readBayesModels.c
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Created: Wed, Jan 15, 14:40

readBayesModels.c
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	#include<stdlib.h>
	#include<float.h>
	#include<string.h>
	#include<math.h>
	#include<fonction.h>
	#include<constant.h>
	#include<dimension.h>
	#include<structure.h>
	#include"lt.h"

	/****************************************************************/
	/* nom: readBayesModels */
	/* auteur: Eric Jullo */
	/* date: 07/08/06 */
	/* place: ESO, Chile *
	*
	* Read the bayes.dat file and return an array[nParam][val].
	* where nParam = [chi2 -> Last param]
	*
	* It also analyse the header of bayes.dat and set
	* the <G.no_lens>, <G.nlens>, <block>, <cblock> and <P.ircut>,
	* <P.isigma> global variables to their corresponding values.
	*
	* Return:
	* - the bayes.dat array and nParam and nVal the size of the array.
	* - 0 for nVal and nParam if bayes.dat cannot be read.
	*
	* Warning :
	* - Theta in <bayes.dat> is in degree but is converted to radian in <array>
	* - sigma in <bayes.dat> is in km/s but is converted according to the lens type
	* in <array>.
	*
	* Then, the user can generate an error mass map even if he doesn't perform
	* an optimisation.
	*/

	static double lhood_mode; // If 1, bayes.dat contains #ln(Lhood), otherwise 0

	static int analyseHeader( char *line );
	static double bayes2lt(long int ilens, int ipx, double val);
	static void convertArray(long int nVal, double **array );
	static double method(long int n, int param, double **array);
	static double *readBayesASCII(int nParam, long int *nVal);
	static double *readBayesFITS(int nParam, long int *nVal);
	static void reset_grad_multi();
	static void reset_grad_arclet();

	double *readBayesModels(int nParam, long int *nVal)
	{
	extern struct g_grille G;
	extern struct g_image I;
	extern struct g_pot P[NPOTFILE];
	extern struct g_source S;

	extern int block[][NPAMAX];
	extern int cblock[NPAMAX];
	extern int sblock[NFMAX][NPAMAX];
	extern struct sigposStr sigposAs;

	double **array;
	char line[LINESIZE];
	long int nLines;
	long int ilens;
	int i, ipx;

	// Initialize ouput variables
	*nParam = 0;
	*nVal = 0;

	//
	// REINITIALIZE ALL VARIABLES
	//

	// Get G.no_lens from bayes.dat
	// Reset G and block global variables
	G.no_lens = 0;
	for ( ilens = 0; ilens < G.nlens; ilens++)
	for ( ipx = CX; ipx <= PMASS; ipx ++)
	block[ilens][ipx] = 0;

	// Source parameters
	// for ( i = 0; i < S.ns; i++ )
	// for( ipx = SCX; ipx <= SFLUX; ipx++ )
	// sblock[i][ipx] = 0;

	// Reset the cblock global variables
	for ( ipx = OMEGAM; ipx <= WA; ipx++)
	cblock[ipx] = 0;

	// Reset the redshift I.nzlim
	// I.nzlim = 0;

	// Reset the potfile
	for( i = 0; i < G.npot; i++ )
	{
	P[i].ircut = 0;
	P[i].isigma = 0;
	P[i].islope = 0;
	P[i].ivdslope = 0;
	P[i].ivdscat = 0;
	P[i].ircutscat = 0;
	}

	// Reset the nuisance
	sigposAs.bk = 0;
	I.dsigell = -1.;

	// Read bayes.dat
	lhood_mode = 0;
	array = readBayesASCII(nParam, nVal);

	if ( array == NULL )
	return 0;

	// Convert <array> to values directly usable in lenstool
	convertArray(*nVal, array);

	return array;
	}

	static int imethod; // use a specified method as parameter estimator
	// -1 : mean value
	// -2 : median value
	// -3 : mode value
	// -4 : best chi2 value
	// -5 : to be used by o_rescale()

