lalsuite 7.26.2.dev20251210__cp312-cp312-macosx_12_0_arm64.whl

lalsuite-7.26.2.dev20251210.data/scripts/cbcBayesCompPos

@@ -0,0 +1,1121 @@
+#!python
+# -*- coding: utf-8 -*-
+#
+#       cbcBayesCompPos.py Copyright 2010--2012 Benjamin Aylott
+#       <benjamin.aylott@ligo.org>, 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.
+
+#standard library imports
+import os
+import sys
+from time import strftime
+import copy
+import getpass
+
+#related third party imports
+import numpy as np
+from numpy import floor
+
+import scipy.stats as ss
+
+import matplotlib as mpl
+mpl.use("AGG")
+from matplotlib import pyplot as plt
+from matplotlib import colors as mpl_colors
+from matplotlib import cm as mpl_cm
+from matplotlib.ticker import ScalarFormatter
+
+#local application/library specific imports
+import lalinference.bayespputils as bppu
+from lalinference import git_version
+
+__author__="Ben Aylott <benjamin.aylott@ligo.org>, Will M. Farr <will.farr@ligo.org>"
+__version__= "git id %s"%git_version.id
+__date__= git_version.date
+
+#List of parameters to plot/bin . Need to match (converted) column names.
+oneDMenu=['mtotal','m1','m2','mchirp','mc','chirpmass','distance','distMPC','dist','iota','psi','eta','q','asym_massratio','spin1','spin2','a1','a2','phi1','theta1','phi2','theta2','costilt1','costilt2','costhetas','cosbeta','phi_orb', 'lambdat', 'dlambdat', 'lambda1', 'lambda2', 'lam_tilde', 'dlam_tilde','theta_jn','a1z','a2z'] + bppu.spininducedquadParams + bppu.snrParams + bppu.spinParams + bppu.cosmoParam + bppu.calParams + bppu.tigerParams + bppu.lorentzInvarianceViolationParams + bppu.qnmtestParams
+#List of parameter pairs to bin . Need to match (converted) column names.
+twoDGreedyMenu=[['mc','eta'],['mchirp','eta'],['chirpmass','eta'],['mc','q'],['mchirp','q'],['chirpmass','q'],['mc','asym_massratio'],['mchirp','asym_massratio'],['chirpmass','asym_massratio'],['m1','m2'],['mtotal','eta'],['distance','iota'],['dist','iota'],['dist','m1'],['ra','dec'],['dist','cos(iota)'],['phi_orb','iota'],['theta_jn','dist'],['spin1','spin2'],['spin1','mchirp'],['spin1','m1'],['a1','a2'],['a1','mchirp'],['a1','m1'],['tilt1','tilt2'],['tilt1','mchirp'],['tilt1','m1'],['a1z','a2z']]
+#Bin size/resolution for binning. Need to match (converted) column names.
+
+#Convert parameter names to LaTeX; if not mentioned here, just use parameter name.
+paramNameLatexMap = {'m1': 'm_1', 'm2' : 'm_2', 'mtotal' : r'M_{\rm tot}', 'mchirp' : r'\mathcal{M}',
+                     'mc': r'\mathcal{M}', 'distance' : 'd', 'distMPC' : 'd', 'dist': 'd',
+                     'iota': r'\iota', 'psi': r'\psi', 'eta': r'\eta', 'asym_massratio': 'q', 'a1': 'a_1',
+                     'a2': 'a_2', 'phi1': r'\phi_1', 'phi2': r'\phi_2', 'theta1': r'\theta_1', 'theta2': r'\theta_2',
+                     'cos(tilt1)': r'\cos t_1', 'cos(tilt2)': r'\cos t_2', 'cos(thetas)': r'\cos \theta_s',
+                     'cosbeta': r'\cos \beta', 'phi_orb': r'\phi_{\rm orb}', 'cos(beta)': r'\cos \beta',
+                     'cos(iota)': r'\cos \iota', 'tilt1': r't_1', 'tilt2': r't_2', 'ra': r'\alpha', 'dec': r'\delta',
+                     'lambdat' : r'\tilde{\Lambda}', 'dlambdat': r'\delta \tilde{\Lambda}',
+                     'lambda1' : r'\lambda_1', 'lambda2': r'\lambda_2',
+                     'lam_tilde' : r'\tilde{\Lambda}', 'dlam_tilde': r'\delta \tilde{\Lambda}','dchiMinus2':r'$d\chi_{-2}$','dchiMinus1':r'$d\chi_{-1}$','dchi0':r'\delta\chi_0','dchi1':r'\delta\chi_1','dchi2':r'\delta\chi_2','dchi3':r'\delta\chi_3','dchi3S':r'\delta\chi_{3S}','dchi3NS':r'\delta\chi_{3NS}','dchi4':r'\delta\chi_4','dchi4S':r'\delta\chi_{4S}','dchi4NS':r'\delta\chi_{4NS}','dchi5':r'\delta\chi_5','dchi5S':r'\delta\chi_{5S}','dchi5NS':r'\delta\chi_{5NS}','dchi5l':r'\delta\chi_{5l}','dchi5lS':r'\delta\chi_{5lS}','dchi5lNS':r'\delta\chi_{5lNS}','dchi6':r'\delta\chi_6','dchi6S':r'\delta\chi_{6S}','dchi6NS':r'\delta\chi_{6NS}','dchi6l':r'\delta\chi_{6l}','dchi7':r'\delta\chi_7','dchi7S':r'\delta\chi_{7S}','dchi7NS':r'\delta\chi_{7NS}','dbeta2':r'\delta\beta_2','dbeta3':r'\delta\beta_3','dsigma2':r'\delta\sigma_2','dsigma3':r'\delta\sigma_3','dsigma4':r'\delta\sigma_4','dbeta2':r'\delta\beta_2','dbeta3':r'\delta\beta_3' ,'log10lambda_a':r'$\log\lambda_{\mathbb{A}}$','log10lambda_eff':r'$\log\lambda_{eff}$','log10livamp':r'$\log \mathbb{A}$','lambda_a':r'$\lambda_{\mathbb{A}}$','lambda_eff':r'$\lambda_{eff}$','liv_amp':r'$\mathbb{A}$','dquadmons':r'\delta\kappa_s','dchikappaS':r'\delta\chi_{kappa_{S}}','dchikappaA':r'\delta\chi_{\kappa_{A}}',
+'domega220': r'$d\omega_{220}$', 'dtau220': r'$d\tau_{220}$',
+                     'domega210': r'$d\omega_{210}$', 'dtau210': r'$d\tau_{210}$',
+                     'domega330': r'$d\omega_{330}$','dtau330': r'$d\tau_{330}$',
+                     'domega440': r'$d\omega_{440}$', 'dtau440': r'$d\tau_{440}$',
+                     'domega550': r'$d\omega_{550}$', 'dtau550': r'$d\tau_{550}$',
+                     'dc1':r'$\delta c_1$', 'dc2':r'$\delta c_2$', 'dc4':r'$\delta c_4$', 'dcl':r'$\delta c_l$', 'db1':r'$\delta b_1$', 'db2':r'$\delta b_2$', 'db3':r'$\delta b_3$', 'db4':r'$\delta b_4$'
+}
+
+# Only these parameters, in this order appear in confidence level table.
