first import

batch/awk/analyze.awk

+BEGIN{
+nerr=0
+nmaxit=0
+fn=FILENAME
+}
+
+/function Value/ { 
+chi2min=$4
+} 
+/calls/{
+niter=$NF
+}
+/TIMER/ { 
+tt=$0
+split($3,a,"=")
+tsec=a[2]
+}
+/Error running/{
+nerr++
+}
+/MAX_IT/{
+nmaxit++
+}
+
+# changement de fichier: dump
+FNR==0{
+print FILENAME
+fn=FILENAME
+}
+
+
+END{
+  if (niter>0)
+    print file,chi2min,niter,tsec/niter,nerr,nmaxit
+}

batch/awk/bestfit.awk

+#!/bin/env awk
+
+BEGIN {
+t=0
+N=0
+it=0
+}
+
+$1==it && NF>10{
+#print $0
+t+=$NF
+N++
+it++
+}
+/Gauss/{
+print $0
+}
+
+/WARNING/ { 
+print $0
+} 
+/function Value/ { 
+chi2min=$4
+ print "chi2min=",chi2min
+
+} 
+/calls/{
+print $0
+niter=$NF
+print "niter=",niter
+}
+/Chi2 from/{
+chi2=$4
+ndof=$6
+}
+/TIMER/ { 
+tt=$0
+print tt
+split($3,a,"=")
+tsec=a[2]
+}
+/===/{
+print $0
+}
+
+/converge/ { print $0 }
+/Name/ {cosmo=0}
+
+
+$2 ~ /\|\|/{
+
+
+  split($0,a,"|")
+num=a[1]
+varname=a[3]
+val=a[7]
+err=a[9]
+type=a[5]
+
+  if (cosmo < 7) 
+   printf("||%d|| %s\t|| %10.5g\t|| %10.5g\t||%s\t||\n",num,varname,val,err,type)
+#   printf("||%d|| %s\t|| %10.5g+-%10.5g\t||\n",num,varname,val,err)
+
+ else
+   printf("||%d|| %s\t|| %5.3g\t|| %5.3g\t||%s\t||\n",num,varname,val,err,type)
+#   printf("||%d|| %s\t|| %5.3g+- %5.3g\t||\n",num,varname,val,err)
+   
+cosmo++
+
+}
+
+END{
+ print "chi2min=",chi2min
+ print "#iter=",niter,"\ttot time=",tsec/3600.," h\ttime/iter=",tsec/niter,"s"
+# print "Hillipop: chi2=",chi2," ndof=",ndof,"(",(chi2-ndof)/sqrt(2*ndof), "sigma)"
+}

batch/awk/genrand.awk

+BEGIN {
+	srand(seed ? seed : 1)
+}
+$1 =="par"{
+  r=2*rand()-1
+  newval=$4+r*$5
+  printf("%s\t%s\t%s\t%f\t%f\t%f\t%f\n",$1,$2,$3,newval,$5,$6,$7)
+}
+$1 !="par"{
+print $0
+}

batch/awk/meansigMC.awk

+NR == 40000{
+N=0
+ for (i=1;i<=NF;i++) {
+   s[i]=0
+   s2[i]=0
+ }
+}
+NR > 40000 {
+N++
+ for (i=1;i<=NF;i++) {
+   s[i]+=$i
+   s2[i]+=($i)**2
+ }
+}
+END{
+
+  for (i=1;i<=NF;i++) {
+    mu=s[i]/N
+    a=sqrt(s2[i]/N)
+    var=(a-mu)*(a+mu)
+    printf("%3.12f\t%3.12f\t",mu,sqrt(var))
+  }
+  printf("\n")
+}

batch/awk/toClass.awk

+BEGIN{
+  print "engine=class"
+}
+
+!/engine/ && !/precisionFile/ && $2 != "m_ncdm" && $2 != "N_nu" && $2 != "YHe"{
+print $0
+}
+
+END{
+print "class     N_ncdm                1"
+print "class     m_ncdm                0.06"
+print "class     N_eff                 2.046"
+print "class     k_pivot               0.05"
+print "class     lensing               yes"
+print "class     sBBN\\ file            bbn/sBBN.dat"
+print "precisionFile=hpjul2.pre"
+}

