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bayesapp.c
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//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Bayesian Inference
//
// Filename: bayesapp.c
//
// Purpose: Test operation of BayeSys with
// UserEmpty,UserTry1,UserTry2,UserInsert1,UserInsert2,UserDelete1.
//=============================================================================
//
// BayeSys3 can operate with arbitrary likelihood functions.
// In this example, an atom has 2 coordinates interpreted as
// location in [0,1] = Cube[0] (restricted to [0.0.75])
// and
// flux in [0,infinity) = -10.0*log(Cube[1])
// to correspond with testing the operation of MassInf with FluxUnit0=10
//
// These are only example programs, involving inefficient calculations that
// repeatedly build an object from scratch with "UserBuild" instructions.
//
//=============================================================================
// History: JS 2 Jan 2002, 4 Jan 2003, 10 Feb 2003, 20 Aug 2003
// Copyright (c) 2002,2003 Maximum Entropy Data Consultants Ltd.
//-----------------------------------------------------------------------------
#include <stdio.h>
#include <string.h>
#include <float.h>
#include <stdlib.h>
#include <math.h>
#include <time.h>
#include "bayesys3.h"
#include "userstr.h"
#include "dimension.h"
#include "structure.h"
#include "fonction.h"
#include "constant.h"
#include "lt.h"
static int minusone; // count chi2 errors in image plane
static double nchi2; // count number of computed chi2
static time_t start, end; // computation time
static int UserBuild(double*, CommonStr*, ObjectStr*, int, int);
#define POTENTIAL 0
struct matrix e_grad2_pot_ptr(const struct point *pi, const struct pot *ilens);
//=============================================================================
// MANAGE THE THREAD SAFE ACCESS TO nchi2
//=============================================================================
#include <pthread.h>
static pthread_mutex_t mp = PTHREAD_MUTEX_INITIALIZER;
void init_mutex()
{
int ret = pthread_mutex_init(&mp, NULL);
if( ret != 0 )
{
fprintf(stderr, "ERROR initilializing mutex in bayesapp.c\n");
exit(1);
}
}
void destroy_mutex()
{
int ret = pthread_mutex_destroy(&mp);
if( ret != 0 )
{
fprintf(stderr, "ERROR destroying mutex in bayesapp.c\n");
exit(1);
}
}
void increase_nchi2()
{
int ret = pthread_mutex_lock(&mp);
nchi2 = nchi2 + 1;
pthread_mutex_unlock(&mp);
}
//=============================================================================
// SIMPLE CODE
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: UserEmpty
//
// Purpose: Set Lhood = logLikelihood(coords) for empty sample
// with 0 atoms in Object, and initialise its other information.
//
// Lhood := log L(empty)
//
// I have already put the number 0 in Object->Natoms,
// so you can use a simple "UserBuild" instruction.
//-----------------------------------------------------------------------------
//
int UserEmpty( // O >=0, or -ve error code
double* Lhood, // O loglikelihood
CommonStr* Common, // I O general information
ObjectStr* Object) // I O sample object, output new Lhood
{
UserBuild(Lhood, Common, Object, 0, 1);
if( Common->Valency )
*Lhood = 0.; // Empty value is set afterwards by FluxEmpty with Mock[]=0
return 1;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: UserTry1
//
// Purpose: d(logLikelihood(coords)) after supposedly adding one new atom
// to Object, without any side effects on it.
//
// If Valency = 0,
// dLtry := d logL(...,x)
// else mimic the above with cool
// dLtry := (1/cool) log INTEGRAL dPrior(z) dlogL(...,x,z)
//
// I have already put the new atom x after the last location
// of the Atoms list, at Object->Cubes[ Object->Natoms ], so
// if Valency=0 you can use simple "UserBuild" instructions.
//-----------------------------------------------------------------------------
//
// External definition
int rescaleParam(int id, int type, int ipx, double *pval);
int UserTry1( // O +ve = OK, 0 = DO NOT USE, -ve = error
double* dLtry, // O trial d(logLikelihood) value
CommonStr* Common, // I general information
ObjectStr* Object) // I sample object (DO NOT UPDATE Lhood)
{
int Natoms = Object->Natoms;
double Lhood = Object->Lhood; // existing Lhood
double Ltry;
int OK;
extern struct g_grille G;
*dLtry = 0.0;
OK = 1;
OK = UserBuild(&Ltry, Common, Object, Natoms + 1, 0); // trial
if ( OK > 0 )
*dLtry = Ltry - Lhood; // increment
return OK; // OK?
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: UserTry2
//
// Purpose: d(logLikelihood(coords)) after supposedly adding one,
// then two new atoms to Object, without any side effects on it.
//
// If Valency = 0,
// dLtry1 := d logL(...,x1)
//
// dLtry2 := d logL(...,x1,x2)
//
// else mimic the above with cool
// dLtry1 := (1/cool) log INTEGRAL dPrior(z1) dlogL(...,x1,z1)
// cool
// dLtry2 := (1/cool) log INTEGRAL dPrior(z1,z2) dlogL(...,x1,z1,x2,z2)
//
// I have already put the new atoms x1,x2 after the last location
// of the Atoms list, at Object->Cubes[ Object->Natoms ] and
// at Object->Cubes[ Object->Natoms + 1 ]
// so if Valency=0 you can use simple "UserBuild" instructions.