+clTableParams = ['mchirp', 'mc', 'chirpmass', 'eta', 'q', 'm1', 'm2', 'distance', 'distMPC', 'dist', 'cos(iota)', 'iota', 'theta_jn', 'psi', 'ra', 'dec', 'time', 'phase', 'a1', 'a2', 'costilt1', 'costilt2','dchiMinus2','dchiMinus1','dchi0','dchi1','dchi2','dchi3','dchi3S','dchi3NS','dchi4','dchi4S','dchi4NS','dchi5','dchi5S','dchi5NS','dchi5l','dchi5lS','dchi5lNS','dchi6','dchi6S','dchi6NS','dchi6l','dchi7','dchi7S','dchi7NS','dbeta2','dbeta3','dsigma2','dsigma3','dsigma4','dbeta2','dbeta3', 'log10lambda_eff','log10lambda_a','log10livamp','lambda_eff','lambda_a','liv_amp','dquadmons','dchikappaS','dchikappaA','domega220', 'dtau220', 'domega210', 'dtau210', 'domega330', 'dtau330', 'domega440', 'dtau440', 'domega550', 'dtau550', 'db1', 'db2', 'db3', 'db4', 'dc1', 'dc2', 'dc4', 'dcl']
+
+
+
+greedyBinSizes={'mc':0.001,'m1':0.1,'m2':0.1,'mass1':0.1,'mass2':0.1,'mtotal':0.1,'eta':0.001,'q':0.001,'asym_massratio':0.001,'iota':0.05,'time':1e-4,'distance':5.0,'dist':1.0,'mchirp':0.01,'chirpmass':0.01,'a1':0.02,'a2':0.02,'phi1':0.05,'phi2':0.05,'theta1':0.05,'theta2':0.05,'ra':0.05,'dec':0.005,'psi':0.1,'cos(iota)':0.01, 'cos(tilt1)':0.01, 'cos(tilt2)':0.01, 'tilt1':0.05, 'tilt2':0.05, 'cos(thetas)':0.01, 'cos(beta)':0.01,'phi_orb':0.2,'inclination':0.05,'theta_jn':0.05,'spin1':0.02,'spin2':0.02}
+for s in bppu.snrParams:
+        greedyBinSizes[s]=0.02
+for s in bppu.calParams:
+        greedyBinSizes[s]=0.02
+for s in bppu.tigerParams + bppu.lorentzInvarianceViolationParams + bppu.qnmtestParams:
+  greedyBinSizes[s]=0.01
+for s in bppu.spinParams:
+        greedyBinSizes[s]=0.02
+for s in bppu.cosmoParam:
+        greedyBinSizes[s]=0.1
+greedyBinSizes['redshift']=0.005
+
+#Confidence levels
+OneDconfidenceLevels=[0.9]#[0.68,0.9,0.95,0.997]
+TwoDconfidenceLevels=OneDconfidenceLevels
+
+#2D plots list
+#twoDplots=[['mc','eta'],['mchirp','eta'],['m1','m2'],['mtotal','eta'],['distance','iota'],['dist','iota'],['RA','dec'],['ra','dec'],['m1','dist'],['m2','dist'],['psi','iota'],['psi','distance'],['psi','dist'],['psi','phi0'],['dist','cos(iota)']]
+twoDplots=[['m1','m2'],['mass1','mass2'],['RA','dec'],['ra','dec'],['cos(thetas)','cos(beta)'],['distance','iota'],['dist','iota'],['dist','cosiota'],['distance','cosiota'],['psi','iota'],['psi','distance'],['psi','phi0'],['dist','cos(iota)'],['phi_orb','iota'],['distance','inclination'],['dist','inclination'],['theta_jn','dist'],['spin1','spin2'],['spin1','mchirp'],['spin1','m1'],['a1','a2'],['a1','mchirp'],['a1','m1'],['tilt1','tilt2'],['tilt1','mchirp'],['tilt1','m1']]
+allowed_params=['mtotal','m1','m2','mchirp','mc','chirpmass','q','asym_massratio','distance','distMPC','dist','iota','psi','eta','ra','dec','a1','a2','spin1','spin2','phi1','theta1','phi2','theta2','cos(iota)','cos(tilt1)','cos(tilt2)','tilt1','tilt2','cos(thetas)','cos(beta)','phi_orb','inclination', 'logl', 'lambdat', 'dlambdat', 'lambda1', 'lambda2', 'lam_tilde', 'dlam_tilde','theta_jn','a1z','a2z','dquadmons','dquadmona','dquadmon1','dquadmon2']+bppu.snrParams + bppu.spinParams + bppu.cosmoParam + bppu.calParams + bppu.tigerParams
+
+def open_url(url,username,password):
+
+    import urllib
+    import urllib2
+    import urlparse
+
+    parsed_url=urlparse.urlparse(url)
+    url=urlparse.urljoin(parsed_url.geturl(),'posterior_samples.dat')
+
+
+    opener = urllib2.build_opener(urllib2.HTTPCookieProcessor())
+    urllib2.install_opener(opener)
+
+    body={'username':username,'password':password}
+    txdata = urllib.urlencode(body) # if we were making a POST type request, we could encode a dictionary of values here - using urllib.urlencode
+    txheaders = {'User-agent' : 'Mozilla/4.0 (compatible; MSIE 5.5; Windows NT)'} # fake a user agent, some websites (like google) don't like automated exploration
+
+    req = urllib2.Request(parsed_url[0]+'://'+parsed_url[1], txdata, txheaders)
+
+    resp = opener.open(req) # save a cookie
+    dump=resp.read()
+    resp.close()
+    try:
+        req = urllib2.Request(url, txdata, txheaders) # create a request object
+        handle = opener.open(req) # and open it to return a handle on the url
+        data = handle.read()
+        f = file('posterior_samples.dat', 'w')
+        f.write(data)
+        f.close()
+
+    except IOError as e:
+        print('We failed to open "%s".' % url)
+        if hasattr(e, 'code'):
+            print('We failed with error code - %s.' % e.code)
+        elif hasattr(e, 'reason'):
+            print("The error object has the following 'reason' attribute :", e.reason)
+            print("This usually means the server doesn't exist, is down, or we don't have an internet connection.")
+            sys.exit()
+    else:
+        print('Here are the headers of the page :')
+        print(handle.info()) # handle.read() returns the page, handle.geturl() returns the true url of the page fetched (in case urlopen has followed any redirects, which it sometimes does)
+
+    return HTMLSource
+
+def all_pairs(L):
+    while L:
+        i = L.pop()
+        for j in L: yield i, j
+
+def open_url_curl(url,args=[]):
+    import subprocess
+
+    kerberos_args = "--insecure -c /tmp/{0}_cookies -b /tmp/{0}_cookies --negotiate --user : --location-trusted".format(getpass.getuser()).split()
+
+    retcode=subprocess.call(['curl'] + kerberos_args + [url] + args)
+
+    return retcode
+
+def test_and_switch_param(common_output_table_header,test,switch):
+    try:
+        idx=common_output_table_header.index(test)
+        common_output_table_header[idx]=switch
+        print("Re-labelled %s -> %s"%(test,switch))
+    except:
+        pass
+
+    return
+
+def compare_plots_one_param_pdf(list_of_pos_by_name,param,analyticPDF=None):
+    """
+    Plots a gaussian kernel density estimate for a set
+    of Posteriors onto the same axis.
