lalsuite 7.26.2.dev20251207__cp313-cp313-manylinux_2_28_x86_64.whl

lalsuite-7.26.2.dev20251207.data/scripts/lalinference_evolve_spins_and_append_samples

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+#!python
+'''
+Code to read in LALInference HDF5 posterior samples, evolve the spins up to a specified value (default: Schwarzschild ISCO), and write the resulting evolved spin samples to the HDF5 file.
+
+Usage:
+python lalinference_evolve_spins_and_append_samples.py --sample_file <directory path to the posterior samples> [--vfinal <final orbital velocity>]
+'''
+# NKJ-M and Anuradha Gupta, 05.2019
+
+import numpy as np
+import argparse
+import lalsimulation as lalsim
+import h5py
+
+from numpy.linalg import norm
+from lal import MSUN_SI, MTSUN_SI
+
+import matplotlib
+matplotlib.use('Agg')
+
+from lalinference.io.hdf5 import read_samples, write_samples, extract_metadata
+from astropy.table import Column, Table, hstack
+
+from lalinference.bayespputils import mc2ms
+
+# Define a convenience function
+def tilts_and_phi12_from_Cartesian_spins_and_L(chi1_v, chi2_v, Ln_v):
+
+        # norms and normalizing
+        chi1_v_norm = norm(chi1_v)
+        chi2_v_norm = norm(chi2_v)
+
+        Ln_v /= norm(Ln_v)
+
+        # dot products
+        chi1dL_v = np.dot(chi1_v, Ln_v)
+        chi2dL_v = np.dot(chi2_v, Ln_v)
+
+        # in-plane spins
+
+        chi1inplane = chi1_v - chi1dL_v*Ln_v
+        chi2inplane = chi2_v - chi2dL_v*Ln_v
+
+        # computing cosine of tilts and phi12
+        cos_tilt1 = chi1dL_v/chi1_v_norm
+        cos_tilt2 = chi2dL_v/chi2_v_norm
+        cos_phi12 = np.dot(chi1inplane,chi2inplane)/(norm(chi1inplane)*norm(chi2inplane))
+
+        # set quadrant of phi12
+        phi12_evol_i = np.arccos(cos_phi12)
+        if np.sign(np.dot(Ln_v,np.cross(chi1_v, chi2_v))) < 0:
+            phi12_evol_i = 2.*np.pi - phi12_evol_i
+
+        return np.arccos(cos_tilt1), np.arccos(cos_tilt2), phi12_evol_i
+
+# Settings
+dt = 0.1 # steps in time for the integration, in terms of the total mass of the binary
+
+# Choose which approximant to use for spin evolution
+approx = lalsim.GetApproximantFromString("SpinTaylorT5")
+
+# Set up the parsing
+parser = argparse.ArgumentParser(description = 'Evolve the LALInference posterior samples of spins and append to HDF5 file of samples')
+parser.add_argument("--sample_file", help = "path to the HDF5 posterior samples file", required=True)
+parser.add_argument("--vfinal", help = "final orbital velocity for the evolution (default is the Schwarzschild ISCO velocity 6**-0.5 ~= 0.408)", type=str, default="ISCO")
+args = parser.parse_args()
+
+hdf_pos_file = args.sample_file
+
+if args.vfinal=='ISCO':
+    v_final = 6.**-0.5
+    label = '_isco'
+else:
+    try:
+        v_final = float(args.vfinal)
+    except ValueError:
+        raise ValueError("vfinal has to either be ISCO or a fraction of the speed of light")
+    label = '_evol_vfinal'
+
+# Functions for table formatting
+
+def _identity(x):
+    return x
