PyCBC 2.3.6__tar.gz → 2.3.7__tar.gz

{PyCBC-2.3.6 → PyCBC-2.3.7}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: PyCBC
-Version: 2.3.6
+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/v2.3.6
+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-2.3.6 → PyCBC-2.3.7}/PyCBC.egg-info/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: PyCBC
-Version: 2.3.6
+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/v2.3.6
+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-2.3.6 → 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-2.3.6 → 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-2.3.6 → 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-2.3.6 → 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-2.3.6 → 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-2.3.6 → 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-2.3.6 → 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-2.3.6 → PyCBC-2.3.7}/pycbc/io/hdf.py

@@ -810,7 +810,21 @@ class ForegroundTriggers(object):
                         curr.append(hdf_dataset[idx])
                     curr = np.array(curr)
                 else:
-                    curr = self.sngl_files[ifo].get_column(variable)[tid]
+                    # Taking code from FileData's get_column
+                    # This needs to be done more cleanly for master!
+                    group = self.sngl_files[ifo].group
+                    if not len(group.keys()):
+                        return np.array([])
+                    dataset = group[variable]
+                    mask = np.zeros(len(dataset), dtype=bool)
+                    mask[tid] = True
+                    needed_data = dataset[mask]
+                    tid_locations = np.where(mask)[0]
+                    new_tid_locations = np.searchsorted(
+                        tid_locations,
+                        tid
+                    )
+                    curr = needed_data[new_tid_locations]
             except IndexError:
                 if len(self.trig_id[ifo]) == 0:
                     curr = np.array([])

{PyCBC-2.3.6 → PyCBC-2.3.7}/pycbc/psd/variation.py

@@ -168,7 +168,7 @@ def calc_filt_psd_variation(strain, segment, short_segment, psd_long_segment,
         fweight = norm * fweight
         fwhiten = numpy.sqrt(2. / srate) / numpy.sqrt(plong)
         fwhiten[0] = 0.
-        full_filt = sig.hann(int(psd_duration * srate)) * numpy.roll(
+        full_filt = sig.windows.hann(int(psd_duration * srate)) * numpy.roll(
             irfft(fwhiten * fweight), int(psd_duration / 2) * srate)
         # Convolve the filter with long segment of data
         wstrain = sig.fftconvolve(astrain, full_filt, mode='same')

{PyCBC-2.3.6 → PyCBC-2.3.7}/pycbc/results/versioning.py

@@ -21,7 +21,7 @@ import subprocess
 import urllib.parse
 
 import lal, lalframe
-import pycbc.version, glue.git_version
+import pycbc.version
 
 def get_library_version_info():
     """This will return a list of dictionaries containing versioning
@@ -88,19 +88,6 @@ def get_library_version_info():
         pass
     library_list.append(lalsimulationinfo)
 
-    glueinfo = {}
-    glueinfo['Name'] = 'LSCSoft-Glue'
-    glueinfo['ID'] = glue.git_version.id
-    glueinfo['Status'] = glue.git_version.status
-    glueinfo['Version'] = glue.git_version.version
-    glueinfo['Tag'] = glue.git_version.tag
-    glueinfo['Author'] = glue.git_version.author
-    glueinfo['Builder'] = glue.git_version.builder
-    glueinfo['Branch'] = glue.git_version.branch
-    glueinfo['Committer'] = glue.git_version.committer
-    glueinfo['Date'] = glue.git_version.date
-    library_list.append(glueinfo)
-
     pycbcinfo = {}
     pycbcinfo['Name'] = 'PyCBC'
     pycbcinfo['ID'] = pycbc.version.version

{PyCBC-2.3.6 → PyCBC-2.3.7}/pycbc/version.py

@@ -1,27 +1,27 @@
 # coding: utf-8
-# Generated by setup.py for PyCBC on 2024-02-22 16:26:33 +0000.
+# Generated by setup.py for PyCBC on 2024-05-28 20:42:01 +0000.
 