+
+    @param list_of_pos_by_name: a dictionary of {name:Posterior} class instances.
+
+    @param param: parameter name to compare
+
+    @param analyticPDF: Optional function to over-plot
+
+    """
+
+    #Create common figure
+    myfig=plt.figure(figsize=(6,4.5),dpi=150)
+
+    list_of_pos=list(list_of_pos_by_name.values())
+    list_of_pos_names=list(list_of_pos_by_name.keys())
+
+    allmins=map(lambda a: np.min(a[param].samples), list_of_pos)
+    allmaxes=map(lambda a: np.max(a[param].samples), list_of_pos)
+    min_pos=np.min(allmins)
+    max_pos=np.max(allmaxes)
+    print('Found global min: %f, max: %f'%(min_pos,max_pos))
+
+    gkdes={}
+    injvals=[]
+    for name,posterior in list_of_pos_by_name.items():
+
+        pos_samps=posterior[param].samples
+        if posterior[param].injval is not None:
+            injvals.append(posterior[param].injval)
+
+        min_pos_temp=np.min(pos_samps)
+        max_pos_temp=np.max(pos_samps)
+
+        if min_pos_temp<min_pos:
+            min_pos=min_pos_temp
+        if max_pos_temp>max_pos:
+            max_pos=max_pos_temp
+
+        injpar=posterior[param].injval
+
+        gkdes[name]=posterior[param].gaussian_kde
+
+    if gkdes:
+        ind=np.linspace(min_pos,max_pos,101)
+
+        kdepdfs=[]
+        for name,gkde in gkdes.items():
+            kdepdf=gkde.evaluate(ind)
+            kdepdfs.append(kdepdf)
+            plt.plot(ind,np.transpose(kdepdf),label=name)
+        plt.grid()
+        plt.legend()
+        plt.xlabel(bppu.plot_label(param))
+        plt.xlim(min_pos,max_pos)
+        plt.ylabel('Probability Density')
+        try:
+          plt.tight_layout()
+        except:
+          pass
+        if injvals:
+            print("Injection parameter is %f"%(float(injvals[0])))
+            injpar=injvals[0]
+            if min(pos_samps)<injpar and max(pos_samps)>injpar:
+                plt.plot([injpar,injpar],[0,max(kdepdf)],'r-.',scalex=False,scaley=False)
+    if analyticPDF is not None:
+        plt.plot(ind,map(analyticPDF,ind),'r')
+    #
+    return myfig#,rkde
+#
+def compare_plots_one_param_line_hist(list_of_pos_by_name,param,cl,color_by_name,cl_lines_flag=True,legend='right',analyticPDF=None):
+
+
+    """
+    Plots a gaussian kernel density estimate for a set
+    of Posteriors onto the same axis.
+
+    @param list_of_pos_by_name: a dict of Posterior class instances indexed by name
+
+    @param param: parameter name to plot
+
+    @param cl: list of credible levels to plot
+
+    @param color_by_name: dict of colours indexed by name
+
+    @param cl_lines_flag: option to plot credible level lines
+
+    @param legend: matplotlib position for legend
+
+    @param analyticPDF: Optional analytic function to over-plot
+
+    """
+
+    #Create common figure
+    myfig=plt.figure(figsize=(6,4.5),dpi=150)
+  #myfig.add_axes([0.1,0.1,0.65,0.85])
+  #myfig.add_axes([0.15,0.15,0.6,0.76])
+    axes=plt.Axes(myfig,[0.15,0.15,0.6,0.76])
+    myfig.add_axes(axes)
+    majorFormatterX=ScalarFormatter(useMathText=True)
+    majorFormatterX.format_data=lambda data:'%.6g'%(data)
+    majorFormatterY=ScalarFormatter(useMathText=True)
+    majorFormatterY.format_data=lambda data:'%.6g'%(data)
+    majorFormatterX.set_scientific(True)
+    majorFormatterY.set_scientific(True)
+
+    list_of_pos=list(list_of_pos_by_name.values())
+    list_of_pos_names=list(list_of_pos_by_name.keys())
+
+    allmins=map(lambda a: np.min(a[param].samples), list_of_pos)
+    allmaxes=map(lambda a: np.max(a[param].samples), list_of_pos)
+    min_pos=np.min(allmins)
+    max_pos=np.max(allmaxes)
+
+    injvals=[]
+
+    patch_list=[]
+    max_y=0
+
+    posbins=np.linspace(min_pos,max_pos,50)
+
+    for name,posterior in list_of_pos_by_name.items():
+        colour=color_by_name[name]
+        #myfig.gca(autoscale_on=True)
+        if posterior[param].injval:
+            injvals.append(posterior[param].injval)
+
+        try:
+            n,bins=np.histogram(posterior[param].samples,bins=posbins,density=True,new=True)
+        except:
+            n,bins=np.histogram(posterior[param].samples,bins=posbins,density=True)
+        if min(bins)==max(bins):
+            print('Skipping '+param)
+            continue
+        locmaxy=max(n)
+        if locmaxy>max_y: max_y=locmaxy
+#(n, bins, patches)=plt.hist(posterior[param].samples,bins=bins,facecolor='white',label=name,normed=True,hold=True,color=color_by_name[name])#range=(min_pos,max_pos)
+        (n, bins, patches)=plt.hist(posterior[param].samples,bins=bins,histtype='step',label=name,density=True,hold=True,color=color_by_name[name])
+        patch_list.append(patches[0])
+
+    Nchars=max(map(lambda d:len(majorFormatterX.format_data(d)),axes.get_xticks()))
+    if Nchars>8:
+      Nticks=3
+    elif Nchars>5:
+      Nticks=4
+    elif Nchars>4:
+      Nticks=6
+    else:
+      Nticks=6
+    locatorX=mpl.ticker.MaxNLocator(nbins=Nticks)
+    locatorX.view_limits(bins[0],bins[-1])
+    axes.xaxis.set_major_locator(locatorX)
+
+    plt.xlim(min_pos,max_pos)
+    top_cl_intervals_list={}
+    pos_names=list(list_of_pos_by_name.keys())
+
+
+    for name,posterior in list_of_pos_by_name.items():
+        #toppoints,injectionconfidence,reses,injection_area,cl_intervals=bppu.greedy_bin_one_param(posterior,{param:greedyBinSizes[param]},[cl])
+        cl_intervals=posterior[param].prob_interval([cl])
+        colour=color_by_name[name]
+        if cl_intervals[0] is not None and cl_lines_flag:
+            try:
+                plt.plot([cl_intervals[0][0],cl_intervals[0][0]],[0,max_y],color=colour,linestyle='--')
+                plt.plot([cl_intervals[0][1],cl_intervals[0][1]],[0,max_y],color=colour,linestyle='--')
+            except:
+                print("MAX_Y",max_y,[cl_intervals[0][0],cl_intervals[0][0]],[cl_intervals[0][1],cl_intervals[0][1]])
+        top_cl_intervals_list[name]=(cl_intervals[0][0],cl_intervals[0][1])
+
+    if cl_lines_flag:
+        pos_names.append(str(int(cl*100))+'%')
+        patch_list.append(mpl.lines.Line2D(np.array([0.,1.]),np.array([0.,1.]),linestyle='--',color='black'))
+
+    plt.grid()
+    plt.xlim(min_pos,max_pos)
+    if legend is not None:
+      oned_legend=plt.figlegend(patch_list,pos_names,'right')
+      for text in oned_legend.get_texts():
+        text.set_fontsize('small')
+    plt.xlabel(bppu.plot_label(param))
+    plt.ylabel('Probability density')
+    plt.draw()
+    #plt.tight_layout()
+    if injvals:
+        print("Injection parameter is %f"%(float(injvals[0])))
+        injpar=injvals[0]
+        #if min(pos_samps)<injpar and max(pos_samps)>injpar:
+        plt.plot([injpar,injpar],[0,max_y],'r-.',scalex=False,scaley=False,linewidth=4,label='Injection')
+
+    #
+    if analyticPDF is not None:
+        plt.plot(posbins,map(analyticPDF,posbins),'r')
+    return myfig,top_cl_intervals_list#,rkde
+
+#
+def compute_ks_pvalue_matrix(list_of_pos_by_name, param):
+    """Returns a matrix of ks p-value tests between pairs of
+    posteriors on the 1D marginalized distributions for param."""
