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fit_oct_model_to_LC_AO.c
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#include<stdio.h>
#include<stdlib.h>
#include"utils.h"
#include"matrix_ops.h"
#include"structs.h"
#include"globals.h"
void fit_oct_model_to_LC_AO(LCstruct *LC,AOstruct *AO,OCstruct *OC,RDstruct *RD,CNTRstruct *CR)
{
char *TEMP_OUT_SHAPE_FILE;
int TEMP_OUT_SHAPE_FILE_index=strlen(OUT_SHAPE_FILE);
TEMP_OUT_SHAPE_FILE=calloc(strlen(OUT_SHAPE_FILE)+6,sizeof(char));
strcpy(TEMP_OUT_SHAPE_FILE,OUT_SHAPE_FILE);
TEMP_OUT_SHAPE_FILE[TEMP_OUT_SHAPE_FILE_index++]='.';
TEMP_OUT_SHAPE_FILE[TEMP_OUT_SHAPE_FILE_index+4]='\0';
//First initialize the initial shape
int *tlist;
double *vlist,*vlist2,*D1,*D2;
int info;
int nfac=8*pow(INI_NROWS,2);
int nvert=4*pow(INI_NROWS,2)+2;
vlist=calloc(3*nvert,sizeof(double));
vlist2=calloc(3*nvert,sizeof(double));
tlist=calloc(3*nfac,sizeof(int));
double *a,*a2;
int alength=3*pow(INI_LMAX+1,2);
int al=pow(INI_LMAX+1,2);
double Albregsum=0;
a=calloc(alength,sizeof(double));
a2=calloc(alength,sizeof(double));
a[0]=log(ELLIPSOID_SEMI_A)/0.2821;
a[1*al]=log(ELLIPSOID_SEMI_B)/0.2821-a[0];
a[2*al]=log(ELLIPSOID_SEMI_C)/0.2821-a[0];
//Setup angles
double angles[]={(90-INI_ANGLE_B)*PI/180,INI_ANGLE_L*PI/180,24*2*PI*1.0/INI_ANGLE_P,INI_ANGLE_PHI0*PI/180};
double angles2[4]={0,0,0,0};
angles2[3]=angles[3];
//This is for calibrated lightcurves
double *params=NULL,*params2=NULL;
int ncalib=0;
int nLCtotal=0;
int USE_CALIB=0;
int nAlbedo=0;
double *eAlbedo=NULL,*eAlbedo2=NULL;
double *dLCdalb=NULL;
double *Alblimits=NULL;
double *Albreg=NULL,*dAlbreg=NULL;
int nAlbreg=0;
if(INI_HAVE_LC)
{
nLCtotal=LC->ntotal;
USE_CALIB=LC->calib;
if(INI_PHASE_PARAMS!=NULL)
{
params=calloc(3,sizeof(double));
params2=calloc(3,sizeof(double));
params[0]=INI_PHASE_PARAMS[0];
params[1]=INI_PHASE_PARAMS[1];
params[2]=INI_PHASE_PARAMS[2];
memcpy(params2,params,sizeof(double)*3);
ncalib=3;
}
if(INI_FIT_ALBEDO==1)
{
nAlbedo=nvert;
eAlbedo=calloc(nAlbedo,sizeof(double));
eAlbedo2=calloc(nAlbedo,sizeof(double));
dLCdalb=calloc(nLCtotal*nAlbedo,sizeof(double));
Alblimits=calloc(2,sizeof(double));
Alblimits[0]=INI_ALBEDO_MIN;
Alblimits[1]=INI_ALBEDO_MAX;
Albreg=calloc(nAlbedo,sizeof(double));
dAlbreg=calloc(nAlbedo*nAlbedo,sizeof(double));
nAlbreg=nAlbedo;
if(INI_ALBEDO_FILE!=NULL)
{
int read_alb=0;
read_alb=read_vector_file(INI_ALBEDO_FILE,eAlbedo,nAlbedo);
if(read_alb<nAlbedo)
{
printf("Wrong number of albedo values in %s\n",INI_ALBEDO_FILE);
zero_array(eAlbedo,nAlbedo);
}
}
}
}
int nCOM=0;
double CoM=0.0;
double *CoMdv;
double *CoMda;
if(INI_COM_WEIGHT>0)
{
nCOM=1;
CoMdv=calloc(3*nvert+3,sizeof(double));
CoMda=calloc(alength+3,sizeof(double));
}
//This is for calibrated lightcurves end
//LC albedo variegation
double ANGres;
double *dANGdv=calloc(3*nvert+3,sizeof(double));
double *dANGda=calloc(alength+3,sizeof(double));
int nAOtotal=0;
int nAOcols=0;
int nAOcolst=0;
int nAO=0;
int nAOoffsets=0;
int nAOscale=0;
double *AOoffset,*AOoffset2,*AOout,*AOda,*AOdv,AOfit,*AOscale,*AOscale2,*AOds,*dAOdAlb,*ao_total_bright;
if(INI_HAVE_AO)
{
nAOtotal=2*(AO->ntotal);
nAOcolst=3*nvert+3+2*(AO->nao);
nAOoffsets=2*(AO->nao);
nAOcols=alength+3+2*(AO->nao);
nAO=AO->nao;
AOoffset=calloc(2*(AO->nao),sizeof(double));
if(INI_INPUT_AO_OFFSET!=NULL)
{
read_vector_file(INI_INPUT_AO_OFFSET,AOoffset,2*(AO->nao));
}
AOoffset2=calloc(2*(AO->nao),sizeof(double));
AOout=calloc(nAOtotal,sizeof(double));
AOdv=calloc(nAOtotal*nAOcolst,sizeof(double));
if(AOdv==NULL)
perror("Could not allocate for AOdv\n");
AOda=calloc(nAOtotal*nAOcols,sizeof(double));
AOfit=0;
AOscale=NULL;
AOscale2=NULL;
