lalsuite 7.26.2.dev20251210__cp312-cp312-macosx_12_0_arm64.whl

lalsuite-7.26.2.dev20251210.data/scripts/cbcBayesDIEvidence

@@ -0,0 +1,68 @@
+#!python
+# -*- coding: utf-8 -*-
+#
+#       cbcBayesDIEvidence.py: compute the direct-integration evidence
+#       from a file of posterior samples.  See arXiv:0911.1777 for the
+#       algorithm.
+#
+#       Copyright 2011
+#       Will M. Farr <will.farr@ligo.org>
+#
+#       This program is free software; you can redistribute it and/or modify
+#       it under the terms of the GNU General Public License as published by
+#       the Free Software Foundation; either version 2 of the License, or
+#       (at your option) any later version.
+#
+#       This program is distributed in the hope that it will be useful,
+#       but WITHOUT ANY WARRANTY; without even the implied warranty of
+#       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#       GNU General Public License for more details.
+#
+#       You should have received a copy of the GNU General Public License
+#       along with this program; if not, write to the Free Software
+#       Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+#       MA 02110-1301, USA.
+#
+#
+
+import numpy as np
+from lalinference import bayespputils as bp
+from lalinference import git_version
+from optparse import OptionParser
+
+__author__="Will M. Farr <will.farr@ligo.org>"
+__version__="git id %s"%git_version.id
+__date__=git_version.date
+
+if __name__=='__main__':
+    parser=OptionParser()
+    parser.add_option("--data",dest="data",action="store",help="file of posterior samples",metavar="FILE")
+    parser.add_option("--Nboxing",dest="Nboxing",action="store",default=64,type="int",metavar="N")
+    parser.add_option("--bootstrap", dest='bootstrap',action='store',default=1,type='int',metavar='N')
+    parser.add_option('--output',dest='output',action='store',default=None,metavar='FILE')
+
+    (opts,args)=parser.parse_args()
+
+    pos_parser=bp.PEOutputParser('common')
+
+    f=open(opts.data, "r")
+    try:
+        pos=bp.Posterior(pos_parser.parse(f))
+    finally:
+        f.close()
+
+    outfile=None
+    if opts.output:
+        outfile=open(opts.output,'w')
+    try:
+        for i in range(opts.bootstrap):
+            if i == 0:
+                log_ev=pos.di_evidence(boxing=opts.Nboxing)
+            else:
+                log_ev=pos.bootstrap().di_evidence(boxing=opts.Nboxing)
+            print('log(evidence) with Nboxing = %d is %.1f (evidence is %g)'%(opts.Nboxing,log_ev,np.exp(ev)))
+            if outfile:
+                outfile.write('%g\n'%log_ev)
+    finally:
+        if outfile:
+            outfile.close()

lalsuite-7.26.2.dev20251210.data/scripts/cbcBayesGraceDBinfo

@@ -0,0 +1,182 @@
+#!python
+# -*- coding: utf-8 -*-
+#
+#       cbcBayesGraceDBinfo
+#
+#       Copyright 2015
+#       Salvatore Vitale <salvatore.vitale@ligo.org>
+#
+#       This program is free software; you can redistribute it and/or modify
+#       it under the terms of the GNU General Public License as published by
+#       the Free Software Foundation; either version 2 of the License, or
+#       (at your option) any later version.
+#
+#       This program is distributed in the hope that it will be useful,
+#       but WITHOUT ANY WARRANTY; without even the implied warranty of
+#       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#       GNU General Public License for more details.
+#
+#       You should have received a copy of the GNU General Public License
+#       along with this program; if not, write to the Free Software
+#       Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+#       MA 02110-1301, USA.
+
+#===============================================================================
+# Preamble
+#===============================================================================
+
+#standard library imports
+import sys
+import numpy as np
+import matplotlib
+matplotlib.use("Agg")
+
+from lalinference import bayespputils as bppu
+from lalinference import git_version
+
+__author__="Salvatore Vitale <salvatore.vitale@ligo.org>"
+__version__= "git id %s"%git_version.id
+__date__= git_version.date
+
+USAGE='''%prog --gid graceDBid --samples posterior_samples.dat
+
+Upload to the pe section of the graceDB page gid information about a lalinference postprocessing run.