+
+    poss=list_of_pos_by_name.values()
+
+    N=len(poss)
+
+    matrix=np.zeros((N,N))
+    matrix[:,:]=float('nan')
+
+    for i in range(N):
+        pi=poss[i]
+        for j in range(i+1, N):
+            pj=poss[j]
+
+            d,pvalue=ss.ks_2samp(pi[param].samples.flatten(), pj[param].samples.flatten())
+
+            matrix[i,j]=pvalue
+            matrix[j,i]=pvalue
+
+    return matrix
+
+def compare_plots_one_param_line_hist_cum(list_of_pos_by_name,param,cl,color_by_name,cl_lines_flag=True,analyticCDF=None,legend='auto'):
+
+    """
+    Plots a gaussian kernel density estimate for a set
+    of Posteriors onto the same axis.
+
+    @param list_of_pos_by_name: a dict of Posterior class instances indexed by name
+
+    @param param: name of parameter to plot
+
+    @param cl: list of confidence levels to show
+
+    @param color_by_name: dict of colours indexed by name
+
+    @param cl_lines_flag: Show confidence level lines
+
+    @param analyticCDF: Analytic CDF function to over-plot
+
+    @param legend: legend position to pass to matplotlib
+
+    """
+
+    #Create common figure
+    myfig=plt.figure(figsize=(6,4.5),dpi=150)
+    myfig.add_axes([0.15,0.15,0.6,0.76])
+    list_of_pos=list(list_of_pos_by_name.values())
+    list_of_pos_names=list(list_of_pos_by_name.keys())
+
+    injvals=[]
+    allmins=map(lambda a: np.min(a[param].samples), list_of_pos)
+    allmaxes=map(lambda a: np.max(a[param].samples), list_of_pos)
+    min_pos=np.min(allmins)
+    max_pos=np.max(allmaxes)
+
+    patch_list=[]
+    max_y=1.
+
+    posbins=np.linspace(min_pos,max_pos,50)
+
+    for name,posterior in list_of_pos_by_name.items():
+        colour=color_by_name[name]
+        #myfig.gca(autoscale_on=True)
+        if posterior[param].injval:
+            injvals.append(posterior[param].injval)
+
+        try:
+            n,bins=np.histogram(posterior[param].samples,bins=posbins,density=True,new=True)
+        except:
+            n,bins=np.histogram(posterior[param].samples,bins=posbins,density=True)
+
+        if min(bins)==max(bins):
+            print('Skipping '+param)
+            continue
+
+        (n, bins, patches)=plt.hist(posterior[param].samples,bins=bins,histtype='step',label=name,density=True,hold=True,color=color_by_name[name],cumulative='True')#range=(min_pos,max_pos)
+
+        patch_list.append(patches[0])
+
+    top_cl_intervals_list={}
+    pos_names=list(list_of_pos_by_name.keys())
+
+
+    for name,posterior in list_of_pos_by_name.items():
+        #toppoints,injectionconfidence,reses,injection_area,cl_intervals=bppu.greedy_bin_one_param(posterior,{param:greedyBinSizes[param]},[cl])
+        cl_intervals=posterior[param].prob_interval([cl])
+        colour=color_by_name[name]
+        if cl_intervals[0] is not None and cl_lines_flag:
+            try:
+                plt.plot([cl_intervals[0][0],cl_intervals[0][0]],[0,max_y],color=colour,linestyle='--')
+                plt.plot([cl_intervals[0][1],cl_intervals[0][1]],[0,max_y],color=colour,linestyle='--')
+            except:
+                print("MAX_Y",max_y,[cl_intervals[0][0],cl_intervals[0][0]],[cl_intervals[0][1],cl_intervals[0][1]])
+        top_cl_intervals_list[name]=(cl_intervals[0][0],cl_intervals[0][1])
+
+    if cl_lines_flag:
+        pos_names.append(str(int(cl*100))+'%')
+        patch_list.append(mpl.lines.Line2D(np.array([0.,1.]),np.array([0.,1.]),linestyle='--',color='black'))
+
+    plt.grid()
+    plt.xlim(min_pos,max_pos)
+    plt.ylim(0,1)
+    if legend:
+      oned_legend=plt.figlegend(patch_list,pos_names,'right')
+      for text in oned_legend.get_texts():
+          text.set_fontsize('small')
+    plt.xlabel(bppu.plot_label(param))
+    plt.ylabel('Cumulative Probability')
+    plt.draw()
+    #plt.tight_layout()
+    if injvals:
+        print("Injection parameter is %f"%(float(injvals[0])))
+        injpar=injvals[0]
+        #if min(pos_samps)<injpar and max(pos_samps)>injpar:
+        plt.plot([injpar,injpar],[0,max_y],'r-.',scalex=False,scaley=False,linewidth=4,label='Injection')
+    if analyticCDF is not None:
+        plt.plot(posbins,map(analyticCDF,posbins),'r')
+    return myfig,top_cl_intervals_list#,rkde
+
+
+def compare_bayes(outdir,names_and_pos_folders,injection_path,eventnum,username,password,reload_flag,clf,ldg_flag,contour_figsize=(4.5,4.5),contour_dpi=250,contour_figposition=[0.15,0.15,0.5,0.75],fail_on_file_err=True,covarianceMatrices=None,meanVectors=None,Npixels2D=50):
+
+    injection=None
+
+    if injection_path is not None and os.path.exists(injection_path) and eventnum is not None:
+        eventnum=int(eventnum)
+        from igwn_ligolw import ligolw, lsctables, utils
+        injections = lsctables.SimInspiralTable.get_table(
+                utils.load_filename(injection_path))
+        if eventnum is not None:
+            if(len(injections)<eventnum):
+                print("Error: You asked for event %d, but %s contains only %d injections" %(eventnum,injection_path,len(injections)))
+                sys.exit(1)
+            else:
+                injection=injections[eventnum]
+
+    #Create analytic likelihood functions if covariance matrices and mean vectors were given
+    analyticLikelihood = None
+    if covarianceMatrices and meanVectors:
+        analyticLikelihood = bppu.AnalyticLikelihood(covarianceMatrices, meanVectors)
+    peparser=bppu.PEOutputParser('common')
+    pos_list={}
+    tp_list={}
+    common_params=None
+    working_folder=os.getcwd()
+    for name,pos_folder in names_and_pos_folders:
+        import urlparse
+
+        pos_folder_url=urlparse.urlparse(pos_folder)
+        pfu_scheme,pfu_netloc,pfu_path,pfu_params,pfu_query,pfu_fragment=pos_folder_url
+
+        if 'http' in pfu_scheme:
+
+            """
+            Retrieve a file over http(s).