INI_AO_TOTAL_BRIGHT=calloc(nAO,sizeof(double));
ao_total_bright=calloc(nAO,sizeof(double));
if(INI_AO_SCALING)
{
AOscale=calloc(1*nAO,sizeof(double));
AOscale2=calloc(1*nAO,sizeof(double));
AOds=calloc(nAOtotal*nAO,sizeof(double));
nAOscale=nAO;
}
if(INI_FIT_AO_ALBEDO)
{
dAOdAlb=calloc(nAOtotal*nAlbedo,sizeof(double));
}
}
int nCRtotal=0;
int nCRcolst=0;
int nCRcols=0;
int nCRoffsets=0;
int nCR=0;
double* CRoffset,*CRoffset2;
double *CRdv,*CRda;
double *CRout;
double *CRdoff;
double CRfit;
if(INI_HAVE_CNTR)
{
if(INI_CNTR_IS_SPARSE)
nCRtotal=(CR->ntotal);
else
nCRtotal=(CR->ntotal)+nvert*CR->ncont;
nCRcolst=3*nvert+3; //Columns in derivative matrix 3*vertices+angles
nCRcols=alength+3;
nCRoffsets=2*(CR->ncont);
nCR=CR->ncont;
CRout=calloc(nCRtotal,sizeof(double));
CRoffset=calloc(2*nCR,sizeof(double));
CRoffset2=calloc(2*nCR,sizeof(double));
CRdv=calloc(nCRtotal*(3*nvert+3),sizeof(double)); //derivative matrix, vertices+angles
CRda=calloc(nCRtotal*(nCRcols),sizeof(double));
CRdoff=calloc(nCRtotal*2*nCR,sizeof(double)); //derivative matrix, offsets
}
//Occultation data
int nOCtotal=0;
int nOCcols=0;
int nOC=0;
int nOCoffsets=0;
int nOCcolst=0;
int nChordoffsets=0;
int nvectorreg=0;
double *OCoffset,*OCoffset2,*OCout,*OCdv,*OCda,OCfit=0,*OCdoff;
double *Chordoffset,*Chordoffset2;
double *dChordoffset; //Derivative matrix for chord offsets
double vectorreg; //regularization for free chord offsets
double *dvectorreg; //derivative matrix for free chord offsets, 1xnChordoffsets
if(INI_HAVE_OC)
{
nOCtotal=4*(OC->ntotal);
nOCcolst=3*nvert+3;
nOCcols=alength+3;
nOCoffsets=2*(OC->noc);
nOC=OC->noc;
OCoffset=calloc(nOCoffsets,sizeof(double));
if(INI_OC_OFFSET!=NULL)
memcpy(OCoffset,INI_OC_OFFSET,sizeof(double)*nOCoffsets);
OCoffset2=calloc(nOCoffsets,sizeof(double));
OCdv=calloc(nOCtotal*nOCcolst,sizeof(double));
OCda=calloc(nOCtotal*(alength+3),sizeof(double));
OCout=calloc(nOCtotal,sizeof(double));
OCdoff=calloc(nOCtotal*nOCoffsets,sizeof(double));
Chordoffset=calloc(OC->ntotal,sizeof(double));
Chordoffset2=calloc(OC->ntotal,sizeof(double));
if(INI_CHORD_OFFSET!=NULL)
{
memcpy(Chordoffset,INI_CHORD_OFFSET,sizeof(double)*OC->ntotal);
memcpy(Chordoffset2,INI_CHORD_OFFSET,sizeof(double)*OC->ntotal);
}
if(INI_FREE_CHORD_NMR>0)
{
nChordoffsets=OC->ntotal;
nvectorreg=1;
dChordoffset=calloc(nOCtotal*nChordoffsets,sizeof(double));
dvectorreg=calloc(nChordoffsets,sizeof(double));
}
}
int nRDtotal=0;
int nRDcols=0,nRDcolst=0;
int nRD=0;
int nRDoffsets=0;
int nRDscale=0;
int nRDexp=0;
double RDexp=INI_RDEXP;
double RDexp2=RDexp;
double RDfit=0;
double *RDda;
double *RDoffset,*RDoffset2,*RDscale,*RDscale2,*RDout,*RDdv,*RDdoff,*RDdscale,*RDdexp;
if(INI_HAVE_RD)
{
nRDtotal=2*(RD->ntotal);
nRDcolst=3*nvert+3;
nRDcols=alength+3;
nRDoffsets=2*(RD->nRD);
nRD=RD->nRD;
nRDscale=nRD;
nRDexp=0;
RDoffset=calloc(nRDoffsets,sizeof(double));
RDoffset2=calloc(nRDoffsets,sizeof(double));
RDscale=calloc(nRDscale,sizeof(double));
RDscale2=calloc(nRDscale,sizeof(double));
RDout=calloc(nRDtotal,sizeof(double));
RDdv=calloc(nRDtotal*nRDcolst,sizeof(double));
RDda=calloc(nRDtotal*nRDcols,sizeof(double));
RDdoff=calloc(nRDtotal*nRDoffsets,sizeof(double));
RDdscale=calloc(nRDtotal*nRD,sizeof(double));
RDdexp=calloc(nRDtotal,sizeof(double));
}
//Variables for regularization terms
double CRres; //Convex reg
double *dCRdv,*dCRda;
double *y,*y2;
dCRdv=calloc(3*nvert+3,sizeof(double));
dCRda=calloc(alength+3,sizeof(double));
//Octantoid regularization
double Ores;
double *dOda;
dOda=calloc(alength,sizeof(double));
double *S,*S2;
double *J,*JTJ,*JTJpd;
////////////////////////////////////