	// Reset the parameters of a potfile
	// Return 1 if the potfile parameters have been updated
	int setpotBayes(struct g_pot pot, int iParam_in, long int nVal, double **array)
	{
	int iParam = *iParam_in;
	int computePot = 0;

	if ( pot->ircut != 0 )
	{
	pot->cut = method(nVal, iParam++, array);
	computePot = 1;
	}
	if ( pot->isigma != 0 )
	{
	pot->sigma = method(nVal, iParam++, array);
	computePot = 1;
	}
	if ( pot->islope != 0 )
	{
	pot->slope = method(nVal, iParam++, array);
	computePot = 1;
	}
	if ( pot->ivdslope != 0 )
	{
	pot->vdslope = method(nVal, iParam++, array);
	computePot = 1;
	}
	if ( pot->ivdscat != 0 )
	{
	pot->vdscat = method(nVal, iParam++, array);
	computePot = 1;
	}
	if ( pot->ircutscat != 0 )
	{
	pot->rcutscat = method(nVal, iParam++, array);
	computePot = 1;
	}
	if ( pot->ia != 0 )
	{
	pot->a = method(nVal, iParam++, array);
	computePot = 1;
	}
	if ( pot->ib != 0 )
	{
	pot->b = method(nVal, iParam++, array);
	computePot = 1;
	}

	*iParam_in = iParam;
	return computePot;
	}

	/* Set all the lenstool parameters to the values contained in the
	* bayes.dat file at line iVal.
	* If iVal < 0 then iVal specifies the method corresponding to the imethod index.
	*/
	void setBayesModel( long int iVal, long int nVal, double **array)
	{
	extern struct g_mode M;
	extern struct g_grille G;
	extern struct g_cosmo C;
	extern struct g_image I;
	extern struct g_pot P[NPOTFILE];

	extern struct galaxie multi[NFMAX][NIMAX];
	extern struct galaxie arclet[NAMAX];
	extern struct z_lim zlim[];
	extern struct z_lim zalim;
	extern struct cline cl[];
	extern struct pot lens[];
	extern int block[][NPAMAX];
	extern int cblock[NPAMAX];
	extern int vfblock[NPAMAX];
	extern struct sigposStr sigposAs;
	extern double *np_b0;
	extern long int narclet;

	int computedr_m, computedr_a, computePot[NPOTFILE]; // flags
	int nimages;
	char limages[ZMBOUND][IDSIZE];
	double tmp;
	double dl0s, dos;
	long int ilens, i;
	int iParam, ipx;
	int j, k, l;

	imethod = iVal;
	if ( imethod == -5 )
	iParam = 0; // assign cube[0][iParam] to the model parameters
	else
	iParam = IDPARAM1;

	computedr_m = computedr_a = 0; // do not recompute dlsds ratio for multiple images
	for( i = 0; i < G.npot; i++ )
	computePot[i] = 0; // potfile parameters are not modified

	for ( ilens = 0; ilens < G.no_lens; ilens++ )
	{
	for ( ipx = CX; ipx <= PMASS; ipx++ )
	if ( block[ilens][ipx] != 0 )
	o_set_lens( ilens, ipx, method(nVal, iParam++, array) );

	// TODO in o_set_lens() assign sigma directly to lens.sigma rather than lens.b0
	if ( block[ilens][B0] != 0 )
	lens[ilens].sigma = lens[ilens].b0;

	if ( block[ilens][ZLENS] != 0 )
	computedr_m = computedr_a = 1;

	set_dynamics(ilens);
	}

	// Compute b0 from msgrid potentials either from sigma or rhos random values
	// if ( G.nmsgrid < G.nlens )
	// {
	// if ( block[G.nmsgrid][B0] != 0 )
	// for ( ilens = G.nmsgrid; ilens < G.nlens; ilens++ )
	// {
	// tmp = method(nVal, iParam++, array);
	// tmp = 6.pia_c2 tmp * tmp;
	// np_b0[ilens-G.nmsgrid] = tmp;
	// lens[ilens].b0 = tmp;
	// }
	// else
	// {
	// double atmp = (double ) malloc((G.nlens - G.nmsgrid ) * sizeof(double));
	// for ( ilens = G.nmsgrid; ilens < G.nlens; ilens++ )
	// atmp[ilens - G.nmsgrid] = method(nVal, iParam++, array);
	//
	// setgrid_rhos2b0(atmp);
	// free(atmp);
	// }
	// }
	for ( ilens = G.nmsgrid; ilens < G.nlens; ilens++ )
	np_b0[ilens - G.nmsgrid] = lens[ilens].b0 = method(nVal, iParam++, array);