+            """
+            downloads_folder=os.path.join(os.getcwd(),"downloads")
+            pos_folder_parse=urlparse.urlparse(pos_folder)
+            pfp_scheme,pfp_netloc,pfp_path,pfp_params,pfp_query,pfp_fragment=pos_folder_parse
+            head,tail=os.path.split(pfp_path)
+            if tail is 'posplots.html' or tail:
+                pos_file_part=head
+            else:
+                pos_file_part=pfp_path
+            pos_file_url=urlparse.urlunsplit((pfp_scheme,pfp_netloc,os.path.join(pos_file_part,'posterior_samples.dat'),'',''))
+            print(pos_file_url)
+            pos_file=os.path.join(os.getcwd(),downloads_folder,"%s.dat"%name)
+
+            if not os.path.exists(pos_file):
+                reload_flag=True
+
+            if reload_flag:
+                if os.path.exists(pos_file):
+                    os.remove(pos_file)
+                if not os.path.exists(downloads_folder):
+                    os.makedirs(downloads_folder)
+                open_url_curl(pos_file_url,args=["-o","%s"%pos_file])
+
+        elif pfu_scheme is '' or pfu_scheme is 'file':
+            pos_file=os.path.join(pos_folder,'%s.dat'%name)
+            # Try looking for posterior_samples.dat if name.dat doesn't exist
+            if not os.path.exists(pos_file):
+                print('%s does not exist, trying posterior_samples.dat'%(pos_file))
+                pos_file=os.path.join(pos_folder,'posterior_samples.dat')
+        else:
+            print("Unknown scheme for input data url: %s\nFull URL: %s"%(pfu_scheme,str(pos_folder_url)))
+            exit(0)
+
+        print("Reading posterior samples from %s ..."%pos_file)
+
+        try:
+            common_output_table_header,common_output_table_raw=peparser.parse(open(pos_file,'r'))
+        except:
+            print('Unable to read file '+pos_file)
+            continue
+
+        test_and_switch_param(common_output_table_header,'distance','dist')
+        test_and_switch_param(common_output_table_header,'chirpmass','mchirp')
+        test_and_switch_param(common_output_table_header,'mc','mchirp')
+        test_and_switch_param(common_output_table_header,'asym_massratio','q')
+        test_and_switch_param(common_output_table_header,'massratio', 'eta')
+        test_and_switch_param(common_output_table_header,'RA','ra')
+        test_and_switch_param(common_output_table_header,'rightascension','ra')
+        test_and_switch_param(common_output_table_header,'declination','dec')
+        test_and_switch_param(common_output_table_header,'tilt_spin1','tilt1')
+        test_and_switch_param(common_output_table_header,'tilt_spin2','tilt2')
+
+        if 'LI_MCMC' in name or 'FU_MCMC' in name:
+
+            try:
+
+                idx=common_output_table_header.index('iota')
+                print("Inverting iota!")
+
+                common_output_table_raw[:,idx]= np.pi*np.ones(len(common_output_table_raw[:,0])) - common_output_table_raw[:,idx]
+
+            except:
+                pass
+
+
+        # try:
+        #     print "Converting phi_orb-> 2phi_orb"
+        #     idx=common_output_table_header.index('phi_orb')
+        #     common_output_table_header[idx]='2phi_orb'
+        #     common_output_table_raw[:,idx]= 2*common_output_table_raw[:,idx]
+        # except:
+        #     pass
+
+        try:
+            print("Converting iota-> cos(iota)")
+            idx=common_output_table_header.index('iota')
+            common_output_table_header[idx]='cos(iota)'
+            common_output_table_raw[:,idx]=np.cos(common_output_table_raw[:,idx])
+        except:
+            pass
+
+        #try:
+        #    print "Converting tilt1 -> cos(tilt1)"
+        #    idx=common_output_table_header.index('tilt1')
+        #    common_output_table_header[idx]='cos(tilt1)'
+        #    common_output_table_raw[:,idx]=np.cos(common_output_table_raw[:,idx])
+        #except:
+        #    pass
+
+        #try:
+        #    print "Converting tilt2 -> cos(tilt2)"
+        #    idx=common_output_table_header.index('tilt2')
+        #    common_output_table_header[idx]='cos(tilt2)'
+        #    common_output_table_raw[:,idx]=np.cos(common_output_table_raw[:,idx])
+        #except:
+        #    pass
+
+        try:
+            print("Converting thetas -> cos(thetas)")
+            idx=common_output_table_header.index('thetas')
+            common_output_table_header[idx]='cos(thetas)'
+            common_output_table_raw[:,idx]=np.cos(common_output_table_raw[:,idx])
+        except:
+            pass
+
+        try:
+            print("Converting beta -> cos(beta)")
+            idx=common_output_table_header.index('beta')
+            common_output_table_header[idx]='cos(beta)'
+            common_output_table_raw[:,idx]=np.cos(common_output_table_raw[:,idx])
+        except:
+            pass
+
+        try:
+            idx=common_output_table_header.index('f_ref')
+            injFrefs=np.unique(common_output_table_raw[:,idx])
+            if len(injFrefs) == 1:
+              injFref = injFrefs[0]
+              print("Using f_ref in results as injected value")
+        except:
+            injFref = None
+            pass
+
+        pos_temp=bppu.Posterior((common_output_table_header,common_output_table_raw),SimInspiralTableEntry=injection, injFref=injFref)
+
+        if 'a1' in pos_temp.names and min(pos_temp['a1'].samples)[0] < 0:
+          pos_temp.append_mapping('spin1', lambda a:a, 'a1')
+          pos_temp.pop('a1')
+          pos_temp.append_mapping('a1', lambda a:np.abs(a), 'spin1')
+        if 'a2' in pos_temp.names and min(pos_temp['a2'].samples)[0] < 0:
+          pos_temp.append_mapping('spin2', lambda a:a, 'a2')
+          pos_temp.pop('a2')
+          pos_temp.append_mapping('a2', lambda a:np.abs(a), 'spin2')
+
+
+        if 'm1' in pos_temp.names and 'm2' in pos_temp.names:
+          print("Calculating total mass")
+          pos_temp.append_mapping('mtotal', lambda m1,m2: m1+m2, ['m1','m2'])
+        if 'mass1' in pos_temp.names and 'mass2' in pos_temp.names:
+          print("Calculating total mass")
+          pos_temp.append_mapping('mtotal', lambda m1,m2: m1+m2, ['mass1','mass2'])
+
+        try:
+            idx=common_output_table_header.index('m1')
+
+            idx2=common_output_table_header.index('m2')
+
+            if pos_temp['m1'].mean<pos_temp['m2'].mean:
+                print("SWAPPING MASS PARAMS!")