// write_matrix_file("/tmp/data0r.txt",AO->datar[0],1,AO->nobs[0]);
// write_matrix_file("/tmp/data0i.txt",AO->datai[0],1,AO->nobs[0]);
// write_matrix_file("/tmp/data1r.txt",AO->datar[1],1,AO->nobs[1]);
// write_matrix_file("/tmp/data1i.txt",AO->datai[1],1,AO->nobs[1]);
// write_matrix_file("/tmp/freqx.txt",AO->freqx[0],1,AO->nobs[0]);
// write_matrix_file("/tmp/freqy.txt",AO->freqy[0],1,AO->nobs[0]);
/////////////////////////////////////////////////////
int Slength;
double zm=0;
double *dzmdz,*dzmdzt,*dzmda;
int softmaxz=0;
if(INI_ZMAX_WEIGHT>0)
{
softmaxz=1;
dzmdz=calloc(nvert,sizeof(double));
dzmdzt=calloc(3*nvert+3,sizeof(double));
dzmda=calloc(alength+3,sizeof(double));
}
int inerreglength=0;
double inerres,inerangle;
double *inerdv=NULL,*inerda=NULL;
if(INI_INER_WEIGHT>0)
{
inerreglength=1;
inerdv=calloc(3*nvert+3,sizeof(double));
inerda=calloc(alength+3,sizeof(double));
}
//Number of rows in J
//If there are no parameters to optimize, add number of additional constraints to be minimized to Slength
//If there are additional parameters, also add number of parameters to nJcols
Slength=nLCtotal+nAOtotal+nOCtotal+nRDtotal+1+1+1+softmaxz+nvectorreg+nAlbreg+nCRtotal+nCOM+inerreglength; //LC points+AO points+OC points+RD points+ convex reg+oct reg+dihedral+[softmaxz]+[vector reg for free chords]
int nJcols=alength+3+ncalib+nAlbedo+nAOoffsets+nAOscale+nOCoffsets+nChordoffsets+nRDoffsets+nRDscale+nRDexp+nCRoffsets;
S=calloc(Slength,sizeof(double));
J=calloc(Slength*(nJcols),sizeof(double));
int padding=3+nAOoffsets;
JTJ=calloc((nJcols)*(nJcols),sizeof(double));
JTJpd=calloc((nJcols)*(nJcols),sizeof(double));
int OCoffsetcolpos=alength+3+nAOoffsets+nAOscale;
int Chordoffsetcolpos=alength+3+nAOoffsets+nAOscale+nOCoffsets;
int OCrowpos=nLCtotal+nAOtotal;
int RDoffsetcolpos=alength+3+nAOoffsets+nAOscale+nOCoffsets+nChordoffsets;
int RDscalecolpos=alength+3+nAOoffsets+nAOscale+nOCoffsets+nChordoffsets+nRDoffsets;
int RDrowpos=nLCtotal+nAOtotal+nOCtotal;
int Albcolpos=alength+3+nAOoffsets+nAOscale+nOCoffsets+nChordoffsets+nRDoffsets+nRDscale+nRDexp;
int regpos=nLCtotal+nAOtotal+nOCtotal+nRDtotal;
int Convregpos=regpos;
int Octregpos=regpos+1;
int Angregpos=regpos+2;
int Zmaxregpos=Angregpos+1;
int Vectorregpos=Zmaxregpos+softmaxz;
int Albregpos=Vectorregpos+nvectorreg;
int phasecolpos=alength+3+nAlbedo+nAOoffsets+nAOscale+nOCoffsets+nChordoffsets+nRDoffsets+nRDscale+nRDexp;
int CRrowpos=nLCtotal+nAOtotal+nOCtotal+nRDtotal+1+1+1+softmaxz+nvectorreg+nAlbreg;
int CRoffsetcolpos=alength+3+ncalib+nAlbedo+nAOoffsets+nAOscale+nOCoffsets+nChordoffsets+nRDoffsets+nRDscale+nRDexp;
int CoMregpos=CRrowpos+nCRtotal; //position of Center of Mass reg (in S and corresponding row in J)
int inerregpos=CoMregpos+nCOM;
double *LCout,*dLCdv,*rhs,*X,*dLCda,*dLCdp=NULL;
LCout=calloc(nLCtotal,sizeof(double));
dLCdv=calloc((nLCtotal)*(3*nvert+3),sizeof(double));
dLCda=calloc((nLCtotal)*(alength+3),sizeof(double));
rhs=calloc(nJcols,sizeof(double));
X=calloc(nJcols,sizeof(double));
//Check if some parameters are fixed:
double *Mask_Matrix;
int *Mask;
int nMask=0;
double *MJTJ;
double *MJTJpd;
double *Mrhs;
double *MX;
int first_time=1;
if(INI_MASK_SET==1)
{
Mask=calloc(nJcols,sizeof(int));
if(INI_FIX_SHAPE==1)
for(int k=0;k<alength;k++)
Mask[k]=1;
if(INI_FIX_PERIOD==1)
Mask[alength+2]=1;
if(INI_FIX_ANGLES==1)
for(int k=alength;k<alength+3;k++)
Mask[k]=1;
if(INI_FIX_A1==1)
Mask[0]=1;
if(INI_STAR_SHAPED==1)
{
for(int k=pow(INI_LMAX+1,2);k<alength;k++)
Mask[k]=1;
a[1*al]=0;
a[2*al]=0;
}
if(INI_FREE_CHORD_NMR>0)
{
for(int k=0;k<nChordoffsets;k++)
Mask[Chordoffsetcolpos+k]=1;
for(int k=0;k<INI_FREE_CHORD_NMR;k++)