//-----------------------------------------------------------------------------
//
int UserTry2( // O +ve = OK, 0 = DO NOT USE, -ve = error
double* dLtry1, // O trial d(logLikelihood) value for 1st atom
double* dLtry2, // O trial d(logLikelihood) value for both atoms
CommonStr* Common, // I general information
ObjectStr* Object) // I sample object (DO NOT UPDATE Lhood)
{
int Natoms = Object->Natoms;
double Lhood = Object->Lhood; // existing Lhood
double Ltry1, Ltry2;
int OK;
extern struct g_grille G;
*dLtry1 = *dLtry2 = 0.0;
OK = 1;
OK = UserBuild(&Ltry1, Common, Object, Natoms + 1, 0); //trial for 1 more
if ( OK > 0 )
{
*dLtry1 = Ltry1 - Lhood; // increment for 1
OK = UserBuild(&Ltry2, Common, Object, Natoms + 2, 0); //trial for 2 more
if ( OK > 0 )
*dLtry2 = Ltry2 - Lhood; // increment for 2
}
return OK; // return OK only if both trials OK
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: UserInsert1
//
// Purpose: Insert 1 new atom into Object, keeping it up-to-date, and
// set d(loglikelihood(coords)).
//
// If Valency = 0,
// dL := d logL(...,x)
//
// else
// cool
// sample z from Prior(z) L(...,x,z)
//
// and set dL := d logL(...,x,z) at the sampled z.
//
// I have already put the new atom x at the last location of
// the updated Atoms list, at Object->Cubes[ Object->Natoms - 1 ],
//-----------------------------------------------------------------------------
//
int UserInsert1( // O >=0, or -ve error code
double* dL, // O d(loglikelihood)
CommonStr* Common, // I general information
ObjectStr* Object) // I O sample object
{
int Natoms = Object->Natoms; // new number
double Lold = Object->Lhood; // not yet updated
double Lnew;
extern struct g_grille G;
UserBuild(&Lnew, Common, Object, Natoms, 1); // new updated state
*dL = Lnew - Lold; // I will update Object->Lhood
return 1;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: UserInsert2
//
// Purpose: Insert 2 new atoms into Object, keeping it up-to-date, and
// set d(loglikelihood(fluxes)).
//
// If Valency = 0,
// dL := d logL(...,x1,x2)
//
// else
// cool
// sample z1,z2 from Prior(z1,z2) L(...,x1,z1,x2,z2)
//
// and set dL := d logL(...,x1,z1,x2,z2) at the sampled z1,z2.
//
// I have already put the new atoms x1,x2 at the last location
// of the Atoms list, at Object->Cubes[ Object->Natoms - 2 ] and
// at Object->Cubes[ Object->Natoms - 1 ]
// so if Valency=0 you can use a simple "UserBuild" instruction.
//-----------------------------------------------------------------------------
//
int UserInsert2( // O >=0, or -ve error code
double* dL, // O d(loglikelihood)
CommonStr* Common, // I general information
ObjectStr* Object) // I O sample object
{
int Natoms = Object->Natoms; // new number
double Lold = Object->Lhood; // not yet updated
double Lnew;
extern struct g_grille G;
UserBuild(&Lnew, Common, Object, Natoms, 1); // new updated state
*dL = Lnew - Lold; // I will update Object->Lhood
return 1;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: UserDelete1
//
// Purpose: Delete 1 old atom from Object, keeping it up-to-date, and
// set d(loglikelihood(fluxes)).
//
// dL := d logL(...)
//
// I have already put the old atom after the last location of
// the updated Atoms list, at Object->Cubes[ Object->Natoms ],
// so if Valency=0 you can use a simple "UserBuild" instruction.
//-----------------------------------------------------------------------------
//
int UserDelete1( // O >=0, or -ve error code
double* dL, // O d(loglikelihood)
CommonStr* Common, // I general information
ObjectStr* Object) // I O sample object
{
int Natoms = Object->Natoms; // new number
double Lold = Object->Lhood; // not yet updated
double Lnew;
extern struct g_grille G;
UserBuild(&Lnew, Common, Object, Natoms, 1); // new updated state
*dL = Lnew - Lold; // I will update Object->Lhood
return 1;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: UserBuild
//
// Purpose: Build Lhood, and any other data info such as Mock from scratch.
