDS progress. Returns: `TimeSeriesDict` : """ #----- Start and stop time for this event. start_time = event_time - block_time / 2 stop_time = event_time + block_time / 2 # Retrieve data and then resample and set epoch data = {} for det in channel_names: data[det] = TimeSeries.read(file_name, path='/noise/aLIGOZeroDetHighPower') data = XTimeSeries(data) for (idet, iseries) in data.items(): # set epoch of timeseries to the event_time iseries.t0 = start_time # set one of the detectors to be the reference detecotr # for any future coherent combinations return data
def get_spectrogram(start, end, axis='X', seis='EXV', **kwargs): ''' Get Spectrogram Parameters ---------- start : `int` start GPS time. end : `int` end GPS time. Returns ------- specgram : `gwpy.spectrogram.Spectrogram` spectrogram. ''' nproc = kwargs.pop('nproc', 3) bandpass = kwargs.pop('bandpass', None) fftlen = kwargs.pop('fftlen', 2**8) diff = kwargs.pop('diff', False) fs = kwargs.pop('fs', 256) fname_hdf5 = fname_specgram(start, end, prefix=seis, axis=axis) # Load specgram from hdf5 file if os.path.exists(fname_hdf5): specgram = Spectrogram.read(fname_hdf5, format='hdf5') return specgram # If no file, make specgram from timeseries data try: chname = get_seis_chname(start, end, axis=axis, seis=seis)[0] fnamelist = existedfilelist(start, end) data = TimeSeries.read(fnamelist, chname, nproc=nproc) data = data.resample(fs) data = data.crop(start, end) except: log.debug(traceback.format_exc()) raise ValueError('!!! {0} {1}'.format(start, end)) # calculate specgram specgram = data.spectrogram2(fftlength=fftlen, overlap=fftlen / 2, nproc=nproc) try: fname_dir = '/'.join(fname_hdf5.split('/')[:4]) if not os.path.exists(fname_dir): os.makedirs(fname_dir) specgram.write(fname_hdf5, format='hdf5', overwrite=True) log.debug('Make {0}'.format(fname_hdf5)) except: log.debug(traceback.format_exc()) raise ValueError('!!!') return specgram
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 get_primary_ts(channel, start, end, filepath=None, frametype=None, cache=None, nproc=1): """Retrieve primary channel timeseries by either reading a .gwf file or querying """ if filepath is not None: LOGGER.info('Reading primary channel file') return TimeSeries.read(filepath, channel=channel, start=start, end=end, format='gwf', nproc=nproc) else: LOGGER.info('Querying primary channel') return get_data(channel, start, end, verbose='Reading primary:'.rjust(30), frametype=frametype, source=cache, nproc=nproc)
def get_lsd(cache, channel, GPSstart, duration, stride, overlap, pltflg=0, filename='', yunit=''): ''' This function calculates linear spectral density. If pltflg==1, make plot. Return: lsd, freq, mu(meanvalue) ''' data = TimeSeries.read(cache, channel, GPSstart, GPSstart + duration, format='lalframe') fs = 1. / data.dt.value # sampling frequency mu = np.mean(data.value) # mean value of data # Define parameters for FFT st = stride # FFT stride in seconds ov = st * overlap # overlap in seconds nfft = int(st * fs) freq, t, Sxx = signal.spectrogram(data.value - mu, window=signal.hann(nfft), nperseg=nfft, fs=fs, noverlap=int(ov * fs)) lspg = np.sqrt(Sxx) lsd = np.mean(lspg, axis=1) if pltflg == 1: plt.figure() plt.loglog(freq, lsd) plt.grid(True) plt.title(channel) plt.xlim(freq[1:].min(), freq[1:].max()) plt.xlabel('Frequency [Hz]') plt.ylabel('LSD [' + yunit + '/rtHz]') plt.tight_layout() fname = filename plt.savefig(fname) plt.close() return lsd, freq, mu