batch/awk/toPico.awk

+BEGIN{
+  print "engine=pico"
+  Alens=0
+  N_nu=0
+  M_ncdm=0
+}
+#############
+NF==3 && $2 == "Alens"{
+Alens=$3
+ print "fix  Alens cosmo ",Alens
+}
+##############
+NF==3 && $2 == "m_ncdm"{
+m_ncdm=$3
+print "fix  m_ncdm cosmo ",m_ncdm
+}
+#############
+$2 == "N_eff"{
+  if (NF==3) {
+    N_nu=$3+1
+    print "fix  N_nu cosmo ",N_nu
+  }
+  else{
+    N_nu=$4+1
+    print $1,"  N_nu cosmo ",N_nu,$5,$6,$7
+  }
+}
+#############
+!/class/ && $2 != "N_eff"{
+print $0
+}
+############
+END{
+#fill if missing
+  if (m_ncdm==0) 
+    print "fix             m_ncdm          cosm       0.06 "
+  
+  if (Alens==0)
+    print "fix             Alens           cosm	   1"
+
+  if (N_nu==0) 
+    print "fix             N_nu           cosm	   3.046"
+
+  print "fix             YHe             cosm       0.248"
+ 
+ 
+
+}

batch/idl/GRRR.scr

+n_chain=4L
+t1=mrdfits(dir+"/samples.fits",1,hdr)
+name=strtrim(hdr[5:n_elements(hdr)-4],2) 
+
+t2=mrdfits(dir+"/samples.fits",2)
+t3=mrdfits(dir+"/samples.fits",3)
+t4=mrdfits(dir+"/samples.fits",4)
+
+sz1=size(t1,/dim)
+sz2=size(t2,/dim)
+sz3=size(t3,/dim)
+sz4=size(t4,/dim)
+
+dim=sz1[1]
+
+stop=min([sz1[0]-1,sz2[0]-1,sz3[0]-1,sz4[0]-1])
+
+
+rec=dblarr(stop+1, dim, n_chain)
+
+flength=dim*stop
+print, flength
+
+
+rec[*,*,0]=t1[0:stop,*]
+rec[*,*,1]=t2[0:stop,*]
+rec[*,*,2]=t3[0:stop,*]
+rec[*,*,3]=t4[0:stop,*]
+
+lenght_min=long(50)
+lenght_max=stop
+gap=1000L
+event=(lenght_max-lenght_min)/gap+1 
+
+
+R=dblarr(dim,event) ;vectore GR
+;vettore di medie delle singole catene
+;vector of means of single chain
+mean_chain=fltarr(dim,n_chain) 
+B_n=fltarr(dim)  ; variance between chains
+W=fltarr(dim)  ; variance of the chain
+W_c=fltarr(dim,n_chain) ; W for fixed n and fixed burn_in=stop/2
+
+mean_dist=fltarr(dim) ; for all dim mean of the chain
+
+index_event=0
+
+for index=lenght_min, lenght_max-1 do begin &$
+  for d=1,dim-1 do begin  &$
+    if stop ne 0 then begin  &$
+    for m=0,n_chain-1 do begin  &$
+     burn_in=index/2  &$
+     mean_chain[d,m]=total(rec[burn_in :index,d,m])/(index-burn_in)  &$
+     W_c[d,m]=total((rec[burn_in :index,d,m]-mean_chain[d,m])^2)/(index-burn_in)  &$
+    endfor  &$
+    endif  &$
+    mean_dist[d]=total(mean_chain[d,*])/n_chain &$ ;mean of the distribution
+    if n_chain gt 1 then begin  &$
+     B_n[d]=total((mean_chain[d,*]-mean_dist[d])^2)/(n_chain-1)  &$
+    endif &$
+    W[d]=total(W_c[d,*])/n_chain  &$
+    if W[d] ne 0 then R[d,index_event]=(float((index-1.)/index)*W[d] + B_n[d]*(1.+1./n_chain))/W[d]  &$
+    endfor &$
+    index_event=index_event+1 &$
+    index=index+gap-1  &$
+  endfor 
+
+;print, R
+;-------------plot  R
+if (n_elements(write) eq 0) then write=0
+if (write ne 0) then openplot, "GR_"+dir+'.ps', xsize=20, ysize=12
+loadct, 39
+x=indgen(event)*gap+lenght_min
+!x.style=1
+
+y=fltarr(event)
+y[*]=0.03
+plot, x ,y, title='Gelman Rubin R vs length of the chain', xtitle='length of the chain', ytitle='R-1',  yrange=[1e-3,1],ylog=ylog
+
+
+linestyle=[0,0,0,0,0,0,2]
+color=[30,90,150,110,200,220,70]
+
+vec_one=fltarr(event)
+vec_one=replicate(1,event)
+
+for i=1,6 do oplot, x, R[i,*]-vec_one, color=color[i-1]
+for i=7,dim-1 do oplot, x, R[i,*]-vec_one, color=color[6], linestyle=linestyle[6]
+
+;items=[ 'omega_b' , 'omega_cdm','100*theta_s', 'tau_reio', 'n_s', 'log(10^10A_s)','nuisances']
+items=name[1:6]
+items=[items,"nuisances"]
+
+legend, items,colors=color,linestyle=linestyle, /top, /right ; textcolors=color
+
+
+
+;add more nuisances here
+
+
+if (write ne 0) then closeplot, /png
+