Mask[Chordoffsetcolpos+INI_FREE_CHORD_LIST[k]-1]=0;
}
if(INI_PHASE_MASK!=NULL)
{
Mask[phasecolpos]=INI_PHASE_MASK[0];
Mask[phasecolpos+1]=INI_PHASE_MASK[1];
Mask[phasecolpos+2]=INI_PHASE_MASK[2];
}
mask_matrix(nJcols,Mask,&Mask_Matrix,&nMask);
MJTJ=calloc(nMask*nMask,sizeof(double));
MJTJpd=calloc(nMask*nMask,sizeof(double));
Mrhs=calloc(nMask,sizeof(double));
MX=calloc(nMask,sizeof(double));
}
//Weights
int nvertn=0;
double angW=INI_DW;
double AOW=INI_AOW;
double lcW=INI_LCW;
double cW=INI_CW;
double oW=INI_OW;
double ocW=INI_OCW;
double RDW=INI_RW;
double lambda=INI_LAMBDA;
int decreased=1;
double chisq=1e9;
double chisq2;
double LCfit=0;
double dec=10;
double prevdec=dec;
double threshold=INI_MINDEC;
int count=0;
int DONE=0;
//Allocate for D matrix
D1=calloc((3*nvert+3)*(alength+3),sizeof(double));
D2=calloc((3*nvert+3+nAOoffsets)*(alength+3+nAOoffsets),sizeof(double));
if(INI_PHASE_PARAMS!=NULL)
dLCdp=calloc(nLCtotal*3,sizeof(double));
//Restore previous state if the state file is available
if(INI_RESTORE_STATE)
{
printf("Restoring previous state from %s\n",INI_RESTORE_STATE);
//Restore angles
read_state_file(INI_RESTORE_STATE,"#Angles",angles,4);
angles[0]=(90-angles[0])*PI/180;
angles[1]=angles[1]*PI/180;
angles[2]=24*2*PI*1.0/angles[2];
angles[3]=angles[3]*PI/180;
//Restore shape
int oldLMAX=0; //oldLMAX is number of spherical harmonics in the state file
double *olda;
read_state_fileI(INI_RESTORE_STATE,"#LMAX",&oldLMAX,1);
int oldalength=3*pow(oldLMAX+1,2);
int oldal=pow(oldLMAX+1,2);
olda=calloc(oldalength,sizeof(double));
read_state_file(INI_RESTORE_STATE,"#aParams",olda,oldalength);
//Copy shape parameters to a
memcpy(a,olda,oldal*sizeof(double));
memcpy(a+al,olda+oldal,oldal*sizeof(double));
memcpy(a+2*al,olda+2*oldal,oldal*sizeof(double));
//Restore AO
read_state_file(INI_RESTORE_STATE,"#AOoffset",AOoffset,nAOoffsets);
read_state_file(INI_RESTORE_STATE,"#AOscale",AOscale,nAOscale);
//Restore OC
read_state_file(INI_RESTORE_STATE,"#OCCoffset",OCoffset,nOCoffsets);
read_state_file(INI_RESTORE_STATE,"#Chordoffset",Chordoffset,nChordoffsets);
//Restore albedo
int albcount=0;
if(INI_HAVE_LC && INI_FIT_ALBEDO==1 && INI_RESTORE_ALBEDO)
{
albcount=read_state_file(INI_RESTORE_STATE,"#Albedolog",eAlbedo,nAlbedo);
printf("Restoring albedo values\n");
if(albcount!=nAlbedo)
{
printf("There are %d albedo values, but %d vertices. Discarding loaded albedos\n",albcount,nAlbedo);
zero_array(eAlbedo,nAlbedo);
}
}
if(INI_HAVE_RD)
{
read_state_file(INI_RESTORE_STATE,"#RDoffset",RDoffset,nRDoffsets);
read_state_file(INI_RESTORE_STATE,"#RDscale",RDscale,nRDscale);
}
}
//Log file
FILE* fidlog=NULL;
if(OUT_LOG_FILE!=NULL)
{
fidlog=fopen(OUT_LOG_FILE,"w");
if(fidlog==NULL)
{
fprintf(stderr,"Cannot open log file %s\n",OUT_LOG_FILE);
exit(-1);
}
}
//This is the main optimization loop
for(int k=0;k<NUM_OF_ROUNDS;k++)
{
start:
if(decreased==1)
{
octantoid_to_trimesh(a,INI_LMAX,INI_NROWS,tlist,vlist,D1,3); //D is 3nvert+3 x alength matrix
octantoid_to_trimesh(a,INI_LMAX,INI_NROWS,tlist,vlist,D2,3+nAOoffsets); //TBD: Fix this ugly thing
//We must pad D before using it to preserve angle and offset derivatives
//Calculate LCs
// write_shape_file("/tmp/Inishape.txt",tlist,vlist,nfac,nvert);
// write_matrix_file("/tmp/a.txt",a,1,alength);
// write_matrix_file("/tmp/D1.txt",D1,3*nvert+3,alength+3);
// write_matrix_file("/tmp/D2.txt",D2,3*nvert+3+nAOoffsets,alength+3+nAOoffsets);
if(INI_HAVE_LC)
{
calculate_lcs(tlist,vlist,nfac,nvert,angles,LC,NULL,nvert,nvert,LCout,dLCdv,eAlbedo,Alblimits,dLCdalb,params,dLCdp,1);
// write_matrix_file("/tmp/LCout.txt",LCout,1,nLCtotal);
