PyCBC 2.3.5__tar.gz → 2.3.7__tar.gz

{PyCBC-2.3.5 → PyCBC-2.3.7}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: PyCBC
-Version: 2.3.5
+Version: 2.3.7
 Summary: Core library to analyze gravitational-wave data, find signals, and study their parameters.
 Home-page: http://www.pycbc.org/
 Author: The PyCBC team
 Author-email: alex.nitz@gmail.org
 License: UNKNOWN
-Download-URL: https://github.com/gwastro/pycbc/tarball/v2.3.5
+Download-URL: https://github.com/gwastro/pycbc/tarball/v2.3.7
 Description: ![GW150914](https://raw.githubusercontent.com/gwastro/pycbc-logo/master/pycbc_logo_name.png)
         
         [PyCBC](http://pycbc.org) is a software package used to explore astrophysical sources of gravitational waves.

{PyCBC-2.3.5 → PyCBC-2.3.7}/PyCBC.egg-info/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: PyCBC
-Version: 2.3.5
+Version: 2.3.7
 Summary: Core library to analyze gravitational-wave data, find signals, and study their parameters.
 Home-page: http://www.pycbc.org/
 Author: The PyCBC team
 Author-email: alex.nitz@gmail.org
 License: UNKNOWN
-Download-URL: https://github.com/gwastro/pycbc/tarball/v2.3.5
+Download-URL: https://github.com/gwastro/pycbc/tarball/v2.3.7
 Description: ![GW150914](https://raw.githubusercontent.com/gwastro/pycbc-logo/master/pycbc_logo_name.png)
         
         [PyCBC](http://pycbc.org) is a software package used to explore astrophysical sources of gravitational waves.

{PyCBC-2.3.5 → PyCBC-2.3.7}/PyCBC.egg-info/SOURCES.txt

@@ -153,6 +153,7 @@ bin/plotting/pycbc_mass_area_plot
 bin/plotting/pycbc_mchirp_plots
 bin/plotting/pycbc_page_banktriggerrate
 bin/plotting/pycbc_page_coinc_snrchi
+bin/plotting/pycbc_page_dq_table
 bin/plotting/pycbc_page_foreground
 bin/plotting/pycbc_page_foundmissed
 bin/plotting/pycbc_page_ifar
@@ -165,6 +166,7 @@ bin/plotting/pycbc_page_sensitivity
 bin/plotting/pycbc_page_snrchi
 bin/plotting/pycbc_page_snrifar
 bin/plotting/pycbc_page_snrratehist
+bin/plotting/pycbc_page_template_bin_table
 bin/plotting/pycbc_page_versioning
 bin/plotting/pycbc_page_vetotable
 bin/plotting/pycbc_plot_background_coincs

{PyCBC-2.3.5 → PyCBC-2.3.7}/bin/all_sky_search/pycbc_bin_trigger_rates_dq

@@ -71,9 +71,9 @@ with HFile(args.trig_file, 'r') as trig_file:
     data_mask = np.zeros(n_triggers_orig, dtype=bool)
     data_mask[idx] = True
 
-    # also get the gated times while we have the file open
+if args.gating_windows:
     gate_times = []
-    if args.gating_windows:
+    with h5.File(args.trig_file, 'r') as trig_file:
         logging.info('Getting gated times')
         try:
             gating_types = trig_file[f'{ifo}/gating'].keys()
@@ -188,6 +188,7 @@ with h5.File(args.output_file, 'w') as f:
             frac_dt = abs(segs) / livetime
             dq_rates[state] = frac_eff / frac_dt
         bin_grp['dq_rates'] = dq_rates
+        bin_grp['num_triggers'] = len(trig_times_bin)
 
     # save dq state segments
     for dq_state, segs in dq_state_segs_dict.items():
@@ -196,7 +197,10 @@ with h5.File(args.output_file, 'w') as f:
         starts, ends = segments_to_start_end(segs)
         dq_grp['segment_starts'] = starts
         dq_grp['segment_ends'] = ends
+        dq_grp['livetime'] = abs(segs)
 
     f.attrs['stat'] = f'{ifo}-dq_stat_info'
+    f.attrs['sngl_ranking'] = args.sngl_ranking
+    f.attrs['sngl_ranking_threshold'] = args.stat_threshold
 
 logging.info('Done!')

