SP_spectrum _SP_addSpectra(SP_spectrum* spectra,size_t nbsp,double width,double clip,double prc,int error_type,double rebin_pixfactor,double rebin_pixshift,int spline,int tclip,int keepnbsp,char* file,size_t line)
{
VC_vector group,factors;
double* work,fct;
double* tmp;
double *dw,*df,*ds;
double fact1,fact2;
double *wmin,*wmax;
VC_vector wlim,wave;
SP_spectrum rslt;
VC_vector eflux,esigm,emask;
VC_vector flx1,flx2,wav1,pds1,pds2;
long *npix;
double y1,y2;
double tmin, tmax,tcen,wpas,old_wpas;
double w1min,w1max,w2min,w2max;
long k1min,k1max,k2min,k2max;
long imin,imax,jmin,jmax;
long *idmin,*idmax;
long *kmin,*kmax;
long nbgroup,igroup,nbcol;
long i,j;
size_t si,sj,k,ngood;
size_t npix_max,npix_tot;
int pourc,old_pourc;
double fsum,wsum,weight,sigm_srianand,mean_srianand;
long nbg_srianand;
long nbg_bastien;
double a1,b1;
SP_spectrum* spline_spectra;
if(nbsp<2) return NULL;
/****************************/
/* Sort and group by setup */
/****************************/
SP_sortSpectrum(spectra,nbsp);
OS_message(0,OS_STD,"[SP_addSpectra] new order for spectra :\n");
for(i=0;i<nbsp;i++)
{
OS_message(0,OS_STD,"[SP_addSpectra] %4d : %s\n",i+1,spectra[i]->name);
}
group=SP_groupSpectrum(spectra,nbsp,prc);
if(!group)
{
OS_message(0,OS_ERR,"not enough memory !!\n");
exit(1);
}
nbgroup=1+group->ldata[nbsp-1];
OS_message(0,OS_STD,"[SP_addSpectra] found %d group%s\n",nbgroup,(nbgroup>1)?"s":" ");
npix_max=0; /*will contain the number of pixel of the biggest spectrum*/
for(si=0;si<nbsp;si++)
npix_max=(spectra[si]->npix>npix_max)?spectra[si]->npix:npix_max;
MMV_malloc(tmp,npix_max,double); /*working buffer*/
MMV_malloc(idmin,nbsp,long);
MMV_malloc(idmax,nbsp,long);
MMV_malloc( kmin,nbsp,long);
MMV_malloc( kmax,nbsp,long);
MMV_malloc( wmin,nbsp,double);
MMV_malloc( wmax,nbsp,double);
for(i=0;i<nbsp;i++)
{
/**********************************************************/
/*Find first and last pixel that not have null flux values*/
/*sort the corresponding wavelength in wmin and wmax and */
/*the pixel index in idmin and idmax. */
/**********************************************************/
VC_getIdxEdge(spectra[i]->data[spectra[i]->colF],idmin+i,idmax+i);
wmin[i]=spectra[i]->wave[idmin[i]];
wmax[i]=spectra[i]->wave[idmax[i]-1];
kmin[i]=kmax[i]=-1;
}
for(i=0;i<nbgroup;i++)
{
k=0;
for(j=0;j<nbsp;j++) if(group->ldata[j]==i) k++;
OS_message(0,OS_STD,"[SP_addSpectra] group #%-2d : %d spectr%s\n",i+1,k,(k>1)?"a":"um");
}
/************************************************/
/*Compute scale factors by group and apply them */
/************************************************/
imax=imin=igroup=0;
while(imax<nbsp)
{
imax=imin;
while((imax<nbsp)&&(group->ldata[imax]==igroup)) ++imax;