// write_matrix_file("/tmp/dLCdv.txt",dLCdv,nLCtotal,3*nvert+3);
//Convert to derivative matrix wrt a
if(INI_FIT_ALBEDO==1)
{
mult_with_cons(dLCdalb,nLCtotal,nAlbedo,lcW);
alb_smooth(eAlbedo,nAlbedo,Albreg,dAlbreg);
//localsmooth(tlist,vlist,nfac,nvert,eAlbedo,Alblimits,Albreg,dAlbreg);
mult_with_cons(dAlbreg,nAlbedo,nAlbedo,-INI_ALBREGW);
mult_with_cons(Albreg,1,nAlbedo,INI_ALBREGW);
set_submatrix(S,1,Slength,Albreg,1,nAlbedo,0,Albregpos);
set_submatrix(J,Slength,nJcols,dLCdalb,nLCtotal,nAlbedo,0,Albcolpos);
set_submatrix(J,Slength,nJcols,dAlbreg,nAlbedo,nAlbedo,Albregpos,Albcolpos);
}
matrix_prod(dLCdv,nLCtotal,3*nvert+3,D1,alength+3,dLCda); //dLCda is nLCtotal x alength+3 matrix
mult_with_cons(LCout,1,nLCtotal,lcW);
mult_with_cons(dLCda,nLCtotal,alength+3,lcW);
matrix_transprod(LCout,nLCtotal,1,&LCfit);
set_submatrix(J,Slength,nJcols,dLCda,nLCtotal,alength+3,0,0);
set_submatrix(S,1,Slength,LCout,1,nLCtotal,0,0);
}
// write_matrix_file("/tmp/dLCda.txt",dLCda,nLCtotal,alength+3);
// printf("Angles: %f %f %f %f\n",angles[0],angles[1],angles[2],angles[3]);
//AO data
// printf("before AOs\n");
if(INI_DW_DEC!=1.0)
angW=INI_DW*pow(INI_DW_DEC,count);
if(INI_HAVE_AO)
{
Calculate_AOs(tlist,vlist,nfac,nvert,angles,AO,AOoffset,NULL,nvert,nvert,INI_AO_WEIGHT,AOscale,AOout,AOdv,AOds,eAlbedo,Alblimits,dAOdAlb,1);
//Convert to derivative wrt params a
matrix_prod(AOdv,nAOtotal,nAOcolst,D2,nAOcols,AOda); //AOda is nAOtotal x (nAOcols)
// write_matrix_file("/tmp/AOda.txt",AOda,nAOtotal,nAOcols);
// write_matrix_file("/tmp/AOdv.txt",AOdv,nAOtotal,nAOcolst);
// write_matrix_file("/tmp/AOout.txt",AOout,1,nAOtotal);
mult_with_cons(AOout,1,nAOtotal,AOW);
mult_with_cons(AOda,nAOtotal,nAOcols,AOW);
set_submatrix(S,1,Slength,AOout,1,nAOtotal,0,nLCtotal);
matrix_transprod(AOout,nAOtotal,1,&AOfit);
set_submatrix(J,Slength,nJcols,AOda,nAOtotal,nAOcols,nLCtotal,0);
if(INI_AO_SCALING)
{
mult_with_cons(AOds,nAOtotal,nAO,AOW);
set_submatrix(J,Slength,nJcols,AOds,nAOtotal,nAO,nLCtotal,nAOcols);
}
if(INI_FIT_AO_ALBEDO)
{
mult_with_cons(dAOdAlb,nAOtotal,nAlbedo,AOW);
set_submatrix(J,Slength,nJcols,dAOdAlb,nAOtotal,nAlbedo,nLCtotal,Albcolpos);
}
}
if(INI_HAVE_CNTR)
{
Calculate_Contours(tlist,vlist,nfac,nvert,angles,CR,CRoffset,NULL,nvert,nvert,CRout,CRdv,CRdoff);
matrix_prod(CRdv,nCRtotal,nCRcolst,D1,nCRcols,CRda);
mult_with_cons(CRout,1,nCRtotal,INI_CNTR_WEIGHT);
mult_with_cons(CRda,nCRtotal,nCRcols,-INI_CNTR_WEIGHT);
mult_with_cons(CRdoff,nCRtotal,nCRoffsets,-INI_CNTR_WEIGHT);
set_submatrix(S,1,Slength,CRout,1,nCRtotal,0,CRrowpos);
set_submatrix(J,Slength,nJcols,CRda,nCRtotal,nCRcols,CRrowpos,0);
set_submatrix(J,Slength,nJcols,CRdoff,nCRtotal,nCRoffsets,CRrowpos,CRoffsetcolpos);
matrix_transprod(CRout,nCRtotal,1,&CRfit);
}
if(INI_HAVE_OC)
{
if(INI_FREE_CHORD_NMR>0)
{
calculate_OCs(tlist,vlist,nfac,nvert,angles,OC,OCoffset,INI_OC_WEIGHT,NULL,nvert,nvert,Chordoffset,OCout,OCdv,OCdoff,dChordoffset);
vector_regularization(Chordoffset,nChordoffsets,&vectorreg,dvectorreg);
mult_with_cons(dChordoffset,nOCtotal,nChordoffsets,-ocW);
mult_with_cons(dvectorreg,1,nChordoffsets,-INI_CHRDW);
vectorreg*=INI_CHRDW;
S[Vectorregpos]=vectorreg;
set_submatrix(J,Slength,nJcols,dChordoffset,nOCtotal,nChordoffsets,OCrowpos,Chordoffsetcolpos); //Chord offsets
set_submatrix(J,Slength,nJcols,dvectorreg,1,nChordoffsets,Vectorregpos,Chordoffsetcolpos);
}
else
calculate_OCs(tlist,vlist,nfac,nvert,angles,OC,OCoffset,INI_OC_WEIGHT,NULL,nvert,nvert,Chordoffset,OCout,OCdv,OCdoff,NULL);
matrix_prod(OCdv,nOCtotal,nOCcolst,D1,alength+3,OCda);
mult_with_cons(OCout,1,nOCtotal,ocW);
mult_with_cons(OCda,nOCtotal,nOCcols,-ocW); //Note the minus here.