// Can be called with any number of atoms
//
// This example implementation has
// Mock[0] = SUM[atoms] flux , flux = - 10*log(Cube[1])
// Mock[1] = SUM[atoms] flux * location , location = Cube[0]
//-----------------------------------------------------------------------------
//
void o_set_lens_ptr(struct pot *ilens, int ipx, double x);
static int UserBuild( // O +ve = OK, 0 = DO NOT USE, -ve = error
double* Lhood, // O loglikelihood
CommonStr* Common, // I General information
ObjectStr* Object, // I(O) Cubes in, perhaps Mock out
int Natoms, // I # atoms
int output) // I +ve if Mock to be written out, -ve if not
{
// MassInf optimization
if( Common->Valency )
{
// Weak-Lensing is done in UserFoot() under the linear approximation
*Lhood = Object->Lhood;
return 1;
// Compute the likelihood for the SL
extern struct g_grille G;
double *np_b0 = (double *)calloc(G.nlens - G.nmsgrid, sizeof(double));
long int ilens;
int k, i, error;
double **Cubes = Object->Cubes;
double C, Lnorm;
UserCommonStr *UserCommon = (UserCommonStr *) Common->UserCommon;
struct point vB[NFMAX];
extern struct g_image I;
extern struct galaxie multi[NFMAX][NIMAX];
int j;
for( i = 0; i < I.n_mult; i++ )
{
vB[i].x = vB[i].y = 0.;
for( j = 0; j < I.mult[i]; j++ )
{
vB[i].x += multi[i][j].C.x;
vB[i].y += multi[i][j].C.y;
}
}
for( k = 0; k < Natoms; k++ )
{
ilens = (int)((G.nlens - G.nmsgrid) * Cubes[k][Common->Ndim - 1]);
np_b0[ilens] += Cubes[k][Common->Ndim];
for( i = 0; i < I.n_mult; i++ )
for( j = 0; j < I.mult[i]; j++ )
{
vB[i].x -= Cubes[k][Common->Ndim] * multi[i][j].np_grad[ilens].x;
vB[i].y -= Cubes[k][Common->Ndim] * multi[i][j].np_grad[ilens].y;
}
}
double *Mock = Object->Mock;
int nimage = 0;
int nmult = Common->Ndata / 2;
for( i = 0; i < I.n_mult; i++ )
for( j = 0; j < I.mult[i]; j++ )
{
Mock[G.nlens - G.nmsgrid + nimage] = vB[i].x / I.mult[i];
Mock[G.nlens - G.nmsgrid + nimage + nmult] = vB[i].y / I.mult[i];
nimage++;
}
free(np_b0);
increase_nchi2();
return 1;
// Compute Likelihood
UserCommon->Nchi2++;
C = 0.; Lnorm = 0.;
error = o_chi_lhood0(&C, &Lnorm, np_b0);
*Lhood = -0.5 * (C + Lnorm);
// Track NaN errors
if ( *Lhood != *Lhood )
{
fprintf(stderr, "ERROR: Lhood=NaN found in bayesapp.c:UserBuild(). Dump cube...\n");
for ( i = 0; i < Common->Ndim; i++ )
fprintf(stderr, "%lf ", np_b0[i]);
fprintf(stderr,"\n");
exit(2);
}
free(np_b0);
increase_nchi2();
if ( error )
{
minusone++;
return 0;
}
return 1;
}
//----------------------------------------------------------------------
// Case with WL only but with moving clumps (Common->Valency == 0)
// Copy lens[G.nmsgrid], Natoms times
//----------------------------------------------------------------------
extern struct g_image I;
extern struct g_grille G;
double** Cubes = Object->Cubes; // I Cubes in [0,1) [Natoms][Ndim]
if( I.stat == 8 && G.nmsgrid != G.nlens )
{
const double Sqrt2Pi = 2.50662827463100050240;
extern struct pot lens[];
extern int block[][NPAMAX];
extern long int narclet;
extern struct galaxie arclet[];
extern double* tmpCube;
UserCommonStr* UserCommon = (UserCommonStr*)Common->UserCommon;
int Ndata = Common->Ndata; // I # data
double* Data = Common->Data; // I Data [Ndata]
double* Acc = Common->Acc; // I Accuracies [Ndata]
int nDim = Common->Ndim;
struct pot mylens = lens[0]; // rough copy, but sufficient
struct matrix grad2;
long int ilens, k;
int ipx, i;
int valid = 1;
*Lhood = 0.;
// Create Mock data
double *Mock = (double *) calloc(Ndata, sizeof(double));
for( i = 0; i < Natoms; i ++ )
{
int iparam = 0;
memcpy(tmpCube, Cubes[i], (unsigned int)(Common->Ndim * sizeof(double)));
for ( ipx = CX; ipx <= PMASS; ipx++ )
if ( block[G.nmsgrid][ipx] != 0 )
{
valid *= rescaleParam(G.nmsgrid, POTENTIAL, ipx, &tmpCube[iparam]);
o_set_lens_ptr(&mylens, ipx, tmpCube[iparam]);
iparam ++;
}
if( block[G.nmsgrid][B0] != 0 )
{
mylens.sigma = mylens.b0;
mylens.b0 = 6.*pia_c2 * mylens.sigma * mylens.sigma;
}
for( k = 0; k < narclet; k++ )
{
grad2 = e_grad2_pot_ptr(&arclet[k].C, &mylens);
Mock[k] += (grad2.a - grad2.c) * arclet[k].dr;