	// Set Multiscale grid SL source positions
	if ( G.nmsgrid != G.nlens && I.n_mult != 0)
	{
	extern struct galaxie source[NFMAX];
	for ( i = 0; i < I.n_mult; i++ )
	source[i].C.x = method(nVal, iParam++, array);

	for ( i = 0; i < I.n_mult; i++ )
	source[i].C.y = method(nVal, iParam++, array);
	}

	// set the source positions
	if( M.iclean == 2 )
	{
	extern struct g_source S;
	extern struct galaxie source[NFMAX];
	extern int sblock[NFMAX][NPAMAX];
	char str[IDSIZE], *pch;

	for ( i = 0; i < S.ns; i++ )
	{
	// if source is attached to an image, reset its coordinates
	strcpy(str, source[i].n);
	pch = strtok(str, "_");
	pch = strtok(NULL, "_");
	if( pch != NULL )
	source[i].C.x = source[i].C.y = 0.;

	for( ipx = SCX ; ipx <= SFLUX; ipx++ )
	if( sblock[i][ipx] != 0 )
	o_set_source( &source[i], ipx, method(nVal, iParam++, array));

	if( sblock[i][SEPS] != 0 )
	source[i].E.b = source[i].E.a * (1. - source[i].eps) / (1. + source[i].eps);
	}
	}

	// Set the cosmological parameters
	for ( ipx = OMEGAM; ipx <= WA; ipx++ )
	if ( cblock[ipx] != 0 )
	{
	o_set_lens( 0, ipx, method(nVal, iParam++, array) );
	computedr_m = computedr_a = 1;
	}

	// Set the optimized redshifts to the corresponding images
	for ( i = 0 ; i < I.nzlim; i++ )
	if ( zlim[i].bk != 0 )
	{
	tmp = method(nVal, iParam++, array);
	nimages = splitzmlimit(zlim[i].n, limages);
	// for all the families in zlim[ipx].n
	for ( j = 0; j < nimages; j++ )
	{
	if( ! strncmp(limages[j], "cl", 2) )
	{
	// loop over the critical lines
	int zmid;
	sscanf(limages[j], "cl%d", &zmid);
	cl[zmid].z = tmp;
	}
	else
	{
	// loop over the images families
	k = 0;
	while ( indexCmp( multi[k][0].n, limages[j] ) && k < I.n_mult ) k++;
	// set the reshift of all the images of the family
	for ( l = 0; l < I.mult[k]; l++ )
	multi[k][l].z = tmp;
	}
	}

	computedr_m = 1;
	}

	// Set the optimized redshifts of the arclets with unknown redshift
	if ( zalim.bk != 0 )
	{
	I.zarclet = method(nVal, iParam++, array);
	for( j = 0; j < zalim.opt; j++ )
	arclet[j].z = I.zarclet;

	computedr_a = 1;
	}

	// Set the velocity field parameters
	for ( ipx = VFCX; ipx <= VFSIGMA; ipx++ )
	if ( vfblock[ipx] != 0 )
	{
	o_set_lens( 0, ipx, method(nVal, iParam++, array) );
	}

	//rescale the pot parameters
	for( i = 0; i < G.npot; i++ )
	if (P[i].ftype != 0 )
	computePot[i] = setpotBayes(&P[i], &iParam, nVal, array);

	//set the nuisance parameters
	if ( sigposAs.bk != 0. )
	{
	for ( i = 0; i < I.n_mult; i++ )
	for ( j = 0; j < I.mult[i]; j++ )
	{
	tmp = method(nVal, iParam++, array);
	I.sig2pos[i][j] = tmp * tmp;
	}
	}

	if ( I.dsigell != -1. )
	{
	I.sigell = method(nVal, iParam++, array);
	I.sig2ell = I.sigell * I.sigell;
	}