+For the moment this is maximum a posteriori and stdev for the parameters in the string pars.
+
+'''
+
+def cbcBayesGraceDBinfo(gid=None,samples=None,skymap=None,analysis='LALInference', bcifile=None,bsnfile=None,email=None,message=None,server="https://gracedb.ligo.org/api/"):
+
+  if gid is None or (samples is None and skymap is None):
+    print("Must provide both a graceDB id and a posterior samples file or skymap file\n")
+    sys.exit(1)
+
+  import ligo.gracedb.rest
+  import os
+  if server is not None:
+    g=ligo.gracedb.rest.GraceDb(server)
+  else:
+    g=ligo.gracedb.rest.GraceDb()
+  if samples is not None:
+    samples=os.path.realpath(samples)
+    if '.hdf' in samples  or '.h5' in samples:
+      peparser = bppu.PEOutputParser('hdf5')
+      commonResultsObj=peparser.parse(samples)
+    else:
+      peparser=bppu.PEOutputParser('common')
+      commonResultsObj=peparser.parse(open(samples,'r'))
+
+    try:
+      pos = bppu.BurstPosterior(commonResultsObj)
+      pars=['frequency','quality','hrss']
+      units={'frequency':'[Hz]','quality':'','hrss':'','loghrss':''}
+    except:
+      pos = bppu.Posterior(commonResultsObj)
+      pars=['mchirp','q','distance']
+    strs=[]
+    outstr='<table><tr><th colspan=2 align=center>%s PE summary</th></tr>'%analysis
+
+    for i in pars:
+      if i in pos.names:
+        _,which=pos._posMap()
+        if i=='hrss':
+          outstr+='<tr><td align=left>%s %s</td>'%(i,units[i])
+          outstr+='<td align=left>%.3e &plusmn; %.3e</td></tr>'%(pos[i].samples[which][0],pos[i].stdev)
+        else:
+          outstr+='<tr><td align=left>%s %s</td>'%(i,units[i])
+          outstr+='<td align=left>%.3f &plusmn; %.3f</td></tr>'%(pos[i].samples[which][0],pos[i].stdev)
+    if bcifile is not None and os.path.isfile(bcifile):
+      bci=np.loadtxt(bcifile)
+    else: bci=None
+    if bci is not None:
+      outstr+='<tr><td align=left>logBCI</td>'
+      outstr+='<td align=center>%.2f</td></tr>'%(bci)
+
+    bsn=None
+    if bsnfile is not None and os.path.isfile(bsnfile):
+      bsn=np.loadtxt(bsnfile)
+      bsn=bsn[0]
+    else:
+      try:
+        import h5py
+        with h5py.File(samples,'r') as h5grp:
+          tmp=h5grp['lalinference']['lalinference_nest'].attrs
+          bsn=tmp['log_bayes_factor']
+      except Exception as e:
+        print("Could not obtain BNS\n")
+        print(e)
+
+    if bsn is not None:
+      outstr+='<tr><td align=left>logBSN</td>'
+      outstr+='<td align=center>%.2f</td></tr>'%(bsn)
+    outstr+='</table>'
+
+    if email is not None and bci is not None:
+      import os
+      import smtplib
+      address=email.split(',')
+      SERVER="localhost"
+      USER=os.environ['USER']
+      import socket
+      HOST=socket.getfqdn()#socket.gethostbyaddr(socket.gethostname())[0]
+      pref=""
+      if bci>3 and bci<6:
+        pref="A promising"
+      elif bci>6 and bci<10:
+        pref="A very interesting"
+      elif bci>10:
+        pref="A SPECTACULAR"
+      FROM="salvatore.vitale@"+HOST
+      SUBJECT="%s LIB result page is ready at "%pref+HOST+" for graceID %s!"%(gid)
+      TEXT="LIB run for graceID %s is done on "%gid+HOST+".\nThe BCI is %lf\n"%bci
+      if bci>10:
+        TEXT+="RUN!!!!!!!!!!\n"
+      message="From: %s\nTo: %s\nSubject: %s\n\n%s"%(FROM,', '.join(address),SUBJECT,TEXT)
+      try:
+        import os
+        os.system('echo "%s" | mail -s "%s" "%s"'%(TEXT,SUBJECT,', '.join(address)))
+        server=smtplib.SMTP(SERVER)
+        server.sendmail(FROM,address,message)
+        server.quit()
