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//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Bayesian Inference
//
// Filename: bayesys3.c
//
// Purpose: Obtain sample objects from posterior atomic distribution.
//
// Dedication: To my intellectual ancestors the late Edwin T Jaynes, and
// Steve Gull, to my descendant Sibusiso Sibisi, and the many
// colleagues and friends over the past quarter-century who
// have inspired and encouraged the development of these ideas.
//
// John Skilling, Kenmare, Ireland, November 2003
// email: skilling@eircom.net
//=============================================================================
/*
Copyright (c) 1999-2003 Maximum Entropy Data Consultants Ltd,
114c Milton Road, Cambridge CB4 1XE, England
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#include "license.txt"
*/
//=============================================================================
//
// An OBJECT is a combination of a-priori-equivalent "atoms":
// statisticians call this construction a "mixture model".
//
// ATOMS
// The number of atoms N in an object can range from MIN to MAX.
// MIN >= 1 is required to avoid the algorithmically special null object N=0.
// Generally, MAX >= MIN is required (with MAX=MIN allowed), but
// MAX=infinity (absence of limit) can be specified with MAX=0.
// [ Technically, this coding allows at most 1 atom per identifiable
// location, so "infinity" means #(locations), perhaps 2^32 . ]
//
// There are three standard priors Pr(N), selected by sign(Alpha).
// Alpha = 0.
// The prior is UNIFORM in MIN <= N <= MAX (and MAX must be finite).
// Alpha > 0.
// The prior is POISSON or BINOMIAL.
// N ~ Alpha +- sqrt(Alpha), subject to MIN and MAX
// Alpha < 0.
// The prior is GEOMETRIC.
// N ~ |Alpha| +- |Alpha|, subject to MIN and MAX
//
// COORDINATES
// The BayeSys prior for locating an atom in space is flat over the hypercube
// (0,1)^Ndim of dimension Ndim . In fact, the hypercube is treated as
// wraparound-continuous, so is more properly described as a "hyper-torus".
// BayeSys gives you coordinate vectors "double Cube[Ndim]" with values in
// (0,1), but you can transform these into other "Coord" if you wish.
//
// The BayeShape procedure lets you modify some or all of your coordinates
// into nine alternative configurations:
//
// Shape Description Prob(Coord[i]) Range of i
//
// 0 Permutation uniform on integers Perm(0...N-1) 0...N-1
// 1 +ve orthant exp(-x) in x > 0 0...N-1
// 2 Simplex volume uniform in SUM(x) < 1 0...N-1
// 3 Simplex surface uniform on SUM(x) = 1 0...N
// 4 Ordered uniform in 0 < x[0] < x[1] < ... < 1 0...N-1
// 5 Bell Normal(0,1) in -inf < x < inf 0...N-1
// 6 Sphere volume uniform in SUM(x^2) < 1 0...N-1
// 7 Hemisphere surface uniform on SUM(x^2) = 1, x[N]>0 0...N
// 8 Sphere surface uniform on SUM(x^2) = 1 0...N
//
// For the interior of an awkward shape, allow a circumscribing volume,
// but return the value 0 from UserTry1 and UserTry2 (instead of the
// usual positive acceptance code) for any location outside the shape.
// The ensemble will keep within the domain, because BayeSys only accepts
// points for which you give strictly positive return codes.
//
// Thus the unit disc x^2 + y^2 < 1 could be programmed in several ways:
// (a) Use BayeShape with Shape=6 which gives the N=2 disc interior directly.
// (b) Use N=2 hypercube (= unit square) but expand it to (-1,1) by setting
// x = 2*Cube[0] - 1, y = 2*Cube[1] - 1
// and reject any point outside the disc by returning 0 from UserTry1
// and UserTry2.
// (c) Use hypercube to yield a unit square, but spread the prior measure
// uniformly through the unit disc with your own transformation, e.g.
// radius^2 = Cube[0], angle = 2 PI Cube[1] .
//
// FLUXES
// The Ndim coordinates can be supplemented by Valency intensities or
// "fluxes" z, being attributes for which the joint distribution
// Prior(z).Likelihood(D|z,...)
// is integrable and can be sampled from.
// The MassInf library incorporated in BayeSys provides Flux procedures for
// its priors and linear data.
//
// DISPLAY
// The coordinates and intensities are supplemented by a guidance width, being
// log(fraction of hypercube volume that atom might plausibly range over).
// This may help you to produce smooth displays from the atomic objects.
//
// The number of atoms in an object is supplied to you as Natoms and
// each atom's attributes are supplied to you consecutively as
// double Cube[ 0,1,...,Ndim-1, Ndim,...,Ndim+Valency-1, Ndim+Valency ]
// coordinates in (0,1) intensities log(width)
//=============================================================================
//
// ENSEMBLE
// The program uses an ensemble of sample objects. Using several objects is
// usually recommended, partly because objects that seem to be getting stuck
// are overwritten by more successful ones which reduces the risk of failure,
// and partly because the geometrical exploration engines only work with
// several objects.
//
//=============================================================================
//
// METHOD
// Internally in the program, hypercube coordinates are mapped to an
// extended-integer label whose range fills the hypercube but which preserves
// a degree of locality: small changes in this integer will necessarily
// correspond to small changes in coordinates.
// The user can use the Method parameter to control the style of this mapping,
// and the operation of the various internal engines that control the
// evolution of the ensemble.
//
// Method = 0 is the simplest algorithm, mapping hypercube coordinates
// onto extended-integer position labels by simple raster,
// and using the "LifeStory1" diffusion engine to create,
// destroy, and move atoms.
// This is very likely to be enhanced by switching on
// various bits of the Method integer.
//
// if( Method & 1 ), hypercube coordinates are mapped to position labels along
// a space-filling Hilbert curve.
// This is generally recommended, but unnecessary if Ndim=1.
//
// if( Method & 2 ), the "LifeStory" diffusion engine will include interactions
// with atoms' neighbours, otherwise not.
// This is generally recommended for its extra power.
//
// if( Method & 4 ), the algorithm includes the Chameleon1 engine, which lets
// atoms jump from one ensemble object to another, without
// changing position.
// This is ineffective if there is only one ensemble object.
//
// if( Method & 8 ), the algorithm includes the Chameleon2 engine, which lets
// atoms from different ensemble objects exchange position.
// This is ineffective if there is only one ensemble object.
//
// if( Method & 16), the algorithm will include the Leapfrog1 engine, which
// inverts atom positions with respect to another atom from
// the same or a different ensemble object.
// This is designed to assist when the posterior distribution
// in more than one dimension is highly non-spherical.
//
// if( Method & 32), the algorithm will include the Leapfrog2 engine, which
// reflects atom positions with respect to two other atoms
// from the same or different ensemble objects.
// This is designed to assist when the posterior distribution
// in more than one dimension is highly non-spherical.
//
// if( Method & 64), the algorithm will include the GuidedWalk engine, which
// moves atoms along directions parallel to displacements
// between neighbours, thus following the local shape of
// the posterior distribution.
// This may supersede the Leapfrog engines.
//
// ________________________________________________________________________
// | |
// | GuidedWalk Leapfrog2 Leapfrog1 Chameleon2 Chameleon1 LifeStory2 Hilbert| 1
// | off off off off off LifeStory1 raster | 0
// |________________________________________________________________________|
// 64 32 16 8 4 2 1 Method
//
// In the interest of overall efficiency, the algorithm tries to equalise the
// computation time between its engines so that even if all the optional
// engines did nothing, the computation cost of including them would be
// limited to the number of engines (currently a factor of 6).
//
// Author generally recommends switching everything in by
// Method = 127 (equivalently -1) .
//
//=============================================================================
//
// The "Massive Inference" (MassInf) option is provided for applications where
// atoms have intensities or "fluxes" about which the data are linear.
//
// The PRIOR for the number of atoms and for their location is as for BayeSys3.
//
// Prior on flux z of atom is Pr(z) = ProbON * P(z) + (1 - ProbON) * delta(z) ,
// i.e. each flux is expected to be distributed as P(z) with probability ProbON
// otherwise it is switched off with zero value.
// Common->ProbON supplies ProbON, and the "units" decimal digit of the switch
// Common->MassInf defines the shape P(z) of the prior according to
//
// (0) "monkeys" P(z) = delta(z-q), i.e. z = q = constant
//
// (1) "positive" P(z) = exp(-z/q) / q in z > 0
//
// (2) "positive/negative" P(z) = exp(-|z|/q) / 2q
// 2 2 2
// (3) "Gaussian" P(z) = exp(-z / 2 q ) / sqrt(2 pi q )
//
// When flux can be positive or negative, the "positive/negative" prior is
// more tolerant of dynamic range than is the Gaussian prior.
// In each case the flux unit q is fixed at the positive value supplied
// in Common->FluxUnit0, or (if <= 0) kept close to its most probable value.
//
// An atom can have Valency (=1,2,...) independent fluxes, provided
// (a) all atoms have the same valency,
// (b) the flux unit is the same for each,
// (c) the mock-data footprints of the different valencies of an atom
// do not overlap (no common cells), and
// (d) (if using LifeStory2 engine) for any pair of atoms, each footprint
// of one overlaps no more than one valency footprint of the other.
//
//
// To specify the LIKELIHOOD (used as its log), define
//
// f = object = sum of atoms
//
// x[j] = positional coordinate of atom j
//
// z[j] = flux(es) of atom j
//
// Footprint(x) = mock data from unit flux at x
//
// Mock = SUM[j] z[j] Footprint(x[j]) = mock data of object
//
// Likeliood Pr(Data | f) can be one of
//
// (0xx) "chisquared", derived from
//
// Data = signal,
//
// Acc = 1/sigma, can be 0, (sigma = standard deviation)
//
// M = # measured data, for which Acc[k] > 0.
// M 2
// Z = PRODUCT[k] sqrt(2 PI sigma[k] )
// 2 2
// Chisq = SUM[k] (Mock[k] - Data[k]) / sigma[k]
// -1 -Chisq / 2
// Pr(Data | f) = Z e
//
// (1xx) "Poisson", for positive problems with "monkey" or "positive" prior;
//
// Data = counts, can be doubleing-point but must be >= 0.0
//
// Acc = extraneous "background", which may be small but
// must be strictly +ve wherever Data > 0.0
// -F[k] D[k]
// Pr(Data | f) = PRODUCT[k] e F[k] / D[k]!
//
// where F = Mock + Acc, D = Data + Acc, x! = GAMMA(x+1) :
// this form of likelihood avoids singularity when active
// cells happen to be empty of mock data, and reduces to
// standard Poisson when the background -> 0
//
// according to the "hundreds" digit of the switch Common->MassInf.