Mock[narclet + k] += 2. * grad2.b * arclet[k].dr;
}
}
// Accumulate logLikelihood from grid
double Lnorm = 0.0; // Likelihood normalisation
double C = 0.0; // chisquared
for( k = 0; k < Ndata; k++ )
{
C += (Mock[k] - Data[k]) * Acc[k] * Acc[k] * (Mock[k] - Data[k]);
Lnorm += log(Acc[k] / Sqrt2Pi); // (fussy to include this)
}
*Lhood += Lnorm - C / 2.0;
UserCommon->Nchi2++;
if( output )
for( k = 0; k < Ndata; k++ )
Object->Mock[k] = Mock[k];
free(Mock);
return 1;
}
//----------------------------------------------------------------------
// Standard case where Common->Valency == 0 and 0 < Natoms < 1 (No MassInf optimization)
//----------------------------------------------------------------------
const double Sqrt2 = 1.414213562373095;
extern double* tmpCube;
int i, j;
int error;
UserCommonStr* UserCommon = (UserCommonStr*)Common->UserCommon;
int valid = 0;
*Lhood = 0.;
if ( G.nmsgrid == G.nlens )
{
// Check for single atom
if ( Natoms != 1 )
return valid;
// Copy by value of the cube (cube is modified in rescaleCube_1Atom)
for( j = 0; j < Common->Ndim; j++ )
tmpCube[j] = Cubes[0][j];
/* Set the clumps parameters from the cube and eventually reject the whole object*/
valid = rescaleCube_1Atom(tmpCube, Common->Ndim);
/* Compute the likelihood for this object */
if ( valid )
{
UserCommon->Nchi2++;
*Lhood = o_lhood(&error);
if ( ! error )
{
// Track NaN errors
if ( *Lhood != *Lhood )
{
fprintf(stderr, "ERROR: Lhood=NaN found in bayesapp.c:UserBuild(). Dump cube...\n");
for ( i = 0; i < Common->Ndim; i++ )
fprintf(stderr, "%lf ", tmpCube[i]);
fprintf(stderr,"\n");
exit(2);
}
increase_nchi2();
}
else
return 0;
#ifdef DEBUG
FILE *dbg;
dbg = fopen("debug.dat", "a");
for( i = 0; i < Common->Ndim; i++ )
fprintf(dbg, "%lf ",tmpCube[i]);
fprintf(dbg, "\n");
fclose(dbg);
#endif
}
}
else
{
extern struct g_grille G;
double *np_b0 = (double *)calloc(G.nlens - G.nmsgrid, sizeof(double));
for( i = 0; i < Natoms; i++ )
{
long int ilens = (int)((G.nlens - G.nmsgrid) * Cubes[i][0]);
np_b0[ilens] += -10.0 * log(Cubes[i][1]);
}
// Compute Likelihood
UserCommon->Nchi2++;
double C = 0.; double Lnorm = 0.;
error = o_chi_lhood0(&C, &Lnorm, np_b0);
*Lhood = -0.5 * (C + Lnorm);
// Track NaN errors
if ( *Lhood != *Lhood )
{
fprintf(stderr, "ERROR: Lhood=NaN found in bayesapp.c:UserBuild(). Dump cube...\n");
for ( i = 0; i < Common->Ndim; i++ )
fprintf(stderr, "%lf ", np_b0[i]);
fprintf(stderr,"\n");
exit(2);
}
free(np_b0);
increase_nchi2();
if ( error )
{
minusone++;
return 0;
}
return 1;
}
return valid;
return 1;
}
//=============================================================================
// Dummy procedure to link to BayeSys3 when not running MassInf
//=============================================================================
int UserFoot(
double* Cube,
CommonStr* Common,
int* ibits,
double* zbits,
int* nbits)
{
extern int *ibitstmp;
extern double **zbitstmp1;
extern struct g_grille G;
extern struct g_image I;
long int ilens;
int nDim = Common->Ndim;
ilens = (int)((G.nlens - G.nmsgrid + I.n_mult) * Cube[nDim-1]);
if( ilens < G.nlens - G.nmsgrid )
{
nbits[0] = Common->Ndata; nbits[1] = 0; nbits[2] = 0;
memcpy(ibits, ibitstmp, (unsigned int)(Common->Ndata * sizeof(int)));;
memcpy(zbits, zbitstmp1[ilens], (unsigned int)(Common->Ndata * sizeof(double)));
}
else
{
int j;
int isrc = ilens - (G.nlens - G.nmsgrid);
nbits[0] = 0; nbits[1] = I.mult[isrc]; nbits[2] = I.mult[isrc];
int nimage = 0;
for( j = 0; j < isrc; j ++ )
nimage += I.mult[j];
int nmult = nimage;
for( j = isrc; j < I.n_mult; j++ )
nmult += I.mult[j];
for( j = 0; j < I.mult[isrc]; j++ )
{
ibits[j] = nimage;
ibits[j+I.mult[isrc]] = nimage + nmult;
zbits[j] = 1.;
zbits[j+I.mult[isrc]] = 1.;
nimage++;
}
}
increase_nchi2();
return (Cube && Common && ibits && zbits && nbits) ? 1 : 1;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: getParName
//
// Purpose: Return the name of the parameter corresponding to the ipx parameters
//=============================================================================