// printf("igroup: %2ld imin: %2ld imax: %2ld\n",igroup,imin,imax);
factors=addiScaleFactors(spectra+imin,imax-imin,width,NULL);
for(i=0,si=imin;si<imax;i++,si++)
for(sj=0;sj<spectra[si]->npix;sj++)
{
spectra[si]->flux[sj]*=factors->ddata[i];
spectra[si]->sigm[sj]*=factors->ddata[i];
}
VC_free(factors);
imin=imax;
igroup++;
}
/*************/
/* Find edge */
/*************/
/****************************************/
/* Compute merge factors and apply them */
/****************************************/
/* Two steps for the computation. */
/* First find scale factor for the edges */
/* Then rebin each edges and compute their */
/* ratio. Fit the ratio by a line and take */
/* max of 1 and the line value for correction */
if(nbgroup>1)
{
OS_message(0,OS_STD,"[SP_addSpectra] Compute factor for the merging\n");
MMV_malloc(work,nbsp,double);
imin=igroup=0;
while(igroup<nbgroup-1)
{
imax=imin;
while((imax<nbsp)&&(group->ldata[imax]==igroup)) imax++;
// printf("igroup: %2ld imin: %2ld imax: %2ld\n",igroup,imin,imax);
++igroup;
if(imax==nbsp)
{
OS_message(0,OS_ERR,"[SP_addSpectra] BUG at line %d of file %s\n",__LINE__,__FILE__);
exit(1);
}
jmin=imax;
jmax=jmin;
while((jmax<nbsp)&&(group->ldata[jmax]==igroup)) jmax++;
//printf("igroup: %2ld jmin: %2ld jmax: %2ld\n",igroup,jmin,jmax);
w1min=wmin[imin];
w1max=wmax[imin];
for(si=imin+1;si<imax;si++)
{
w1min=(w1min<wmin[si])?w1min:wmin[si];
w1max=(w1max>wmax[si])?w1max:wmax[si];
}
w2min=wmin[jmin];
w2max=wmax[jmin];
for(sj=jmin+1;sj<jmax;sj++)
{
w2min=(w2min<wmin[sj])?w2min:wmin[sj];
w2max=(w2max>wmax[sj])?w2max:wmax[sj];
}
tmin=(w1min>w2min)?w1min:w2min;
tmax=(w1max<w2max)?w1max:w2max;
if(tmin>=tmax) /* no overlap*/
{
w1min=w1max-width/10.;
w2max=w2min+width/10.;
}
else
{
w1min=w2min=tmin;
w1max=w2max=tmax;
}
for(si=imin;si<imax;si++)
{
k1min=findNear(spectra[si]->data[spectra[si]->colW],w1min);
k1max=findNear(spectra[si]->data[spectra[si]->colW],w1max)+1;
for(i=0,j=k1min;j<k1max;j++,i++)
tmp[i]=spectra[si]->flux[j];
work[si]=median(tmp,k1max-k1min);
}
for(sj=jmin;sj<jmax;sj++)
{
k2min=findNear(spectra[sj]->data[spectra[sj]->colW],w2min);
k2max=findNear(spectra[sj]->data[spectra[sj]->colW],w2max)+1;
for(i=0,j=k2min;j<k2max;j++,i++)
tmp[i]=spectra[sj]->flux[j];
work[sj]=median(tmp,k2max-k2min);
}
fact1=median(work+imin,imax-imin);
fact2=median(work+jmin,jmax-jmin);
if(fact1<=0) fact1=1;
if(fact2<=0) fact2=1;
/* Factor are computed. Now rebin edges*/
/* imin->imax index of spectra in group 1 */
/* jmin->jmax index of spectra in group 2 */
/* Compute flx1 and flx2 */
if(tmin>=tmax)
{
fact1/=fact2;
OS_message(0,OS_STD,"[SP_addSpectra] Factor for merging for group #%d : %f\n",1+igroup,fact1);
for(sj=jmin;sj<jmax;sj++)
for(j=0;j<spectra[sj]->npix;j++)