+      except:
+        print("Cound not send email\n")
+
+    g.writeLog(gid,outstr,filename=None,tagname='pe')
+  elif skymap is not None:
+    if bcifile is not None and os.path.isfile(bcifile):
+      bci=np.loadtxt(bcifile)
+    else: bci=None
+    if bsnfile is not None and os.path.isfile(bsnfile):
+      bsn=np.loadtxt(bsnfile)
+    else: bsn=None
+    tag=['sky_loc']
+    """
+    if bci is not None and bsn is not None:
+      if bsn>5. and bci>2.:
+        tag.append('lvem')
+    """
+    g.writeLog(gid,message,filename=skymap,tagname=tag)
+
+
+if __name__=='__main__':
+
+    from optparse import OptionParser
+    parser=OptionParser(USAGE)
+    parser.add_option("-g","--gid", dest="gid",help="GraceDB id", metavar="G123456",default=None)
+    parser.add_option("-s","--samples",dest="samples",help="posterior_samples.hdf5/dat",default=None)
+    parser.add_option("--analysis",help="Prefix to use for the graceDB entries. Should be the name of the analysis (default LALInference)",default='LALInference')
+    parser.add_option("--bci",dest="bci",help="coherence test file: bci.dat",default=None)
+    parser.add_option("--bsn",dest="bsn",help="evidence file: bsn.dat [Deprecated, now is read from samples.hdf5]",default=None)
+    parser.add_option("--skymap",dest="skymap",help="FITS file skymap",default=None)
+    parser.add_option("--message",dest="message",type='str', help="Message to go with skymap uplaod",default=None)
+    parser.add_option('--email',dest='email',help="Will email when run is done.",default=None)
+    parser.add_option('--server',dest='server',help="GraceDB server to interact with.",default="https://gracedb.ligo.org/api/")
+
+    (opts,args)=parser.parse_args()
+    if opts.gid is None:
+      print("Must provide a graceDB id with --gid/-g ")
+      sys.exit(1)
+    if opts.samples is None and opts.skymap is None:
+      print("Must provide lalinference posterior samples with --samples/-s or FITS skymap with --skymap ")
+      sys.exit(1)
+    cbcBayesGraceDBinfo(opts.gid, opts.samples,analysis=opts.analysis,bcifile=opts.bci,bsnfile=opts.bsn,email=opts.email,skymap=opts.skymap,message=opts.message,server=opts.server)

lalsuite-7.26.2.dev20251210.data/scripts/cbcBayesMCMC2pos

@@ -0,0 +1,314 @@
+#!python
+# -*- coding: utf-8 -*-
+#
+#       cbcBayesMCMC2pos.py
+#
+#       Copyright 2016
+#       Carl-Johan Haster <carl-johan.haster@ligo.org>
+#
+#       Following methodology from cbcBayesThermoInt.py and lalapps_nest2pos.py
+#
+#       This program is free software; you can redistribute it and/or modify
+#       it under the terms of the GNU General Public License as published by
+#       the Free Software Foundation; either version 2 of the License, or
+#       (at your option) any later version.
+#
+#       This program is distributed in the hope that it will be useful,
+#       but WITHOUT ANY WARRANTY; without even the implied warranty of
+#       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#       GNU General Public License for more details.
+#
+#       You should have received a copy of the GNU General Public License
+#       along with this program; if not, write to the Free Software
+#       Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+#       MA 02110-1301, USA.
+
+import sys
+from functools import reduce
+
+import matplotlib
+matplotlib.use('Agg') #sets backend to not need to open windows
+
+import numpy as np
+import astropy.table as apt
+try:
+	from scipy.integrate import trapezoid
+except ImportError:
+	# FIXME: Remove this once we require scipy >=1.6.0.