batch/idl/add1.pro

+;Alens
+sig2=0.07^2
+ipos=6
+
+cov=readmatrix("covmat.dat")
+
+sz=size(cov,/dim)
+
+cov_new=make_array(sz+1,/double,val=0)
+cov_new[0:sz[0]-1,0:sz[1]-1]=cov
+cov_new[sz[0],sz[1]]=sig2
+
+w=lindgen(sz[0])
+w_new=[w[0:ipos-1],sz[0]+1,w[ipos:*]]
+c1=cov_new[*,w_new]
+c2=c1[w_new,*]
+
+cov_new=c2
+name_new=[name,"Alens"]
+
+cor_new=cov2cor(cov_new)
+plotcor,cor_new,name_new[w_new]
+
+writematrix,cov_new,f="covmat_new.dat"

batch/idl/autozone.pro

+pro autozone,n
+
+ncol=long(sqrt(n))
+nrow=N/ncol
+if (N mod nrow ne 0) then nrow++
+
+!p.multi=[0,ncol,nrow]
+
+
+return
+end

batch/idl/bestbest.scr

+file=dir+"/bestfit.det"
+
+if (not file_test(file)) then stop,'error file'+file 
+t=read_ascii(file)
+t=transpose(t.(0))
+readcol,file,files,f='A'
+n=n_elements(files)
+sz=size(t,/dim)
+n=sz[0]
+
+;look for names 
+camels=file_search(dir+"/*/camel*.par")
+
+names=parnames(camels[0],fix=fix)
+namevar=fix[n_elements(fix)-1]
+print,"profile on: ",namevar
+print,+"# free params="+strn(n_elements(names))
+print,names
+
+; prof2
+;ichi=sz[1]-12
+
+;Mnu
+ichi=sz[1]-11
+;
+imu=ichi-1
+;imu=ichi-2 ; Alens class
+m=t[*,imu]
+chi2=t[*,ichi]
+dchi2=chi2-min(chi2)
+
+zone
+window,/free,tit=file
+plot,m,chi2-min(chi2),/ys,/psym,xtit=namevar,ytit=textoidl('\Delta \chi^2'),tit=file,yr=[0,4]
+
+;best fit uniq
+u=uniq(m)
+mu=m[u]
+mu=mu[sort(mu)]
+Nu=n_elements(u)
+bf=make_array(Nu,sz[1],/double)
+
+for iu=0,Nu-1 do begin &$
+w=where(m eq mu[iu]) &$
+sub=t[w,*] &$
+c=min(sub[*,ichi],imin) &$
+print,mu[iu],double(c) &$
+bf[iu,*]=transpose(sub[imin,*]) &$
+  endfor
+
+oplot,mu,bf[*,ichi]-min(bf[*,ichi],imin),col=red
+
+;imin=2
+!x.margin=[15,5]
+;window,/free,xs=1200,ys=700,tit=file
+;cgdisplay,/free,xs=1200,ys=700,tit=file
+
+cgdisplay,900,700,/free,tit=file
+autozone,n_elements(names)
+
+ii=0
+for i=0,sz[1]-1 do begin &$
+if (stddev(bf[*,i]) eq 0) then continue &$
+if (ii ge n_elements(names)) then break &$
+cgplot,mu,bf[*,i],/ys,xtit=namevar,ytit=names[ii],psym=-16,symsize=0.1 &$
+print,names[ii],bf[imin,i] &$
+ii++ &$
+  endfor
+print,namevar,mu[imin]
+
+;fichier avec mnu rajoute chi2 rajoute au debut
+print,"writing",dir+"/bestfit.all"
+openw,lun,dir+"/bestfit.all",/get_lun
+for i=0,n_elements(mu)-1 do begin &$
+line=[bf[i,imu],bf[i,ichi],transpose(bf[i,*])] &$
+printf,lun,strjoin(strtrim(string(line),2),"   ") &$
+endfor
+free_lun,lun
+
+print,bf[imin,*]