+                common_output_table_header[idx]='x'
+                common_output_table_header[idx2]='m1'
+                common_output_table_header[idx]='m2'
+                pos_temp=bppu.Posterior((common_output_table_header,common_output_table_raw),SimInspiralTableEntry=injection)
+        except:
+            pass
+
+        pos_list[name]=pos_temp
+
+        if common_params is None:
+            common_params=pos_temp.names
+        else:
+            set_of_pars = set(pos_temp.names)
+            common_params=list(set_of_pars.intersection(common_params))
+
+    print("Common parameters are %s"%str(common_params))
+
+    if injection is None and injection_path is not None:
+        injections = SimInspiralUtils.ReadSimInspiralFromFiles([injection_path])
+        injection=bppu.get_inj_by_time(injections,pos_temp.means['time'])
+    if injection is not None:
+        for pos in pos_list.values():
+            pos.set_injection(injection)
+
+    set_of_pars = set(allowed_params)
+    common_params=list(set_of_pars.intersection(common_params))
+
+    print("Using parameters %s"%str(common_params))
+
+    if not os.path.exists(os.path.join(os.getcwd(),'results')):
+        os.makedirs('results')
+
+    if not os.path.exists(outdir):
+        os.makedirs(outdir)
+
+    pdfdir=os.path.join(outdir,'pdfs')
+    if not os.path.exists(pdfdir):
+        os.makedirs(pdfdir)
+
+    greedy2savepaths=[]
+
+    if common_params is not [] and common_params is not None: #If there are common parameters....
+        colorlst=bppu.__default_color_lst
+
+        if len(common_params)>1: #If there is more than one parameter...
+            temp=copy.copy(common_params)
+            #Plot two param contour plots
+
+            #Assign some colours to each different analysis result
+            color_by_name={}
+            hatches_by_name={}
+            my_cm=mpl_cm.Dark2
+            cmap_size=my_cm.N
+            color_idx=0
+            color_idx_max=len(names_and_pos_folders)
+            cmap_array=my_cm(np.array(range(cmap_size)))
+            #cmap_array=['r','g','b','c','m','k','0.5','#ffff00']
+            hatches=['/','\\','|','-','+','x','o','O','.','*']
+            ldg='auto'
+            if not ldg_flag:
+              ldg=None
+            for name,infolder in names_and_pos_folders:
+                #color_by_name=cmap_array[color_idx]
+                color_by_name[name]=cmap_array[int(floor(color_idx*cmap_size/color_idx_max)),:]
+                color_idx=(color_idx+1) % color_idx_max
+                hatches_by_name[name]=hatches[color_idx]
+
+            for i,j in all_pairs(temp):#Iterate over all unique pairs in the set of common parameters
+                pplst=[i,j]
+                rpplst=pplst[:]
+                rpplst.reverse()
+
+                pplst_cond=(pplst in twoDplots)
+                rpplst_cond=(rpplst in twoDplots)
+                if pplst_cond or rpplst_cond:#If this pair of parameters is in the plotting list...
+
+                    try:
+                        print('2d plots: building ',i,j)
+                        greedy2Params={i:greedyBinSizes[i],j:greedyBinSizes[j]}
+                    except KeyError:
+                        continue
+
+                    name_list=[]
+                    cs_list=[]
+
+                    slinestyles=['solid', 'dashed', 'dashdot', 'dotted']
+
+                    fig=bppu.plot_two_param_kde_greedy_levels(pos_list,greedy2Params,TwoDconfidenceLevels,color_by_name,figsize=contour_figsize,dpi=contour_dpi,figposition=contour_figposition,legend=ldg,line_styles=slinestyles,hatches_by_name=hatches_by_name,Npixels=Npixels2D)
+                    if fig is None: continue
+                    #fig=bppu.plot_two_param_greedy_bins_contour(pos_list,greedy2Params,TwoDconfidenceLevels,color_by_name,figsize=contour_figsize,dpi=contour_dpi,figposition=contour_figposition)
+                    greedy2savepaths.append('%s-%s.png'%(pplst[0],pplst[1]))
+                    fig.savefig(os.path.join(outdir,'%s-%s.png'%(pplst[0],pplst[1])),bbox_inches='tight')
+                    fig.savefig(os.path.join(pdfdir,'%s-%s.pdf'%(pplst[0],pplst[1])),bbox_inches='tight')
+
+
+            plt.clf()
+        oned_data={}
+        #confidence_levels={}
+        confidence_levels=[{},{},{},{}]
+        confidence_uncertainty={}
+        for param in common_params:
+            print("Plotting comparison for '%s'"%param)
+
+            cl_table_header='<table><th>Run</th>'
+            cl_table={}
+            save_paths=[]
+            cl_table_min_max_str='<tr><td> Min | Max </td>'
+            level_index=0
+            for confidence_level in OneDconfidenceLevels:
+                if analyticLikelihood:
+                    pdf=analyticLikelihood.pdf(param)
+                    cdf=analyticLikelihood.cdf(param)
+                else:
+                    pdf=None
+                    cdf=None
+                cl_table_header+='<th colspan="2">%i%% (Lower|Upper)</th>'%(int(100*confidence_level))
+                hist_fig,cl_intervals=compare_plots_one_param_line_hist(pos_list,param,confidence_level,color_by_name,cl_lines_flag=clf,legend=ldg,analyticPDF=pdf)
+                hist_fig2,cl_intervals=compare_plots_one_param_line_hist_cum(pos_list,param,confidence_level,color_by_name,cl_lines_flag=clf,analyticCDF=cdf,legend=ldg)
+
+                # Save confidence levels and uncertainty
+                #confidence_levels[param]=[]
+                confidence_levels[level_index][param]=[]
+
+                for name,pos in pos_list.items():
+                    median=pos[param].median
+                    low,high=cl_intervals[name]
+                    #confidence_levels[param].append((name,low,median,high))
+                    confidence_levels[level_index][param].append((name,low,median,high))
+
+                level_index=level_index+1
+                cl_bounds=[]
+                poses=[]
+                for name,pos in pos_list.items():
+                    cl_bounds.append(cl_intervals[name])
+                    poses.append(pos[param])
+                confidence_uncertainty[param]=bppu.confidence_interval_uncertainty(confidence_level, cl_bounds, poses)
+
+                save_path=''
+                if hist_fig is not None:
+                    save_path=os.path.join(outdir,'%s_%i.png'%(param,int(100*confidence_level)))
+                    save_path_pdf=os.path.join(pdfdir,'%s_%i.pdf'%(param,int(100*confidence_level)))
+                    try:
+                      plt.tight_layout(hist_fig)
+                      plt.tight_layout(hist_fig2)
+                    except:
+                      pass
+                    hist_fig.savefig(save_path,bbox_inches='tight')
+                    hist_fig.savefig(save_path_pdf,bbox_inches='tight')
+                    save_paths.append(save_path)
+                    save_path=os.path.join(outdir,'%s_%i_cum.png'%(param,int(100*confidence_level)))
+                    save_path_pdf=os.path.join(pdfdir,'%s_%i_cum.pdf'%(param,int(100*confidence_level)))
+                    hist_fig2.savefig(save_path,bbox_inches='tight')
+                    hist_fig2.savefig(save_path_pdf,bbox_inches='tight')
+                    save_paths.append(save_path)