	// recompute the dlsds ratios if necessary
	if ( computedr_a && computedr_m )
	{
	if ( C.kcourb == 0. )
	C.omegaX = 1 - C.omegaM;
	else
	C.kcourb = C.omegaM + C.omegaX - 1;

	// ...same for the critical line dlsds
	for ( i = 0 ; i < I.npcl; i++ )
	{
	if ( lens[0].z < cl[i].z )
	cl[i].dl0s = distcosmo2(lens[0].z, cl[i].z);
	else
	cl[i].dl0s = 0.;
	cl[i].dos = distcosmo1(cl[i].z);
	cl[i].dlsds = cl[i].dl0s / cl[i].dos;
	}
	}

	if ( computedr_m )
	{
	// set the DLS/DS ratio for all the images according
	// to the new cosmological parameters
	for ( i = 0 ; i < I.n_mult; i++ )
	for ( j = 0; j < I.mult[i]; j++ )
	{
	dos = distcosmo1(multi[i][0].z);

	if ( lens[0].z < multi[i][0].z )
	dl0s = distcosmo2(lens[0].z, multi[i][0].z);
	else
	dl0s = 0.;

	for ( j = 0 ; j < I.mult[i]; j++ )
	{
	multi[i][j].dos = dos;
	multi[i][j].dl0s = dl0s;
	multi[i][j].dr = dl0s / dos;
	}
	}
	}

	//...the same for the arclets
	if( computedr_a )
	{
	//... arclets with optimized redshifts
	if( zalim.bk != 0 )
	{
	dos = distcosmo1(I.zarclet);
	if ( lens[0].z < I.zarclet )
	dl0s = distcosmo2(lens[0].z, I.zarclet);
	else
	dl0s = 0.;

	for ( i = 0 ; i < zalim.opt; i++ )
	{
	arclet[i].dos = dos;
	arclet[i].dl0s = dl0s;
	arclet[i].dr = dl0s / dos;
	}
	}

	// ... the rest of the arclets
	if( computedr_m )
	for( i = zalim.opt; i < narclet; i++ )
	dratio_gal(&arclet[i], lens[0].z);
	}

	// recompute the potfile if necessary
	for( i = 0; i < G.npot; i++ )
	if ( computePot[i] )
	{
	scale_pot(&P[i]);
	computedr_a = computedr_m = 1;
	}

	// Reset the image->grad and image->grad2 accelerators
	if( computedr_m )
	reset_grad_multi();

	if( computedr_a )
	reset_grad_arclet();
	}

	// Read the header of bayes.dat and call analyseHeader()
	// to process each line
	static double ** readBayesASCII(int nParam, long int nVal)
	{
	extern struct g_grille G;
	long int nLines;
	FILE *bayes;
	int error;
	char line[LINESIZE];
	char *pch; // token to split a line
	double **array;
	int j;

	// Read bayes.dat
	#ifdef DEBUG
	bayes = fopen( "bayes.dbg.dat", "r");
	#else
	bayes = fopen( "bayes.dat" , "r" );
	#endif

	if ( bayes == NULL )
	{
	//fprintf(stderr, "WARNING: Reading bayes.dat. No such file found.\n");
	return 0;
	}

	// Read header
	error = 0;
	nLines = wc(bayes);
	fgets( line, LINESIZE, bayes);
	line[strlen(line)-1] = '\0'; // replace ending \n by \0
	while ( !feof(bayes) && !ferror(bayes) && line[0] == '#' && !error )
	{
	(*nParam)++;
	error = analyseHeader( line );
	fgets( line, LINESIZE, bayes);
	line[strlen(line)-1] = '\0';
	}

	// Deal with error code
	if ( error )
	{
	fclose(bayes);
	return 0;
	}

	// Reinitialise G.no_lens in case part of the clumps are accelerated
	if ( G.no_lens > G.nmsgrid )
	G.no_lens = G.nmsgrid;

	// Initialize array
	nParam = (nParam) - 1; //because Nsample is excluded from array
	array = alloc_square_double( nParam , nLines - (nParam) - 1);