mult_with_cons(OCdoff,nOCtotal,nOCoffsets,-ocW);
set_submatrix(S,1,Slength,OCout,1,nOCtotal,0,OCrowpos);
set_submatrix(J,Slength,nJcols,OCda,nOCtotal,nOCcols,OCrowpos,0);
set_submatrix(J,Slength,nJcols,OCdoff,nOCtotal,nOCoffsets,OCrowpos,OCoffsetcolpos);
matrix_transprod(OCout,nOCtotal,1,&OCfit);
}
if(INI_HAVE_RD)
{
Calculate_RDs(tlist,vlist,nfac,nvert,angles,RD,RDoffset,NULL,nvert,nvert,INI_RD_WEIGHT,RDscale,RDexp,RDout,RDdv,RDdoff,RDdscale,RDdexp,1);
matrix_prod(RDdv,nRDtotal,nRDcolst,D1,nRDcols,RDda);
mult_with_cons(RDout,1,nRDtotal,RDW);
mult_with_cons(RDda,nRDtotal,nRDcols,RDW); //NO minus here
mult_with_cons(RDdoff,nRDtotal,nRDoffsets,RDW);
mult_with_cons(RDdscale,nRDtotal,nRDscale,RDW);
if(nRDexp>0)
{
mult_with_cons(RDdexp,nRDtotal,1,RDW);
set_submatrix(J,Slength,nJcols,RDdexp,nRDtotal,1,RDrowpos,RDscalecolpos+nRDscale);
}
set_submatrix(S,1,Slength,RDout,1,nRDtotal,0,RDrowpos);
set_submatrix(J,Slength,nJcols,RDda,nRDtotal,nRDcols,RDrowpos,0);
set_submatrix(J,Slength,nJcols,RDdoff,nRDtotal,nRDoffsets,RDrowpos,RDoffsetcolpos); //[RDda 0 RDdoff RDdscale RDdexp]
set_submatrix(J,Slength,nJcols,RDdscale,nRDtotal,nRDscale,RDrowpos,RDscalecolpos);
matrix_transprod(RDout,nRDtotal,1,&RDfit);
}
convex_reg(tlist,vlist,nfac,nvert,NULL,nvertn,nvert,&CRres,dCRdv);
dihedral_angle_reg(tlist,vlist,nfac,nvert,NULL,nvert,nvert,&ANGres,dANGdv);
matrix_prod(dANGdv,1,3*nvert+3,D1,alength+3,dANGda);
//Convert to derivative wrt a
matrix_prod(dCRdv,1,3*nvert+3,D1,alength+3,dCRda);
//Octantoid regularization
octantoid_reg(a,INI_LMAX,&Ores,dOda);
if(INI_ZMAX_WEIGHT>0)
{
soft_maxdimz(tlist,vlist,nfac,nvert,NULL,nvert,INI_ZMAX,1.0,&zm,dzmdz);
zm*=INI_ZMAX_WEIGHT;
memcpy(dzmdzt+2*nvert,dzmdz,nvert*sizeof(double));
matrix_prod(dzmdzt,1,3*nvert+3,D1,alength+3,dzmda);
mult_with_cons(dzmda,1,alength+3,-INI_ZMAX_WEIGHT);
S[Zmaxregpos]=zm;
set_submatrix(J,Slength,nJcols,dzmda,1,alength,Zmaxregpos,0);
}
if(INI_COM_WEIGHT>0)
{
CoM=center_of_mass(tlist,vlist,nfac,nvert,NULL,nvert,nvert,CoMdv,1);
matrix_prod(CoMdv,1,3*nvert+3,D1,alength+3,CoMda);
CoM=INI_COM_WEIGHT*CoM;
mult_with_cons(CoMda,1,alength+3,-INI_COM_WEIGHT);
S[CoMregpos]=CoM;
set_submatrix(J,Slength,nJcols,CoMda,1,alength,CoMregpos,0);
}
if(INI_INER_WEIGHT>0)
{
inertia(tlist,vlist,nfac,nvert,NULL,0,0,&inerres,&inerangle,inerdv);
printf("Inerres: %f Inerangle: %f\n",inerres,inerangle);
matrix_prod(inerdv,1,3*nvert+3,D1,alength+3,inerda);
inerres*=INI_INER_WEIGHT;
mult_with_cons(inerda,1,alength+3,-INI_INER_WEIGHT);
S[inerregpos]=inerres;
set_submatrix(J,Slength,nJcols,inerda,1,alength,inerregpos,0);
}
CRres*=cW;
mult_with_cons(dANGda,1,alength+3,-angW);
ANGres*=angW;
mult_with_cons(dCRda,1,alength+3,-cW);
Ores*=oW;
mult_with_cons(dOda,1,alength,-oW);
//Build the res vector and matrix
S[Convregpos]=CRres; //Convex reg terms
S[Octregpos]=Ores; //Octantoid reg
S[Angregpos]=ANGres;
matrix_transprod(S,Slength,1,&chisq);
printf("Round: %d chisq: %4.2f LCfit: %4.2f AOfit: %4.2f OCfit: %4.2f RDfit: %4.2f Convex reg: %4.2f Octantoid reg: %4.2f Dihedral reg: %4.2f",k,chisq,LCfit,AOfit,OCfit,RDfit,pow(CRres,2),pow(Ores,2),pow(ANGres,2));
//printf("scale: %f %f\n",AOscale[0],AOscale[1]);
//Construct Jacobian matrix
if(INI_HAVE_CNTR>0)
printf(" CNTRfit: %4.2f",CRfit);
if(INI_COM_WEIGHT>0)
printf(" CoM reg: %4.2f",pow(CoM,2));
if(INI_INER_WEIGHT>0)
printf(" Iner reg: %4.2f",pow(inerres,2));
if(INI_ZMAX_WEIGHT>0)
printf(" Zmax reg: %f\n",pow(zm,2));
else
printf("\n");
if(fidlog!=NULL)
{
fprintf(fidlog,"Round: %d chisq: %4.2f LCfit: %4.2f AOfit: %4.2f OCfit: %4.2f RDfit: %4.2f Convex reg: %4.2f Octantoid reg: %4.2f Dihedral reg: %4.2f",k,chisq,LCfit,AOfit,OCfit,RDfit,pow(CRres,2),pow(Ores,2),pow(ANGres,2));
//printf("scale: %f %f\n",AOscale[0],AOscale[1]);
//Construct Jacobian matrix
if(INI_HAVE_CNTR>0)
fprintf(fidlog," CNTRfit: %4.2f",CRfit);
if(INI_COM_WEIGHT>0)
fprintf(fidlog," CoM reg: %4.2f",pow(CoM,2));