+                min_low,max_high=cl_intervals.values()[0]
+                for name,interval in cl_intervals.items():
+                    low,high=interval
+                    if low<min_low:
+                        min_low=low
+                    if high>max_high:
+                        max_high=high
+                    try:
+                        cl_table[name]+='<td>%s</td><td>%s</td>'%(low,high)
+                    except:
+                        cl_table[name]='<td>%s</td><td>%s</td>'%(low,high)
+                cl_table_min_max_str+='<td>%s</td><td>%s</td>'%(min_low,max_high)
+            cl_table_str=cl_table_header
+            for name,row_contents in cl_table.items():
+                cl_table_str+='<tr><td>%s<font color="%s"></font></td>'%(name,str(mpl_colors.rgb2hex(color_by_name[name][0:3])))#,'&#183;'.encode('utf-8'))
+
+                cl_table_str+=row_contents+'</tr>'
+            cl_table_str+=cl_table_min_max_str+'</tr>'
+            cl_table_str+='</table>'
+
+            cl_uncer_str='<table> <th>Confidence Relative Uncertainty</th> <th>Confidence Fractional Uncertainty</th> <th>Confidence Percentile Uncertainty</th>\n'
+            cl_uncer_str+='<tr> <td> %g </td> <td> %g </td> <td> %g </td> </tr> </table>'%(confidence_uncertainty[param][0], confidence_uncertainty[param][1], confidence_uncertainty[param][2])
+
+            ks_matrix=compute_ks_pvalue_matrix(pos_list, param)
+
+            N=ks_matrix.shape[0]+1
+
+            # Make up KS-test table
+            ks_table_str='<table><th colspan="%d"> K-S test p-value matrix </th>'%N
+
+            # Column headers
+            ks_table_str+='<tr> <td> -- </td> '
+            for name,pos in pos_list.items():
+                ks_table_str+='<td> %s </td>'%name
+            ks_table_str+='</tr>'
+
+            # Now plot rows of matrix
+            for i in range(len(pos_list)):
+                ks_table_str+='<tr> <td> %s </td>'%(pos_list.keys()[i])
+                for j in range(len(pos_list)):
+                    if i == j:
+                        ks_table_str+='<td> -- </td>'
+                    elif ks_matrix[i,j] < 0.05:
+                        # Failing at suspiciously low p-value
+                        ks_table_str+='<td> <b> %g </b> </td>'%ks_matrix[i,j]
+                    else:
+                        ks_table_str+='<td> %g </td>'%ks_matrix[i,j]
+
+                ks_table_str+='</tr>'
+
+            ks_table_str+='</table>'
+
+            oned_data[param]=(save_paths,cl_table_str,ks_table_str,cl_uncer_str)
+
+    # Watch out---using private variable _logL
+    max_logls = [[name,max(pos._logL)] for name,pos in pos_list.items()]
+    dics = [pos.DIC for name, pos in pos_list.items()]
+
+    return greedy2savepaths,oned_data,confidence_uncertainty,confidence_levels,max_logls,dics
+
+def output_confidence_levels_tex(clevels,outpath):
+    """Outputs a LaTeX table of parameter and run medians and confidence levels."""
+    outfile=open(os.path.join(outpath,'confidence_table.tex'), 'w')
+    for level_index in range(len(OneDconfidenceLevels)):
+        params=list(clevels[level_index].keys())
+
+        clevels_by_name={}
+        for param in clTableParams:
+            if param in params:
+                for name,low,med,high in clevels[level_index][param]:
+                    if name in clevels_by_name:
+                        clevels_by_name[name].append((param,low,med,high))
+                    else:
+                        clevels_by_name[name] = [(param,low,med,high)]
+
+        try:
+            outfile.write('confidence level %1.3g\n'%OneDconfidenceLevels[level_index])
+            outfile.write(r'\begin{tabular}{|l||')
+            for param in clTableParams:
+                if param in params:
+                    outfile.write('c|')
+            outfile.write('}\n')
+
+            outfile.write(r'\hline ')
+            for param in clTableParams:
+                if param in params:
+                    tparam=paramNameLatexMap.get(param,param)
+                    outfile.write(r'& $%s$ '%tparam)
+            outfile.write('\\\\ \n \\hline \\hline ')
+
+            for name,levels in clevels_by_name.items():
+                outfile.write(name)
+                for param,low,med,high in levels:
+                    outfile.write(r' & $%0.5g^{%0.5g}_{%0.5g}$ '%(med,high,low))
+                outfile.write('\\\\ \n')
+
+            outfile.write('\\hline \n \\end{tabular}')
+        finally:
+            outfile.write('\n\n')
+
+    outfile.close()
+
+def output_confidence_levels_dat(clevels,outpath):
+    """Outputs a LaTeX table of parameter and run medians and confidence levels."""
+    outfile=open(os.path.join(outpath,'confidence_table.dat'), 'w')
+    for level_index in range(len(OneDconfidenceLevels)):
+        params=list(clevels[level_index].keys())
+
+        clevels_by_name={}
+        for param in clTableParams:
+            if param in params:
+                for name,low,med,high in clevels[level_index][param]:
+                    if name in clevels_by_name:
+                        clevels_by_name[name].append((param,low,med,high))
+                    else:
+                        clevels_by_name[name] = [(param,low,med,high)]
+
+        try:
+            outfile.write('%1.3g\t'%OneDconfidenceLevels[level_index])
+            for param in clTableParams:
+                if param in params:
+                    tparam=paramNameLatexMap.get(param,param)
+                    outfile.write('%s\t'%param)
+            outfile.write('\n')
+
+            for name,levels in clevels_by_name.items():
+                outfile.write(name)
+                for param,low,med,high in levels:
+                    outfile.write('\t%6.6g - %6.6g'%(low,high))
+                outfile.write('\n')
+        finally:
+            outfile.write('\n')
+
+    outfile.close()
+
+def output_confidence_uncertainty(cluncertainty, outpath):
+    outfile=open(os.path.join(outpath, 'confidence_uncertainty.dat'), 'w')
+    try:
+        params=list(cluncertainty.keys())
+        uncer=list(cluncertainty.values())
+
+        outfile.write('# Uncertainty in confidence levels.\n')
+        outfile.write('# First row is relative uncertainty (wrt to parameter mean).\n')
+        outfile.write('# Second row is fractional uncertainty (wrt to combined conf interval).\n')
+        outfile.write('# Third row is percentile uncertainty (wrt combined samples).\n')
+        outfile.write('# ')
+        for param in params:
+            outfile.write(str(param) + ' ')
+        outfile.write('\n')
+
+        rel = np.array([d[0] for d in uncer])
+        fracs = np.array([d[1] for d in uncer])
+        quants = np.array([d[2] for d in uncer])
+
+        np.savetxt(outfile, np.reshape(rel, (1, -1)))
+        np.savetxt(outfile, np.reshape(fracs, (1, -1)))
+        np.savetxt(outfile, np.reshape(quants, (1,-1)))
+    finally:
+        outfile.close()
+
+if __name__ == '__main__':
+    from optparse import OptionParser
+    parser=OptionParser()
+    parser.add_option("-o","--outpath", dest="outpath",help="Make page and plots in DIR.", metavar="DIR")
+    parser.add_option("-p","--pos",dest="pos_list",action="append",help="Path to folders containing output of cbcBayesPostProc.")