//
// For example, Common->MassInf = 1 is Gaussian data with "positive" prior;
// Common->MassInf = 101 is Poisson data with "positive" prior.
//=============================================================================
// History:
// MassInf1 v1.12-2.36 1998-2000
// BayeSys1 code 1999-2000
// BayeSys2 v1.02-1.05 1 May - 10 Sep 2001
// BayeSys3 v1.01-1.32 2 Jan 2002 - 4 Feb 2003
// v2.00 10 Feb 2003
// v2.01 11 Jul 2003 Fixed-q0 option to fix FluxUnit0 in MassInf
// v2.02 19 Jul 2003 MassInf options extended to allow flux=0
// v2.10 12 Aug 2003 MassInf needs FluxUnit0 from user
// v2.20 14 Aug 2003 Remove any overlay in MassInf user's "bits"
// v3.00 20 Aug 2003 Poisson data as MassInf option
// v3.01 12 Sep 2003 MassInf control of flux=0 by ProbON
// v3.02 18 Sep 2003 BayeShape coordinate options
// v3.03 11 Oct 2003 "Hilbert" name used instead of Peano
// v3.04 20 Oct 2003 Display width of atom roughy halved
// v3.05 27 Oct 2003 BayeShape permutation option
// v3.10 29 Nov 2003 Free software under GNU LGPL
// v3.11 3 Feb 2004 Control uses <#copies>. Better Evid & Info
//-----------------------------------------------------------------------------
//
#include <stdlib.h>
#include <float.h>
#include <math.h>
#include "bayesys3.h"
#include "random.h"
#include "hilbert.h"
#include <time.h>
#include <stdio.h>
#undef PARALLEL
#define PARALLEL 0 // # slaved parallel processors [0 = none]
#undef DEBUG
#define DEBUG 0 // check Cube/Link consistency [0 = off]
/***********************/
/* Internal structures */
/***********************/
typedef struct
{
int i; // 1st object
int j; // [2nd object]
int k; // [3rd object]
signed char engine; // operation type
signed char iType; // type of 1st object, -1=WRITE, 0=Unused, 1=read
signed char jType; // type of 2nd object, -1=WRITE, 0=Unused, 1=read
signed char kType; // type of 3rd object, -1=WRITE, 0=Unused, 1=read
int iEarly; // min start time # for 1st object i
int jEarly; // min start time # for 2nd object j
int kEarly; // min start time # for 3rd object k
int iLate; // max start time # for 1st object i
int jLate; // max start time # for 2nd object j
int kLate; // max start time # for 3rd object k
int slave; // assigned processor
int CPU; // CPU time in this operation
int Success; // # successes in this operation
} OperStr; // Operation
/*********************************/
/* Internal constants and macros */
/*********************************/
//
// CALLOC(p,n,t) allocates vector p[0:n-1] of type t
// REALLOC(p,n,t) (re-)allocates vector p[0:n-1] of type t
// FREE(p) frees CALLOC or REALLOC or NULL vector p[0:*], sets p=NULL
// CALL catches negative error codes
// PLUS(x,y) log(exp(x)+exp(y))
// SWAP(x,y) exchange
//
#undef CALLOC
#define CALLOC(p,n,t) {p=NULL;\
if((n)>0&&!(p=(t*)calloc((size_t)(n),sizeof(t))))\
{CALLvalue=E_MALLOC;goto Exit;}/*printf("%p %d\n",p,(size_t)(n)*sizeof(t));*/}
#undef REALLOC
#define REALLOC(p,n,t) {/*printf("%p -1\n",p);*/\
if((n)>0&&!(p=(t*)realloc(p,(size_t)(n)*sizeof(t))))\
{CALLvalue=E_MALLOC;goto Exit;}/*printf("%p %d\n",p,(size_t)(n)*sizeof(t));*/}
#undef FREE
#define FREE(p) {if(p){/*printf("%p -1\n",p);*/(void)free((void*)p);} p=NULL;}
#undef CALL
#define CALL(x) {if( (CALLvalue = (x)) < 0 ) goto Exit;}
#undef PLUS
#define PLUS(x,y) ((x)>(y)?(x)+log(1.+exp((y)-(x))):(y)+log(1.+exp((x)-(y))))
#undef SWAP
#define SWAP(a,b) {swap = a; a = b; b = swap;}
/***********************/
/* Internal prototypes */
/***********************/
// BayeSys3 main procedures
static void ShapeSolve (int, double, double, double*, double*);
static double ShapeCumul (int, double, double*);
static void ShapeIndex (int, double*, double*);
static int BayesAlloc (CommonStr*, ObjectStr*, Node*, Node*);
static int BayesInit (CommonStr*, ObjectStr*);
static int PriorInit (CommonStr*, ObjectStr*, Node*, int, double*);
static int Control (CommonStr*, ObjectStr*, int, double*, double*);
static double Copies (double*, int);
static int Anneal (CommonStr*, ObjectStr*, int, double);
static void Sort2 (int*, double*, int);
static int FillOcean (CommonStr*, ObjectStr*, Node*, int);
static int MCMCengines (CommonStr*, ObjectStr*, Node*);
static void BayesFree (CommonStr*, ObjectStr*, Node*, Node*);
// Engines
static int DoOperations(OperStr*, CommonStr*, ObjectStr*, Node*, int);
static int Do1operation(OperStr*, CommonStr*, ObjectStr*, Node*, int);
static int SetPrior (OperStr*, CommonStr*, ObjectStr*, Node*);
static int CopyObject (OperStr*, CommonStr*, ObjectStr*);
static int MCMCsetup (OperStr*, CommonStr*, ObjectStr*, Node*);
static int LifeStory1 (OperStr*, CommonStr*, ObjectStr*, Node*);
static int LifeStory2 (OperStr*, CommonStr*, ObjectStr*, Node*);
static int Chameleon1 (OperStr*, CommonStr*, ObjectStr*, Node*);
static int Chameleon2 (OperStr*, CommonStr*, ObjectStr*, Node*);
static int Leapfrog1 (OperStr*, CommonStr*, ObjectStr*, Node*);
static int Leapfrog2 (OperStr*, CommonStr*, ObjectStr*, Node*);
static int GuidedWalk (OperStr*, CommonStr*, ObjectStr*, Node*);
static int MCMCexit (OperStr*, CommonStr*, ObjectStr*, Node*);
// Event library
static double Birth (CommonStr*, int);
static double Death (CommonStr*, int);
static int SafeCube (CommonStr*, ObjectStr*);
// Atom control
static int Empty (CommonStr*, ObjectStr*);
static int Try1 (double*, CommonStr*, ObjectStr*);
static int Try2 (double*, double*, CommonStr*, ObjectStr*);
static int Insert1 (CommonStr*, ObjectStr*, Node*);
static int Insert2 (CommonStr*, ObjectStr*, Node*);
static int Delete1 (int, double*, double*, CommonStr*, ObjectStr*, Node*);
// Label library
static void Topology (CommonStr*);
static void CubetoLabel (unsigned*, ObjectStr*, CommonStr*);
static void LabeltoCube (ObjectStr*, unsigned*, CommonStr*);
static void RanLabel (unsigned*, int, unsigned*);
static void CopyLabel (unsigned*, unsigned*, int);
static void NewLabel (unsigned*, unsigned*, unsigned*, int,
int, int, unsigned*);
static int Outside (unsigned*, unsigned*, unsigned*, int);
// MassInf ancillary library
static int FluxAlloc (CommonStr*, ObjectStr*);
static int FluxInit (CommonStr*, ObjectStr*);
static int FluxCalib0 (CommonStr*, ObjectStr*, Node*);
static void FluxCalib (CommonStr*, ObjectStr*);
static void FluxFree (CommonStr*, ObjectStr*);
// MassInf outer procedures
static void FluxEmpty (double*, CommonStr*, ObjectStr*);
static int FluxTry1 (double*, CommonStr*, ObjectStr*);
static int FluxTry2 (double*, double*, CommonStr*, ObjectStr*);
static int FluxInsert1 (double*, CommonStr*, ObjectStr*);
static int FluxInsert2 (double*, CommonStr*, ObjectStr*);
static int FluxDelete1 (double*, CommonStr*, ObjectStr*);
// MassInf application procedures for user Footprints
static int AtomBits (double*, CommonStr*, int*, double*, int*, int*);
static int Overlap1 (int*, int*, int*, int);
static int Overlap2 (int*, int*, int*, int*, int*, int*, int);
static void SetIndex (int, int*, int*, int*, int*, int*, int*);
static void InsBits (double*, double*, int*, int*, double*, int);
static void DelBits (double*, double*, int*, int*, double*, int);
// MassInf application procedures for quadratic chisquared
static void SetGrad1 (double*, double*, double*, int, int*, int*, double*,
double*, double*);
static void SetGrad2 (double*, double*, double*, double*, int, int*, int*,
double*, int*, int*, double*, double*, double*,
double*, double*, double*, int*);
// MassInf application procedures for quadratic probabilities
static double GaussLhood (int, double*, double*, double*);
static double GaussTry1 (int, double, double, double, int, double*, double*);
static void GaussTry2 (int, double, double, double, int, double*, double*,
double*, double*, double*, int*, double*, double*);
static void GaussInsert1(int, Rand_t, double, double, double, int, double*,
double*, double*);
static void GaussInsert2(int, Rand_t, double, double, double, int, double*,
double*, double*, double*, double*, int*, double*,
double*);
static double GaussLhood1 (int, double*, double*, double*, int);
static double GaussLhood2 (int, double*, double*, double*, double*, double*,
int*, double*, double*);
// without Valency ....
static double Gauss1Marginal(int, double, double, double, double, double);
static double Gauss2Marginal(int, double, double, double, double, double,
double, double, double);
static double Gauss1Sample (int, Rand_t, double, double, double, double,
double);
static void Gauss2Sample (int, Rand_t, double, double, double, double,
double, double, double, double, double*, double*);
// without ProbON ....
static double gauss1marginal(int, double, double, double, double);
static double gauss2marginal(int, double, double, double, double, double,
double, double);
static double gauss1sample (int, Rand_t, double, double, double, double);
static void gauss2sample (int, Rand_t, double, double, double, double,
double, double, double, double*, double*);
// MassInf application procedures for Poisson probabilities
static double PoissLhood (int, double*, double*, double*);
static int PoissTry1 (int, double, double, double, double*, double*,
double*, int*, int, int*, int*, double*, double*);
static int PoissTry2 (int, double, double, double, double*, double*,
double*, int*, double*, int, int*, int*, double*,
int*, int*, double*, int*, double*, double*);
static int PoissInsert1 (int, Rand_t, double, double, double, double*,
double*, double*, int*, int, int*, int*, double*,
double*);
static int PoissInsert2 (int, Rand_t, double, double, double, double*,
double*, double*, int*, double*, int, int*, int*,
double*, int*, int*, double*, int*, double*,
double*);
static double PoissLhood1 (double*, double*, double*, int, int*, int*,
double*, double*, int);
static double PoissLhood2 (double*, double*, double*, double*, int, int*,
int*, double*, int*, int*, double*, int*,
double*, double*);
// without Valency ....