char* getParName(int ipx, char* name, int type)
{
switch (ipx)
{
case(CX):
strcpy( name, "x (arcsec)");
break;
case(CY):
strcpy( name, "y (arcsec)");
break;
case(EPOT):
strcpy( name, "epot");
break;
case(EMASS):
if ( type == 14 )
strcpy( name, "gamma" );
else
strcpy( name, "emass" );
break;
case(THETA):
strcpy( name, "theta (deg)" );
break;
case(PHI):
strcpy( name, "phi (deg)" );
break;
case(RC):
if ( type == 13 )
strcpy( name, "Re (arcsec)" );
else if ( type == 12 || type == 16 )
strcpy( name, "rs (arcsec)" );
else
strcpy( name, "rc (arcsec)" );
break;
case(B0):
if ( type == 13 )
strcpy( name, "Sigma_e (10^8 Msol/kpc^2)" );
else
strcpy( name, "sigma (km/s)" );
break;
case(ALPHA):
if ( type == 13 )
strcpy( name, "n" );
else
strcpy( name, "alpha" );
break;
case(BETA):
if ( type == 12 )
strcpy( name, "c" );
else
strcpy( name, "beta" );
break;
case(RCUT):
if ( type == 12 )
strcpy( name, "r200 (arcsec)" );
else
strcpy( name, "rcut (arcsec)" );
break;
case(MASSE):
strcpy( name, "M200 (Msol)" );
break;
case(ZLENS):
strcpy( name, "z_lens" );
break;
case(RCSLOPE):
strcpy( name, "rc_slope" );
break;
case(PMASS):
if ( type == 12 )
strcpy( name, "rhos (Msol/Mpc^3)" );
else
strcpy( name, "pmass (g/cm2)" );
break;
case(OMEGAM):
strcpy( name, "omegaM" );
break;
case(OMEGAX):
strcpy( name, "omegaX" );
break;
case(WX):
strcpy( name, "wX" );
break;
case(WA):
strcpy( name, "wa" );
break;
case(SCX):
strcpy( name, "x (arcsec)" );
break;
case(SCY):
strcpy( name, "y (arcsec)" );
break;
case(SA):
strcpy( name, "a (arcsec)" );
break;
case(SB):
strcpy( name, "b (arcsec)" );
break;
case(SEPS):
strcpy( name, "eps" );
break;
case(STHETA):
strcpy( name, "theta (deg)" );
break;
case(SINDEX):
strcpy( name, "index" );
break;
case(SFLUX):
strcpy( name, "mag" );
break;
case(VFCX):
strcpy( name, "velocity x (arcsec)");
break;
case(VFCY):
strcpy( name, "velocity y (arcsec)");
break;
case(VFVT):
strcpy( name, "vt (km/s)");
break;
case(VFRT):
strcpy( name, "rt (kpc)");
break;
case(VFI):
strcpy( name, "inclination (deg)");
break;
case(VFTHETA):
strcpy( name, "velocity theta (deg)");
break;
case(VFLCENT):
strcpy( name, "lambda (Angstroms)");
break;
case(VFSIGMA):
strcpy( name, "velocity dispersion (km/s)");
break;
}
return name;
}
/* Convert input Lenstool values to the corresponding values in <bayes.dat> file.
* bayes2lt() function in readBayesModels.c
*/
static double lt2bayes(int i, int ipx, double val)
{
extern struct pot lens[];
extern struct g_cosmo C;
switch (ipx)
{
case(THETA):
val *= RTD;
break;
case(B0):
// copied from o_print_res()
if ( lens[i].type <= 1 )
val = sqrt(val / 4. / pia_c2);
else if ( lens[i].type == 13 )
val = val * 1e4 * (cH0_4piG * C.h / distcosmo1(lens[i].z)); // in 10^8 Msol/kpc^2
else
val = sqrt(val / 6. / pia_c2);
break;
/* Everything in solar masses
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;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: getParVal
//
// Purpose: Return the parameter value corresponding to the ilens and ipx parameters
//=============================================================================
static double getParVal(int i, int ipx)
{
double x;
x = o_get_lens(i, ipx);
return lt2bayes(i, ipx, x);
}
static void addStat(double val, UserCommonStr *UserCommon, int param, long int samp)
{
double var, var1, mean;
UserCommon->err[param] += val * val;
UserCommon->avg[param] += val;
mean = UserCommon->avg[param] / samp;
var1 = UserCommon->err[param] / samp - mean * mean;
var = abs(var1); //TV
UserCommon->sum += var / mean / mean;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: UserMonitor
//
// Purpose: I have provided a new ensemble of objects.
//
// 1. For probabilistic exploration, restrict Common->cool to <= 1.
// cool = 0 is prior, seen at the first call.
// 0 < cool < 1 is "burn-in"
// cool = 1 is evolve posterior,
// cool -> infinity is maximum likelihood
// Return with a POSITIVE return code to exit BayeSys,
// usually after the end of an evolution stage with cool = 1.
// You can use Common->Nsystem, which counts calls to UserMonitor.