+    parser.add_option("-n","--name",dest="names",action="append",help="Name of posterior result e.g. followupMCMC 2.5PN (optional)")
+    parser.add_option("-i","--inj",dest="inj",help="Path of injection XML containing SimInspiralTable (optional).")
+    parser.add_option("-e","--eventnum",dest="eventnum",help="Sim ID of injection described in injection XML (optional).")
+    parser.add_option("-u",dest="username",help="User name for https authenticated content (optional).")
+    parser.add_option("-x",dest="password",help="Password for https authenticated content (optional).")
+    parser.add_option("--reload",dest="reload_flag",action="store_true",help="Re-download all pos files (optional).")
+    parser.add_option("--hide-cl-lines",dest="clf",action="store_false",default=True,help="Hide confidence level lines on 1D plots for clarity (optional).")
+    parser.add_option("--contour-dpi",dest="cdpi",default=250,help="DPI for contour plot (optional).")
+    parser.add_option("--contour-width",dest="cw",default=7,help="Width (in inches) of contour plots (optional).")
+    parser.add_option("--contour-height",dest="ch",default=6,help="Height (in inches) of contour plots (optional).")
+    parser.add_option("--contour-plot-width",dest="cpw",default=0.5,help="Relative width of plot element 0.15<width<1 (optional).")
+    parser.add_option("--contour-plot-height",dest="cph",default=0.76,help="Relative height of plot element 0.15<width<1 (optional).")
+    parser.add_option("--no-legend",dest="ldg_flag",action="store_false",default=True,help="Hide legend (optional).")
+    parser.add_option("--ignore-missing-files",dest="readFileErr",default=False,action="store_true",help="Do not fail when files are missing (optional).")
+    parser.add_option("-c","--covarianceMatrix",dest="covarianceMatrices",action="append",default=None,help="CSV file containing covariance (must give accompanying mean vector CSV. Can add more than one matrix.")
+    parser.add_option("-m","--meanVectors",dest="meanVectors",action="append",default=None,help="Comma separated list of locations of the multivariate gaussian described by the correlation matrix.  First line must be list of params in the order used for the covariance matrix.  Provide one list per covariance matrix.")
+    parser.add_option("--no2D",dest="no2d",action="store_true",default=False,help="Disable 2D plots")
+    parser.add_option("--npixels-2d",dest="npixels_2d",action="store",type="int",default=50,help="Number of pixels on a side of the 2D plots (default 50)",metavar="N")
+
+    (opts,args)=parser.parse_args()
+
+    if opts.outpath is None:
+        print("No output directory specified. Output will be saved to PWD : %s"%os.getcwd())
+        outpath=os.getcwd()
+    else:
+        outpath=opts.outpath
+
+    if opts.pos_list is None:
+        print("No input paths given!")
+        exit(1)
+
+    if opts.names is None:
+        print("No names given, making some up!")
+        names=[]
+        for i in range(len(opts.pos_list)):
+            names.append(str(i))
+    else:
+        names=opts.names
+
+    if len(opts.pos_list)!=len(names):
+        print("Either add names for all posteriors or dont put any at all!")
+
+    # Sort inputs alphabetically
+    names,pos_list = zip(*sorted(zip(names,opts.pos_list)))
+
+    if opts.no2d:
+        twoDplots=[]
+
+
+    greedy2savepaths,oned_data,confidence_uncertainty,confidence_levels,max_logls,dics=compare_bayes(outpath,zip(names,pos_list),opts.inj,opts.eventnum,opts.username,opts.password,opts.reload_flag,opts.clf,opts.ldg_flag,contour_figsize=(float(opts.cw),float(opts.ch)),contour_dpi=int(opts.cdpi),contour_figposition=[0.15,0.15,float(opts.cpw),float(opts.cph)],fail_on_file_err=not opts.readFileErr,covarianceMatrices=opts.covarianceMatrices,meanVectors=opts.meanVectors,Npixels2D=int(opts.npixels_2d))
+
+    ####Print Confidence Levels######
+    output_confidence_levels_tex(confidence_levels,outpath)
+    output_confidence_levels_dat(confidence_levels,outpath)
+
+    ####Save confidence uncertainty#####
+    output_confidence_uncertainty(confidence_uncertainty,outpath)
+
+    ####Print HTML!#######
+
+    compare_page=bppu.htmlPage('Compare PDFs (single event)',css=bppu.__default_css_string)
+
+    param_section=compare_page.add_section('Meta')
+
+    param_section_write='<div><p>This comparison was created from the following analyses</p>'
+    param_section_write+='<table border="1">'
+    param_section_write+='<th>Analysis</th> <th> max(log(L)) </th> <th> DIC </th>'
+    for (name,logl_max), dic in zip(max_logls, dics):
+        param_section_write+='<tr><td><a href="%s">%s</a></td> <td>%g</td> <td>%.1f</td></tr>'%(dict(zip(names,pos_list))[name],name,logl_max,dic)
+    param_section_write+='</table></div>'
+
+    param_section.write(param_section_write)
+    param_section.write('<div><p><a href="confidence_table.tex">LaTeX table</a> of medians and confidence levels.</p></div>')
+    if oned_data:
+
+        param_section=compare_page.add_section('1D marginal posteriors')
+
+        for param_name,data in oned_data.items():
+            param_section.h3(param_name)
+            save_paths,cl_table_str,ks_table_str,cl_uncer_str=data
+            clf_toggle=False
+            for save_path in save_paths:
+                head,plotfile=os.path.split(save_path)
+                param_section.write('<img src="%s"/>'%str(plotfile))
+
+            param_section.write(cl_table_str)
+            param_section.write(cl_uncer_str)
+            param_section.write(ks_table_str)
+
+    if greedy2savepaths:
+
+        param_section=compare_page.add_section('2D greedy bin histograms')
+        for plot_path in greedy2savepaths:
+            temp,param_name=os.path.split(plot_path)
+            param_name=param_name.split('.')[0]
+            head,plotfile=os.path.split(plot_path)
+            param_section.write('<img src="%s"/>'%str(plotfile))#str(os.path.relpath(plot_path,outpath)))
+
+
+
+    compare_page_footer=compare_page.add_section('')
+    compare_page_footer.p('Produced using cbcBayesCompPos.py at '+strftime("%Y-%m-%d %H:%M:%S")+' .')
+
+    cc_args=copy.deepcopy(sys.argv)
+
+    #remove username and password
+    try:
+        user_idx=cc_args.index('-u')
+        cc_args[user_idx+1]='<LIGO username>'
+    except:
+        pass
+
+    try:
+        pass_idx=cc_args.index('-x')
+        cc_args[pass_idx+1]='<LIGO password>'
+    except:
+        pass
+
+    cc_args_str=''
+    for cc_arg in cc_args:
+        cc_args_str+=cc_arg+' '
+
+    compare_page_footer.p('Command line: %s'%cc_args_str)
+    compare_page_footer.p(git_version.verbose_msg)
+
+
+    resultspage=open(os.path.join(outpath,'index.html'),'w')
+    resultspage.write(str(compare_page))
+    resultspage.close()