if(INI_INER_WEIGHT>0)
fprintf(fidlog," Iner reg: %4.2f",pow(inerres,2));
if(INI_ZMAX_WEIGHT>0)
fprintf(fidlog," Zmax reg: %f\n",pow(zm,2));
else
fprintf(fidlog,"\n");
}
set_submatrix(J,Slength,nJcols,dCRda,1,alength+3,Convregpos,0);
set_submatrix(J,Slength,nJcols,dOda,1,alength,Octregpos,0);
set_submatrix(J,Slength,nJcols,dANGda,1,alength,Angregpos,0);
if(INI_HAVE_LC && INI_PHASE_PARAMS!=NULL)
{
mult_with_cons(dLCdp,nLCtotal,3,lcW);
set_submatrix(J,Slength,nJcols,dLCdp,nLCtotal,3,0,phasecolpos);
}
// write_matrix_file("/tmp/S.txt",S,1,Slength);
// write_matrix_file("/tmp/J.txt",J,Slength,nJcols);
//Calculate J^TJ+lambda*J
// matrix_transprod(J,Slength,nJcols,JTJ);
matrix_transprod(J,Slength,nJcols,JTJ);
matrix_vectorprod(J,Slength,nJcols,S,rhs,1); //rhs=J^T*S;
//////////////////
// write_matrix_file("/tmp/a.txt",a,alength,1);
// write_matrix_file("/tmp/dOda.txt",dOda,1,alength);
// write_matrix_file("/tmp/dCRda.txt",dCRda,1,alength);
if(INI_MASK_SET==1)
{
matrix_prod_ATBA(Mask_Matrix,nJcols,nMask,JTJ,MJTJ);
matrix_prod_ATB(Mask_Matrix,nJcols,nMask,rhs,1,Mrhs);
}
}
if(INI_MASK_SET==1)
{
matrix_adddiag(MJTJ,MJTJpd,nMask,lambda);
info=solve_matrix_eqS(MJTJpd,nMask,Mrhs,MX);
matrix_prod(Mask_Matrix,nJcols,nMask,MX,1,X);
}
else
{
matrix_adddiag(JTJ,JTJpd,nJcols,lambda); //JTJpd=JTJ+lambda*diag(JTJ)
info=solve_matrix_eqS(JTJpd,nJcols,rhs,X); //Solve the LM
}
//THIS IS A NASTY HACK, IF MATRIX EQUATION IS NOT SOLVABLE, WE FIX ALBEDO AND CONTINUE
if(info>0 && INI_HAVE_LC && INI_FIT_ALBEDO && first_time==1)
{
printf("Solving the matrix failed, fixing the albedo\n");
if(fidlog!=NULL)
fprintf(fidlog,"Solving the matrix failed, fixing the albedo\n");
first_time=0;
INI_MASK_SET=1;
int INI_FIX_ALBEDO=1;
if(INI_MASK_SET==1)
{
Mask=calloc(nJcols,sizeof(int));
if(INI_FIX_SHAPE==1)
for(int k=0;k<alength;k++)
Mask[k]=1;
if(INI_FIX_ANGLES==1)
for(int k=alength;k<alength+3;k++)
Mask[k]=1;
if(INI_FIX_A1==1)
Mask[0]=1;
if(INI_STAR_SHAPED==1)
{
for(int k=pow(INI_LMAX+1,2);k<alength;k++)
Mask[k]=1;
a[1*al]=0;
a[2*al]=0;
}
if(INI_FREE_CHORD_NMR>0)
{
for(int k=0;k<nChordoffsets;k++)
Mask[Chordoffsetcolpos+k]=1;
for(int k=0;k<INI_FREE_CHORD_NMR;k++)
Mask[Chordoffsetcolpos+INI_FREE_CHORD_LIST[k]-1]=0;
}
if(INI_FIX_ALBEDO==1)
for(int k=0;k<nAlbedo;k++)
Mask[Albcolpos+k]=1;
if(INI_PHASE_MASK!=NULL)
{
Mask[phasecolpos]=INI_PHASE_MASK[0];
Mask[phasecolpos+1]=INI_PHASE_MASK[1];
Mask[phasecolpos+2]=INI_PHASE_MASK[2];
}
mask_matrix(nJcols,Mask,&Mask_Matrix,&nMask);
MJTJ=calloc(nMask*nMask,sizeof(double));
MJTJpd=calloc(nMask*nMask,sizeof(double));
Mrhs=calloc(nMask,sizeof(double));
MX=calloc(nMask,sizeof(double));
}
decreased=1;
goto start;
}
//END HACK
// add_vector_to_vlist(vlist,X,vlist2,nvert);
matrix_plus2(a,1,alength,X,a2);
if(INI_HAVE_AO)
{
matrix_plus2(AOoffset,1,nAOoffsets,&X[alength+3],AOoffset2);
if(INI_AO_SCALING)
matrix_plus2(AOscale,1,nAO,&X[alength+3+nAOoffsets],AOscale2);
}
if(INI_HAVE_CNTR)
matrix_plus2(CRoffset,1,nCRoffsets,&X[CRoffsetcolpos],CRoffset2);
if(INI_HAVE_OC)
{
matrix_plus2(OCoffset,1,nOCoffsets,&X[OCoffsetcolpos],OCoffset2);
if(INI_FREE_CHORD_NMR>0)
matrix_plus2(Chordoffset,1,nChordoffsets,&X[Chordoffsetcolpos],Chordoffset2);
}
if(INI_HAVE_LC && INI_FIT_ALBEDO==1)
{
for(int j=0;j<nAlbedo;j++)
eAlbedo2[j]=eAlbedo[j]+X[Albcolpos+j];
}
angles2[0]=angles[0]+X[alength];
angles2[1]=angles[1]+X[alength+1];
angles2[2]=angles[2]+X[alength+2];
angles2[3]=angles[3];
if(INI_HAVE_LC && INI_PHASE_PARAMS!=NULL)
{
params2[0]=params[0]+X[phasecolpos];
params2[1]=params[1]+X[phasecolpos+1];
params2[2]=params[2]+X[phasecolpos+2];
}
if(INI_HAVE_RD)
{
matrix_plus2(RDoffset,1,nRDoffsets,&X[RDoffsetcolpos],RDoffset2);
matrix_plus2(RDscale,1,nRDscale,&X[RDscalecolpos],RDscale2);
if(nRDexp>0)
RDexp2=X[RDscalecolpos+nRDscale]+RDexp;
}
//New shape is a2. Check for fit
octantoid_to_trimesh(a2,INI_LMAX,INI_NROWS,tlist,vlist2,D1,3);