+	from scipy.integrate import trapz as trapezoid
+from optparse import OptionParser
+
+from lalinference import git_version
+from lalinference import bayespputils as bppu
+from lalinference.io import read_samples, write_samples, extract_metadata
+
+from lalinference import LALINFERENCE_PARAM_FIXED as FIXED
+from lalinference import LALINFERENCE_PARAM_OUTPUT as OUTPUT
+
+__author__="Carl-Johan Haster <carl-johan.haster@ligo.org>>"
+__version__= "git id %s"%git_version.id
+__date__= git_version.date
+
+def multipleFileCB(opt, opt_str, value, parser):
+    args=[]
+
+    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
+      args.append(arg)
+
+    del parser.rargs[:len(args)]
+    #Append new files to list if some already specified
+    if getattr(parser.values, opt.dest):
+        oldargs = getattr(parser.values, opt.dest)
+        oldargs.extend(args)
+        args = oldargs
+    setattr(parser.values, opt.dest, args)
+
+mcmc_group_id = '/lalinference/lalinference_mcmc'
+
+def reassign_metadata(new_posterior, original_hdf5):
+	# Make sure output file has same metadata as original
+	# input hdf5 file
+
+	base_file = read_samples(original_hdf5)
+
+	mcmc_diagnostics_params = ['nLocalTemps','randomSeed']
+
+	meta_dict = {}
+
+	for colname, column in base_file.columns.items():
+		meta_dict[colname] = column.meta
+
+	for colname, column in new_posterior.columns.items():
+		if colname in mcmc_diagnostics_params:
+			column.meta = {'vary': OUTPUT}
+			# these parameters are fixed within a run,
+			# but doesn't have to be equal between runs.
+		elif colname in meta_dict:
+			column.meta = meta_dict[colname]
+		elif 'cos'+colname in meta_dict:
+			column.meta = meta_dict['cos'+colname]
+		elif 'sin'+colname in meta_dict:
+			column.meta = meta_dict['sin'+colname]
+		elif 'log'+colname in meta_dict:
+			column.meta = meta_dict['log'+colname]
+		elif colname.startswith('chain_'):
+			column.meta = {'vary': OUTPUT}
+			# same argument as with mcmc_diagnostics_params
+		else:
+			column.meta = {'vary': FIXED}
+
+	return new_posterior
+
+def downsample_and_evidence(data_hdf5, deltaLogP=None, fixedBurnin=None, nDownsample=None, verbose=False):
+
+    # Remove burnin from beginning of MCMC-chains, downsample by the chain's respective autocorrelation length.
+    # Compute the evidence for the set of parallel tempered chains through a thermodynamic integral
+
+	if not data_hdf5.lower().endswith(('.hdf5', '.hdf', '.h5')):
+		print('cbcBayesMCMC2pos only suports hdf5 input, for older file formats plese revert to cbcBayesThermoInt and cbcBayesPosProc')
+		sys.exit(1)
+
+	peparser = bppu.PEOutputParser('hdf5')
+
+	ps, samps = peparser.parse(data_hdf5, deltaLogP=deltaLogP, fixedBurnins=fixedBurnin,
+		nDownsample=nDownsample, tablename=None)
+	posterior_samples = apt.Table(samps, names=ps)
+
+	highTchains = []
+	for i in range(1,int(posterior_samples['nTemps'][0])):
+		ps, samps = peparser.parse(data_hdf5, deltaLogP=deltaLogP, fixedBurnins=fixedBurnin,
+			nDownsample=nDownsample, tablename='chain_'+str('%02.f' %i))
+		highTchains.append(apt.Table(samps, names=ps))
+		if verbose: print('chain_'+str('%02.f' %i)+' at a temperature '+str(highTchains[i-1]['temperature'].mean()))
+
+	betas = np.zeros(len(highTchains)+1)
+	logls = np.zeros_like(betas)
+
+	betas[0] = 1./np.median(posterior_samples['temperature'])
+	logls[0] = np.mean(posterior_samples['logl'])
+
+	for i in range(len(highTchains)):
+		betas[i+1] = 1./np.median(highTchains[i]['temperature'])
+		logls[i+1] = np.mean(highTchains[i]['logl'])
+
+	inds = np.argsort(betas)[::-1]
+
+	betas = betas[inds]
+	logls = logls[inds]
+
+	# Now extend to infinite temperature by copying the last <log(L)>.