{PyCBC-2.3.5 → PyCBC-2.3.7}/bin/all_sky_search/pycbc_make_bayestar_skymap

@@ -23,8 +23,14 @@ import glob
 import sys
 import random
 import tempfile
+
+from ligo.lw import lsctables, utils as ligolw_utils
+
 import pycbc.version
 from pycbc import init_logging
+from pycbc.waveform import bank as wavebank
+from pycbc.io import WaveformArray
+from pycbc.io.ligolw import LIGOLWContentHandler
 
 parser = argparse.ArgumentParser(description=__doc__)
 parser.add_argument('--version', action="version",
@@ -38,14 +44,12 @@ parser.add_argument('--bayestar-executable',
 parser.add_argument('--event-xml', required=True,
                     help="XML file containing event information, SNR "
                          "timeseries and PSD to pass to bayestar")
-parser.add_argument('--waveform', default='TaylorF2',
-                    help="Waveform used in the matched-filtering "
-                         "to generate the SNR timeseries.")
 parser.add_argument('--low-frequency-cutoff', type=float, default=20,
                     help="Low-frequency cutoff used in the matched-filtering "
                          "to generate the SNR timeseries")
 parser.add_argument('--output-file', required=True,
                     help="Filename to output the fits file to.")
+wavebank.add_approximant_arg(parser)
 args, unknown = parser.parse_known_args()
 
 # Default logging is set higher than normal for this job
@@ -57,12 +61,36 @@ bayestar_exe = args.bayestar_executable or 'bayestar-localize-coincs'
 
 tmpdir = tempfile.mkdtemp()
 
+# Work out which approximant is being used
+# Load the file
+xmldoc = ligolw_utils.load_filename(
+    args.event_xml,
+    contenthandler=LIGOLWContentHandler
+)
+
+# Grab the single inspiral table(s) which contain the template information
+sngl_inspiral_table = lsctables.SnglInspiralTable.get_table(xmldoc)
+
+# turn this into a waveform array
+row = WaveformArray.from_ligolw_table(
+    sngl_inspiral_table,
+)
+
+# Work out which waveform is used based on the template information
+# Note that as there are multiple single inspiral tables (one per ifo)
+# with the same information, we use [0] here
+waveform = wavebank.parse_approximant_arg(args.approximant, row)[0]
+
+# BAYESTAR uses TaylorF2 instead of SPAtmplt
+if waveform == 'SPAtmplt':
+    waveform = 'TaylorF2'
+
 # Set up the command to pass to bayestar.
 # The XML file path being passed twice is a legacy requirement, not a mistake.
 cmd = [bayestar_exe,
        args.event_xml,
        args.event_xml,
-       '--waveform', args.waveform,
+       '--waveform', waveform,
        '--f-low', str(args.low_frequency_cutoff),
        '-o', tmpdir]
 

{PyCBC-2.3.5 → PyCBC-2.3.7}/bin/all_sky_search/pycbc_prepare_xml_for_gracedb

@@ -96,7 +96,7 @@ def read_psds(psd_files):
         psd = [group["psds"][str(i)] for i in range(len(group["psds"].keys()))]
         psds[ifo] = segmentlist(psd_segment(*segargs) for segargs in zip(
             psd, group["start_time"], group["end_time"]))
-        return psds
+    return psds
 
 psds = read_psds(args.psd_files)
 

{PyCBC-2.3.5 → PyCBC-2.3.7}/bin/all_sky_search/pycbc_sngls_findtrigs

@@ -43,6 +43,8 @@ parser.add_argument('--cluster-window', type=float,
                     help='Window (seconds) during which to keep the trigger '
                          'with the loudest statistic value. '
                          'Default=do not cluster')
+parser.add_argument("--minimum-stat", type=float,
+                    help="Minimum statistic value to store.")
 parser.add_argument("--output-file",
                     help="File to store the candidate triggers")
 stat.insert_statistic_option_group(parser)
@@ -159,6 +161,12 @@ for tnum in template_ids:
         tids_full = tids_full[cid]
         trigger_times = trigger_times[cid]
 