+
+_colname_map = (('tilt_spin1' + label, 'tilt1' + label, _identity),
+                 ('tilt_spin2' + label, 'tilt2' + label, _identity))
+
+def _remap_colnames(table):
+    for old_name, new_name, func in _colname_map:
+        if old_name in table.colnames:
+            table[new_name] = func(table.columns.pop(old_name))
+
+# read the posterior samples and metadata
+data = read_samples(hdf_pos_file)
+metadata = {}
+run_identifier = extract_metadata(hdf_pos_file, metadata)
+
+# extract mass and spin samples
+if ('mc' in data.dtype.names) and ('q' in data.dtype.names):
+  q = np.atleast_1d(data['q'])
+  eta = q/(1. + q)/(1. + q)
+  m1, m2 = mc2ms(np.atleast_1d(data['mc']), eta) # We use the redshifted masses here, since the starting frequency is in the detector frame
+else:
+  raise ValueError("Chirp mass and mass ratio are not found in %s. There is likely something wrong with this posterior file."%hdf_pos_file)
+if ('a1' in data.dtype.names) and ('a2' in data.dtype.names):
+  chi1, chi2 = np.atleast_1d(data['a1']), np.atleast_1d(data['a2'])
+else:
+  raise ValueError("No spin magnitude samples were found in %s. There are no spins to evolve."%hdf_pos_file)
+if ('tilt1' in data.dtype.names) and ('tilt2' in data.dtype.names):
+  tilt1, tilt2 = np.atleast_1d(data['tilt1']), np.atleast_1d(data['tilt2'])
+else:
+  raise ValueError("No tilt angle samples were found in %s; cannot evolve spins."%hdf_pos_file)
+if 'phi12' in data.dtype.names:
+  phi12 = np.atleast_1d(data['phi12'])
+else:
+  raise ValueError("No phi12 samples were found in %s; cannot evolve spins."%hdf_pos_file)
+
+# Extract start frequency appropriate for the waveform used in the analysis
+
+if 'LAL_APPROXIMANT' not in data.dtype.names:
+    raise ValueError('LAL_APPROXIMANT is missing--unable to determine which waveform was used to obtain the samples.')
+
+spinfreq_enum = np.array([lalsim.SimInspiralGetSpinFreqFromApproximant(int(lal_approx)) for lal_approx in data['LAL_APPROXIMANT']])
+
+if len(np.where(spinfreq_enum == lalsim.SIM_INSPIRAL_SPINS_CASEBYCASE)[0]) > 0:
+        raise ValueError('Unable to evolve spins since approximant does not have a set frequency at which the spins are defined.')
+
+f_start = np.where(np.array(spinfreq_enum == lalsim.SIM_INSPIRAL_SPINS_FLOW), data['flow'], data['f_ref'])
+
+# Evolve spins
+tilt1_evol = np.zeros_like(m1)
+tilt2_evol = np.zeros_like(m1)
+phi12_evol = np.zeros_like(m1)
+
+for i, _ in enumerate(m1):
+    # Only evolve spins if at least one spin magnitude is above 1e-3
+    if np.logical_or(chi1[i] > 1e-3, chi2[i] > 1e-3):
+        mtot_s = (m1[i] + m2[i])*MTSUN_SI # total mass in seconds
+        f_final = v_final*v_final*v_final/(mtot_s*np.pi)
+