def get_spectrogram(cache, channel, GPSstart, duration, stride, overlap, pltflg=0, filename='', rtnflg=0): ''' This function calculated linear spectrogram. If pltflg==1, makes plot. If rtnflg==1, returns lspg, time, freq, mu ''' data = TimeSeries.read(cache, channel, GPSstart, GPSstart + duration, format='lalframe') fs = 1. / data.dt.value # sampling frequency mu = np.mean(data.value) # mean value of data # Define parameters for FFT st = stride # FFT stride in seconds ov = st * overlap # overlap in seconds nfft = int(st * fs) freq, t, Sxx = signal.spectrogram(data.value - mu, window=signal.hann(nfft), nperseg=nfft, fs=fs, noverlap=int(ov * fs)) lspg = np.sqrt(Sxx) if pltflg == 1: T, FREQ = np.meshgrid(t, freq) fig2, ax = plt.subplots() pc = ax.pcolor(T, FREQ, 10 * np.log10(lspg), cmap='rainbow') cb = fig2.colorbar(pc) fname = filename plt.sacefig(fname) plt.close() if rtnflg == 1: return lspg, t, freq, mu
def hoge(gps): if np.isnan(gps): return None from gwpy.time import tconvert #print tconvert(gps) from gwpy.timeseries import TimeSeries from glue.lal import Cache channel = 'K1:PEM-EXV_SEIS_Z_SENSINF_OUT_DQ' start = gps #- 5*60 end = gps + 30*60 gwf_cache = 'full_Sep01-Nov01.cache' with open(gwf_cache, 'r') as fobj: cache = Cache.fromfile(fobj) #print cache data = TimeSeries.read(cache,channel,start=start,end=end,verbose=True,nproc=2,pad=np.nan,format='gwf.lalframe') plot = data.plot( title = 'hoge' #ylabel='Strain amplitude', ) plot.savefig('{0}.png'.format(gps)) plot.close()
parser.add_option("--condor-cluster", type="float",help="Cluster ID") parser.add_option("--proc", type="float", help="Job ID") (opts, args) = parser.parse_args() starttime = opts.starttime endtime = opts.endtime h0_max = opts.h0 wm = 'all/fg500' #-------- Importing, filtering and timeshifting data ----------# durationH = endtime - starttime oldstarttime = starttime oldendtime = endtime Xspacing = 2.44140625E-4 pathtoinput = "/home/spxha/" strainH = TimeSeries.read(pathtoinput+'S6framesH1.lcf',channel='H1:LDAS-STRAIN', start=starttime, end=endtime) strainL = TimeSeries.read(pathtoinput+'S6framesL1.lcf',channel='L1:LDAS-STRAIN', start=starttime, end=endtime) num_points = int(durationH/Xspacing) h0_min = 0.0000001 h0_vals_num = 30 #---------------------------- # Applying a bandpass filter #---------------------------- coefsL = get_filter_coefs('L1') coefsH = get_filter_coefs('H1') strainL = filter_data(strainL,coefsL) strainH = filter_data(strainH,coefsH) timeH = np.arange(starttime, endtime, Xspacing) timeL = timeH detMap = {'H1': lal.LALDetectorIndexLHODIFF, 'L1': lal.LALDetectorIndexLLODIFF}
def validity_test(starttime, endtime, h0_max=0.001): #------- Packages ---------# print 'Importing packages' import numpy as np import astropy, gwpy, h5py, lal, sys, os from astropy.coordinates import get_sun import astropy.time as Time from scipy.signal import butter, filtfilt from gwpy.timeseries import TimeSeries from antres import antenna_response as ant_res from scipy.misc import logsumexp from notchfilt import get_filter_coefs, filter_data from optparse import OptionParser #-------- Importing, filtering and timeshifting data ----------# print 'Reading data' durationH = endtime - starttime # same for durationL, but not used anyway oldstarttime = starttime # for use later oldendtime = endtime # for use later Xspacing = 2.44140625E-4 gpsTime = np.linspace(starttime,endtime,int(1/Xspacing)) pathtoinput = "/home/spxha/" strainH = TimeSeries.read(pathtoinput+'S6framesH1.lcf',channel='H1:LDAS-STRAIN', start=starttime, end=endtime) strainL = TimeSeries.read(pathtoinput+'S6framesL1.lcf',channel='L1:LDAS-STRAIN', start=starttime, end=endtime) num_points = int(durationH/Xspacing) h0_min=0.00005 h0_vals_num=30 # Adding in a fake signal # frequency in the middle of the range we're interested in 125 Hz omega = 250.0*np.pi amplitude = 0.5e-24 # (hopefully) middle of h0 values # the signal to introduce is of the form amplitude*np.sin(omega*t) # first get timeL and timeH in synch with the sun's position print 'Getting the detectors in sync' timeH = np.arange(starttime, endtime, Xspacing) timeL = timeH detMap = {'H1': lal.LALDetectorIndexLHODIFF, 'L1': lal.LALDetectorIndexLLODIFF} detH1 = lal.CachedDetectors[detMap['H1']] detL1 = lal.CachedDetectors[detMap['L1']] tgps = lal.LIGOTimeGPS(starttime, 0) #---------- Get right ascension and declination of source in radians ----------# numseg30 = int((endtime-starttime)/30.) seg30 = starttime + 30*np.linspace(1,numseg30,numseg30) # 30 second update rate tdelay = [[0] for _ in range(numseg30)] tdelay = [[0] for _ in range(numseg30)] for i in range(numseg30-1): for j in range(int(len(timeL)*Xspacing)): if ((timeL[j/Xspacing]>seg30[i])&(timeL[j/Xspacing]<seg30[i+1])): coordstime=seg30[i] coords = get_sun(Time.Time(coordstime,format='gps')) tdelay[i] = lal.ArrivalTimeDiff(detH1.location, detL1.location, coords.ra.hour*np.pi/12, coords.dec.hour*np.pi/12, tgps) coordstime = seg30[-1] coords = get_sun(Time.Time(coordstime,format='gps')) tdelay[-1] = lal.ArrivalTimeDiff(detH1.location, detL1.location, coords.ra.hour*np.pi/12, coords.dec.hour*np.pi/12, tgps) tdelay = np.array(tdelay) tdelay = np.repeat(tdelay,int(30/Xspacing)) # make sure tdelay and timeL are of same length in case integer-ing caused slight inconsistency. b = np.ones(len(timeL)-len(tdelay))*tdelay[-1] tdelay = np.append(tdelay,b) timeL = timeL - tdelay #------------ Down-sampling ------------# print 'Down-sampling' Xspacing = Xspacing*8 num_points = int(durationH/Xspacing) newtimeL, newtimeH, newstrainH, newstrainL, newtdelay = [[0 for _ in range(num_points)] for _ in range(5)] for i in range(num_points): j = 8*i + 4 newstrainH[i] = np.mean(strainH[j-4:j+4]) newstrainL[i] = np.mean(strainL[j-4:j+4]) newtimeH[i] = timeH[j] newtimeL[i] = timeL[j] newtdelay[i] = tdelay[j] newstrainH = newstrainH[76800:len(newstrainH)] newstrainL = newstrainL[76800:len(newstrainL)] newtimeH = newtimeH[76800:len(newtimeH)] newtimeL = newtimeL[76800:len(newtimeL)] newtdelay = newtdelay[76800:len(newtdelay)] starttime = starttime + 150 durationH = int(newtimeH[-1]) - int(newtimeH[0]) num_points = int(durationH/Xspacing) del timeL, timeH, tdelay, strainH, strainL #----------- add in fake signal ------------# newtimeH = newtimeH[0:num_points] newtimeL = newtimeL[0:num_points] newtdelay = newtdelay[0:num_points] print 'Insert fake signal' numseg = int((durationH)/600) segs = np.linspace(0,numseg,numseg+1)*600 segs = segs + newtimeL[0] psi1=np.pi/4 ra,dec,fp,fc = [[0 for _ in range(numseg+1)] for _ in range(4)] for i in range(numseg+1): coordstime = segs[i] coords = get_sun(Time.Time(coordstime,format='gps')) ra[i] = coords.ra.hour*np.pi/12 dec[i] = coords.dec.hour*np.pi/12 FcX0, FpX0, FcY0, FpY0 = [[0 for _ in range(num_points)] for _ in range(4)] for i in range(num_points): FpX0[i], FcX0[i] = ant_res(gpsTime[int(i*Xspacing/600.)], ra[int(i*Xspacing/600.)], dec[int(i*Xspacing/600.)], 0, 'H1') FpY0[i], FcY0[i] = ant_res(gpsTime[int(i*Xspacing/600.)], ra[int(i*Xspacing/600.)], dec[int(i*Xspacing/600.)], 0, 'L1') cos2pi1 = np.cos(2*psi1) sin2pi1 = np.sin(2*psi1) fakeH, fakeL, FpX, FcX, FpY, FcY = [[0 for _ in range(num_points)] for _ in range(6)] for i in range(num_points): FpX[i] = FpX0[i]*cos2pi1 + FcX0[i]*sin2pi1 FcX[i] = FcX0[i]*cos2pi1 - FpX0[i]*sin2pi1 FpY[i] = FpY0[i]*cos2pi1 + FcY0[i]*sin2pi1 FcY[i] = FcY0[i]*cos2pi1 - FpY0[i]*sin2pi1 for i in range(len(newtimeH)): fakeH[i] = amplitude*(FpX[i]*np.sin(omega*newtimeH[i]) + FcX[i]*np.cos(omega*newtimeH[i])) fakeL[i] = amplitude*(FpY[i]*np.sin(omega*newtimeL[i]) + FcY[i]*np.cos(omega*newtimeL[i])) tdelayidx = [0 for _ in range(len(newtdelay))] for i in range(len(newtdelay)): tdelayidx[i] = int(newtdelay[i]*Xspacing) idxmax= np.max(tdelayidx) print len(newtdelay), len(newstrainL) newstrainL0,newstrainH0 = [[0 for _ in range(len(newtdelay)-idxmax)] for _ in range(2)] for i in range(idxmax,len(newtdelay)): newstrainL0[i-idxmax]=newstrainL[i-tdelayidx[i]] newstrainH0=newstrainH[0:len(newstrainL0)] newstrainH0 = newstrainH0 + fakeH newstrainL0 = newstrainL0 + fakeL del newstrainL, newstrainH, fakeL, fakeH # H1 and L1 are now in sync and filtered between 100 and 150 Hz. del FcX,FcX0,FpX,FpX0,FcY,FcY0,FpY,FpY0 #----- Applying a bandpass filter -----# print 'Filtering data' coefsL = get_filter_coefs('L1') coefsH = get_filter_coefs('H1') newstrainL0 = np.array(newstrainL0) newstrainH0 = np.array(newstrainH0) newstrainL = filter_data(newstrainL0,coefsL) newstrainH = filter_data(newstrainH0,coefsH) del coefsL, coefsH ############################################################ #------------ Finding probability distribution ------------# # ------------ Defining some stuff for p ------------- # print 'Finding likelihood Part 1/2' psi_array = np.linspace(0,np.pi,10) dpsi = psi_array[1]-psi_array[0] sigmaA = 10.0 h0min = h0_min*np.std(newstrainH) h0max = h0_max*np.std(newstrainH) h0_array = np.linspace(h0min,h0max,h0_vals_num) invSigma0 = np.array([[(1./sigmaA**2), 0.], [0., (1./sigmaA**2)]]) detSigma0 = sigmaA**4 dX = newstrainH dY = newstrainL del newstrainH, newstrainL, newstrainH0, newstrainL0, newtimeL, newtimeH FcX0, FpX0, FcY0, FpY0 = [[0 for _ in range(num_points)] for _ in range(4)] for i in range(num_points): FpX0[i], FcX0[i] = ant_res(gpsTime[int(i*Xspacing/600.)], ra[int(i*Xspacing/600.)], dec[int(i*Xspacing/600.)], 0, 'H1') FpY0[i], FcY0[i] = ant_res(gpsTime[int(i*Xspacing/600.)], ra[int(i*Xspacing/600.)], dec[int(i*Xspacing/600.)], 0, 'L1') p = [0 for _ in range(len(h0_array))] ppsi = [0 for _ in range(len(psi_array))] logdpsi_2 = np.log(0.5*dpsi) cos2pi, sin2pi = [[0 for _ in range(len(psi_array))] for _ in range(2)] FpX, FcX, FpY, FcY = [[[0 for _ in range(num_points)] for _ in range(len(psi_array))] for _ in range(4)] for k in range(len(psi_array)): cos2pi[k] = np.cos(2*psi_array[k]) sin2pi[k] = np.sin(2*psi_array[k]) for i in range(num_points): FpX[k][i] = FpX0[i]*cos2pi[k] + FcX0[i]*sin2pi[k] FcX[k][i] = FcX0[i]*cos2pi[k] - FpX0[i]*sin2pi[k] FpY[k][i] = FpY0[i]*cos2pi[k] + FcY0[i]*sin2pi[k] FcY[k][i] = FcY0[i]*cos2pi[k] - FpY0[i]*sin2pi[k] print 'Finding likelihoot Part 2/2. This will take a while... ' for i in range(num_points): d = np.array([dX[i], dY[i]]) d.shape = (2,1) if (i + int(60/Xspacing)<num_points): int1 = i + int(60/Xspacing) else: int1 = i if (i - int(60/Xspacing)>0): int0 = i - int(60/Xspacing) else: int0 = 0 sigmaX = np.std(dX[int0:int1]) sigmaY = np.std(dY[int0:int1]) C = np.array([[sigmaX**2, 0.], [0., sigmaY**2]]) invC = np.array([[(1./sigmaX**2), 0.], [0., (1/sigmaY**2)]]) detC = sigmaX**2 * sigmaY**2 for j in range(len(h0_array)): for k in range(len(psi_array)): M = h0_array[j]*np.array([[FpX[k][i], FpY[k][i]], [FcX[k][i], FcY[k][i]]]) M = np.array([[M[0][0][0],M[0][1][0]],[M[1][0][0], M[1][1][0]]]) invSigma = np.dot(M.T, np.dot(invC, M)) + invSigma0 Sigma = np.linalg.inv(invSigma) detSigma = np.linalg.det(Sigma) chi = np.dot(Sigma, np.dot(M.T, np.dot(invC, d))) ppsi[k] = 0.5*np.log(detSigma) - 0.5*np.log(16.*np.pi**4*detSigma0*detC) - 0.5*(np.vdot(d.T, np.dot(invC, d)) + np.vdot(chi.T, np.dot(invSigma, chi))) p[j] += logdpsi_2 + logsumexp([logsumexp(ppsi[:-1]), logsumexp(ppsi[1:])]) # Write into a file. wm = 'all/siginj' if os.path.exists(wm)==False: os.mkdir(wm) else: pass np.savetxt(wm+'/p'+str(oldstarttime)+'.txt',p) np.savetxt(wm+'/h0'+str(oldstarttime)+'.txt',h0_array)
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
__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. signal = signal.taper() # Since the time samples overlap, we can inject this into our noise data # using :meth:`~gwpy.types.series.Series.inject`: data = noise.inject(signal) # Finally, we can visualize the full process in the time domain:
ifo = str(sys.argv[5]) frames = ifo + '1_M' channel_list = str(sys.argv[3]) out_file = str(sys.argv[4]) fP = open(out_file,'w') chan_list = [] chan_read = open(channel_list) for line in chan_read.readlines(): chan_list.append(line) connection = datafind.GWDataFindHTTPConnection() cache = connection.find_frame_urls(ifo, frames, start_gps, end_gps, urltype='file') for chan in chan_list: chan1 = chan[:-1] data1=TimeSeries.read(cache, chan1, start=start_gps, end=end_gps) if any(diff(data1.value)>0): print >> fP, chan1 fP.close()
def generate_triggers(channel,gps_start,gps_end,ifo,frames,outdir,segments,padding): # generate frame cache and connection pad_gps_end = gps_end - padding print "Processing segment: " + str(gps_start) + " - " + str(pad_gps_end) connection = datafind.GWDataFindHTTPConnection() cache = connection.find_frame_urls(ifo, frames, int(gps_start), int(gps_end), urltype='file') data=TimeSeries.read(cache, channel, start=int(gps_start), end=int(pad_gps_end)) time_vec=data.times.value ''' We are interested in times when the channels switch from a normal state to an overflowing state or vice versa. We're not checking the first and last data point of each set because it's not possible to tell whether or not a channel has just started overflowing at our first data point or if it had been overflowing