+	# This works as long as the chains have extended to high enough
+	# temperature to sample the prior.
+	# If infinite temperature is already included, this 'duplicate'
+	# will not change the final evidence.
+	ebetas = np.concatenate((betas, [0.0]))
+	elogls = np.concatenate((logls, [logls[-1]]))
+
+	ebetas2 = np.concatenate((betas[::2], [0.0]))
+	elogls2 = np.concatenate((logls[::2], [logls[::2][-1]]))
+
+	evidence = -trapezoid(elogls, ebetas)
+	evidence2 = -trapezoid(elogls2, ebetas2)
+
+	posterior_samples['chain_log_evidence'] = evidence
+	posterior_samples['chain_delta_log_evidence'] = np.absolute(evidence - evidence2)
+	posterior_samples['chain_log_noise_evidence'] = posterior_samples['nullLogL']
+	posterior_samples['chain_log_bayes_factor'] = posterior_samples['chain_log_evidence'] - posterior_samples['chain_log_noise_evidence']
+
+	if verbose:
+		print('logZ = '+str(posterior_samples['chain_log_evidence'][0])+'+-'+str(posterior_samples['chain_delta_log_evidence'][0]))
+		print('logB_SN = '+str(posterior_samples['chain_log_bayes_factor'][0]))
+
+	posterior_samples = reassign_metadata(posterior_samples, data_hdf5)
+
+	return posterior_samples
+
+
+def weight_and_combine(pos_chains, verbose=False, evidence_weighting=True, combine_only=False):
+
+	# Combine several posterior chains into one
+        # If evidence_weighting == True, they are
+	# weighted by their relative evidence
+
+        # Otherwise they are just combined
+
+	log_evs = np.zeros(len(pos_chains))
+	log_noise_evs = np.zeros_like(log_evs)
+
+	for i in range(len(pos_chains)):
+		log_evs[i] = pos_chains[i]['chain_log_evidence'][0]
+		log_noise_evs[i] = pos_chains[i]['chain_log_noise_evidence'][0]
+	if verbose: print('Computed log_evidences: %s'%(str(log_evs)))
+
+	max_log_ev = log_evs.max()
+
+	if evidence_weighting:
+	    fracs=[np.exp(log_ev-max_log_ev) for log_ev in log_evs]
+	else:
+	    fracs = [1.0 for _ in log_evs]
+	if verbose: print('Relative weights of input files: %s'%(str(fracs)))
+
+	Ns=[fracs[i]/len(pos_chains[i]) for i in range(len(fracs))]
+	Ntot=max(Ns)
+	fracs=[n/Ntot for n in Ns]
+	if combine_only:
+	    fracs = [1.0 for _ in fracs]
+	if verbose: print('Relative weights of input files taking into account their length: %s'%(str(fracs)))
+
+	final_posterior = pos_chains[0][np.random.uniform(size=len(pos_chains[0]))<fracs[0]]
+
+	for i in range(1,len(pos_chains)):
+		final_posterior = apt.vstack([final_posterior,
+			pos_chains[i][np.random.uniform(size=len(pos_chains[i]))<fracs[i]]])
+
+	final_log_evidence = reduce(np.logaddexp, log_evs) - np.log(len(log_evs))
+	final_log_noise_evidence = reduce(np.logaddexp, log_noise_evs) - np.log(len(log_noise_evs))
+
+	run_level= 'lalinference/lalinference_mcmc'
+	metadata = {}
+	metadata[run_level] = {}
+	metadata[run_level]['log_bayes_factor'] = final_log_evidence - final_log_noise_evidence
+	metadata[run_level]['log_evidence'] = final_log_evidence
+	metadata[run_level]['log_noise_evidence'] = final_log_noise_evidence
+	metadata[run_level]['log_max_likelihood'] = final_posterior['logl'].max()
+	# This has already been burned-in and downsampled,
+	# remove the cycle column to stop cbcBayesPosProc
+	# from doing it again.