batch/idl/compnufit.scr

+!x.margin=[6,5]
+
+xfit=0.2
+yup=18
+
+
+xr=[-.5,.5]
+yr=[0,yup]
+
+;dirs=["hlpTT_bflike_vhl_LCDMClass_nuscan","hlpTT_vhl_lensing_LCDMClass_nuscan"]
+;dirs=["hlpTT_bflike_vhl_LCDMClass_nuscan","hlpTT_bflike_vhl_LCDMClass_nuscan0"]
+dirs=["hlpTT_bflike_vhl_LCDMClass_nuscan","hlpTT_bflike_vhl_JLA_LCDMClass_nuscan"]
+
+names=dirs
+
+cols=['black','red','blue','green','orange','magenta','violet','purple','navy']
+
+;paires
+;cols=['red','red5','blue','navy','green','forest green','violet','violet red']
+
+varname=textoidl('\Sigma m_\nu [eV]')
+
+cgplot,findgen(10),xr=xr,yr=yr,xtit=varname,ytit=textoidl('\Delta \chi^2'),ys=1,/xs,/nodata
+
+xp=[xr[0],0,0,xr[0]]
+yp=[yr[0],yr[0],yup,yup]
+polyfill,xp,yp,/data,/line_fill,ORIENTATION=45, THICK=1.5, SPACING=0.1,col=grey
+
+in=''
+N=n_elements(dirs)
+for i=0,N-1 do begin &$
+if (i eq 0) then over=0 else over=1 &$
+t=read_ascii(dirs[i]+'/bestfit.all') &$
+t=transpose(t.(0)) &$
+sz=size(t,/dim) &$
+ichi=1 &$
+itau=0 &$
+chi2=t[*,ichi] &$
+dchi2=chi2-min(chi2,imin) &$
+tau=t[*,itau] &$
+iord=sort(tau) &$
+tau=tau[iord] &$
+dchi2=dchi2[iord] &$
+diff=dchi2-shift(dchi2,-1) &$
+w=where(dchi2 lt 5 and abs(diff) lt 1) &$ ; points used 
+;w=where(dchi2 gt 0) &$
+x=tau &$
+chi2min1=min(chi2) &$
+chi2-=chi2min1 &$
+cut=where(x lt xfit) &$
+par=svdfit(x[cut],chi2[cut],3,/double) &$
+xmle=-par[1]/(2*par[2]) &$
+chi2min=poly(xmle,par) &$
+sig=1/sqrt(par[2]) &$
+print,dirs[i]+' xmle=',+strn(xmle),'  sigma='+strn(sig)+'  nsig='+strn(xmle/sig) &$
+cgplot,x,chi2-chi2min,psym=16,col=cols[i],/over &$
+xx=range(xr[0],xr[1],N=100) &$
+cgplot,xx,poly(xx,par)-chi2min,linestyle=2,col=cols[i],/over &$
+xx=range(0,xfit,N=100) &$
+cgplot,xx,poly(xx,par)-chi2min,col=cols[i],/over &$
+;feldman
+xf=[-.5,-.4,-.3,-.2,-.1,0.,.1,.2,.3,.4,.5]  &$
+yf95=[1.49,1.58,1.67,1.77,1.86,1.96,2.06,2.16,2.26,2.36,2.46]  &$
+mu2=interpol(yf95,xf,xmle/sig)  &$
+x0=mu2*sig  &$
+print, 'FC=',x0  &$
+y0=poly(x0,par)-chi2min  &$
+cgplot,[0,x0],[y0,y0],col=cols[i],thick=2,/over   &$
+cgplot,[x0,x0],[0,y0],col=cols[i],thick=2,/over  &$
+endfor
+
+;hlp
+;plik
+;cgtext,0.6,0.8,names[0],/normal,col=cols[0]
+;cgtext,0.6,0.75,names[1],/normal,col=cols[1]
+
+al_legend,names,textcol=cgcolor(cols),/top,/right,box=0