beforehand. This big loop will test every data point (that isn't an endpoint) and record it in the trigger vector if it's an overflow transition. ''' # trig_segs = seg.segmentlist() # # for j in np.arange(np.size(data,0)): # if (0 < j < (np.size(data,0) - 1)): # if cumu_seg_test(data[j-1],data[j],data[j+1]): # trig_segs |= seg.segmentlist([seg.segment(time_vec[j+1],time_vec[j+1]+1)]) # # trig_segs = trig_segs.coalesce() trigger_vec = [] for j in np.arange(np.size(data,0)): if (0 < j < (np.size(data,0) - 1)): if cumu_seg_test(data[j-1],data[j],data[j+1]): trigger_vec.append(time_vec[j+1]) if (np.size(trigger_vec) == 0): print "No triggers found for " + str(channel) return else: print "Found triggers for " + str(channel) # map triggers into float type and then convert them all into LIGOTimeGPS notation trig_times = map(LIGOTimeGPS,map(float,trigger_vec)) # create mocked up frequency and SNR vectors to fill in XML tables freqs = np.empty(np.size(trigger_vec)) freqs.fill(100) snrs = np.empty(np.size(trigger_vec)) snrs.fill(10) sngl_burst_table_up = lsctables.New(lsctables.SnglBurstTable, ["peak_time", "peak_time_ns","peak_frequency","snr"]) for t,f,s in zip(trig_times, freqs, snrs): row = sngl_burst_table_up.RowType() row.set_peak(t) row.peak_frequency = f row.snr = s sngl_burst_table_up.append(row) xmldoc_up = ligolw.Document() xmldoc_up.appendChild(ligolw.LIGO_LW()) xmldoc_up.childNodes[0].appendChild(sngl_burst_table_up) directory_up = (outdir + '/' + channel[:2] + "/" + channel[3:] + "/" + str(gps_start)[:5] + "/") if not os.path.exists(directory_up): os.makedirs(directory_up) utils.write_filename(xmldoc_up, directory_up + channel[:2] + "-" + channel[3:6] + "_" + channel[7:] + "_ADC-" + str(gps_start) + "-" + str(gps_end - gps_start) + ".xml.gz", gz=True)
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]
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: self.start_list = list(set(map(int, arg_list.start))) 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.") sys.exit(2) return
a, b = 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(polyfit(data[idx1:idx2, 0], data[idx1:idx2, 1], 1, w=weights[idx1 - idx + width:idx2 - idx + width])) coeffs = array(coeffs) times = 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 = arange(len(imc)) / 256. coeffs0 = interp(samp_times, times, coeffs[:, 0]) coeffs1 = 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 setUp(self): # read data self.data = TimeSeries.read(self.framefile, 'L1:LDAS-STRAIN') # calculate PSD self.psd = self.data.psd(0.4, 0.2, window=('kaiser', 24))
# plotting all the data from gwpy.timeseries import TimeSeries import matplotlib.pyplot as plt import numpy as np import gwpy import glue data = np.loadtxt('/home/spxha/solarGW/intersect6.txt',dtype='f8') TimesStart = data[:,0] TimesEnd = data[:,1] Xspacing = 2.44140625E-4 for i in range(len(TimesStart)): print i duration = TimesEnd[i]-TimesStart[i] timeseriesi = np.linspace(TimesStart[i], TimesEnd[i], int(duration/Xspacing)) straini = TimeSeries.read('/home/spxha/S6framesH1.lcf',channel='H1:PSL-ODC_CHANNEL_OUT_DQ',start=TimesStart[i], end=TimesEnd[i], format='lcf') if i==0: strain = straini timeseries = timeseriesi else: strain = np.append(strain, straini) timeseries = np.append(timeseries, timeseriesi) del