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bayesys3.h
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bayesys3.h
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//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Bayesian Inference
//
// Filename: bayesys3.h
//
// Purpose: Header for bayesys3.c
//
// History: JS 28 Jan 2002 - 18 Sep 2003
//-----------------------------------------------------------------------------
#ifndef BAYESYS3
#define BAYESYS3
/**************/
/* Structures */
/**************/
typedef struct // GENERAL INFORMATION AND WORKSPACE
{
// BayeSys3 external
int Ndim; // I Hypercube dimension = # variables in atom
int MinAtoms; // I Min #atoms >= 1
int MaxAtoms; // I Max #atoms >= MinAtoms (or 0 for unlimited)
double Alpha; // I Hyperparameter for #atoms (+ve or 0 or -ve)
int ENSEMBLE; // I # sample objects in ensemble
int Method; // I Method of algorithm
double Rate; // I Annealing rate
int Iseed; // I O Random seed, +ve = fixed, -ve = time seed
double cool; //(I)O Annealing (burnin<1, Bayes=1, maxLhood=inf)
double Evidence; // O log[e] Pr(Data)
double Information;// O -log"Volume" = INT post log(post/prior) dx
int Nsystem; // O Elapsed iterates
double CPU; // O CPU in units of 1-atom Del|Try|Ins changes
double Success; // O # successes (as internally defined)
// (100% efficiency would be Success ~ CPU)
int Valency; // I 0, or MassInf valency
// MassInf external (referenced by BayeSys3 and used if Valency > 0)
int MassInf; // I Method of analysing Gaussian or Poisson data
// 0=monkeys, 1=positive, 2=pos/neg, 3=gauss,
// add 10 to allow flux=0: add 100 if Poisson data
int Ndata; // I # data
double* Data; // I Data [Ndata]
double* Acc; // I 1/Gaussian_sigma, or Poisson background [Ndata]
double ProbON; // I Prob(individual flux != 0), > 0
double FluxUnit0; // I O Hyperparameter for unit of flux
// BayeSys3 internal
int Nbits; // O # bits per word
unsigned* offset; // (O)Cube-to-Label mapping [Ndim]
int* permute; // (O)Cube-to-Label mapping [Ndim]
unsigned Rand[4]; // O Random generator
// MassInf internal (referenced by BayeSys3 and used if Poisson data)
int* Counts; // (O)Annealed data counts [Ndata]
// USER monitoring information
void* UserCommon;
} CommonStr;
typedef struct // MEMBER OBJECT OF ENSEMBLE
{
// BayeSys3 external
double Lhood; // O log Prob(Data|object)
int Natoms; // O # atoms in object (used dimension of Cube)
double** Cubes; // O Atomic output [Natoms][Ndim+Valency+1]
// Ndim cube position, Valency fluxes, log(width)
// De-allocated before exiting BayeSys3
// MassInf external (referenced by BayeSys3 and used there iff Valency > 0)
double* Mock; // (O)Workspace for Mock data [Ndata]
// De-allocated before exiting BayeSys3
double FluxUnit; // O Unit of flux
// BayeSys3 internal
int Nstore; // # atoms allocated (physical dim of Cube)
unsigned* xLabel; // Label control [Ndim]
unsigned* yLabel; // Label control [Ndim]
unsigned* xOrigin; // Label control [Ndim]
unsigned* yOrigin; // Label control [Ndim]
unsigned* xTry; // Label control [Ndim]
unsigned* yTry; // Label control [Ndim]
unsigned* work; // Cube-to-Label workspace [Ndim]
int clock; // parallel operation
int flowcheck; // parallel operation
unsigned Rand[4]; // Random generator
// MassInf internal (referenced by BayeSys3 and used there if Valency > 0)
int reset; // Reset inserted MassInf fluxes?