static int Poiss1Marginal(int, double, double, double, double*, double*,
double*, int*, int, int*, double*, double*);
static int Poiss2Marginal(int, double, double, double, double*, double*,
double*, int*, double*, int, int*, double*, int,
int*, double*, double*, double*);
static int Poiss1Sample (int, Rand_t, double, double, double, double*,
double*, double*, int*, int, int*, double*,
double*);
static int Poiss2Sample (int, Rand_t, double, double, double, double*,
double*, double*, int*, double*, int, int*,
double*, int, int*, double*, double*, double*);
// without ProbON ....
static int Poisson1 (int, Rand_t, double, double, double*, double*,
double*, int*, int, int*, double*, double*);
static int Poisson2 (int, Rand_t, double, double, double*, double*,
double*, int*, double*, int, int*, double*, int,
int*, double*, double*, double*);
static double poiss1lhood (double, double*, double*, double*, int, int*,
double*);
static void poiss2lhood (double, double, double*, double*, double*,
double*, int, int*, double*, int, int*, double*,
double*, double*);
//=============================================================================
//
// BayeSys3 main procedures
// main
// |
//>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
// BayeSys3
// | \_____________________________________________________________
// | | | | | | |
// | PriorInit Control MCMCengines BayesAlloc BayesFree FillOcean
// | \ Anneal / \ BayesInit
// | \ | / \ /
// | DoOperations Topology
// | |
// | Do1operation
// | _____________|______________________________________________
// | | | | | | |
// | CopyObject SetPrior MCMCsetup LifeStory1 LifeStory2 MCMCexit
// | | | Chameleon1 /|
// | | | Chameleon2 / |
// | | | Leapfrog1 / |
// | | | Leapfrog2 / |
// | | | GuidedWalk / |
// | | | \ / |
// | Empty Empty Insert1 Insert2
// | Insert1 Insert1 Delete1 Try2
// | Try1 Try1
// |
// | Empty Insert1 Try1 Delete1 Insert2 Try2
// | | | \_________|_\______|_\_________|_\_________|_\___
// | | | | | | | |
//<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
// | | | | | | | |
// | UserEmpty UserInsert1 UserTry1 UserDelete1 UserInsert2 UserTry2 |
// | |
// | |
// UserMonitor UserFoot
//=============================================================================
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: BayeSys3
//
// Purpose: Perform Markov chain Monte Carlo algorithm for
// Bayesian analysis or maximisation over unit hypercube,
// using an ensemble of one or more objects.
//
// History: JS BayeSys1 3 Mar 1999 - 3 Nov 2000
// BayeSys2 25 Apr 2001 - 10 Sep 2001
// BayeSys3 12 Jan 2002 - 3 Feb 2004
//-----------------------------------------------------------------------------
//
int BayeSys3( // O +ve finish code from UserMonitor (or error)
CommonStr* Common, // I O General information
ObjectStr* Objects) // O ENSEMBLE of objects
{
static const double BIG = DBL_MAX / 3.0000; // for annealing protection
static const int NOCEAN = 50000; // max # atoms in Ocean, for atom-widths
int NTABLE = 1000; // current size of evidence table
#undef NEXTRA
#define NEXTRA 12 /* # likelihoods in prior settings */
int ENSEMBLE = Common->ENSEMBLE;
int Valency = Common->Valency;
double Lextra[NEXTRA]; // Old likelihoods for stability
Node* Links = NULL; // Linked lists of atom labels
Node Ocean[1]; // Linked list of accumulated atoms
double cold; // Old reciprocal temperature
double dcool; // Cooling increment
double Lbar; // <logL>
double* Ltable = NULL; // table of strictly increasing logL values
double* ctable = NULL; // table of strictly increasing cool values
int* ntable = NULL; // table of occupation numbers for averaging
double Evid; // SUM[1..] Ltable[i] * (ctable[i]-ctable[i-1])
int j; // table counter
int k; // object counter
int finish; // exit code from UserMonitor
double t; // temporary
int CALLvalue = 0;
#if DEBUG
printf("WARNING: DEBUG switched on\n");
#endif
// Check input parameters
if ( Common->ENSEMBLE < 1 ) return E_BAYESYS_PARMS;
if ( Common->MinAtoms < 1 ) return E_BAYESYS_PARMS;
if ( Common->MaxAtoms && Common->MaxAtoms < Common->MinAtoms )
return E_BAYESYS_PARMS;
if ( Common->MaxAtoms < Common->MinAtoms && Common->Alpha == 0.0 )
return E_BAYESYS_PARMS;
if ( Common->Rate <= 0.0 ) return E_BAYESYS_PARMS;
if ( Common->Ndim < 1 ) return E_BAYESYS_PARMS;
if ( Valency )
{
if ( Common->MassInf != 0 && Common->MassInf != 1
&& Common->MassInf != 2 && Common->MassInf != 3
&& Common->MassInf != 100 && Common->MassInf != 101 )
return E_MASSINF_PARMS;
if ( Common->Ndata < 0 ) return E_MASSINF_PARMS;
if ( ! Common->Data ) return E_MASSINF_PARMS;
if ( ! Common->Acc ) return E_MASSINF_PARMS;
if ( Common->ProbON <= 0.0 ) return E_MASSINF_PARMS;
if ( Common->MassInf >= 100 )
for ( k = 0; k < Common->Ndata; k++ )
{
if ( Common->Acc[k] < 0. || Common->Data[k] + Common->Acc[k] < 0. )
return E_MASSINF_DATA;
if ( Common->Acc[k] == 0.0 && Common->Data[k] != 0.0 )
return E_MASSINF_DATA;
}
}
// Allocate memory
CALLOC(Ltable, NTABLE, double)
CALLOC(ctable, NTABLE, double)
CALLOC(ntable, NTABLE, int)
CALLOC(Links, ENSEMBLE, Node)
CALL( BayesAlloc(Common, Objects, Links, Ocean) )
// Initialise system
CALL( BayesInit(Common, Objects) )
// Initialise prior objects
CALL( PriorInit(Common, Objects, Links, NEXTRA, Lextra) )
// Enter at prior (infinite temperature)
dcool = BIG;
ntable[0] = j = 0;
ctable[0] = Ltable[0] = Evid = 0.0;
do
{
Common->Nsystem ++;
// Update Ocean
CALL( FillOcean(Common, Objects, Ocean, NOCEAN) )
// Controlled cooling
cold = Common->cool; // previous value
CALL( Control(Common, Objects, NEXTRA, Lextra, &t) )
Common->cool += t;
if ( Common->cool > cold + 2.0000 * dcool ) // MAX allowable cooling to
Common->cool = cold + 2.0000 * dcool; // prevent fast acceleration
// User-limited cooling, at posterior (= 1) or beyond (> 1)
// Reset any nuisance parameters
// Collect statistics and display diagnostics
CALL( UserMonitor(Common, Objects) ) // should not increase dcool
finish = CALLvalue; // enables user to exit
if ( Common->cool > BIG ) // avoid overflow
Common->cool = BIG;
dcool = Common->cool - cold;
// Cool ensemble by copying (user's nuisance parameters won't be copied)
CALL( Anneal(Common, Objects, NEXTRA, dcool) )
// Evolve
CALL( MCMCengines(Common, Objects, Links) )
// Evidence and Information diagnostics
Lbar = 0.0;
for ( k = 0; k < ENSEMBLE; k++ )
Lbar += Objects[k].Lhood;
Lbar /= ENSEMBLE;
if ( j == NTABLE - 1 )
{
NTABLE += NTABLE / 2;
REALLOC(Ltable, NTABLE, double)
REALLOC(ctable, NTABLE, double)
REALLOC(ntable, NTABLE, int)
}
if ( Common->cool > ctable[j] ) // new table value
{
j++;
ctable[j] = Common->cool;
Ltable[j] = Lbar;
ntable[j] = 1;
Evid += (ctable[j] - ctable[j-1]) * Ltable[j];
}
else // update existing top value
{
Evid -= (ctable[j] - ctable[j-1]) * Ltable[j];
Ltable[j] = (ntable[j] * Ltable[j] + Lbar) / (ntable[j] + 1);
ntable[j] ++;
Evid += (ctable[j] - ctable[j-1]) * Ltable[j];
}
// Prune tables to satisfy known constraint: logL increasing function of cool
// If logL tries to decrease, feed the deficit backwards
while ( j > 1 && Ltable[j-1] >= Ltable[j] )
{
Evid -= (ctable[j] - ctable[j-1]) * Ltable[j];
j--;
Evid -= (ctable[j] - ctable[j-1]) * Ltable[j];
ctable[j] = ctable[j+1];
Ltable[j] = (ntable[j] * Ltable[j] + ntable[j+1] * Ltable[j+1])
/ (ntable[j] + ntable[j+1]);
ntable[j] += ntable[j+1];
Evid += (ctable[j] - ctable[j-1]) * Ltable[j];
}
Common->Evidence = Evid;
Common->Information = ctable[j] * Ltable[j] - Evid;
// Exit?
}
while ( ! finish );
CALLvalue = finish;
Exit:
// Free memory
BayesFree(Common, Objects, Links, Ocean);
FREE(Links)
FREE(ntable)
FREE(ctable)
FREE(Ltable)
return CALLvalue;
#undef NEXTRA
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: BayeShape
//
// Purpose: Transfer BayeSys hypercube to User's shape.
//
// Shape Description Prob(Coord[i]) Range of i
//
// 0 Permutation uniform on integers Perm(0...N-1) 0...N-1
// 1 Positive orthant exp(-x) in x > 0 0...N-1
// 2 Simplex volume uniform in SUM(x) < 1 0...N-1
// 3 Simplex surface uniform on SUM(x) = 1 0...N
// 4 Ordered uniform in 0 < x[0] < x[1] < ... < 1 0...N-1
// 5 Bell Normal(0,1) in -inf < x < inf 0...N-1
// 6 Sphere volume uniform in SUM(x^2) < 1 0...N-1
// 7 Hemisphere surface uniform on SUM(x^2) = 1, x[N]>0 0...N
// 8 Sphere surface uniform on SUM(x^2) = 1 0...N
//
// Notes: The hypercube has 2^N corners, at which there may be singular
// anisotropy in the exploration. It is better to keep any such
// singularities separated and diluted.
//
// 0 Permutation of integers 0,1,...,N-1.