duration, timeseriesi, straini plt.figure() plt.plot(timeseries,strain) plt.savefig('/home/spxha/Timeseries.png')
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') if __name__ == '__main__': ifo = sys.argv[1] st = int(sys.argv[2]) dur = int(sys.argv[3]) et = st + dur connection = datafind.GWDataFindHTTPConnection() cache = connection.find_frame_urls( ifo[0], '%s_R' % ifo, st, et, urltype='file') print "Get IMC" imc = TimeSeries.read(cache, chan2_pat % ifo, st, et) print "Get psl" pslvco = TimeSeries.read(cache, chan1_pat % ifo, st, et + 1) print "Downsample psl" pslvco = pslvco[16 + 8::16] print "Downsample imc" imc_srate = int(imc.sample_rate.value) imc = imc[imc_srate / 2::imc_srate] print "Saving" data = numpy.array((imc.data, pslvco.data)).T fname = "%s-imc-vco-%u-%u.npy" % (ifo, st, dur) numpy.save("%s-imc-vco-%u-%u.npy" % (ifo, st, dur), data) dump_calibrated_data(fname)
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 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}
def setUp(self): self.ts = TimeSeries.read(TEST_HDF_FILE, 'H1:LDAS-STRAIN')
# for now let's just assume you're not looking at a lock # longer than a day... for i in range(int(86400 / t)): new_times = [] new_freqs = [] for time, snr, freq in zip(times, snrs, freqs): if time > st and time < st + t: new_times.append(time) new_freqs.append(freq) if len(new_times) == 0: st += t continue connection = datafind.GWDataFindHTTPConnection() cache = connection.find_frame_urls( 'L', 'L1_C', st, st + t, urltype='file') data = TimeSeries.read(cache, channel, st, st + t) data2 = detrend(data) data = TimeSeries( data2, dx=data.dx, sample_rate=data.sample_rate, x0=data.x0) specgram = data.spectrogram2(fftlength=.1, overlap=0.1 * 0.9) specgram = specgram.ratio('median') plot = specgram.plot(vmin=1, vmax=10, norm='log') plot.add_colorbar(label='amplitude relative to median') ax = plot.gca() ax.set_ylim(40, 7e4) ax.set_yscale('log') # ax.scatter(new_times,new_freqs,'x',color='r') for time, freq in zip(new_times, new_freqs): ax.scatter(time, freq, marker='x', color='r', s=160) ax.set_title('expect %d triggers' % (len(new_times))) plotfile = '%s/%s/%s/%d/%d' % (dir2, extra_dir,
if (x == y != z) and (z != 0): return True else: return False # check if an overflow channel is cumulative by crosschecking ndcuid_list and model_list # model list lines are recorded as <model_name.mdl> <cumulative status> <ndcuid=num> def checkCumulative(chan_name,model_list,ndcuid_list): ID = 'ndcuid=' + str(chan_name)[str(chan_name).find('-')+1:str(chan_name).find('_')] if (model_list[ndcuid_list.index(ID)][1] == 'cumulative'): return True else: return False data=TimeSeries.read(cache, channel, start=gps_start, end=gps_end) time_vec = linspace(gps_start,gps_end,(gps_end - gps_start)*16,endpoint=False) ''' We are interested in times when the channels switch from a normal state to an overflowing state or vice versa. We're not checking the first and last data point of each set because it's not possible to tell whether or not a channel has just started overflowing at our first data point or if it had been overflowing beforehand. This big loop will test every data point (that isn't an endpoint) and record it in the trigger vector if it's an overflow transition. '''
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)