+    if args.minimum_stat is not None:
+        keep = stat_t >= args.minimum_stat
+        stat_t = stat_t[keep]
+        tids_full = tids_full[keep]
+        trigger_times = trigger_times[keep]
+
     trigger_ids_all += list(tids_full)
     template_ids_all += list(tnum * np.ones_like(tids_full))
     trigger_times_all += list(trigger_times)

{PyCBC-2.3.5 → PyCBC-2.3.7}/bin/all_sky_search/pycbc_upload_single_event_to_gracedb

@@ -72,7 +72,7 @@ if args.production_server:
 else:
     gracedb = GraceDb(service_url='https://gracedb-playground.ligo.org/api/')
 
-labels = [l.upper() for l in args.labels]
+labels = [l.upper() for l in (args.labels or [])]
 allowed_labels = gracedb.allowed_labels
 
 if set(labels) - set(allowed_labels):

{PyCBC-2.3.5 → PyCBC-2.3.7}/bin/minifollowups/pycbc_page_coincinfo

@@ -151,7 +151,7 @@ for ifo in files.keys():
     mchirp = (pycbc.pnutils.mass1_mass2_to_mchirp_eta(bank['mass1'][tid],
                                                       bank['mass2'][tid]))[0]
 
-    time = d['end_time'][:][i]
+    time = d['end_time'][i]
     utc = lal.GPSToUTC(int(time))[0:6]
 
     # Headers will store the headers that will appear in the table.

{PyCBC-2.3.5 → PyCBC-2.3.7}/bin/plotting/pycbc_page_coinc_snrchi

@@ -6,6 +6,7 @@ from matplotlib import colors
 matplotlib.use('Agg')
 import pylab, pycbc.results
 from pycbc.io import get_chisq_from_file_choice, chisq_choices
+from pycbc.io import SingleDetTriggers
 from pycbc import conversions
 from pycbc.detector import Detector
 import pycbc.version
@@ -54,11 +55,22 @@ for tmpifo in ifos:
 
 f = h5py.File(args.single_trigger_file, 'r')
 ifo = tuple(f.keys())[0]
-f = f[ifo]
 tid = b_tids[ifo][:]
-bkg_snr = f['snr'][:][tid]
-
-bkg_chisq = get_chisq_from_file_choice(f, args.chisq_choice)[tid]
+mask = numpy.zeros(len(f[f'{ifo}/snr']), dtype=bool)
+f.close()
+mask[tid] = True
+trigs = SingleDetTriggers(
+    args.single_trigger_file,
+    None,
+    None,
+    None,
+    None,
+    ifo,
+    premask=mask
+)
+bkg_snr = trigs['snr']
+
+bkg_chisq = get_chisq_from_file_choice(trigs, args.chisq_choice)
 
 # don't plot if chisq is not calculated
 bkg_pos = bkg_chisq > 0
@@ -107,11 +119,32 @@ if 'optimal_snr_{}'.format(ifo) in f['injections']:
     opt_snr = f[opt_snr_str][:][inj_idx]
     coloring['optimal_snr'] = (opt_snr, 'Optimal SNR', colors.LogNorm())
 
-f = h5py.File(args.single_injection_file, 'r')[ifo]
 tid = inj_tids[ifo][:]
 if len(tid):
-    inj_snr = f['snr'][:][tid]
-    inj_chisq = get_chisq_from_file_choice(f, args.chisq_choice)[tid]
+    f = h5py.File(args.single_injection_file, 'r')
+    mask = numpy.zeros(len(f[f'{ifo}/snr']), dtype=bool)
+    f.close()
+    mask[tid] = True
+    inj_trigs = SingleDetTriggers(
+        args.single_injection_file,
+        None,
+        None,
+        None,
+        None,
+        ifo,
+        premask=mask
+    )
+    inj_snr_data = inj_trigs['snr']
+    inj_chisq_data = get_chisq_from_file_choice(inj_trigs, args.chisq_choice)
+    # But the stuff above would have removed ordering and duplicates now
+    # need something of the right length!
+    tid_locations = numpy.where(mask)[0]
+    new_tid_locations = numpy.searchsorted(
+        tid_locations,
+        tid
+    )
+    inj_snr = inj_snr_data[new_tid_locations]
+    inj_chisq = inj_chisq_data[new_tid_locations]
 else:
     inj_snr = numpy.array([])
     inj_chisq = numpy.array([])