+        _, _, chi1x_v_data, chi1y_v_data, chi1z_v_data, chi2x_v_data, chi2y_v_data, chi2z_v_data, Lnx_v_data, Lny_v_data, Lnz_v_data, _, _, _ = lalsim.SimInspiralSpinTaylorPNEvolveOrbit(deltaT=dt*mtot_s, m1=m1[i]*MSUN_SI, m2=m2[i]*MSUN_SI, fStart=f_start[i], fEnd=f_final, s1x=chi1[i]*np.sin(tilt1[i]), s1y=0., s1z=chi1[i]*np.cos(tilt1[i]), s2x=chi2[i]*np.sin(tilt2[i])*np.cos(phi12[i]), s2y=chi2[i]*np.sin(tilt2[i])*np.sin(phi12[i]), s2z=chi2[i]*np.cos(tilt2[i]), lnhatx=0., lnhaty=0., lnhatz=1., e1x=1., e1y=0., e1z=0., lambda1=0., lambda2=0., quadparam1=1., quadparam2=1., spinO=6, tideO=0, phaseO=7, lscorr=0, approx=approx)
+
+        # Set index to take from array output by lalsim.SimInspiralSpinTaylorPNEvolveOrbit: -1 for evolving forward in time and 0 for evolving backward in time
+        if f_start[i] <= f_final:
+            idx_use = -1
+        else:
+            idx_use = 0
+
+        chi1_v = np.array([chi1x_v_data.data.data[idx_use], chi1y_v_data.data.data[idx_use], chi1z_v_data.data.data[idx_use]])
+        chi2_v = np.array([chi2x_v_data.data.data[idx_use], chi2y_v_data.data.data[idx_use], chi2z_v_data.data.data[idx_use]])
+
+        Ln_v = np.array([Lnx_v_data.data.data[idx_use], Lny_v_data.data.data[idx_use], Lnz_v_data.data.data[idx_use]])
+
+        tilt1_evol[i], tilt2_evol[i], phi12_evol[i] = tilts_and_phi12_from_Cartesian_spins_and_L(chi1_v, chi2_v, Ln_v)
+    else:
+        tilt1_evol[i], tilt2_evol[i], phi12_evol[i] = tilt1[i], tilt2[i], phi12[i]
+
+# Setup for output
+
+# Get the names of the columns
+colnames = np.array(data.colnames)
+
+tilt1_id = np.where(colnames=='tilt1')[0][0]
+tilt2_id = np.where(colnames=='tilt2')[0][0]
+phi12_id = np.where(colnames=='phi12')[0][0]
+f_ref_id = np.where(colnames=='f_ref')[0][0]
+
+# Get the meta for tilt1, tilt2, phi12
+meta_tilt1 = tuple(data.columns.items())[tilt1_id][1].meta
+meta_tilt2 = tuple(data.columns.items())[tilt2_id][1].meta
+meta_phi12 = tuple(data.columns.items())[phi12_id][1].meta
+meta_f_ref = tuple(data.columns.items())[f_ref_id][1].meta
+
+# Create an astropy table with the evolved spin samples
+tilts_evol = Table([Column(tilt1_evol, name='tilt1' + label, meta=meta_tilt1), Column(tilt2_evol, name='tilt2' + label, meta=meta_tilt2), Column(phi12_evol, name='phi12' + label, meta=meta_phi12)])
+
+# Append the columns to the existing astropy table of samples from the HDF5 file
+data_joined = hstack([data, tilts_evol])
+
+if v_final != "ISCO":
+    vfinal_col = Table([Column(v_final*np.ones_like(tilt1_evol), name='vfinal', meta=meta_f_ref)])
+    data_joined = hstack([data_joined, vfinal_col])
+
+_remap_colnames(data_joined)
+
+f = h5py.File(hdf_pos_file, 'r')
+path = '/lalinference/'+run_identifier+'/posterior_samples'
+level = f[path]
+arrt = level.attrs
+names = np.array([list(arrt.items())[i][0] for i in range(len(list(arrt.items())))])
+num_names = 0
+for name in names:
+    if 'NAME' in name:
+        num_names += 1
+
+# Updating the metadata
+metadata[path]['FIELD_{0}_NAME'.format(num_names+1)]='tilt_spin1' + label
+metadata[path]['FIELD_{0}_NAME'.format(num_names+2)]='tilt_spin2' + label
+metadata[path]['FIELD_{0}_NAME'.format(num_names+3)]='phi12' + label
+
+# Write the joined table
+write_samples(data_joined, hdf_pos_file, path=path, metadata=metadata, overwrite=True)