//
// 2. You should reset any nuisance parameters x in UserCommon and/or
// each of your UserObject structures, preferably by sampling from
// their conditonal probabilities Pr(x|Objects) and/or Pr(x|Object).
//
// 3. Collect your statistics and display your diagnostics.
//-----------------------------------------------------------------------------
//
int UserMonitor( // O 0 = continue, +ve = finish, -ve = abort
CommonStr* Common, // I Full general information
ObjectStr* Objects) // I Full ensemble of sample objects [ENSEMBLE]
{
// Track NaN errors
if ( Common->cool != Common->cool )
{
fprintf(stderr, "ERROR: Common->cool=NaN found in bayesapp.c:UserMonitor().\n");
exit(2);
}
// Variables used everywhere
const double Sqrt2Pi = 2.50662827463100050240;
extern struct g_mode M;
extern struct g_grille G;
UserCommonStr* UserCommon = (UserCommonStr*)Common->UserCommon;
extern double *tmpCube;
char bayesName[30],burninName[30];
FILE *bayes;
int k, ipx; // counters
long int i, j;
double lhood0, chi2;
//.............................................................................
// USER IMPOSES FINAL TEMPERATURE AND TERMINATION CONDITION !
if ( Common->cool >= 1.0 && M.inverse == 3 )
Common->cool = 1.0;
//.............................................................................
// Save the models in burnin.dat/bayes.dat
strcpy(bayesName, "bayes");
strcpy(burninName, "burnin");
#ifdef DEBUG
sprintf(bayesName, "%s.dbg", bayesName);
sprintf(burninName, "%s.dbg", burninName);
#endif
#ifdef MPI
sprintf(bayesName, "%s.%d", bayesName, ltID);
sprintf(burninName, "%s.%d", burninName, ltID);
#endif
sprintf(bayesName, "%s.dat", bayesName);
sprintf(burninName, "%s.dat", burninName);
if ( Common->cool < 1. )
bayes = fopen( burninName, "a");
else
bayes = fopen( bayesName, "a");
UserCommon->sum = 0;
for ( k = 0; k < Common->ENSEMBLE; k++ )
{
double **Cubes = Objects[k].Cubes;
extern double *np_b0;
if( Common->Valency )
{
extern struct g_image I;
extern double **zbitstmp1;
int Ndata = Common->Ndata;
double *Data = Common->Data;
double *Acc = Common->Acc;
long int ilens;
// Initialize arrays
double *Mock = (double *) calloc(Ndata, sizeof(double));
memset(np_b0, 0, (unsigned long int)((G.nlens - G.nmsgrid) * sizeof(double)));
// MassInf optimization (commented: 1 optimized pot.)
for( i = 0; i < Objects[k].Natoms; i++ )
{
// Not implemented in UserBuild()
// for( j = 0; j < Common->Ndim - 2; j ++ )
// tmpCube[j] += Cubes[i][j]; // TODO: rescale between 0..1 with Unif prior
// Cubes[][Common->Ndim - 1] is coordinate
ilens = (int)((G.nlens - G.nmsgrid + I.n_mult) * Cubes[i][Common->Ndim - 1]);
if( ilens < G.nlens - G.nmsgrid )
{
np_b0[ilens] += Cubes[i][Common->Ndim];
for( j = 0; j < Ndata; j++ )
Mock[j] += Cubes[i][Common->Ndim] * zbitstmp1[ilens][j];
}
else
{
int isrc = ilens - (G.nlens - G.nmsgrid);
int nimage = 0;
for( j = 0; j < isrc; j ++ )
nimage += I.mult[j];
int nmult = nimage;
for( j = isrc; j < I.n_mult; j++ )
nmult += I.mult[j];
for( j = 0; j < I.mult[isrc]; j++ )
{
Mock[nimage] += Cubes[i][Common->Ndim + 1];
Mock[nimage + nmult] += Cubes[i][Common->Ndim + 2];
nimage++;
}
}
}
// Compute Likelihood from SL
chi2 = 0.; lhood0 = 0.;
// Accumulate logLikelihood from grid
for( j = 0; j < Ndata; j++ )
{
chi2 += (Mock[j] - Data[j]) * Acc[j] * Acc[j] * (Mock[j] - Data[j]);
lhood0 += log(Sqrt2Pi / Acc[j]);
}
// Compute Likelihood (not to include otherwise there is no match
// when reading with readBayesModel.c)
//int error = o_chi_lhood0(&chi2, &lhood0, np_b0); // TODO: catch error
free(Mock);
}
else if( G.nmsgrid != G.nlens )
{
// CONDITION NOT USED BECAUSE EVERYTHING IS DONE WITH MASSINF NOW
long int ilens;
memset(np_b0, 0, (unsigned long int)((G.nlens - G.nmsgrid) * sizeof(double)));
for( i = 0; i < Objects[k].Natoms; i++ )
{
ilens = (int)((G.nlens - G.nmsgrid) * Cubes[i][0]);