	// Read the data (first line comes from header analysis)
	nLines = *nParam + 1;
	while ( !feof(bayes) && !ferror(bayes) )
	{
	// Test for line too long
	if ( strlen(line) + 1 == LINESIZE )
	{
	fprintf(stderr, "ERROR: while reading bayes.dat line %ld. Increase LINESIZE(current value is=%d) to match the line size in bayes.dat.\n", nLines, LINESIZE);
	exit(1);
	}

	// Skip the fist column and read the 2nd one
	pch = strtok( line, " " );

	// Fill array[][*nVal]
	j = 0;
	while ( j < *nParam && pch != NULL )
	{
	pch = strtok (NULL, " ");
	if ( pch != NULL )
	{
	int lnval;
	double val;
	if( sscanf( pch, "%dx%lf", &lnval, &val ) == 2 )
	{
	long int i;
	for ( i = 0; i < lnval; i++ )
	array[j++][*nVal] = val;
	}
	else if( sscanf( pch, "%lf", &array[j++][*nVal] ) != 1 )
	{
	fprintf( stderr, "ERROR: while reading bayes.dat line %ld, column %d. pch = %s\n", *nVal, j + 1, pch);
	pch = NULL;
	*nVal -= 1;
	}
	}
	}
	// normal exit: (j == *nParam && pch != NULL) \|\| pch == NULL (it points on the last element)

	if( j < *nParam ) // if true pch != NULL
	{
	fprintf( stderr, "ERROR: while reading bayes.dat line %ld, not enough parameters (%d/%d).\n", nLines, j+1, *nParam+1);
	*nVal -= 1;
	}

	fgets(line, LINESIZE, bayes);
	line[strlen(line)-1] = '\0';

	nLines ++;

	(*nVal) ++;
	}
	fprintf( stderr, "INFO: %ld good lines found in bayes.dat\n", *nVal);

	// Catch errors
	if ( ferror(bayes) \|\| ( feof(bayes) && *nVal == 0 ) )
	{
	// fprintf( stderr, "WARNING : reading bayes.dat\n" );
	nVal = nParam = 0;
	fclose(bayes);
	return array;
	}
	fclose(bayes);

	return array;

	}

	// Read the header of bayes.fits and call analyseHeader()
	// to process each line
	static double ** readBayesFITS(int nParam, long int nVal)
	{
	}

	/* Analyse a line of the bayes.dat header and eventually
	* In the case of reading a best.par file, reset the
	* <G.no_lens>, <block>, <cblock>, <zlim> and <P.ircut>, <P.isigma>
	* global variables as if they were optimized
	*/
	static int analyseHeader( char *line )
	{
	extern struct g_grille G;
	extern struct g_image I;

	extern struct pot lens[];
	extern struct z_lim zlim[];
	extern int block[][NPAMAX];
	extern int cblock[NPAMAX];
	extern struct sigposStr sigposAs;

	long int i;
	int ipx;
	char pch, pch2, name[50];
	int updated; // flag to prevent the case when the clump is already set as optimised

	// skip the '#'
	line = line + 1;

	if ( !strcmp(line, "Nsample") \|\|
	!strcmp(line, "Evidence") \|\|
	!strcmp(line, "Chi2") )
	return 0; // not an error

	if ( !strcmp(line, "ln(Lhood)") )
	{
	lhood_mode = 1;
	return 0; // not an error
	}


	// Get the first word
	pch = strtok( line, " " );

	// Skip the "O" if it exists in the <bayes.dat> file... <pch> in bayes.dat
	// "O" means a lens[] element
	if ( pch[0] == 'O' )
	{
	pch++;

	// Look for the right lens to change
	updated = 0;
	for ( i = 0; i < G.nlens && updated == 0 ; i++ )
	{
	// ... and in Lenstool... <pch2> in Lenstool
	pch2 = lens[i].n;
	if ( pch2[0] == 'O' )
	pch2++;

	if ( !strcmp( pch, pch2 ) )
	{
	pch = strtok( NULL, " " ); // skip the ':'
	pch = strtok( NULL, " " );
	// Look for the right parameter to change
	for ( ipx = CX; ipx <= PMASS; ipx++ )
	{
	pch2 = strtok( getParName(ipx, name, lens[i].type), " "); // remove the unit if any
	if ( !strcmp( pch, pch2) && block[i][ipx] == 0 )
	block[i][ipx] = 1;
	}
	// Prevent the case when the clump is already set as optimised
	for ( ipx = CX; ipx <= PMASS; ipx++ )
	updated += block[i][ipx];