lalsuite-7.26.2.dev20251207.data/scripts/lalinference_injectedlike

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+#!python
+import os
+import sys
+from importlib.resources import files, as_file
+with as_file(files('lalapps') / 'bin' / 'lalinference_injectedlike') as path:
+    os.execv(path, sys.argv)

lalsuite-7.26.2.dev20251207.data/scripts/lalinference_merge_posteriors

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+#!python
+
+# resample posteriors (C) John Veitch, 2015
+
+from numpy import vstack,log
+from optparse import OptionParser
+import sys
+from lalinference import bayespputils as bppu
+
+from lalinference.nest2pos import draw_posterior, draw_N_posterior
+
+usage='''%prog [-N NPOS]-o output.dat -p pos1.dat -w weight1 [-p pos2.dat -w weight2 ...]
+%prog takes a list of posterior files and weights and draws samples from the combined,
+reweighted distribution
+'''
+
+def load_data(filename,header=None):
+    peparser=bppu.PEOutputParser('common')
+    commonObj=peparser.parse(open(filename,'r'),info=[header,None])
+    pos=bppu.Posterior(commonObj)
+    return pos
+
+if __name__=='__main__':
+    parser=OptionParser(usage)
+    parser.add_option('-o','--output',action='store',type='string',default=None,help='output file',metavar='output.dat')
+    parser.add_option('-p','--posterior',action='append',type='string',default=[],metavar='pos.dat',help='posterior input file')
+    parser.add_option('-w','--weight',action='append',type='float',default=[],metavar='NUM',help='weight of an input file')
+    parser.add_option('-N','--npos',action='store',default=None,metavar='NPOS',help='Optional number of posterior samples to draw')
+    parser.add_option('--verbose',action='store_true',default=False,help='Prints additional information')
+    (opts,args) = parser.parse_args()
+
+    if len(opts.posterior)==0:
+        sys.stderr.write('No input files given\n')
+        sys.exit(1)
+    if len(opts.weight) != len(opts.posterior):
+        sys.stderr.write('Error: must specify same number of weights and posteriors\n')
+        sys.exit(1)
+
+    # Create posterior samples for each input file
+    datas=map(load_data,opts.posterior)
+    weights=[]
+    for d,w in zip(datas,opts.weight):
+        theseweights = (log(w) + logl + logp for logl,logp in zip(d['logl'].samples,d['logprior'].samples))
+        weights.extend(theseweights)
+    bigdata=vstack([d.samples()[0] for d in datas])
+
+    # Call reweighting function
+    if opts.npos is not None:
+        merged=draw_N_posterior(bigdata,weights,opts.npos,verbose=opts.verbose)
+    else:
+        merged=draw_posterior(bigdata,weights,verbose=opts.verbose)
+
+    outObj=bppu.Posterior((datas[0].names,merged))
+
+    # Write output file
+    if opts.output is not None:
+        outObj.write_to_file(opts.output)

lalsuite-7.26.2.dev20251207.data/scripts/lalinference_mpi_wrapper

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+#!python
+import os
+import sys
+from importlib.resources import files, as_file
+with as_file(files('lalapps') / 'bin' / 'lalinference_mpi_wrapper') as path:
+    os.execv(path, sys.argv)