if(INI_HAVE_LC)
{
calculate_lcs(tlist,vlist2,nfac,nvert,angles2,LC,NULL,nvertn,nvert,LCout,dLCdv,eAlbedo2,Alblimits,dLCdalb,params2,dLCdp,0);
if(INI_FIT_ALBEDO==1)
{
alb_smooth(eAlbedo2,nAlbedo,Albreg,dAlbreg);
// localsmooth(tlist,vlist2,nfac,nvert,eAlbedo2,Alblimits,Albreg,dAlbreg);
mult_with_cons(Albreg,1,nAlbedo,INI_ALBREGW);
set_submatrix(S,1,Slength,Albreg,1,nAlbedo,0,Albregpos);
}
mult_with_cons(LCout,1,nLCtotal,lcW);
set_submatrix(S,1,Slength,LCout,1,nLCtotal,0,0);
}
if(INI_HAVE_AO)
{
Calculate_AOs(tlist,vlist2,nfac,nvert,angles2,AO,AOoffset2,NULL,nvertn,nvert,INI_AO_WEIGHT,AOscale2,AOout,AOdv,NULL,eAlbedo2,Alblimits,dAOdAlb,0);
mult_with_cons(AOout,1,nAOtotal,AOW);
set_submatrix(S,1,Slength,AOout,1,nAOtotal,0,nLCtotal);
}
if(INI_HAVE_OC)
{
calculate_OCs(tlist,vlist2,nfac,nvert,angles2,OC,OCoffset2,INI_OC_WEIGHT,NULL,nvert,nvert,Chordoffset2,OCout,OCdv,OCdoff,NULL);
mult_with_cons(OCout,1,nOCtotal,ocW);
set_submatrix(S,1,Slength,OCout,1,nOCtotal,0,OCrowpos);
if(INI_FREE_CHORD_NMR>0)
{
vector_regularization(Chordoffset2,nChordoffsets,&vectorreg,dvectorreg);
S[Vectorregpos]=INI_CHRDW*vectorreg;
}
}
if(INI_HAVE_CNTR)
{
Calculate_Contours(tlist,vlist2,nfac,nvert,angles2,CR,CRoffset2,NULL,nvert,nvert,CRout,CRdv,CRdoff);
mult_with_cons(CRout,1,nCRtotal,INI_CNTR_WEIGHT);
set_submatrix(S,1,Slength,CRout,1,nCRtotal,0,CRrowpos);
matrix_transprod(CRout,nCRtotal,1,&CRfit);
}
if(INI_HAVE_RD)
{
Calculate_RDs(tlist,vlist2,nfac,nvert,angles2,RD,RDoffset2,NULL,nvert,nvert,INI_RD_WEIGHT,RDscale2,RDexp2,RDout,RDdv,RDdoff,RDdscale,RDdexp,0);
mult_with_cons(RDout,1,nRDtotal,RDW);
set_submatrix(S,1,Slength,RDout,1,nRDtotal,0,RDrowpos);
}
if(INI_COM_WEIGHT>0)
{
CoM=center_of_mass(tlist,vlist2,nfac,nvert,NULL,nvert,nvert,CoMdv,0);
CoM=INI_COM_WEIGHT*CoM;
S[CoMregpos]=CoM;
}
if(INI_INER_WEIGHT>0)
{
inertia(tlist,vlist2,nfac,nvert,NULL,0,0,&inerres,&inerangle,inerdv);
inerres*=INI_INER_WEIGHT;
S[inerregpos]=inerres;
}
dihedral_angle_reg(tlist,vlist2,nfac,nvert,NULL,nvert,nvert,&ANGres,dANGdv);
convex_reg(tlist,vlist2,nfac,nvert,NULL,nvertn,nvert,&CRres,dCRdv);
octantoid_reg(a2,INI_LMAX,&Ores,dOda);
CRres*=cW;
Ores*=oW;
ANGres*=angW;
if(INI_ZMAX_WEIGHT>0)
{
soft_maxdimz(tlist,vlist,nfac,nvert,NULL,nvert,INI_ZMAX,1.0,&zm,dzmdz);
zm*=INI_ZMAX_WEIGHT;
S[Zmaxregpos]=zm;
}
S[Convregpos]=CRres; //Convex reg terms
S[Octregpos]=Ores;
S[Angregpos]=ANGres;
matrix_transprod(S,Slength,1,&chisq2);
matrix_transprod(AOout,nAOtotal,1,&AOfit);
printf("Round: %d chisq2: %7.2f\n",k,chisq2);
if(fidlog!=NULL)
fprintf(fidlog,"Round: %d chisq2: %7.2f\n",k,chisq2);
if(chisq2<chisq)
{
prevdec=dec;
dec=chisq-chisq2;
count++;
printf("decreased!\n");
if(fidlog!=NULL)
fprintf(fidlog,"decreased!\n");
// write_matrix_file("/tmp/albedo_test.txt",eAlbedo,1,nfac);
memcpy(a,a2,sizeof(double)*(alength));
if(INI_HAVE_AO)
{
memcpy(AOoffset,AOoffset2,sizeof(double)*(nAOoffsets));
memcpy(ao_total_bright,INI_AO_TOTAL_BRIGHT,sizeof(double)*nAO);
if(INI_AO_SCALING)
memcpy(AOscale,AOscale2,sizeof(double)*nAO);
}
if(INI_HAVE_CNTR)
memcpy(CRoffset,CRoffset2,sizeof(double)*nCRoffsets);
if(INI_HAVE_OC)
{
memcpy(OCoffset,OCoffset2,sizeof(double)*(nOCoffsets));
if(INI_FREE_CHORD_NMR>0)
memcpy(Chordoffset,Chordoffset2,sizeof(double)*(nChordoffsets));
}
if(INI_PHASE_PARAMS!=NULL)
memcpy(params,params2,3*sizeof(double));
if(INI_HAVE_RD)
{
memcpy(RDoffset,RDoffset2,sizeof(double)*(nRDoffsets));
memcpy(RDscale,RDscale2,sizeof(double)*nRDscale);
RDexp=RDexp2;
}
decreased=1;
angles[0]=angles2[0];
angles[1]=angles2[1];
angles[2]=angles2[2];
if(INI_HAVE_LC && INI_FIT_ALBEDO==1)
memcpy(eAlbedo,eAlbedo2,sizeof(double)*nAlbedo);
lambda=lambda/INI_LAMBDADEC;
zero_array(J,Slength*nJcols);
zero_array(S,Slength);
sprintf(TEMP_OUT_SHAPE_FILE+TEMP_OUT_SHAPE_FILE_index,"%03d",k);
write_shape_file(TEMP_OUT_SHAPE_FILE,tlist,vlist2,nfac,nvert);
}
else
{
lambda=INI_LAMBDAINC*lambda;
decreased=0;