np_b0[ilens] += -10.0 * log(Cubes[i][1]);
}
int error = o_chi_lhood0(&chi2, &lhood0, np_b0); // TODO: catch error
}
else
{
// Reset the tmpCube array
memset(tmpCube, 0, (unsigned long int)(UserCommon->Ndim * sizeof(double)));
int iparam = 0;
// Natoms should be 1, but still allow case with Natoms > 1
for( i = 0; i < Objects[k].Natoms; i++ )
for( j = 0; j < Common->Ndim; j ++ )
tmpCube[iparam++] = Cubes[i][j];
// Normal case: UserCommon->Ndim is the number of free parameters
// But eg, UserCommon->Ndim can be Natoms times the same pot
rescaleCube_1Atom(tmpCube, UserCommon->Ndim);
// Compute Likelihood
int error = o_chi_lhood0(&chi2, &lhood0, NULL); // TODO: catch error
// Loop to the next iteration if error
if( error )
continue;
}
double o_lhood_rez = (-0.5*(chi2 + lhood0));
fprintf( bayes, "%ld %lf ", UserCommon->Nsample + 1, o_lhood_rez);
// SAVE: save lens parameters
int iparam = 0;
long int samp = UserCommon->Nsample * Common->ENSEMBLE + k + 1;
extern int block[][NPAMAX];
double val = 0.;
for ( i = 0; i < G.no_lens; i++ )
for ( ipx = CX; ipx <= PMASS; ipx++ )
if ( block[i][ipx] != 0 )
{
val = getParVal(i, ipx);
fprintf(bayes, "%lf ", val );
addStat(val, UserCommon, iparam++, samp);
}
int nzeros= 0;
for ( i = 0; i < G.nlens - G.nmsgrid; i++ )
{
val = np_b0[i];
if ( fabs(val) > 1E-6 )
{
if( nzeros > 0 )
fprintf(bayes, "%dx0.0 %lf ", nzeros, val);
else
fprintf(bayes, "%lf ", val);
nzeros = 0;
}
else
nzeros++;
addStat(val, UserCommon, iparam++, samp);
}
if ( nzeros > 0 )
fprintf(bayes, "%dx0.0 ", nzeros);
// SAVE: source positions for grid model (for DEBUG purposes for now)
extern struct g_image I;
if ( Common->Valency && I.n_mult != 0)
{
double *Ps = (double *)calloc(I.n_mult * 2, sizeof(double));
long int ilens;
for ( i = 0; i < Objects[k].Natoms; i++ )
{
ilens = (int)((G.nlens - G.nmsgrid + I.n_mult) * Cubes[i][Common->Ndim - 1]);
if( ilens >= G.nlens - G.nmsgrid )
{
int isrc = ilens - (G.nlens - G.nmsgrid);
Ps[isrc] += Cubes[i][Common->Ndim + 1];
Ps[isrc + I.n_mult] += Cubes[i][Common->Ndim + 2];
}
}
for ( i = 0; i < I.n_mult * 2; i++ )
fprintf(bayes, "%lf ", Ps[i]);
free(Ps);
}
// SAVE: source parameters for M.iclean == 2
if ( M.iclean == 2 )
{
extern int sblock[NFMAX][NPAMAX];
extern struct g_source S;
extern struct galaxie source[NFMAX];
for( i = 0; i < S.ns; i++ )
for( ipx =SCX; ipx <= SFLUX; ipx++ )
if( sblock[i][ipx] != 0 )
{
val = o_get_source(&source[i], ipx);
if( ipx == STHETA ) val *= RTD;
fprintf(bayes, "%f ", val);
addStat(val, UserCommon, iparam++, samp);
}
}
// SAVE: save cosmological parameters
extern int cblock[NPAMAX];
for ( ipx = OMEGAM; ipx <= WA; ipx++ )
if ( cblock[ipx] != 0 )
{
val = getParVal(0, ipx);
fprintf(bayes, "%lf ", val);
addStat(val, UserCommon, iparam++, samp);
}
// SAVE: save zmlimit parameters
extern struct g_image I;
extern struct z_lim zlim[];
extern struct galaxie multi[NFMAX][NIMAX];
char limages[ZMBOUND][IDSIZE];
int nimages;
for ( ipx = 0; ipx < I.nzlim; ipx++ )
if ( zlim[ipx].bk != 0 )
{
// look for the images families corresponding to the zmlimit to optimize
nimages = splitzmlimit(zlim[ipx].n, limages);
i = 0;
while ( indexCmp( multi[i][0].n, limages[0] ) ) i++;
val = multi[i][0].z;
fprintf( bayes, "%lf ", val );
addStat(val, UserCommon, iparam++, samp);
/* i = 0;
while( indexCmp( multi[i][0].n, zlim[ipx].n ) ) i++;
for( k = 0; k < I.mult[i]; k++ )
fprintf( bayes, "%lf ", multi[i][k].z );
*/
}
// SAVE: save z_a_limit parameter
extern struct z_lim zalim;
if( zalim.bk != 0 )
{
val = I.zarclet;
fprintf( bayes, "%lf ", val);
addStat(val, UserCommon, iparam++, samp);
}
// SAVE: save velocity field parameters
extern int vfblock[NPAMAX];
for ( ipx = VFCX; ipx <= VFSIGMA; ipx++ )
if ( vfblock[ipx] != 0 )
{
val = getParVal(0, ipx);
if( ipx == VFTHETA ) val *= RTD;
if( ipx == VFI ) val *= RTD;
fprintf(bayes, "%lf ", val);