{
spectra[sj]->flux[j]*=fact1;
spectra[sj]->sigm[j]*=fact1;
}
}
else
{
/*First crude addition of the edge 2*/
k1min=findNear(spectra[imin]->data[spectra[imin]->colW],w1min);
k1max=findNear(spectra[imin]->data[spectra[imin]->colW],w1max)+1;
// printf("%d %d\n",k1min,k1max);
VCV_allocate(flx1,k1max-k1min,VCTDOUBLE);
VCV_allocate(wav1,k1max-k1min,VCTDOUBLE);
VCV_allocate(flx2,k1max-k1min,VCTDOUBLE);
VCV_allocate(pds1,k1max-k1min,VCTDOUBLE);
VCV_allocate(pds2,k1max-k1min,VCTDOUBLE);
// printf("flx1 %x \n",flx1);
// printf("flx2 %x \n",flx2);
// printf("wav1 %x \n",wav1);
for(i=k1min,j=0;i<k1max;i++,j++)
{
wav1->ddata[j]=spectra[imin]->wave[i];
flx1->ddata[j]=0.;
pds1->ddata[j]=0.;
flx2->ddata[j]=0.;
pds2->ddata[j]=0.;
}
for(si=imin;si<imax;si++)
{
k2min=k2max=-1;
dw=spectra[si]->wave+idmin[si];
df=spectra[si]->flux+idmin[si];
ds=spectra[si]->sigm+idmin[si];
for(i=k1min,j=0;i<k1max;i++,j++)
{
if(j==0) tmin=0.5*(3*wav1->ddata[0]-wav1->ddata[1]);
else tmin=0.5*(wav1->ddata[j-1]+wav1->ddata[j]);
if(j==(wav1->size-1)) tmax=0.5*(3*wav1->ddata[j]-wav1->ddata[j-1]);
else tmax=0.5*(wav1->ddata[j+1]+wav1->ddata[j]);
rebinLocal(df,ds,dw,idmax[si]-idmin[si],
tmin,tmax,&k2min,&k2max,
&fsum,&wsum);
if(wsum<=0) continue;
weight=fsum/wsum;
weight*=weight;
pds1->ddata[j]+=weight;
flx1->ddata[j]+=weight*fsum;
}
}
for(sj=jmin;sj<jmax;sj++)
{
k2min=k2max=-1;
dw=spectra[sj]->wave+idmin[sj];
df=spectra[sj]->flux+idmin[sj];
ds=spectra[sj]->sigm+idmin[sj];
for(i=k1min,j=0;i<k1max;i++,j++)
{
if(j==0) tmin=0.5*(3*wav1->ddata[0]-wav1->ddata[1]);
else tmin=0.5*(wav1->ddata[j-1]+wav1->ddata[j]);
if(j==(wav1->size-1)) tmax=0.5*(3*wav1->ddata[j]-wav1->ddata[j-1]);
else tmax=0.5*(wav1->ddata[j+1]+wav1->ddata[j]);
rebinLocal(df,ds,dw,idmax[sj]-idmin[sj],
tmin,tmax,&k2min,&k2max,
&fsum,&wsum);
if(wsum<=0) continue;
weight=fsum/wsum;
weight*=weight;
pds2->ddata[j]+=weight;
flx2->ddata[j]+=weight*fsum;
}
}
ngood=0;
for(j=0;j<wav1->size;j++)
{
if((!pds1->ddata[j])||(!pds2->ddata[j])) continue;
y1=flx1->ddata[j]/(fact1*pds1->ddata[j]);
y2=flx2->ddata[j]/(fact2*pds2->ddata[j]);
if((y1<0.2)||(y2<0.2)) continue;
flx1->ddata[ngood]=y1/y2;
wav1->ddata[ngood]=wav1->ddata[j];
ngood++;
}
if(ngood)
fitLineIter(flx1->ddata,wav1->ddata,ngood,&a1,&b1);
else
{
a1=0;
b1=1;
}
wpas=0.1/(wav1->ddata[1]-wav1->ddata[0]);
fact1/=fact2;
/* apply correction */
for(sj=jmin;sj<jmax;sj++)
for(j=0;j<spectra[sj]->npix;j++)
{
wsum=spectra[sj]->wave[j];
weight=(fact1*(a1*wsum+b1)*expFilter(wsum,w1max,-wpas))+
(fact1*(a1*w1max+b1)*expFilter(wsum,w1max,wpas));
spectra[sj]->flux[j]*=weight;
spectra[sj]->sigm[j]*=weight;
}
VC_free(pds2);
VC_free(pds1);
VC_free(flx1);
VC_free(flx2);
VC_free(wav1);
}
imin=jmin;
}