 # general info
-version = '2.3.6'
-date = '2024-02-22 14:14:35 +0000'
+version = '2.3.7'
+date = '2024-05-28 20:15:34 +0000'
 release = 'True'
 last_release = '2.4.0'
 
 # git info
-git_hash = '4606ff7e39717505df757ac7e0f5538ec9e25cb3'
+git_hash = '2e0f835b436827ce1626c53bad647a96ced7e9d0'
 git_branch = 'None'
-git_tag = 'v2.3.6'
+git_tag = 'v2.3.7'
 git_author = 'Ian Harry <ian.harry@ligo.org>'
 git_committer = 'GitHub <noreply@github.com>'
 git_status = 'CLEAN: All modifications committed'
 git_builder = 'Unknown User <>'
-git_build_date = '2024-02-22 16:26:33 +0000'
-git_verbose_msg = """Version: 2.3.6
+git_build_date = '2024-05-28 20:42:01 +0000'
+git_verbose_msg = """Version: 2.3.7
 Branch: None
-Tag: v2.3.6
-Id: 4606ff7e39717505df757ac7e0f5538ec9e25cb3
+Tag: v2.3.7
+Id: 2e0f835b436827ce1626c53bad647a96ced7e9d0
 Builder: Unknown User <>
-Build date: 2024-02-22 16:26:33 +0000
+Build date: 2024-05-28 20:42:01 +0000
 Repository status is CLEAN: All modifications committed"""
 
 from pycbc._version import *

{PyCBC-2.3.6 → PyCBC-2.3.7}/pycbc/waveform/parameters.py

@@ -545,6 +545,18 @@ dbeta2 = Parameter("dbeta2",
 dbeta3 = Parameter("dbeta3",
                 dtype=float, default=0., label=r"$d\beta_3$",
                 description="Intermediate testingGR parameter.")
+
+## Specific waveform parameters
+
+threshmband = Parameter("ThresholdMband",
+                dtype=float, default=None, label="ThresholdMband",
+                description="PhenomXHM Multibanding")
+
+precthreshmband = Parameter("PrecThresholdMband",
+                dtype=float, default=None, label="PrecThresholdMband",
+                description="PhenomXPHM Multibanding")
+
+
 #
 # =============================================================================
 #
@@ -575,7 +587,7 @@ extrinsic_params = orientation_params + location_params
 testingGR_params = ParameterList\
     ([dchi0, dchi1, dchi2, dchi3, dchi4, dchi5, dchi5l, dchi6, dchi6l,
       dchi7, dalpha1, dalpha2, dalpha3, dalpha4, dalpha5,
-      dbeta1, dbeta2, dbeta3])
+      dbeta1, dbeta2, dbeta3, precthreshmband, threshmband])
 
 # intrinsic parameters of a CBC waveform. Some of these are not recognized
 # by every waveform model

{PyCBC-2.3.6 → PyCBC-2.3.7}/pycbc/waveform/waveform.py

@@ -170,6 +170,16 @@ def _check_lal_pars(p):
         lalsimulation.SimInspiralWaveformParamsInsertNonGRDBeta2(lal_pars,p['dbeta2'])
     if p['dbeta3'] is not None:
         lalsimulation.SimInspiralWaveformParamsInsertNonGRDBeta3(lal_pars,p['dbeta3'])
+    if p['PrecThresholdMband'] is not None:
+        lalsimulation.SimInspiralWaveformParamsInsertPhenomXPHMThresholdMband(
+            lal_pars,
+            p['PrecThresholdMband'],
+        )
+    if p['ThresholdMband'] is not None:
+        lalsimulation.SimInspiralWaveformParamsInsertPhenomXHMThresholdMband(
+            lal_pars,
+            p['ThresholdMband'],
+        )
     return lal_pars
 
 def _lalsim_td_waveform(**p):

{PyCBC-2.3.6 → PyCBC-2.3.7}/pycbc/workflow/minifollowups.py

@@ -1104,11 +1104,12 @@ def make_upload_files(workflow, psd_files, snr_timeseries, xml_all,
         '--output-file',
     )
 
+    # This will be called if the approximant is within the bank
     if approximant == b'SPAtmplt':
         # Bayestar doesn't use the SPAtmplt approximant
         approximant = b'TaylorF2'
     if approximant is not None:
-        bayestar_node.add_opt('--waveform', approximant.decode())
+        bayestar_node.add_opt('--approximant', approximant.decode())
 
     workflow += bayestar_node
 

{PyCBC-2.3.6 → PyCBC-2.3.7}/setup.py

@@ -119,7 +119,7 @@ def get_version_info():
         vinfo = _version_helper.generate_git_version_info()
     except:
         vinfo = vdummy()
-        vinfo.version = '2.3.6'
+        vinfo.version = '2.3.7'
         vinfo.release = 'True'
 
     version_script = f"""# coding: utf-8