// No singularity, permutation given by ranked order of Cube[0...N-1].
//
// 1 Positive orthant
// No singularity.
// The origin remains unchanged.
// Other corners are at infinity.
//
// 2 Simplex volume
// The origin remains unchanged.
// Its N adjacent corners go to the remaining N vertices x[i]=1
// of the simplex.
// The remaining 2^N-N-1 corners are isolated singularities
// distributed over the simplex roof SUM(x)=1.
//
// 3 Simplex surface
// The origin moves to the upper vertex x[N]=1.
// Its N adjacent corners go to the other surface vertices x[i]=1.
// The remaining 2^N-N-1 corners are isolated singularities
// distributed over the floor x[N]=0.
//
// 4 Ordered
// The origin does not move.
// Its N adjacent corners go to the other vertices (0,..0,0,1,1,..,1).
// The remaining 2^N-N-1 corners are isolated singularities
// distributed over the roof x[N-1]=1.
// This is better than just sorting the x[i] from a hypercube,
// with its N!-to-1 overlapping.
//
// 5 Bell
// No singularity.
// The hypercube centre becomes the origin.
// All corners project out to infinity.
//
// 6 Sphere volume
// All corners are isolated singularities on the sphere surface
// SUM(x^2)=1, distributed with their original cubic symmetry.
// This is much better than concentrating all the singularity at
// the centre, as with using polar coordinates.
//
// 7 Hemisphere surface
// All corners are isolated singularities at the equator x[N]=0,
// distributed with their original cubic symmetry.
//
// 8 Sphere surface
// All corners are isolated singularities at the surface's equator
// x[N]=0, distributed with their original cubic symmetry.
// The penalty for having this arrangement is that the north and south
// hemispheres touch everywhere, with even Hilbert points defined as
// north x[N]>0 and odd Hilbert points defined as south x[N]<0.
// This will slow exploration because about half of the trial
// points will be in the wrong hemisphere. And there will be trouble
// if an over-intelligent user tries to hide some information of his
// own in this bit of lowest arithmetical significance.
// The alternative, of collecting all the singularities together
// down at the south pole, is worse.
//
// History: JS 18 Sep 2003, 20 Oct 2003
//-----------------------------------------------------------------------------
//
void BayeShape(
double* Coord, // O coordinates [N] or [N+1]
double* Cube, // I hypercube position [N]
int N, // I dimension
int Shape) // I choice of shape
{
static const double logG1[20] = // log( (N/2)! )
{
0.0000000000000000, -0.1207822376352452, 0.0000000000000000,
0.2846828704729193, 0.6931471805599453, 1.2009736023470752,
1.7917594692280550, 2.4537365708424432, 3.1780538303479458,
3.9578139676187183, 4.7874917427820458, 5.6625620598571409,
6.5792512120101012, 7.5343642367587300, 8.5251613610654147,
9.5492672573009951, 10.6046029027452509, 11.6893334207972703,
12.8018274800814691, 13.9406252194037652
};
static const double Z = (unsigned)(-1) + 1.0; // 2^32
static const double logpibytwo = 0.45158270528945486473;
unsigned hemisphere;
double p, q, r, rr, s, t, inward, inwardN, outward, scale;
int i;
switch ( Shape )
{
case 0:
ShapeIndex(N, Cube, Coord);
break;
case 1:
case 2:
case 3:
case 4:
for ( i = 0; i < N; i++ )
Coord[i] = -log(Cube[i]);
if ( Shape == 1 )
break;
r = 0.0;
for ( i = 0; i < N; i++ )
r += Coord[i]; // Old radius
s = t = q = exp(-r / N);
p = r * q;
for ( i = 1; i < N; i++ )
{
t *= p / i;
s = s * q + t;
} // Outward cumulant
s = (s * s < DBL_EPSILON) ? 1.0 - s / N
: pow(1.0 - s, 1.0 / N); // New radius
s /= r;
for ( i = 0; i < N; i++ ) // Rescale
Coord[i] *= s;
if ( Shape == 2 )
break;
t = 1.0;
for ( i = 0; i < N; i++ )
t -= Coord[i];
Coord[N] = t;
if ( Shape == 3 )
break;
for ( i = 1; i <= N; i++ )
Coord[i] += Coord[i-1];
break;
case 5:
case 6:
case 7:
case 8:
for ( i = 0; i < N; i++ )
Coord[i] = InvNorm(Cube[i]);
if ( Shape == 5 )
break;
rr = 0.0;
for ( i = 0; i < N; i++ )
{
Coord[i] = t = InvNorm(Cube[i]);
rr += t * t;
}
r = sqrt(rr);
scale = (N < 20) ? logG1[N] : logGamma(N / 2. + 1.);
scale = sqrt(2.0) / exp(scale / N);
inwardN = r * scale;
inward = pow(inwardN, N);
outward = 1.0 - inward; // polar limit
if ( inward * inward > DBL_EPSILON ) // non-polar evaluation
{
if ( N & 1 )
{
q = exp(-rr / (N + 1.0));
p = q * rr;
t = q / rr;
s = 0.0;
for ( i = 1; i < N; i += 2 )
{
t *= p / i;
s = s * q + t;
}
s = exp(logerf(r, 1) - 0.5 * (rr + logpibytwo)) + r * s;
}
else
{
t = s = q = exp(- rr / N);
p = q * rr;
for ( i = 2; i < N; i += 2 )
{
t *= p / i;
s = s * q + t;
}
}
outward = s;
inward = 1.0 - outward;
inwardN = pow(inward, 1.0 / N);
}
if ( Shape == 6 )
{
scale = (outward * outward < DBL_EPSILON)
? (1.0 - outward / N) / r : inwardN / r;
for ( i = 0; i < N; i++ )
Coord[i] *= scale;
break;
}
ShapeSolve(N, outward, inwardN, &scale, &Coord[N]);
scale /= r;
for ( i = 0; i < N; i++ )
Coord[i] *= scale;
if ( Shape == 7 )
break;
hemisphere = 0;
for ( i = 0; i < N; i++ )
hemisphere ^= (unsigned)(Cube[i] * Z); // Hilbert parity
if ( hemisphere & 1 )
Coord[N] = -Coord[N];
break;
default:
for ( i = 0; i < N; i++ )
Coord[i] = Cube[i];
break;
}
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: ShapeSolve
//
// Purpose: Latitude phi for which
// ShapeCumul(phi) / ShapeCumul(PI/2) = outward
// Equator is outward = 0, phi = 0
// North pole is outward = 1, phi = PI/2
//
// Method: FROWN(a) = ShapeCumul(a) is concave,
// FROWN''(a) < 0,
// so if a < aim, tangent meets aim at better lower bound
// SMILE(b) = - (ShapeCumul(PI/2) - ShapeCumul(b))^(1/N) is convex,
// SMILE''(b) > 0,
// so if b > aim, tangent meets aim at better upper bound
// Chop between lower and upper bounds
//
// History: JS 18 Sep 2003
//-----------------------------------------------------------------------------
static
void ShapeSolve(
int N, // I dimension of surface of sphere
double outward, // I poleward cumulant
double inwardN, // I (equator-ward cumulant)^(1/N)
double* cosp, // O cos(latitude)
double* sinp) // O sin(latitude)
{
static const double pibytwo = 1.57079632679489661923;
double frac = 1.0 / N;
double a; // left bound
double ya; // FROWN(a)
double ma; // FROWN'(a) > 0
double b; // right bound
double yb; // SMILE(b)
double mb; // SMILE'(b) > 0
double c; // central estimate
double yc; // ShapeCumul(c)
double mc; // ShapeCumul'(c)
double top; // ShapeCumul(PI/2)
double aim; // required value for FROWN
double bim; // required value for SMILE
int iter; // 5 chops suffice for full accuracy
if ( N == 1 )
{
a = outward * pibytwo;
*cosp = cos(a);
*sinp = sin(a);
return;
}
if ( N == 2 )
{
*cosp = sqrt(1.0 - outward * outward);
*sinp = outward;
return;
}
top = ShapeCumul(N, pibytwo, &mc);
a = outward * top;
b = a * a * (N - 2) / 6.0;
if ( b * b <= DBL_EPSILON )
{
*sinp = a * (1.0 + b);
*cosp = sqrt(1.0 - *sinp * *sinp);
return;
}
a = inwardN * pow(N * top, frac);
b = a * a / (2.0 * N + 4.0);
if ( b * b <= DBL_EPSILON )
{
*cosp = a * (1.0 - b);
*sinp = sqrt(1.0 - *cosp * *cosp);
return;
}
aim = outward * top;
bim = - pow(top - aim, frac);
a = 0.0;
ya = 0.0;
ma = 1.0;
b = pibytwo;
yb = 0.0;
mb = pow(frac, frac);
for ( iter = 0; iter < 5; iter++ )
{
c = (a + b) / 2.0;
yc = ShapeCumul(N, c, &mc);
if ( yc < aim )
{
a = c;
ya = yc;
ma = mc;
a += (aim - ya) / ma;
}
else
{
b = c;
yb = - pow(top - yc, frac);
mb = - mc * frac * yb / (top - yc);
b += (bim - yb) / mb;
}
}
// protected interpolation
ya = ShapeCumul(N, a, &ma) - aim;
yb = ShapeCumul(N, b, &mb) - aim;
if ( ya >= yb )
c = (a + b) / 2.0; // unusual
else
{
c = (a * yb - b * ya) / (yb - ya); // linear
mc = (mb - ma) / (yb - ya);
c += 0.5 * mc * (b - c) * (c - a); // quadratic correction
}
if ( c < a ) c = a; // final protection
if ( c > b ) c = b; // final protection
*cosp = cos(c);
*sinp = sin(c);
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: ShapeCumul
//
// Purpose: phi N-1
// INTEGRAL cos (theta) d(theta)
// 0
//
// History: JS 18 Sep 2003
//-----------------------------------------------------------------------------
static
double ShapeCumul( // O integral
int N, // I dimension of surface of hemisphere
double phi, // I latitude
double* deriv) // O cos(phi)^(N-1)
{
double r, s, t, u, sinp, cosp, cos2;
int i;
sinp = sin(phi);
cosp = cos(phi);
cos2 = cosp * cosp;
s = t = u = 1.0;
for ( i = (N & 1) + 2; i < N; i += 2 )
{
r = 1.0 / i;
t *= 1.0 - r;
u *= cos2;
s += t * u;
}
t *= N - 1.0;
s *= sinp;
u *= cosp;
if ( N & 1 )
{
s = (phi + cosp * s) / 2.0;
u *= cosp;
t /= 2.0;
}
*deriv = u;
return s / t;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: ShapeIndex
//
// Purpose: Index vector y into increasing order
// y[p[0]] <= y[p[1]] <= .... <= y[p[n-1]]
//
// History: JS 27 Apr 1999, 27 Oct 2003
//-----------------------------------------------------------------------------
static
void ShapeIndex(
int N, // I dimension
double* y, // I vector being indexed by value
double* p) // O index (integer values)
{
int j, k, l, m, q;
double r;
if ( N <= 1 )
{
p[0] = 0.0;
return;
}
for ( j = 0; j < N; j++ )
p[j] = (double)j;
l = N / 2;
k = N - 1;
while ( 1 )
{
if ( l > 0 )
{
q = (int)p[--l];
r = y[q];
}
else
{
q = (int)p[k];
r = y[q];
p[k--] = p[0];
if ( k == 0 )
{
p[0] = (double)q;
return;
}
}
m = l;
j = l + l + 1;
while ( j <= k )
{
if ( j < k && y[(int)p[j]] < y[(int)p[j+1]] )
j++;
if ( r < y[(int)p[j]] )
{
p[m] = p[j];
m = j;
j = j + j + 1;
}
else
j = k + 1;
}
p[m] = (double)q;
}
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: BayesAlloc
//
// Purpose: Allocate memory for BayeSys (and MassInf)
//
// History: JS 16 Oct 2002, 1 Feb 2003, 13 Sep 2003
//-----------------------------------------------------------------------------