+	final_posterior.remove_column('cycle')
+
+	return final_posterior, metadata
+
+USAGE='''%prog [options] PTMCMC_datafile.hdf5 [PTMCMC_datafile2.hdf5 ...]
+Compute the evidence for a set of parallel tempered MCMC chains
+thourgh thermodynamical integration. If using several input PTMCMC files,
+combine them into one set of posterior samples, weighted by their relative
+evidences.
+'''
+
+if __name__ == '__main__':
+	parser = OptionParser(USAGE)
+	parser.add_option(
+		'-p', '--pos', action='store', type='string', default=None,
+		help='Output file for posterior samples', metavar='posterior.hdf5')
+	parser.add_option(
+		'-v', '--verbose', action='store_true', default=False,
+		help='Print some additional information')
+	parser.add_option('-d','--data',dest='data',action='callback',
+		callback=multipleFileCB,help='datafile')
+	parser.add_option(
+		'-s','--downsample',action='store',default=None,
+		help='Approximate number of samples to record in the posterior',type='int')
+	parser.add_option(
+		'-l','--deltaLogP',action='store',default=None,
+		help='Difference in logPosterior to use for convergence test.',type='float')
+	parser.add_option(
+		'-b','--fixedBurnin',dest='fixedBurnin',action="callback",
+		callback=multipleFileCB,help='Fixed number of iteration for burnin.')
+	parser.add_option(
+		'--equal-weighting',action='store_true',default=False,
+		help = 'Disable evidence weighting and just combine chains so they have equal\
+                        contribution to the final result')
+	parser.add_option(
+                '--combine-only', action='store_true',default=False,
+                help = "Don't weight the chains at all, just concatenate them (different length\
+                        inputs will have different representation in the output)")
+	opts, args = parser.parse_args()
+
+	datafiles=[]
+	if args:
+		datafiles = datafiles + args
+	if opts.data:
+		datafiles = datafiles + opts.data
+
+	if opts.fixedBurnin:
+	# If only one value for multiple chains, assume it's to be applied to all chains
+		if len(opts.fixedBurnin) == 1:
+			fixedBurnins = [int(opts.fixedBurnin[0]) for df in datafiles]
+		else:
+			fixedBurnins = [int(fixedBurnin) for fixedBurnin in opts.fixedBurnin]
+	else:
+		fixedBurnins = [None]*len(datafiles)
+
+	chain_posteriors = []
+
+	for i in range(len(datafiles)):
+		chain_posteriors.append(downsample_and_evidence(datafiles[i],
+			deltaLogP=opts.deltaLogP, fixedBurnin=fixedBurnins[i], nDownsample=opts.downsample, verbose=opts.verbose))
+
+	final_posterior, metadata = weight_and_combine(chain_posteriors, verbose=opts.verbose,
+                evidence_weighting = not opts.equal_weighting,
+                combine_only = opts.combine_only)
+
+	for path in datafiles:
+		run_identifier = extract_metadata(path, metadata)
+
+	# Remove duplicate metadata
+	path_to_samples = '/'.join(['','lalinference',run_identifier,'posterior_samples'])
+	if path_to_samples in metadata:
+		for colname in final_posterior.columns:
+			metadata[path_to_samples].pop(colname, None)
+
+	# for metadata which is in a list, take the average.
+	for level in metadata:
+		for key in metadata[level]:
+			#if isinstance(metadata[level][key], list) and all(isinstance(x, (int,float)) for x in metadata[level][key]):
+			#    metadata[level][key] = mean(metadata[level][key])
+			if isinstance(metadata[level][key], list) and all(isinstance(x, (str)) for x in metadata[level][key]):
+				print("Warning: only printing the first of the %d entries found for metadata %s/%s. You can find the whole list in the headers of individual hdf5 output files\n"%(len(metadata[level][key]),level,key))
+				metadata[level][key] = metadata[level][key][0]
+
+	write_samples(final_posterior, opts.pos,
+		path=path_to_samples, metadata=metadata)