double* g1; // grad chisquared [Valency]
double* g2; // grad chisquared [Valency]
double* A11; // grad grad chisquared [Valency]
double* A12; // grad grad chisquared [Valency]
double* A22; // grad grad chisquared [Valency]
int* Xindex; // Index to cross-terms [Valency]
int* nbits; // Fragment numbers [Valency]
int* nbitx; // Fragment numbers [Valency]
int* ibits; // Fragment identifiers [<=Ndata]
int* ibitx; // Fragment identifiers [<=Ndata]
double* zbits; // Fragment quantities [<=Ndata]
double* zbitx; // Fragment quantities [<=Ndata]
double* Foot; // Footprint of unit flux [Ndata]
int* flags; // Valency identifiers [Ndata]
// USER information for individual objects
void* UserObject;
} ObjectStr;
/**************/
/* Procedures */
/**************/
#ifdef __cplusplus
extern "C" {
#endif
// Full Bayesian calculation ended by UserMonitor
extern int BayeSys3( // O +ve = UserMonitor return code, -ve = abort
CommonStr* Common, // I O General information
ObjectStr* Objects); // O ENSEMBLE of sample objects
extern void BayeShape( // Transform cube position to other shape
double* Coord, // O Coordinates
double* Cube, // I Cube (or part of)
int N, // I Dimension of (part of) Cube
int Shape); // I Choice of coordinate shape
// Set empty object with 0 atoms
extern int UserEmpty( // O >=0 is OK, -ve is error abort
double* Lhood, // O loglikelihood
CommonStr* Common, // I General information
ObjectStr* Object); // O Sample object
// Try one new atom
extern int UserTry1( // O +ve = OK, 0 = DO NOT USE, -ve = error abort
double* Ltry, // O DELTA(logLikelihood) from 1 trial atom
CommonStr* Common, // I General information
ObjectStr* Object); // I Sample object (DO NOT UPDATE Lhood)
// Try two new atoms
extern int UserTry2( // O +ve = OK, 0 = DO NOT USE, -ve = error abort
double* Ltry1, // O DELTA(logLikelihood) from 1st trial atom
double* Ltry2, // O DELTA(logLikelihood) from both trial atoms
CommonStr* Common, // I General information
ObjectStr* Object); // I Sample object (DO NOT UPDATE Lhood)
// Insert one atom and update
extern int UserInsert1( // O >=0 is OK, -ve is error abort
double* Lhood, // O DELTA(loglikelihood)
CommonStr* Common, // I General information
ObjectStr* Object); // I O Sample object
// Insert two atoms and update
extern int UserInsert2( // O >=0 is OK, -ve is error abort
double* Lhood, // O DELTA(loglikelihood)
CommonStr* Common, // I General information
ObjectStr* Object); // I O Sample object
// Delete one atom and update
extern int UserDelete1( // O >=0 is OK, -ve is error abort
double* Lhood, // O DELTA(loglikelihood)
CommonStr* Common, // I General information
ObjectStr* Object); // I O Sample object
// Mock data from unit flux for MassInf
extern int UserFoot( // O +ve = OK, 0 = DO NOT USE, -ve = error abort
double* Cube, // I Atom coordinates
CommonStr* Common, // I General information
int* ibits, // O Fragment coords
double* zbits, // O Fragment quantities
int* nbits); // O # fragments >= 0, SUM(nbits) <= Ndata
// Inspect progress and collect statistics
extern int UserMonitor( // O 0 = continue, +ve = finish, -ve = abort
CommonStr* Common, // I General information
ObjectStr* Objects); // I ENSEMBLE of sample objects
#ifdef __cplusplus
};
#endif
/*************/
/* Constants */
/*************/
#undef E_BAYESYS_PARMS
#define E_BAYESYS_PARMS -220 // Wrong input parameters
#undef E_BAYESYS_SYSERR
#define E_BAYESYS_SYSERR -221 // Global error (atom insertion failure)
#undef E_MASSINF_PARMS
#define E_MASSINF_PARMS -210 // Wrong input parameters
#undef E_MASSINF_OVERLAP
#define E_MASSINF_OVERLAP -211 // Valency footprints overlap wrongly
#undef E_MASSINF_NBITS
#define E_MASSINF_NBITS -212 // Too many fragments
#undef E_MASSINF_RANGE
#define E_MASSINF_RANGE -213 // Fragment outside data range
#undef E_MASSINF_DATA
#define E_MASSINF_DATA -214 // Negative count data supplied
#undef E_MASSINF_COUNTS
#define E_MASSINF_COUNTS -215 // Count data too large threatening overflow
#undef E_MALLOC
#define E_MALLOC -130 // Can't allocate memory
#endif

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