MM_free(work);
}
/**************************/
/* Compute the wave range */
/**************************/
OS_message(0,OS_STD,"[SP_addSpectra] Compute wavelength range\n");
/*****************************************/
/* merge all the wave limits and compute */
/* average pixel size for each group */
/*****************************************/
VCV_allocate(wlim,2*nbgroup,VCTDOUBLE);
imin=igroup=0;
while(imin<nbsp)
{
imax=imin;
tmin=wmin[imin];
tmax=wmax[imin];
while((imax<nbsp)&&(group->ldata[imax]==igroup))
{
tmin=(tmin<wmin[imax])?tmin:wmin[imax];
tmax=(tmax>wmax[imax])?tmax:wmax[imax];
imax++;
}
wlim->ddata[ 2*igroup]=tmin;
wlim->ddata[1+2*igroup]=tmax;
imin=imax;
igroup++;
}
VC_hpsort(wlim);
/* Compute pixel size */
MMV_malloc(npix,(2*nbgroup-1),long);
wpas=0;
for(i=0;i<2*nbgroup-1;i++)
{
k=0;
npix[i]=0;
tcen=0.5*(wlim->ddata[i]+wlim->ddata[i+1]);
old_wpas=wpas;
wpas=0;
for(j=0;j<nbsp;j++)
{
if((tcen>=wmax[j])||(tcen<=wmin[j])) continue;
k++;
wpas+=(wmax[j]-wmin[j])/(float)(idmax[j]-idmin[j]);
}
// printf("chunck %2ld k: %2ld swpas: %f rap:%f\n",i,k,wpas,(k>0)?(wpas/(double)k):0);
if(k)
wpas/=(double)k;
else
if(!i)
{
OS_message(0,OS_ERR,"Bug at %s line %d !!!\n",__FILE__,__LINE__);
exit(1);
}
else
wpas=old_wpas;
wpas*=rebin_pixfactor;
npix[i]=(long)((wlim->ddata[i+1]-wlim->ddata[i])/wpas+0.5);
if(!npix[i])
{
OS_message(0,OS_ERR,"Bug at %s line %d !!!\n",__FILE__,__LINE__);
exit(1);
}
}
npix_tot=0;
for(i=0;i<2*nbgroup-1;i++) npix_tot+=npix[i]-1;
npix_tot++;
/* Fill the final wave array */
VCV_allocate(wave,npix_tot,VCTDOUBLE);
k=0;
for(i=0;i<2*nbgroup-1;i++)
{
wpas=(wlim->ddata[i+1]-wlim->ddata[i])/(double)(npix[i]);
for(j=0;j<npix[i]-1;j++)
wave->ddata[k++]=wlim->ddata[i]+((float)j+rebin_pixshift)*wpas;
}
wave->ddata[k++]=wlim->ddata[2*nbgroup-1]+rebin_pixshift*wpas;
/* display some information */
OS_message(0,OS_STD,"\n[SP_mergeSpectra] New wavelength range (%d chunks) \n",2*nbgroup-1);
for(i=0;i<2*nbgroup-1;i++)
OS_message(0,OS_STD,"[SP_mergeSpectra] chunks #%-2d : %10.2f %10.2f %9.4f\n",
i+1,wlim->ddata[i],wlim->ddata[i+1],
(wlim->ddata[i+1]-wlim->ddata[i])/(double)npix[i]);
// for(i=0;i<nbsp;i++) printf("i:%2d wmin:%f wmax:%f\n",(int)i,wmin[i],wmax[i]);
MM_free( npix);
VC_free( wlim);
MM_free(wmin);
MM_free(wmax);
/**********************************/
/* if spline is set rebin spectra */
/* with cubic spline */
/**********************************/
if(spline)
{
OS_message(0,OS_STD,"[SP_mergeSpectra] Doing spline rebinning : \n");
MMV_malloc(spline_spectra,nbsp,SP_spectrum);
if(!spline_spectra)
{
OS_message(0,OS_ERR,"not enough memory !!\n");
MM_free( kmax);
MM_free( kmin);
MM_free(idmax);
MM_free(idmin);
MM_free( tmp);
return NULL;
}
for(i=0;i<nbsp;i++)
{