static
int BayesAlloc( // O 0, or -ve error
CommonStr* Common, // I(O) general information
ObjectStr* Objects, // (O) new ENSEMBLE of objects [ENSEMBLE]
Node* Links, // (O) new trees [ENSEMBLE]
Node* Ocean) // (O) new ocean [1]
{
int ENSEMBLE = Common->ENSEMBLE;
int Ndim = Common->Ndim;
int Valency = Common->Valency;
int Nsize = Ndim + Valency + 1;
ObjectStr* Object;
int j, k;
int CALLvalue = 0;
// Allow subsequent CALLOC memory allocation to fail gracefully
Common->offset = NULL;
Common->permute = NULL;
// Allocate
// Common
CALLOC(Common->offset, Ndim, unsigned)
CALLOC(Common->permute, Ndim, int)
// Objects
for ( k = 0; k < ENSEMBLE; k++ )
{
Object = &Objects[k];
Object->xLabel = NULL;
Object->yLabel = NULL;
Object->xOrigin = NULL;
Object->yOrigin = NULL;
Object->xTry = NULL;
Object->yTry = NULL;
Object->work = NULL;
Object->Cubes = NULL;
CALLOC(Object->xLabel, Ndim, unsigned)
CALLOC(Object->yLabel, Ndim, unsigned)
CALLOC(Object->xOrigin, Ndim, unsigned)
CALLOC(Object->yOrigin, Ndim, unsigned)
CALLOC(Object->xTry, Ndim, unsigned)
CALLOC(Object->yTry, Ndim, unsigned)
CALLOC(Object->work, Ndim, unsigned)
Object->Nstore = Common->MinAtoms + 2;
CALLOC(Object->Cubes, Object->Nstore, double*)
for ( j = 0; j < Object->Nstore; j++ )
CALLOC(Object->Cubes[j], Nsize, double)
CALL( SetLink(Ndim, &Links[k]) )
}
if ( Valency )
CALL( FluxAlloc(Common, Objects) )
// Ocean
CALL( SetLink(Ndim, Ocean) )
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: BayesInit
//
// Purpose: Initialise BayeSys (and MassInf)
//
// History: JS 16 Oct 2002, 1 Feb 2003
//-----------------------------------------------------------------------------
static
int BayesInit( // O 0, or -ve error
CommonStr* Common, // I O general information
ObjectStr* Objects) // O new ENSEMBLE of objects
{
unsigned* Rand = Common->Rand;
int ENSEMBLE = Common->ENSEMBLE;
int Ndim = Common->Ndim;
int Valency = Common->Valency;
int Nsize = Ndim + Valency + 1;
ObjectStr* Object;
int i, j, k;
int CALLvalue = 0;
// Initialise BayeSys
Common->Nbits = 0;
for ( Rand[0] = 1; Rand[0]; Rand[0] <<= 1 )
Common->Nbits++;
CALL( RanInit(Rand, Common->Iseed) )
Common->Iseed = CALLvalue;
Common->cool = 0.0;
Common->Evidence = 0.0;
Common->Information = 0.0;
Common->Nsystem = 0;
Common->Success = 0.0;
Common->CPU = 0.0;
for ( k = 0; k < ENSEMBLE; k++ )
{
Object = &Objects[k];
j = Ranint(Rand);
if ( j < 0 )
j = ~j;
CALL( RanInit(Object->Rand, j) )
Objects[k].Natoms = 0;
for ( j = 0; j < Object->Nstore; j++ )
for ( i = 0; i < Nsize; i++ )
Object->Cubes[j][i] = 0.0;
Object->reset = 1;
}
Topology(Common);
if ( Valency )
CALL( FluxInit(Common, Objects) )
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: PriorInit
//
// Purpose: Initialise prior objects and extra loglikelihood values
//
// History: JS 16 Oct 2002, 1 Feb 2003
//-----------------------------------------------------------------------------
static
int PriorInit( // O 0, or -ve error
CommonStr* Common, // I O general information
ObjectStr* Objects, // O ENSEMBLE of objects
Node* Links, // (O) empty on exit
int NEXTRA, // I # extra loglikelihood values
double* Lextra) // O extra loglikelihood values [NEXTRA]
{
int ENSEMBLE = Common->ENSEMBLE;
OperStr* Operations = NULL; // list of operations [ENSEMBLE]
OperStr* Oper; // & individual operation
int i, j, k;
int CALLvalue = 0;
// Pre-calibrate objects
if ( Common->Valency )
CALL( FluxCalib0(Common, Objects, Links) )
CALLOC(Operations, ENSEMBLE, OperStr)
// Find O(10) preliminary prior objects, preferably all with different L
Operations->engine = 0; // SetPrior
Operations->iType = -1;
Operations->i = 0; // operate on objects[0]
Operations->jType = 0;
Operations->kType = 0;
for ( k = 0; k < NEXTRA; k++ )
{
for ( i = 0; i < NEXTRA; i++ )
{ // try to ensure all L different but don't insist
CALL( DoOperations(Operations, Common, Objects, Links, 1) )
for ( j = 0; j < k; j++ )
if ( Objects->Lhood == Lextra[j] )
break;
if ( j == k )
break;
}
Lextra[k] = Objects->Lhood;
}
// Set ENSEMBLE of prior objects
for ( i = 0; i < ENSEMBLE; i++ )
{
Oper = &Operations[i];
Oper->engine = 0; // SetPrior
Oper->iType = -1;
Oper->i = i;
Oper->jType = 0;
Oper->kType = 0;
}
CALL( DoOperations(Operations, Common, Objects, Links, ENSEMBLE) )
Exit:
FREE(Operations)
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Control
//
// Purpose: Rate-limited allowable cooling.
// Aim for about Rate copy operations per object
// (see Anneal for documentation on this).
//
// Guard against accidental near-coalescence of likelihood values
// (which would allow arbitrarily large cooling), by including
// artificial extra loglikelihood values, perhaps from old ensembles
//
// History: John Skilling 28 Jan 2002, 25 Mar 2002, 18 Jul 2002
// 17 Sep 2002 Rate pertains to most likely object
// 17 Dec 2002 Lextra kept different
// 20 Aug 2003 Separate Sort2 call
// 3 Feb 2004 Use <# copies> not #copies(Lmax)
//-----------------------------------------------------------------------------
static
int Control( // O 0, or -ve error
CommonStr* Common, // I General information
ObjectStr* Objects, // I Sample objects, with Lhood [ENSEMBLE]
int Nextra, // I # extra objects
double* Lextra, // I O Extra objects for stability [Nextra]
double* dcool) // O cooling increment allowed by Rate
{
double Rate = Common->Rate;
int ENSEMBLE = Common->ENSEMBLE;
unsigned* Rand = Common->Rand;
double Lmid; // central likelihood value
double R; // Rate, adjusted for finite allowable # copies
int N; // total # likelihoods
int i, j; // counters
int chop; // binary chop counter
double a, copya; // binary chop x and y (left)
double b, copyb; // binary chop x and y (mid)
double c, copyc; // binary chop x and y (right)
double* wa; // binary chop data vector (left)
double* wb; // binary chop data vector (mid)
double* wc; // binary chop data vector (right)
double* work1 = NULL; // workspace
double* work2 = NULL; // workspace
double* work3 = NULL; // workspace
double* Lvalue = NULL; // workspace for sorted likelihoods
double* swap; // exchange pointer
double Lmax; // largest logL
int CALLvalue = 0;
// Default if all L equal or other anomaly
*dcool = 0.0;
// Read all likelihoods
N = ENSEMBLE + Nextra;
CALLOC(Lvalue, N, double)
CALLOC(work1, N, double)
CALLOC(work2, N, double)
CALLOC(work3, N, double)
for ( j = 0; j < ENSEMBLE; j++ )
Lvalue[j] = Objects[j].Lhood;
for ( ; j < N; j++ )
Lvalue[j] = Lextra[j-ENSEMBLE];
if ( N <= 1 )
return 0;
// Offset loglikelihoods to MAX=0 for safety
Lmax = Lvalue[0];
for ( i = 1; i < N; i++ )
if ( Lmax < Lvalue[i] )
Lmax = Lvalue[i];
for ( i = 0; i < N; i++ )
Lvalue[i] -= Lmax;
// Max # possible copies = max # recipients (per sample)
R = N;
for ( i = 0; i < N; i++ )
if ( Lvalue[i] == 0.0 )
R -= 1.0;
R /= N;
if ( R > 0.0 )
{
// Ensure # copies < max possible (the 3. is for rough backward compatibility)
R = 1.0 / (3. / Rate + 1.0 / R);
// Guess initial value for dcool from normally distributed Lvalues
a = b = 0.0;
for ( i = 0; i < N; i++ )
a += Lvalue[i];
a /= N;
for ( i = 0; i < N; i++ )
{
c = Lvalue[i] - a;
b += c * c;
}
b = sqrt(b / N);
a = b = 2.5066 * R / b;
// Bracket dcool by interval [a,b] a factor of 2 wide
wa = work1;
wb = work2;
for ( i = 0; i < N; i++ )
wa[i] = wb[i] = exp(a * Lvalue[i]);
copya = copyb = Copies(wa, N);
if ( copya < R )
{
do
{
a = b;
copya = copyb;
swap = wa;
wa = wb;
wb = swap;
b = 2.0 * a;
for ( i = 0; i < N; i++ )
wb[i] = wa[i] * wa[i];
copyb = Copies(wb, N);
}
while ( copyb < R );
}
else
{
do
{
b = a;
copyb = copya;
swap = wb;
wb = wa;
wa = swap;
a = b / 2.0;
for ( i = 0; i < N; i++ )
wa[i] = sqrt(wb[i]);
copya = Copies(wa, N);
}
while ( copya > R );
}
// Binary chop to accuracy 1 in 1000
wc = work3;
for ( chop = 0; chop < 10; chop++ )
{
c = (a + b) / 2;
for ( i = 0; i < N; i++ )
wc[i] = sqrt(wa[i] * wb[i]);
copyc = Copies(wc, N);
if ( copyc < R )
{
a = c;
copya = copyc;
swap = wa;
wa = wc;
wc = swap;
}
else
{
b = c;
copyb = copyc;
swap = wb;
wb = wc;
wc = swap;
}
}
// Final linear interpolation
*dcool = (b * (R - copya) + a * (copyb - R)) / (copyb - copya);
}
if ( Nextra )
{
// Keep Lextra up-to-date enough, trying to keep all different
for ( j = 0; j < Nextra; j++ )
{
Lmid = Objects[Rangrid(Rand, ENSEMBLE)].Lhood;
for ( i = 0; i < Nextra; i++ )
if ( Lextra[i] == Lmid )
break;
if ( i == Nextra )
{
Lextra[Rangrid(Rand, Nextra)] = Lmid;
break;
}
}
}
// Phenomenological correction for finite ENSEMBLE, reducing effective dcool
// (Undo correction at top of Anneal)
*dcool *= (N - 1.0) / N;
Exit:
FREE(work3);
FREE(work2);
FREE(work1);
FREE(Lvalue);
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Copies
//
// Purpose: <# copy operations per object> for weights w
//
// = SUM | w - <w> | / 2 SUM w
//
// History: JS 3 Feb 2004
//-----------------------------------------------------------------------------
static
double Copies(
double* w, // I weights
int N) // I dimension
{
double sumw, wbar, copy;
int i;
sumw = 0.0;
for ( i = 0; i < N; i++ )
sumw += w[i];
wbar = sumw / N;
copy = 0.0;
for ( i = 0; i < N; i++ )
copy += fabs(w[i] - wbar);
return copy / (2.0 * sumw);
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Anneal
//
// Purpose: Anneal ensemble by dcool, by copying from source objects "src"
// to destination objects "dest", as uniformly as possible
// consistently with excess/deficit real multiplicities N:-
//
// N(src) = exp(dcool * (Lhood[src] - Lbar)) - 1.0
// for Lhood[src] > Lbar only
// N(dest) = 1.0 - exp(dcool * (Lhood[dest] - Lbar))
// for Lhood[dest] < Lbar only
// where Lbar is adjusted for equality in
// # copy operations = SUM[src] N(src) = SUM[dest] N(dest).