addStat(val, UserCommon, iparam++, samp);
}
// SAVE : save pot parameters
extern struct g_pot P[NPOTFILE];
for( i = 0; i < G.npot; i++ )
{
struct g_pot *pot = &P[i];
if ( pot->ftype != 0 )
{
if ( pot->ircut != 0 )
{
fprintf( bayes, "%lf ", pot->cut );
addStat(pot->cut, UserCommon, iparam++, samp);
}
if ( pot->isigma != 0 )
{
fprintf( bayes, "%lf ", pot->sigma );
addStat(pot->sigma, UserCommon, iparam++, samp);
}
if ( pot->islope != 0 )
{
fprintf( bayes, "%lf ", pot->slope );
addStat(pot->slope, UserCommon, iparam++, samp);
}
if ( pot->ivdslope != 0 )
{
fprintf( bayes, "%lf ", pot->vdslope );
addStat(pot->vdslope, UserCommon, iparam++, samp);
}
if ( pot->ivdscat != 0 )
{
fprintf( bayes, "%lf ", pot->vdscat );
addStat(pot->vdscat, UserCommon, iparam++, samp);
}
if ( pot->ircutscat != 0 )
{
fprintf( bayes, "%lf ", pot->rcutscat );
addStat(pot->rcutscat, UserCommon, iparam++, samp);
}
if ( pot->ia != 0 )
{
fprintf( bayes, "%lf ", pot->a );
addStat(pot->rcutscat, UserCommon, iparam++, samp);
}
if ( pot->ib != 0 )
{
fprintf( bayes, "%lf ", pot->b );
addStat(pot->rcutscat, UserCommon, iparam++, samp);
}
}
}
// SAVE: the nuisance parameters
extern struct sigposStr sigposAs;
if ( sigposAs.bk != 0 )
{
for ( i = 0; i < I.n_mult; i++ )
for ( j = 0; j < I.mult[i]; j++ )
{
val = sqrt(I.sig2pos[i][j]);
fprintf( bayes, "%lf ", val );
addStat(val, UserCommon, iparam++, samp);
}
}
if ( I.dsigell != -1. )
{
val = sqrt(I.sig2ell);
fprintf( bayes, "%lf ", val );
addStat(val, UserCommon, iparam++, samp);
}
// append the evidence
if ( Common->cool < 1. ) fprintf( bayes, "%lf ", Common->Evidence);
//append #Chi2 in last column in bayes.dat
if ( Common->cool >= 1. ) fprintf( bayes, "%lf ", chi2);
fprintf( bayes, "\n" );
}
fclose(bayes);
//.............................................................................
// Print the status line of STDOUT
int Nrem;
if( Common->cool < 1. )
{
double chi2rate = difftime(end, start);
chi2rate = chi2rate > 0 ? chi2rate : -1;
chi2rate = nchi2 / chi2rate;
Nrem = Common->Nsystem; // # to go, as (2 * Nsample++) catches up with Nsystem++
printf(" \r");
fprintf(stdout, // (stderr flushes output immediately)
"Burn-in : %10.6lf %5d %12.3lf %10.3lf %d/%.0lf %.0lfchi2/s\r",
Common->cool, Nrem, chi2, Common->Evidence, minusone, nchi2, chi2rate);
}
else
{
if ( M.itmax == 0 )
M.itmax = Common->Nsystem;
Nrem = M.itmax - UserCommon->Nsample; // or any other setting
UserCommon->sum /= Common->ENSEMBLE * Common->Ndim;
fprintf(stdout, "Sampling : %10.6lf %7ld/%d %12.3lf %10.3lf[CTRL-C to interrupt]\r",
Common->cool, UserCommon->Nsample + 1, M.itmax + 1, chi2, sqrt(UserCommon->sum));
}
fflush(stdout);
minusone = 0;
nchi2 = 0.;
start = end;
time(&end);
//.............................................................................
// Set any NUISANCE PARAMETERS you may have here
// Could over-ride system's choices of FluxUnit (both Common and Objects) here
// Could CALIBRATE data here (corrupting Evidence and Information)
//.............................................................................
// BURN-IN
extern int optInterrupt; // Global variable modified in o_run_bayes.c/signalReset()
if ( Common->cool < 1.0 && !optInterrupt) // final temperature not reached..
return 0; // ...normal return, keep going
//.............................................................................
// EVOLUTION: Accumulate any desired statistics
for ( k = 0; k < Common->ENSEMBLE; k++ )
UserCommon->atoms += Objects[k].Natoms; // # atoms
// # samples of full ensemble
UserCommon->Nsample ++;
if ( Nrem > 0 && !optInterrupt) // not finished...
return 0; // ..normal return
//.............................................................................
// EXIT WITH POSITIVE FINISH CODE WHEN EVOLUTION IS DEEMED COMPLETE
NPRINTF(stderr, "\n" );
return 1;
}

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