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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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