tmin=spectra[i]->wave[idmin[i]];
tmax=spectra[i]->wave[idmax[i]-1];
if(wave->ddata[0]>tmin)
imin=0;
else
while((imin<wave->size)&&(wave->ddata[imin]<tmin)) ++imin;
imax=imin;
while((imax<wave->size)&&(wave->ddata[imax]<tmax)) ++imax;
spline_spectra[i]=SP_allocate(imax-imin,3);
if(!spline_spectra[i])
{
OS_message(0,OS_ERR,"not enough memory !!\n");
MM_free(spline_spectra);
MM_free( kmax);
MM_free( kmin);
MM_free(idmax);
MM_free(idmin);
MM_free( tmp);
return NULL;
}
/*Copy Wavelength array*/
for(k=0,j=imin;j<imax;j++,k++)
spline_spectra[i]->wave[k]=wave->ddata[j];
/*********************************/
/* do the cubic spline estimation*/
/* for the flux */
NRspline(spectra[i]->wave,spectra[i]->flux,spectra[i]->npix,1e30,1e30,tmp);
NRasplint(spectra[i]->wave,spectra[i]->flux,tmp,spectra[i]->npix,
spline_spectra[i]->wave,spline_spectra[i]->flux,spline_spectra[i]->npix);
/* for the error */
/* (strange, maybe to fix latter)*/
NRspline(spectra[i]->wave,spectra[i]->sigm,spectra[i]->npix,1e30,1e30,tmp);
NRasplint(spectra[i]->wave,spectra[i]->sigm,tmp,spectra[i]->npix,
spline_spectra[i]->wave,spline_spectra[i]->sigm,spline_spectra[i]->npix);
/* Rebin Done */
/* Put index instead of wavelenght */
for(k=0,j=imin;j<imax;j++,k++)
spline_spectra[i]->wave[k]=j;
/*********************************/
/*Old spectra[i] useless, set it to spline_spectra[i] */
SP_free(spectra[i]);
spectra[i]=spline_spectra[i];
}
}
/***************************************/
/* Allocate memory for output spectrum */
/***************************************/
nbcol=3;
if(keepnbsp) ++nbcol;
if(error_type==_BOTH_ERRORS_) ++nbcol;
rslt=_SP_allocate(wave->size,nbcol,file,line);
if(!rslt)
{
OS_message(0,OS_ERR,"not enough memory !!\n");
MM_free( kmax);
MM_free( kmin);
MM_free(idmax);
MM_free(idmin);
MM_free( tmp);
return NULL;
}
VC_free(rslt->data[rslt->colW]);
rslt->data[rslt->colW]=wave;
/*******************/
/* Do the addition */
/*******************/
VCV_allocate(eflux,nbsp,VCTDOUBLE);
VCV_allocate(esigm,nbsp,VCTDOUBLE);
VCV_allocate(emask,nbsp,VCTDOUBLE);
OS_message(0,OS_STD,"\n[SP_addSpectra] Do the addition : 0%%");
old_pourc=pourc=0;
for(j=0;j<rslt->npix;j++)
{
pourc=(int)(j*100/(rslt->npix-1));
if(pourc>old_pourc)
{
old_pourc=pourc;
OS_message(0,OS_STD,"\b\b\b\b%3ld%%",pourc);
OS_flush();
}
if(spline)
{
ngood=0;
for(i=0;i<nbsp;i++)
{
eflux->ddata[ngood]=esigm->ddata[ngood]=0.;
dw=spectra[i]->wave;
df=spectra[i]->flux;
ds=spectra[i]->sigm;
if(getSplineInter(df,ds,dw,spectra[i]->npix,j,kmin+i,
eflux->ddata+ngood,esigm->ddata+ngood)) continue;
emask->ddata[ngood]=1.;
++ngood;
}
}
else
{
if(j==0) tmin=0.5*(3*wave->ddata[0]-wave->ddata[1]);
else tmin=0.5*(wave->ddata[j-1]+wave->ddata[j]);