	// Increment G.no_lens only once per clump
	if ( updated == 1 )
	{
	G.no_lens ++;
	}
	else if ( updated == 0 )
	{
	fprintf( stderr, "ERROR: bayes.dat header format unrecognised\n");
	exit(-1);
	}
	}
	}
	}

	// Look for a source parameter
	// TODO: Not finished. Find a way to check the number of sources
	if ( !strcmp(pch, "src") )
	{
	extern struct g_source S;
	extern struct galaxie source[NFMAX];
	pch = strtok( NULL, " " );
	i = 0;
	while( strcmp(pch, source[i].n) && i < S.ns ) i++;

	if ( i == S.ns && strcmp(pch, source[i - 1].n) )
	{
	fprintf(stderr, "ERROR: number of sources in lenstool (%ld) and found in bayes.dat mismatch\n", S.ns);
	exit(-1);
	}
	}

	// Look for cosmological parameters
	if ( !strcmp(pch, "omegaM") )
	cblock[OMEGAM] = 1;
	if ( !strcmp(pch, "omegaX") )
	cblock[OMEGAX] = 1;
	if ( !strcmp(pch, "wX") )
	cblock[WX] = 1;
	if ( !strcmp(pch, "wa") )
	cblock[WA] = 1;

	// Look for the redshifts
	// THIS HAS TO BE DEFINED IN THE .PAR FILE
	// if ( !strcmp(pch, "Redshift") )
	// {
	// pch = strtok( NULL, " " ); // pch contains 'of'
	// pch += 3; // pch points on the last part of line
	// strcpy(zlim[I.nzlim].n, pch);
	// // Append an image to optimize
	// zlim[I.nzlim].opt = 1;
	// COMMENTED EJ20100306 : trust .par input file
	// I.nzlim++;
	// }

	// Look for the Potfile keyword "Pot" or "Pot1" or "Pot2" etc...
	int ipot = 0;
	if ( !strcmp(pch, "Pot") \|\| sscanf(pch, "Pot%d", &ipot) == 1 )
	{
	extern struct g_pot P[NPOTFILE];
	struct g_pot *pot = &P[ipot]; // default with P[0]

	// if ( pot->core == -1 )
	// {
	// fprintf( stderr, "WARNING : Potfile parameters in bayes.dat not found in parfile.\n");
	// return 1;
	// }
	pch = strtok( NULL, " " ); // pch contains rcut or sigma
	if ( !strcmp(pch, "rcut") )
	pot->ircut = 1;
	if ( !strcmp(pch, "sigma") )
	pot->isigma = 1;
	if ( !strcmp(pch, "rcut_slope") \|\| !strcmp(pch, "m200slope") )
	pot->islope = 1;
	if ( !strcmp(pch, "sigma_slope") \|\| !strcmp(pch, "c200slope") )
	pot->ivdslope = 1;
	if ( !strcmp(pch, "vdscatter") )
	pot->ivdscat = 1;
	if ( !strcmp(pch, "rcutscatter") )
	pot->ircutscat = 1;
	if ( !strcmp(pch, "a") \|\| !strcmp(pch, "m200") )
	pot->ia = 1;
	if ( !strcmp(pch, "b") \|\| !strcmp(pch, "c200") )
	pot->ib = 1;
	}

	// Look for the nuisance
	if ( !strcmp(pch, "SigposArcsec") )
	sigposAs.bk = 1; // this is not the correct sigma but it doesn't matter
	// since the values are written in the bayes.dat file

	if ( !strcmp(pch, "Sigell") )
	I.dsigell = 1.;

	return 0;
	}

	/* Convert input <bayes.dat> values to the corresponding values readily usable
	* in lenstool.
	*/
	static double bayes2lt(long int i, int ipx, double val)
	{
	extern struct g_cosmo C;
	extern struct pot lens[];