//
// A source will be copied either n or n+1 times, where
// n = (int)N(src) = 0,1,2,...
// A destination will be overwritten, with probability N(dest).
//
// History: John Skilling 28 Jan 2002, 25 Mar 2002, 18 Jul 2002
// 17 Sep 2002 Return # copies
// 3 Feb 2004 Internal vector allocations
//-----------------------------------------------------------------------------
static
int Anneal( // O #copies diagnostic, or -ve error
CommonStr* Common, // I CopyObject info
ObjectStr* Objects, // I Sample objects [ENSEMBLE]
int Nextra, // I # extra objects, for phenomenological de-correction
double dcool) // I Cooling increment
{
int ENSEMBLE = Common->ENSEMBLE;
unsigned* Rand = Common->Rand;
OperStr* Operations = NULL; // list of operations [ENSEMBLE]
OperStr* Oper; // & individual operation
double Lmid; // Central likelihood value
double r; // Excess accumulator, also used for indexing
double s; // Deficit accumulator
double p; // COPY accumulator
double pmax; // Accumulator limit
double w; // Excess/deficit = weight - 1
int src; // Identifier for duplication
int dest; // Identifier for destruction
int i; // ENSEMBLE counter
int copy; // # copies
double* Lvalue = NULL; // workspace for sorted likelihoods
int* Lindex = NULL; // workspace for sorted likelihoods
int CALLvalue = 0;
if ( ENSEMBLE <= 1 )
return CALLvalue; // (nothing to do)
// Undo phenomenological correction for finite ENSEMBLE
// (Correction defined at bottom of Control)
i = ENSEMBLE + Nextra;
dcool /= (i - 1.0) / i;
// Read all likelihoods
CALLOC(Lindex, ENSEMBLE, int)
CALLOC(Lvalue, ENSEMBLE, double)
for ( i = 0; i < ENSEMBLE; i++ )
{
Lindex[i] = i;
Lvalue[i] = Objects[i].Lhood;
}
// Sort (index,likelihood) to increasing likelihood
Sort2(Lindex, Lvalue, ENSEMBLE);
// Offset loglikelihoods to MAX=0 for safety and convenience
for ( i = 0; i < ENSEMBLE; i++ )
Lvalue[i] -= Lvalue[ENSEMBLE - 1];
// Central likelihood value
r = 0.0;
for ( i = 0; i < ENSEMBLE; i++ )
r += exp(dcool * Lvalue[i]);
Lmid = log(r / ENSEMBLE) / dcool;
// Find total excess and (equal) total deficit weights
r = s = 0.0;
for ( i = 0; i < ENSEMBLE; i++ )
{
w = Lvalue[i] - Lmid;
if ( w > 0.0 )
r += exp(dcool * w) - 1.0;
if ( w < 0.0 )
s -= exp(dcool * w) - 1.0;
}
pmax = (r < s) ? r : s; // (use the smaller for safety)
// Copy whenever cumulant excess/deficit weights step another integer
// Use ordered likelihoods as a refinement to cool more accurately
CALLOC(Operations, ENSEMBLE, OperStr)
copy = 0;
r = s = 0.0;
dest = src = -1;
for ( p = Randouble(Rand); p < pmax; p += 1.0 )
{
while ( r < p )
{
w = Lvalue[++src] - Lmid;
if ( w > 0.0 )
r += exp(dcool * w) - 1.0;
}
while ( s < p )
{
w = Lvalue[++dest] - Lmid;
if ( w < 0.0 )
s -= exp(dcool * w) - 1.0;
}
Oper = &Operations[copy];
Oper->engine = 1; // CopyObject
Oper->iType = -1;
Oper->i = Lindex[dest];
Oper->jType = 1;
Oper->j = Lindex[src];
Oper->kType = 0;
copy++;
}
CALL( DoOperations(Operations, Common, Objects, NULL, copy) )
CALLvalue = copy;
Exit:
FREE(Operations)
FREE(Lvalue)
FREE(Lindex)
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Sort2
//
// Purpose: Sort on value into increasing order
//
// History: JS 20 Aug 2003 From Qsort of 29 Aug 1991
//-----------------------------------------------------------------------------
static
void Sort2(
int* Lindex, // I O subsidiary to Lvalue
double* Lvalue, // I O sort on this
int N) // I dimension
{
double r; // accumulator
int j, k, l, m, q; // indexing counters
l = N / 2;
k = N - 1;
while ( 1 )
{
if ( l > 0 )
{
q = Lindex[--l];
r = Lvalue[l];
}
else
{
q = Lindex[k];
r = Lvalue[k];
Lindex[k] = Lindex[0];
Lvalue[k--] = Lvalue[0];
if ( k == 0 )
{
Lindex[0] = q;
Lvalue[0] = r;
break;
}
}
m = l;
j = l + l + 1;
while ( j <= k )
{
if ( j < k && Lvalue[j] < Lvalue[j+1] )
j++;
if ( r < Lvalue[j] )
{
Lindex[m] = Lindex[j];
Lvalue[m] = Lvalue[j];
m = j;
j = j + j + 1;
}
else
j = k + 1;
}
Lindex[m] = q;
Lvalue[m] = r;
}
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: FillOcean
//
// Purpose: Width of atom = occupiable fraction of hypercube (as logarithm).
//
// Method: Fill Ocean of previous atoms ('o' in diagram) along Hilbert line.
// Estimate semi-width (diagram shows 2 atoms) for each current
// atom ('|') in the Ocean, allowing a safety reduction below the
// obvious estimate 0.5 * (# atoms in Ocean) / (# atoms in Object).
//
// .o..oo...oo.oo.....oo.ooo....ooooooo..ooooo...ooo.o...o...o....o.
// <--|--> <--|--> <-|-> <-|-> <-----|----->
//
// Construct symmetric window ('<-- -->' in diagram), to
// whichever left or right displacement across Ocean is closer.
// Then cancel the safety reduction to get "typical" width of atom.
//
// Dense regions of Ocean have small widths,
// sparse regions with isolated atoms have large widths.
//
// Notes: (1) Uses one standard Hilbert line so boundaries might become visible
// (2) This procedure is for display, it's not solid Bayesian analysis.
// (3) Not parallelisable.
//
// History: JS 25 Jan 2003, 20 Oct 2003
//-----------------------------------------------------------------------------
static
int FillOcean( // O 0, or -ve error
CommonStr* Common, // I O general information
ObjectStr* Objects, // I ENSEMBLE of objects [ENSEMBLE]
Node* Ocean, // I O new ocean [1]
int NOCEAN) // I max # atoms in Ocean
{
static const double Z = (unsigned)(-1) + 1.0; // 2^32
static const double SAFE = 0.3000; // safety
int ENSEMBLE = Common->ENSEMBLE; // I # objects of ensemble
int Nbits = Common->Nbits; // I # bits per word
int Ndim = Common->Ndim; // I # dimensions
int Valency = Common->Valency; // I # fluxes
unsigned* Rand = Common->Rand; // I O random generator
int Nsize = Ndim + Valency + 1;
ObjectStr* Object; // object of ensemble
int Natoms; // # atoms in object
double* Cube; // location in hypercube
unsigned* Axes; // location in hypercube, size 2^32
Atom atom[1]; // Hilbert length (standard orientation)
Atom* pCentre; // position in Ocean
int semiwidth; // atom count to windowframe either side
Atom* pLeft; // left windowframe
Atom* pRight; // right windowframe
unsigned* uleft; // distance to left windowframe
unsigned* uright; // distance to right windowframe
unsigned* uwide; // distance to closer windowframe
double logvol; // log(fraction of hypercube)
int i, j, k, n; // counters
int CALLvalue = 0;
// For each atom in ensemble...