lalsuite-7.26.2.dev20251207.data/scripts/lalinference_multi_pipe

@@ -0,0 +1,144 @@
+#!python
+# DAG generation code for running LALInference pipeline
+# (C) 2012 John Veitch
+# 2013 Salvatore Vitale: extended to work with several ini files
+
+from lalinference import lalinference_pipe_utils as pipe_utils
+import configparser
+from optparse import OptionParser
+import sys
+
+usage=""" %prog [options] config1.ini config2.ini ... configN.ini
+Setup a Condor DAG file to run the LALInference pipeline based on
+N config.ini files.
+
+The user must specify either an injection file to analyse, with the --inj option,
+a list of SnglInspiralTable or CoincInspiralTable triggers with the --<x>-triggers options,
+or an ASCII list of GPS times with the --gps-time-file option.
+
+The user must also specify and ini file which will contain the main analysis config.
+
+"""
+
+import os
+def vararg_callback(option, opt_str, value, parser):
+    assert value is None
+    value = []
+    def floatable(str):
+        try:
+            float(str)
+            return True
+        except ValueError:
+            return False
+    for arg in parser.rargs:
+        # stop on --foo like options
+        if arg[:2] == "--" and len(arg) > 2:
+            break
+        # stop on -a, but not on -3 or -3.0
+        if arg[:1] == "-" and len(arg) > 1 and not floatable(arg):
+            break
+        value.append(arg)
+    del parser.rargs[:len(value)]
+    setattr(parser.values, option.dest, value)
+
+parser=OptionParser(usage)
+parser.add_option("-r","--run-path",default=None,action="store",type="string",help="Directory to run pipeline in (default: $PWD)",metavar="RUNDIR")
+parser.add_option("-p","--daglog-path",default=None,action="store",type="string",help="Path to directory to contain DAG log file. SHOULD BE LOCAL TO SUBMIT NODE",metavar="LOGDIR")
+parser.add_option("-g","--gps-time-file",action="store",type="string",default=None,help="Text file containing list of GPS times to analyse",metavar="TIMES.txt")
+parser.add_option("-t","--single-triggers",action="store",type="string",default=None,help="SnglInspiralTable trigger list",metavar="SNGL_FILE.xml")
+parser.add_option("-C","--coinc-triggers",action="store",type="string",default=None,help="CoinInspiralTable trigger list",metavar="COINC_FILE.xml")
+parser.add_option("-L","--lvalert",action="store",type="string",default=None,help="LVAlert coinc file",metavar="coinc_G0000.xml")
+parser.add_option("--gid",action="store",type="string",default=None,help="Optional GraceDB ID for submitting results")
+parser.add_option("-I","--injections",action="store",type="string",default=None,help="List of injections to perform and analyse",metavar="INJFILE.xml")
+parser.add_option("-P","--pipedown-db",action="store",type="string",default=None,help="Pipedown database to read and analyse",metavar="pipedown.sqlite")
+parser.add_option("-F","--folder-names",dest="fnames",action="callback", callback=vararg_callback,help="Space separated list of folders that will be created, corresponding to the TIGER parameters that are being tested or GR. The order has to be the same used with the ini files!",default=None,metavar="GR phi1")
+parser.add_option("--condor-submit",action="store_true",default=False,help="Automatically submit the condor dag")
+
+(opts,args)=parser.parse_args()
+
+if len(args)>1:
+  print('Using %s ini files\n'%len(args))
+elif len(args)==1:
+  inifile=args[0]
+
+inits=args
+ninits=len(inits)
+fnames=opts.fnames
+nfnames=len(fnames)
+
+if not ninits==nfnames:
+  print("You seem to be using %d parser files and %d foldernames. These two numbers must be the same. Exiting...\n"%(ninits,nfnames))
+  sys.exit(1)
+
+fnames_dic={}
+for fname in fnames:
+  fnames_dic[fnames.index(fname)]=str(fname)
+
+glob_hyp=fnames
+hyp_str=" "
+
+for hy in glob_hyp:
+  hyp_str+=hy+" "
+
+cp=configparser.ConfigParser()
+cp.optionxform = str
+
+first_dag=True
+common_path=opts.run_path
+
+for inifile in inits:
+  try:
+    cp.read_file(open(inifile))
+  except AttributeError:
+    cp.readfp(open(inifile))
+  if opts.run_path is not None:
+    cp.set('paths','basedir',opts.run_path)
+  if opts.daglog_path is not None:
+    cp.set('paths','daglogdir',opts.daglog_path)
+  else:
+    cp.set('paths','daglogdir',opts.run_path)
+  if opts.gps_time_file is not None:
+    cp.set('input','gps-time-file',opts.gps_time_file)
+  if opts.single_triggers is not None:
+    cp.set('input','sngl-inspiral-file',opts.single_triggers)
+  if opts.injections is not None:
+    cp.set('input','injection-file',opts.injections)
+  if opts.coinc_triggers is not None:
+    cp.set('input','coinc-inspiral-file',opts.coinc_triggers)
+  if opts.lvalert is not None:
+    cp.set('input','lvalert-file',opts.lvalert)
+  if opts.gid is not None:
+    cp.set('input','gid',opts.gid)
+  if opts.pipedown_db is not None:
+    cp.set('input','pipedown-db',opts.pipedown_db)
+
+  if opts.run_path is not None:
+    cp.set('paths','basedir',os.path.join(str(common_path),str(fnames_dic[inits.index(inifile)])))
+    # Create the DAG from the configparser object
+  if first_dag:
+    dag=pipe_utils.LALInferencePipelineDAG(cp)
+    first_dag=False
+    dag.write_sub_files()
+    dag2=dag
+  else:
+    dag2=pipe_utils.LALInferencePipelineDAG(cp,first_dag=False,previous_dag=dag)
+    dag2.write_sub_files()
+    dag=dag2
+
+# Create the DAG from the configparser object
+dag2.set_dag_file(os.path.join(common_path,'common_dag'))
+dag2.write_dag()
+dag2.write_script()
+# End of program
+print('Successfully created DAG file.')
+print('Now run condor_submit_dag %s\n'%(dag2.get_dag_file()))
+
+if opts.condor_submit:
+    import subprocess
+
+    x = subprocess.Popen(['condor_submit_dag',dag.get_dag_file()])
+    x.wait()
+    if x.returncode==0:
+      print('Submitted DAG file')
+    else:
+      print('Unable to submit DAG file')

lalsuite-7.26.2.dev20251207.data/scripts/lalinference_nest

@@ -0,0 +1,6 @@
+#!python
+import os
+import sys
+from importlib.resources import files, as_file
+with as_file(files('lalapps') / 'bin' / 'lalinference_nest') as path:
+    os.execv(path, sys.argv)