batch/idl/convMC1.scr

+.r parnames
+
+if (n_elements(write) eq 0) then write=0
+fileout=dir+'.ps'
+
+if (n_elements(t) eq 0) then begin &$
+file=dir+'/samples_cut.fits' &$
+print,"reading : ",file &$ 
+t=mrdfits(file,1,hdr)&$ 
+sz=size(t,/dim) &$
+n=sz[0] &$
+;name=parnames(dir+'/camel.par') &$
+;name=['chi2',name] &$
+name=strtrim(hdr[5:n_elements(hdr)-4],2) &$
+derived,t,name &$
+endif
+;noms/val
+;if (write eq 0) then 
+if (write ne 0) then openplot,fileout,xs=30,ys=30,charsize=2 else cgdisplay,900,700,tit=dir,/free
+
+N=n_elements(name)
+autozone,N
+
+!p.charsize=1.2
+
+delvar,name2
+if (file_test(dir+"/bf")) then begin &$
+print, "best fit file found",dir+"/bf" &$
+readcol,dir+'/bf',delim='||',f='x,a,f',name2,bf &$
+name2=strtrim(name2,2)  &$
+endif
+
+
+line=['']
+!x.margin=[5,5]
+for i=1,N-1 do begin &$
+if (total(t[*,i]-t[0,i]) eq 0) then continue &$
+m=mean(t[*,i]) &$
+s=stddev(t[*,i]) &$
+hist_plot,t[*,i],/noplot,x=x,y=y,nbin=101 &$
+;hist_plot,t[*,i],/noplot,x=x,y=y,nbin=50 &$
+yy=smooth(y,15,/edge_trunc)&$
+yy/=max(yy) &$
+cgplot,x,yy,xtit=name[i],yr=[0,1],/xs,xticks=3,yticks=3,ytickv=[0.,0.5,1] &$
+ibf=-1 &$
+if (n_elements(name2) ne 0)  then begin &$
+ibf=strindex(name2,name[i],/silent)  &$
+cgplot,[bf[ibf],bf[ibf]],!y.crange,/over,line=2  &$
+  endif  &$
+if (i le 6 ) then dec=5 else dec=3 &$
+ss=cgNumber_Formatter(m,dec=dec)+'+-'+cgNumber_Formatter(s,dec=dec) &$
+cgtext,m-2*s,0.6,ss,/data,charsize=1,col='blue' &$  
+if (ibf ge 0) then  begin&$
+print,'||',name[i],'||',cgNumber_Formatter(bf[ibf],dec=3),'||',ss,'||' &$
+endif else begin &$
+print,'||',name[i],'|| ||',ss,'||' &$
+  endelse  &$
+line=[line,strn(m)] &$
+endfor
+
+
+if (write ne 0) then closeplot,/pdf,/view
+;if (write ne 0) then closeplot,/png

batch/idl/convMC2.scr

+.r strindex
+.r derived
+
+;if (n_elements(mcr) eq 0) then mcr=[80000L,150000L]
+;print,'range=',mcr
+
+!X.OMargin = [5, 2]
+!Y.OMargin = [5, 5]
+!y.margin=[3,2]
+!x.margin=[5,2]
+
+if (n_elements(write) eq 0) then write=0
+fileout=dir+'_vs_'+dir2+'.ps'
+
+delvar,t
+file=dir+'/samples_cut.fits' &$
+print,"reading : ",file &$ 
+t=mrdfits(file,1,hdr)&$ 
+name=strtrim(hdr[5:n_elements(hdr)-4],2) &$
+derived,t,name
+sz=size(t,/dim) &$
+
+;le plus grand
+delvar,t2
+file=dir2+'/samples_cut.fits' &$
+print,"reading : ",file&$
+t2=mrdfits(file,1,hdr)  &$
+name2=strtrim(hdr[5:n_elements(hdr)-4],2) &$
+derived,t2,name2
+
+if (n_elements(write) eq 0) then write=0
+if (write ne 0) then openplot,fileout,xs=30,ys=30,charsize=1.5 else cgdisplay,900,700,tit=dir,/free
+if (write eq 0) then !p.thick=3 else !p.thick=8
+if (write eq 0) then !p.charsize=1
+
+
+N=n_elements(name)
+autozone,N
+
+
+!x.margin=[5,5]
+
+for i=1,N-1 do begin &$
+if (total(t[*,i]-t[0,i]) eq 0) then continue &$
+;dans liste2
+j=strindex(name2,name[i],/silent) &$
+print,name[i],j &$
+if (j lt 0) then continue &$
+print,i,j,name[i],name2[j] &$
+hist_plot,t[*,i],/noplot,x=x,y=y,nbin=101 &$
+yy=smooth(y,15,/edge_trunc)&$
+yy/=max(yy) &$
+hist_plot,t2[*,j],/noplot,x=x2,y=y2,nbin=101 &$
+yy2=smooth(y2,15,/edge_trunc)&$
+yy2/=max(yy2) &$
+xx=[x,x2] &$
+cgplot,x,yy,xtit=name[i],xr=minmax(xx),color='dark green',yticks=4,yr=[0,1] &$