	switch (ipx)
	{
	case(THETA):
	val *= DTR;
	break;
	case(B0):
	if ( lens[i].type == 13 )
	val *= 1e8;
	break;
	/* now it is in solar mass in bayes.dat also
	case(PMASS):
	if( lens[i].type == 12 )
	val *= 1e14; // rhos in 10^14 Msol -> Msol
	break;
	case(MASSE):
	if( lens[i].type == 12 )
	val *= 1e14; // masse in 10^14 Msol -> Msol
	break;
	*/
	default:
	break;
	}

	return val;
	}

	static void convertArray(long int nVal, double **array )
	{
	extern struct g_mode M;
	extern struct g_grille G;
	extern struct g_source S;
	extern int sblock[NFMAX][NPAMAX];
	extern int block[][NPAMAX];

	long int iVal, i;
	int nParam, ipx;

	for ( iVal = 0; iVal < nVal; iVal++ )
	{
	nParam = IDPARAM1; // position of the first parameter in array
	// 1st column in array is chi2
	if ( lhood_mode ) array[0][iVal] *= -1.; // so that the best lhood has the lowest value
	// ie same behavior as chi2

	// Optimized clumps
	for ( i = 0; i < G.no_lens; i++ )
	for ( ipx = CX; ipx <= PMASS; ipx++ )
	if ( block[i][ipx] != 0 )
	{
	array[nParam][iVal] = bayes2lt( i, ipx, array[nParam][iVal] );
	nParam++;
	}

	// Grid clumps
	for ( i = G.nmsgrid; i < G.nlens; i++ )
	nParam++;

	// Sourcelimit parameters
	if( M.iclean == 2 )
	for ( i = 0; i < S.ns; i++ )
	for( ipx = SCX; ipx <= SFLUX; ipx ++ )
	if( sblock[i][ipx] != 0 )
	{
	if( ipx == STHETA )
	array[nParam][iVal] = array[nParam][iVal] * DTR;

	nParam ++;
	}
	}
	}

	/* Return the value in <list> that has produced the best chi2*/
	static double bestchi2(long int n, double chi2, double list)
	{
	double chi2min;
	long int i, imin;

	imin = 0;
	chi2min = DBL_MAX;

	for ( i = 0; i < n; i++)
	if ( chi2[i] < chi2min )
	{
	chi2min = chi2[i];
	imin = i;
	}

	return( list[imin] );
	}

	/* Return an estimated value of the values in <array> depending
	* on the value of the <imethod> value.
	* <imethod> may also be a line number in array[param].
	* n is the number of elements in array[param].
	*/
	static double method(long int n, int param, double **array)
	{
	double val;

	switch ( imethod )
	{
	case(-1):
	val = mean(n, array[param]);
	break;
	case(-2):
	val = median(n, array[param]);
	break;
	case(-3):
	val = mode(n, array[param]);
	break;
	case(-4):
	val = bestchi2(n, array[0], array[param]);
	break;
	case(-5): // o_rescale Atoms, with n parameters per atom
	val = array[0][param];
	break;
	default:
	val = array[param][imethod];
	break;
	}

	return val;
	}

	/*
	* reset the multi.grad(2) parameters for the optimisation.
	*/
	static void reset_grad_multi()
	{
	extern struct g_image I;
	extern struct galaxie multi[][NIMAX];

	long int i;
	int k;

	// reset the grad and grad2 arclet temporary structure for optimisation
	for ( i = 0; i < I.n_mult; i++ )
	for ( k = 0; k < I.mult[i]; k++ )
	{
	multi[i][k].grad2.a = 0;
	multi[i][k].grad2.c = 0;
	multi[i][k].grad.x = 0;
	multi[i][k].grad.y = 0;
	}
	}

	/*
	* reset the arclet.grad(2) parameters for the optimisation.
	*/
	static void reset_grad_arclet()
	{
	extern struct galaxie arclet[NAMAX];
	extern long int narclet;

	long int i;

	// reset the grad and grad2 arclet temporary structure for optimisation
	for ( i = 0 ; i < narclet ; i++ )
	{
	arclet[i].grad2.a = arclet[i].grad2.c = 0;
	arclet[i].grad.x = arclet[i].grad.y = 0;
	}
	}

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