for ( k = 0; k < ENSEMBLE; k++ )
{
Object = &Objects[k];
Natoms = Object->Natoms;
semiwidth = (int)(0.5 * SAFE * (1.0 + NumAtoms(Ocean)) / Natoms) / 2;
Axes = Object->yLabel;
atom->Label = Object->xLabel;
uleft = Object->xTry;
uright = Object->yTry;
for ( j = 0; j < Natoms; j++ )
{
// Erode old atoms
if ( NumAtoms(Ocean) && Rangrid(Rand, 2) )
{
i = Rangrid(Rand, NumAtoms(Ocean));
pCentre = FindAtom(i, Ocean);
CALL( DelAtom(pCentre, Ocean) )
}
// Don't overfill Ocean
while ( NumAtoms(Ocean) >= NOCEAN - 1 )
{
i = Rangrid(Rand, NumAtoms(Ocean));
pCentre = FindAtom(i, Ocean);
CALL( DelAtom(pCentre, Ocean) )
}
// New atom
Cube = Object->Cubes[j];
for ( i = 0; i < Ndim; i++ )
Axes[i] = (unsigned)(Z * Cube[i]);
AxestoLine(atom->Label, Axes, Nbits, Ndim);
CALL( InsAtom(atom, Ocean) )
pCentre = FindHere(atom->Label, Ocean); // necessarily present
// Window around it
i = OrderNum(pCentre);
n = i - semiwidth;
while ( n < 0 )
n += NumAtoms(Ocean);
pLeft = FindOrder(n, Ocean);
n = i + semiwidth;
while ( n >= NumAtoms(Ocean) )
n -= NumAtoms(Ocean);
pRight = FindOrder(n, Ocean);
// Closer distance
SubLabel(uleft, pCentre->Label, pLeft->Label, Ndim);
SubLabel(uright, pRight->Label, pCentre->Label, Ndim);
uwide = (CmpLabel(uright, uleft, Ndim) > 0) ? uleft : uright;
// Translate back to hypercube volume
logvol = 0.0;
for ( i = Ndim - 1; i >= 0; i-- )
{
if ( uwide[i] )
logvol = log((double)uwide[i] + exp(logvol));
logvol -= log(Z); // fraction of hypercube
}
logvol -= log(SAFE); // cancel safety factor
logvol -= log(1.0 + (1.0 - SAFE) * exp(logvol)); // ensure vol < 1
// Store
Cube[Nsize-1] = logvol;
}
}
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: MCMCengines
//
// Purpose: Apply MCMC engines for standard timestep
//
// History: JS 2 Jan 2002 - 14 Jan 2003
//-----------------------------------------------------------------------------
static
int MCMCengines( // O 0, or -ve error
CommonStr* Common, // I(O) general information
ObjectStr* Objects, // I O ENSEMBLE of objects
Node* Links) //(I O) empty on entry and exit
{
static double oldcool = 0.0; // previous cool, initialise on first call only
static double Ncall[] = {1, 1, 1, 1, 1, 1, 1, 1, 1, 1}; // # calls weighted by cool
static double CPU[] = {1, 1, 1, 1, 1, 1, 1, 1, 1, 1}; // CPU time weighted by cool
int ENSEMBLE = Common->ENSEMBLE;
unsigned* Rand = Common->Rand;
double cool = Common->cool;
OperStr* Operations = NULL; // list of operations [total]
OperStr* Oper; // & individual operation
OperStr swap; // permutation exchange
int total; // # operations
int i, j, k; // object numbers
int count; // operation counter
int engine; // engine id
int n3, n4, n5, n6, n7, n8, n9; // numbers of engine calls per object
double t; // mean CPU time in LifeStory
int CALLvalue = 0;
// Initialisation
if ( oldcool == 0.0 && cool > 0.0 )
{
t = 4.0000 * cool;
Ncall[3] = Ncall[4] = Ncall[5] = Ncall[6] = Ncall[7] = Ncall[8] = Ncall[9] = t;
CPU[3] = CPU[4] = CPU[5] = CPU[6] = CPU[7] = CPU[8] = CPU[9] = t;
}
// Regenerate Links with revised Cube-to-Label mapping
Topology(Common);
// Count MCMC operations
n3 = n4 = n5 = n6 = n7 = n8 = n9 = 0;
if ( Common->Method & 2 && Common->MaxAtoms != 1 )
{
n4 = 1;
t = CPU[4] / Ncall[4];
}
else
{
n3 = 1;
t = CPU[3] / Ncall[3];
}
if ( Common->Method & 4 && ENSEMBLE > 1 )
n5 = (int)(t / (CPU[5] / Ncall[5]));
if ( Common->Method & 8 && ENSEMBLE > 1 )
n6 = (int)(t / (CPU[6] / Ncall[6]));
if ( Common->Method & 16 )
n7 = (int)(t / (CPU[7] / Ncall[7]));
if ( Common->Method & 32 )
n8 = (int)(t / (CPU[8] / Ncall[8]));
if ( Common->Method & 64 && ENSEMBLE > 1 )
n9 = (int)(t / (CPU[9] / Ncall[9]));
total = (n3 + n4 + n5 + n6 + n7 + n8 + n9) * ENSEMBLE;
CALLOC(Operations, total, OperStr)
// Set and perform MCMC entry operations
for ( count = 0; count < ENSEMBLE; count++ )
{
Oper = &Operations[count];
Oper->engine = 2; // MCMCsetup
Oper->iType = -1;
Oper->i = count;
Oper->jType = 0;
Oper->kType = 0;
}
CALL( DoOperations(Operations, Common, Objects, Links, ENSEMBLE) )
// Set MCMC operations
Oper = Operations;
for ( count = 0; count < n3; count++ )
for ( i = 0; i < ENSEMBLE; i++ )
{
Oper->engine = 3; // LifeStory1
Oper->iType = -1;
Oper->i = i;
Oper->jType = 0;
Oper->kType = 0;
Oper++;
}
for ( count = 0; count < n4; count++ )
for ( i = 0; i < ENSEMBLE; i++ )
{
Oper->engine = 4; // LifeStory2
Oper->iType = -1;
Oper->i = i;
Oper->jType = 0;
Oper->kType = 0;
Oper++;
}
for ( count = 0; count < n5; count++ )
for ( i = 0; i < ENSEMBLE; i++ )
{
Oper->engine = 5; // Chameleon1
do j = Rangrid(Rand, ENSEMBLE);
while ( j == i ); // objects must be different
Oper->iType = -1;
Oper->i = i;
Oper->jType = -1;
Oper->j = j;
Oper->kType = 0;
Oper++;
}
for ( count = 0; count < n6; count++ )
for ( i = 0; i < ENSEMBLE; i++ )
{
Oper->engine = 6; // Chameleon2
do j = Rangrid(Rand, ENSEMBLE);
while ( j == i ); // objects must be different
Oper->iType = -1;
Oper->i = i;
Oper->jType = -1;
Oper->j = j;
Oper->kType = 0;
Oper++;
}
for ( count = 0; count < n7; count++ )
for ( i = 0; i < ENSEMBLE; i++ )
{
Oper->engine = 7; // Leapfrog1
j = Rangrid(Rand, ENSEMBLE); // objects can be same
Oper->iType = -1;
Oper->i = i;
Oper->jType = (j == i) ? 0 : 1;
Oper->j = j;
Oper->kType = 0;
Oper++;
}
for ( count = 0; count < n8; count++ )
for ( i = 0; i < ENSEMBLE; i++ )
{
Oper->engine = 8; // Leapfrog2
j = Rangrid(Rand, ENSEMBLE);
if ( j == i )
k = i;
else // either both or neither neighbour from original object
do k = Rangrid(Rand, ENSEMBLE);
while ( k == i );
Oper->iType = -1;
Oper->i = i;
Oper->jType = (j == i) ? 0 : 1;
Oper->j = j;
Oper->kType = (k == j) ? 0 : 1;
Oper->k = k;
Oper++;
}
for ( count = 0; count < n9; count++ )
for ( i = 0; i < ENSEMBLE; i++ )
{
Oper->engine = 9; // GuidedWalk
do j = Rangrid(Rand, ENSEMBLE);
while ( j == i );
do k = Rangrid(Rand, ENSEMBLE);
while ( k == i );
Oper->iType = -1;
Oper->i = i;
Oper->jType = 1;
Oper->j = j;
Oper->kType = (k == j) ? 0 : 1;
Oper->k = k;
Oper++;
}
// Perform MCMC operations
// Individual engines have detailed balance, but only LifeStory explores
// fully, so LifeStory alone ought to equilibrate (eventually).
// Other engines are slaved to LifeStory's CPU time: the slaving ratio
// is locked after burn-in, so evolution has exact detailed balance.
// Permute operations for visible detailed balance.