if(j==(rslt->npix-1)) tmax=0.5*(3*wave->ddata[rslt->npix-1]-wave->ddata[rslt->npix-2]);
else tmax=0.5*( wave->ddata[j+1]+ wave->ddata[j]);
ngood=0;
for(i=0;i<nbsp;i++)
{
eflux->ddata[ngood]=esigm->ddata[ngood]=0.;
dw=spectra[i]->wave+idmin[i];
df=spectra[i]->flux+idmin[i];
ds=spectra[i]->sigm+idmin[i];
if(rebinLocal(df,ds,dw,idmax[i]-idmin[i],
tmin,tmax,kmin+i,kmax+i,
eflux->ddata+ngood,esigm->ddata+ngood)) continue;
emask->ddata[ngood]=1.;
++ngood;
}
}
/* if((tmin>5156)&&(tmax<5158)) */
/* printf("tmin:%f tmax:%f ngood: %d\n",tmin,tmax,ngood); */
mean_srianand=sigm_srianand=fsum=wsum=0.0;
nbg_srianand=nbg_bastien=0;
if(ngood)
{
eflux->size=ngood;
esigm->size=ngood;
emask->size=ngood;
if(tclip==_DATACLIPPING_)
dataClipping(eflux,esigm,&emask,clip);
else if (tclip!=_NOCLIPPING_)
sigmaClipping(eflux,&emask,clip,0);
for(i=0;i<ngood;i++)
{
if(emask->ddata[i])
{
weight=esigm->ddata[i];
mean_srianand+=eflux->ddata[i];
sigm_srianand+=eflux->ddata[i]*eflux->ddata[i];
++nbg_srianand;
if(weight<=0) continue;
++nbg_bastien;
weight=1./(weight*weight);
wsum+=weight;
fsum+=eflux->ddata[i]*weight;
}
}
}
if(nbg_srianand>0)
{
/* mean_srianand*=mean_srianand; */
/* mean_srianand/=(double)(nbg_srianand); /\* n.<X>^2 *\/ */
/* sigm_srianand-=mean_srianand; // n<X^2>-n<X>^2 */
/* sigm_srianand/=(double)(nbg_srianand); //(n/n-1)(<X^2>-<X>^2) */
mean_srianand/=(double)(nbg_srianand);
mean_srianand*=mean_srianand;
sigm_srianand/=(double)(nbg_srianand);
sigm_srianand=(sigm_srianand-mean_srianand)/(double)(nbg_srianand);
}
else
sigm_srianand=0.;
if(wsum>0)
{
wsum=1./wsum;
fsum*=wsum;
switch (error_type)
{
case _BOTH_ERRORS_ :
case _BASTIEN_ :
{
wsum=sqrt(wsum);
sigm_srianand=sqrt(sigm_srianand);
}
break;
case _SRIANAND_ : wsum=sqrt(sigm_srianand);
break;
case _BASTIEN_AND_SRIANAND_ : wsum=sqrt(wsum+sigm_srianand);
break;
case _MAX_BASTIEN_AND_SRIANAND_ : wsum=sqrt((sigm_srianand>wsum)?sigm_srianand:wsum);
break;
case _MAX_BASTIEN_AND_MAX_SRIANAND_ :
if(nbg_srianand>1)
fct=(1+sqrt(2./(nbg_srianand-1)));
else
fct=1.;
wsum=sqrt((sigm_srianand>wsum)?sigm_srianand*fct:wsum);
break;
default : wsum=sqrt((sigm_srianand>wsum)?sigm_srianand:wsum);
}
}
else
fsum=wsum=0;
if((!IS_NAN(fsum))&&(!IS_NAN(wsum)))
{
rslt->flux[j]=fsum;
rslt->sigm[j]=wsum;
}
if((error_type==_BOTH_ERRORS_)&&(!IS_NAN(sigm_srianand)))
rslt->cont[j]=sigm_srianand;
if(keepnbsp)
rslt->data[rslt->ndata-1]->ddata[j]=nbg_bastien;
eflux->size=nbsp;
esigm->size=nbsp;
emask->size=nbsp;
}
OS_message(0,OS_STD,"\b\b\b\b%3ld%%\n",100);
VC_free(emask);
VC_free(esigm);
VC_free(eflux);
MM_free( kmin);
MM_free( kmax);
MM_free(idmin);
MM_free(idmax);
MM_free(tmp);
return rslt;
}
void Cloud::loopForever()
{
overlapOctaves(map32, map256);
expFilter(map256);
}