PyCBC-2.3.7/bin/plotting/pycbc_page_dq_table

@@ -0,0 +1,54 @@
+#!/usr/bin/env python
+""" Make a table of dq state information
+"""
+import sys
+import argparse
+import h5py as h5
+import numpy as np
+
+import pycbc
+import pycbc.results
+from pycbc.version import git_verbose_msg as version
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--version", action="version", version=version)
+parser.add_argument('--ifo', required=True)
+parser.add_argument('--dq-file', required=True)
+parser.add_argument('--verbose', action='count')
+parser.add_argument('--output-file')
+args = parser.parse_args()
+
+dq_states = {
+    'dq_state_0': 'Clean',
+    'dq_state_1': 'DQ Flag',
+    'dq_state_2': 'Autogating',
+}
+
+f = h5.File(args.dq_file, 'r')
+grp = f[args.ifo]['dq_segments']
+
+livetimes = []
+total_livetime = 0
+for dq_state in dq_states:
+    livetime = grp[dq_state]['livetime'][()]
+    livetimes.append(livetime)
+    total_livetime += livetime
+livetimes.append(total_livetime)
+
+frac_livetimes = [lt / total_livetime for lt in livetimes]
+state_names = list(dq_states.values()) + ['Total']
+columns = [state_names, livetimes, frac_livetimes]
+columns = [np.array(c) for c in columns]
+col_names = ['DQ State', 'Livetime', '% of Livetime']
+
+format_strings = [None, '0.0', '0.00%']
+
+html_table = pycbc.results.html_table(columns, col_names,
+                                      page_size=len(state_names),
+                                      format_strings=format_strings)
+title = f'{args.ifo} DQ State Livetimes'
+caption = 'Table of DQ state livetimes'
+
+pycbc.results.save_fig_with_metadata(
+    str(html_table), args.output_file, title=title,
+    caption=caption, cmd=' '.join(sys.argv))

{PyCBC-2.3.5 → PyCBC-2.3.7}/bin/plotting/pycbc_page_snrchi

@@ -3,7 +3,8 @@ import numpy, h5py, argparse, matplotlib, sys
 matplotlib.use('Agg')
 import pylab, pycbc.results, pycbc.version
 from pycbc.events import veto
-from pycbc.io import get_chisq_from_file_choice, chisq_choices
+from pycbc.io import get_chisq_from_file_choice, chisq_choices, HFile
+from pycbc.io import SingleDetTriggers
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--trigger-file', help='Single ifo trigger file')
@@ -21,9 +22,32 @@ args = parser.parse_args()
 
 f = h5py.File(args.trigger_file, 'r')
 ifo = tuple(f.keys())[0]
-f = f[ifo]
-snr = f['snr'][:]
-chisq = get_chisq_from_file_choice(f, args.chisq_choice)
+f.close()
+if args.min_snr:
+    with HFile(args.trigger_file, 'r') as trig_file:
+        n_triggers_orig = trig_file[f'{ifo}/snr'].size
+        idx, _ = trig_file.select(
+            lambda snr: snr >= args.min_snr,
+            f'{ifo}/snr',
+            return_indices=True
+        )
+        data_mask = numpy.zeros(n_triggers_orig, dtype=bool)
+        data_mask[idx] = True
+else:
+    data_mask = None
+
+trigs = SingleDetTriggers(
+    args.trigger_file,
+    None,
+    args.veto_file,
+    args.segment_name,
+    None,
+    ifo,
+    premask=data_mask
+)
+
+snr = trigs['snr']
+chisq = get_chisq_from_file_choice(trigs, args.chisq_choice)
 
 def snr_from_chisq(chisq, newsnr, q=6.):
     snr = numpy.zeros(len(chisq)) + float(newsnr)
@@ -31,18 +55,6 @@ def snr_from_chisq(chisq, newsnr, q=6.):
     snr[ind] = float(newsnr) / ( 0.5 * (1. + chisq[ind] ** (q/2.)) ) ** (-1./q)
     return snr
 
-if args.veto_file:
-    time = f['end_time'][:]
-    locs, segs = veto.indices_outside_segments(time, [args.veto_file], 
-                                       segment_name=args.segment_name, ifo=ifo)
-    snr = snr[locs]
-    chisq = chisq[locs]
-
-if args.min_snr is not None:
-    locs = snr > args.min_snr
-    snr = snr[locs]
-    chisq = chisq[locs]
-
 fig = pylab.figure(1)
 
 r = numpy.logspace(numpy.log(chisq.min()), numpy.log(chisq.max()), 300)

PyCBC-2.3.7/bin/plotting/pycbc_page_template_bin_table

@@ -0,0 +1,75 @@
+#!/usr/bin/env python
+""" Make a table of template bin information
+"""
+import sys
+import argparse
+import h5py as h5
+import numpy as np
+
+import pycbc
+import pycbc.results
+from pycbc.version import git_verbose_msg as version
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--version", action="version", version=version)
+parser.add_argument('--ifo', required=True)
+parser.add_argument('--dq-file', required=True)
+parser.add_argument('--verbose', action='count')
+parser.add_argument('--output-file')
+args = parser.parse_args()
+
+f = h5.File(args.dq_file, 'r')
+grp = f[args.ifo]['bins']
+bin_names = list(grp.keys())
+
+sngl_ranking = f.attrs['sngl_ranking']
+sngl_thresh = f.attrs['sngl_ranking_threshold']
+
+livetime = 0
+seg_grp = f[args.ifo]['dq_segments']
+for k in seg_grp.keys():
+    livetime += seg_grp[k]['livetime'][()]
+
+num_templates = []
+num_triggers = []
+total_templates = 0
+total_triggers = 0
+for bin_name in bin_names:
+    bin_grp = grp[bin_name]
+
+    n_tmp = len(bin_grp['tids'][:])
+    num_templates.append(n_tmp)
+    total_templates += n_tmp
+
+    n_trig = bin_grp['num_triggers'][()]
+    num_triggers.append(n_trig)
+    total_triggers += n_trig
+
+bin_names.append('Total')
+num_triggers.append(total_triggers)
+num_templates.append(total_templates)
+frac_triggers = [n / total_triggers for n in num_triggers]
+frac_templates = [n / total_templates for n in num_templates]
+trigger_rate = [n / livetime for n in num_triggers]
+
+col_names = ['Template Bin', 'Number of Templates', '% of Templates',
+             'Number of Loud Triggers', '% of Loud Triggers',
+             'Loud Trigger Rate (Hz)']
+columns = [bin_names, num_templates, frac_templates,
+           num_triggers, frac_triggers, trigger_rate]
+columns = [np.array(c) for c in columns]
+
+format_strings = [None, '#', '0.000%', '#', '0.0%', '0.00E0']
+
+html_table = pycbc.results.html_table(columns, col_names,
+                                      page_size=len(bin_names),
+                                      format_strings=format_strings)
+title = f'{args.ifo} DQ Template Bin Information'
+caption = 'Table of information about template bins ' \
+           + 'used for DQ trigger rate calculations. ' \
+           + 'Loud triggers are defined as those with ' \
+           + f'{sngl_ranking} > {sngl_thresh}.'
+
+pycbc.results.save_fig_with_metadata(
+    str(html_table), args.output_file, title=title,
+    caption=caption, cmd=' '.join(sys.argv))

{PyCBC-2.3.5 → PyCBC-2.3.7}/bin/plotting/pycbc_plot_dq_flag_likelihood

@@ -77,7 +77,10 @@ ax2.set_ylabel('DQ Log Likelihood Penalty')
 ax2.set_ylim(numpy.log(ymin), numpy.log(ymax))
 
 # add meta data and save figure
-plot_title = f'{ifo} DQ Trigger Rates'
+plot_title = f'{ifo}:{args.dq_label} DQ Trigger Rates'
+
+ax.set_title(plot_title)
+
 plot_caption = 'The log likelihood correction \
       during during each dq state for each template bin.'
 pycbc.results.save_fig_with_metadata(

{PyCBC-2.3.5 → PyCBC-2.3.7}/bin/plotting/pycbc_plot_hist

@@ -46,10 +46,31 @@ pycbc.init_logging(args.verbose)
 f = h5py.File(args.trigger_file, 'r')
 ifo = tuple(f.keys())[0]
 
+# This is fixed better on master, but should work here
+if args.x_var == 'snr' or args.x_var == 'newsnr_sgveto':
+    with pycbc.io.HFile(args.trigger_file, 'r') as trig_file:
+        n_triggers_orig = trig_file[f'{ifo}/snr'].size
+        logging.info("Trigger file has %d triggers", n_triggers_orig)
+        logging.info('Generating trigger mask')
+        # psd_var_val may not have been calculated
+        idx, _ = trig_file.select(
+            lambda snr: snr >= args.x_min,
+            f'{ifo}/snr',
+            return_indices=True
+        )
+        data_mask = numpy.zeros(n_triggers_orig, dtype=bool)
+        data_mask[idx] = True
+else:
+    logging.warn(
+        'With %s as --x-var, this is going to be very memory intensive!',
+        args.x_var
+    )
+    data_mask = None
+
 # read single-detector triggers
 trigs = pycbc.io.SingleDetTriggers(args.trigger_file, args.bank_file,
                                    args.veto_file, args.segment_name,
-                                   None, ifo)
+                                   None, ifo, premask=data_mask)
 
 # get x values and find the maximum x value
 val = getattr(trigs, args.x_var)

{PyCBC-2.3.5 → PyCBC-2.3.7}/bin/pycbc_convertinjfiletohdf

@@ -150,7 +150,11 @@ class LVKNewStyleInjectionSet(object):
             elif lvk_name == 't_co_gps_add':
                 continue
             else:
-                data[pycbc_name] = self.inj_file[f'{self.subdir}/{lvk_name}'][:]
+                lvk_file_dset = self.inj_file[f'{self.subdir}/{lvk_name}']
+                if lvk_file_dset.dtype.char in ['U', 'O']:
+                    data[pycbc_name] = lvk_file_dset[:].astype('S')
+                else:
+                    data[pycbc_name] = lvk_file_dset[:]
         return data
 
 

{PyCBC-2.3.5 → PyCBC-2.3.7}/bin/workflows/pycbc_make_offline_search_workflow

@@ -561,19 +561,25 @@ for key in final_bg_files:
 
 # DQ log likelihood plots
 for dqf, dql in zip(dqfiles, dqfile_labels):
+    ifo = dqf.ifo
+    outdir = rdir[f'data_quality/{dqf.ifo}_DQ_results']
+
     # plot rates when flag was on
-    outdir = rdir[f'data_quality/{dqf.ifo}_{dql}_trigger_rates']
     wf.make_dq_flag_trigger_rate_plot(workflow, dqf, dql, outdir, tags=[dql])
 
-# DQ background binning plot
-ifo_bins = workflow.cp.get_subsections('bin_templates')
-for ifo in ifo_bins:
+    # make table of dq segment info
+    wf.make_dq_segment_table(workflow, dqf, outdir, tags=[dql])
+
+    # plot background bins
     background_bins = workflow.cp.get_opt_tags(
         'bin_templates', 'background-bins', tags=[ifo])
-    wf.make_template_plot(workflow, hdfbank, rdir['data_quality'],
+    wf.make_template_plot(workflow, hdfbank, outdir,
                           bins=background_bins,
                           tags=[ifo, 'dq_bins'] + bank_tags)
 
+    # make table of template bin info
+    wf.make_template_bin_table(workflow, dqf, outdir, tags=[ifo])
+
 ############################## Setup the injection runs #######################
 
 splitbank_files_inj = wf.setup_splittable_workflow(workflow, [hdfbank],