for ( count = 0; count < total; count++ )
{
i = Rangrid(Rand, total - count);
if ( i )
SWAP(Operations[count], Operations[count + i])
}
// Perform in permuted order
CALL( DoOperations(Operations, Common, Objects, Links, total) )
// Statistics for tuning
for ( count = 0; count < total; count++ )
{
Oper = &Operations[count];
Common->Success += Oper->Success;
Common->CPU += Oper->CPU;
if ( cool > oldcool )
{
engine = (int)Oper->engine;
CPU [engine] = CPU [engine] + cool * Oper->CPU;
Ncall[engine] = Ncall[engine] + cool;
}
}
// Set and perform MCMC exit operations
for ( count = 0; count < ENSEMBLE; count++ )
{
Oper = &Operations[count];
Oper->engine = 10; // MCMCexit
Oper->iType = -1;
Oper->i = count;
Oper->jType = 0;
Oper->kType = 0;
}
CALL( DoOperations(Operations, Common, Objects, Links, ENSEMBLE) )
oldcool = cool;
Exit:
FREE(Operations)
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: BayesFree
//
// Purpose: Free allocated memory for BayeSys (and MassInf)
//
// History: JS 16 Oct 2002, 16 Nov 2002, 1 Feb 2003
//-----------------------------------------------------------------------------
static
void BayesFree (
CommonStr* Common, // I(O) general information
ObjectStr* Objects, // (O) old objects
Node* Links, // (O) old trees
Node* Ocean) // (O) old ocean
{
int ENSEMBLE = Common->ENSEMBLE;
int Valency = Common->Valency;
ObjectStr* Object; // local object
int j; // atom counter
int k; // object counter
FreeLink(Ocean);
if ( Valency )
FluxFree(Common, Objects);
for ( k = 0; k < ENSEMBLE; k++ )
{
Object = &Objects[k];
if ( Object->Cubes )
for ( j = 0; j < Object->Nstore; j++ )
FREE(Object->Cubes[j])
FREE(Object->Cubes)
FREE(Object->work)
FREE(Object->yTry)
FREE(Object->xTry)
FREE(Object->yOrigin)
FREE(Object->xOrigin)
FREE(Object->yLabel)
FREE(Object->xLabel)
FreeLink(&Links[k]);
}
FREE(Common->permute)
FREE(Common->offset)
}
//=============================================================================
//
// Engines
//
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: DoOperations
//
// Purpose: Perform list of operations with parallelisable engine calls
//
// History: JS 25 Oct 2002
//-----------------------------------------------------------------------------
#if ! PARALLEL
static
int DoOperations( // O 0, or -ve error
OperStr* Operations, // I O all operations
CommonStr* Common, // I O general information
ObjectStr* Objects, // I O ENSEMBLE of objects
Node* Links, // I O linked lists of labels
int nOper) // I # operations
{
int op; // operation counter
int CALLvalue = 0;
time_t start, end;
int CPU;
//printf( "%d operations to do\n",nOper);
time(&start);
CPU = 0;
for ( op = 0; op < nOper; op++ )
{
Operations[op].slave = 0;
CALL( Do1operation(Operations, Common, Objects, Links, op) )
CPU += Operations[op].CPU;
}
Exit:
time(&end);
//printf("%d/%d operations done in %lf\n",nOper,CPU, difftime(end,start));
return CALLvalue;
}
#endif
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Do1operation
//
// Purpose: Distribution procedure for parallelisable engine calls
//
// History: JS 25 Oct 2002, 1 Feb 2003
//-----------------------------------------------------------------------------
static
int Do1operation( // O 0, or -ve error
OperStr* Operations, // I O all operations
CommonStr* Common, // I O general information
ObjectStr* Objects, // I O ENSEMBLE of objects
Node* Links, // I O linked lists of labels
int op) // I individual operation
{
OperStr* Oper = &Operations[op];
int CALLvalue = 0;
switch ( Oper->engine )
{
case 0:
CALL( SetPrior (Oper, Common, Objects, Links) ) break;
case 1:
CALL( CopyObject(Oper, Common, Objects ) ) break;
case 2:
CALL( MCMCsetup (Oper, Common, Objects, Links) ) break;
case 3:
CALL( LifeStory1(Oper, Common, Objects, Links) ) break;
case 4:
CALL( LifeStory2(Oper, Common, Objects, Links) ) break;
case 5:
CALL( Chameleon1(Oper, Common, Objects, Links) ) break;
case 6:
CALL( Chameleon2(Oper, Common, Objects, Links) ) break;
case 7:
CALL( Leapfrog1 (Oper, Common, Objects, Links) ) break;
case 8:
CALL( Leapfrog2 (Oper, Common, Objects, Links) ) break;
case 9:
CALL( GuidedWalk(Oper, Common, Objects, Links) ) break;
case 10:
CALL( MCMCexit (Oper, Common, Objects, Links) ) break;
}
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: SetPrior Parallel engine #0
//
// Purpose: Sample the prior to set an Object of ENSEMBLE.
// The prior on the number of atoms is as follows.
//
// (1) Alpha = 0.
// The prior is UNIFORM (and MAX must be finite).
//
// Pr(N) = 1 / (MAX+1-MIN)
//
// <N> = (MAX+MIN) / 2, var(N) = (MAX-MIN) (MAX-MIN+2) / 12
//
// (2) Alpha > 0.
// The prior is BINOMIAL.
//
// (MAX-MIN)! N-MIN MAX-N Alpha
// Pr(N) = ---------------- q (1-q) , q = -------------
// (N-MIN)!(MAX-N)! Alpha+MAX-MIN
//
// <N> = (1-q) MIN + q MAX , var(N) = (MAX-MIN) q (1-q)
//
//
// Special case MAX = infinity becomes POISSON in (N-MIN).
// -alpha N-MIN
// Pr(N) = e alpha / (N-MIN)! , N >= MIN
//
// <N> = MIN + alpha , var(N) = alpha
//
//
// (3) Alpha < 0.
// The prior is truncated GEOMETRIC.
//
// N-MIN MAX-MIN+1
// Pr(N) = a (1-a) / (1-a ) , a = |Alpha| / (|Alpha|+1)
//
// The mean <N> and variance var(N) have explicit but uninformative forms.
//
//
// Special case MAX = infinity becomes GEOMETRIC with ratio a .
// N-MIN
// Pr(N) = (1-a) a , N >= MIN
//
// <N> = MIN + alpha , var(N) = alpha (alpha + 1)
//
//
// History: JS 24 Jan 2002, 30 Sep 2002, 16 Oct 2002, 14 Jan 2003
// 1 Feb 2003, 8 Feb 2002
//-----------------------------------------------------------------------------
static
int SetPrior( // O 0, or -ve error
OperStr* Oper, // I O operation
CommonStr* Common, // I general information
ObjectStr* Objects, // O sample objects
Node* Links) //(I O) empty on entry and exit
{
Node* Link = &Links [Oper->i];
ObjectStr* Object = &Objects[Oper->i];
unsigned* Label = Object->xLabel;
unsigned* Rand = Object->Rand;
int MinAtoms = Common->MinAtoms;
int MaxAtoms = Common->MaxAtoms;
int Ndim = Common->Ndim;
double Alpha = Common->Alpha;
double Ltry;
int j;
int Natoms;
Atom* pAtom;
int CALLvalue = 0;
// # atoms
Natoms = MinAtoms;
if ( MaxAtoms > MinAtoms )
{
j = MaxAtoms - MinAtoms;
if ( Alpha == 0.0 )
Natoms += Rangrid(Rand, 1 + j);
else if ( Alpha > 0.0 )
Natoms += Ranbinom(Rand, j, Alpha / (Alpha + j));
else // Alpha < 0.0
Natoms += Rangeom(Rand, -Alpha, 1 + j);
}
else if ( MaxAtoms == 0 )
do
{
Natoms = MinAtoms;
if ( Alpha > 0.0 )
Natoms += Ranpoiss(Rand, Alpha);
else // Alpha < 0.0 (Alpha=0 excluded)
Natoms += (int)(log(Randouble(Rand)) / log(Alpha / (Alpha - 1.0)));
}
while ( Natoms < MinAtoms ); // technical overflow protection
Object->Natoms = Natoms;
CALL( SafeCube(Common, Object) )
// Sample the Cube and avoid spatial coincidences by filling Link
do
{
Object->Natoms = 0; // no Cubes exist
CALL( Empty(Common, Object) )
for ( j = 0; j < Natoms; j++ )
{
do
{
do
{
RanLabel(Label, Ndim, Rand);
LabeltoCube(Object, Label, Common);
}
while ( FindHere(Label, Link) );
CALL( Try1(&Ltry, Common, Object) )
}
while ( CALLvalue == 0 ); // repeat until atom accepted by user
CALL( Insert1(Common, Object, Link) )
}
for ( pAtom = BeginLink(Link); pAtom; pAtom = BeginLink(Link) )
CALL( DelAtom(pAtom, Link) ) // empty Link for later use
}
while ( j < Natoms );
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: CopyObject Parallel engine #1
//
// Purpose: Copy source ensemble object to destination, "*dest = *src".
// Ideally, destination object should be rebuilt afterwards to
// recover any nuisance parameters.
//
// History: JS 25 Apr 2001, 2 Jan 2002, 21 Mar 2002, 30 Sep 2002,
// 1 Feb 2003, 8 Feb 2003, 20 Aug 2003
//-----------------------------------------------------------------------------
static
int CopyObject( // O 0, or -ve error
OperStr* Oper, // I O operation
CommonStr* Common, // I(O) General information
ObjectStr* Objects) // I O Ensemble of objects
{
int Ndim = Common->Ndim;
int Valency = Common->Valency;
int Nsize = Ndim + Valency + 1;
int dest = Oper->i;
int src = Oper->j;
ObjectStr* yObject = &Objects[dest];
ObjectStr* xObject = &Objects[src];
int Natoms = xObject->Natoms;
int i, j;
int CALLvalue = 0;
if ( dest != src )
{
yObject->Lhood = xObject->Lhood;
yObject->Natoms = Natoms;
CALL( SafeCube(Common, yObject) )
for ( j = 0; j < Natoms; j++ )
for ( i = 0; i < Nsize; i++ )
yObject->Cubes[j][i] = xObject->Cubes[j][i];
if ( Valency )
yObject->FluxUnit = xObject->FluxUnit;
}
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: MCMCsetup Parallel engine #2
//
// Purpose: Re-generate Links in new topology
//
// History: JS 16 Oct 2002, 8 Feb 2003, 20 Aug 2003
//-----------------------------------------------------------------------------
static
int MCMCsetup( // O 0, or -ve error
OperStr* Oper, // I O operation
CommonStr* Common, // I general information
ObjectStr* Objects, // I O ENSEMBLE of objects
Node* Links) // O new trees
{
int MinAtoms = Common->MinAtoms;
int MaxAtoms = Common->MaxAtoms;
ObjectStr* Object = &Objects[Oper->i];
Node* Link = &Links [Oper->i];
int Natoms = Object->Natoms;
int j;
int CALLvalue = 0;
Object->Natoms = 0;
CALL( Empty(Common, Object) )
Object->reset = 0; // keep MassInf fluxes
for ( j = 0; j < Natoms; j++ )
CALL( Insert1(Common, Object, Link) )
if ( Object->Natoms < MinAtoms )
return E_BAYESYS_SYSERR;
if ( MaxAtoms && Object->Natoms > MaxAtoms )
return E_BAYESYS_SYSERR;
Object->reset = 1; // recover default state
if ( Common->Valency )
FluxCalib(Common, Object); // Re-calibrate object
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: LifeStory1 Parallel engine #3
//
// Purpose: MCMC engine, cutdown alternate to 2-atom version LifeStory2.
//
// Birth/Move/Death for one atom in an object. Explores all space.
// Success defined as birth or death if this is allowed,
// else as movement.
//
// History: JS 2 Jan 2002 - 8 Feb 2003
//-----------------------------------------------------------------------------
static
int LifeStory1( // O 0, or -ve error
OperStr* Oper, // I O operation
CommonStr* Common, // I(O) general information
ObjectStr* Objects, // I O ENSEMBLE of objects
Node* Links) // I O linked lists of labels
{
// Sampling interval: each atom is investigated about TIMESTEP times
static const double TIMESTEP = 2.0000;
int Ndim = Common->Ndim;
double cool = Common->cool;
int Nbits = Common->Nbits;
int MinAtoms = Common->MinAtoms;
int MaxAtoms = Common->MaxAtoms;
ObjectStr* Object = &Objects[Oper->i];
Node* Link = &Links [Oper->i];
unsigned* xLabel = Object->xLabel;
unsigned* Origin = Object->xOrigin;
unsigned* xTry = Object->xTry;
unsigned* Rand = Object->Rand;
int n;
int del;
int jbits;
double accept;
double Ltry;
double L0;
double L1;
double b;
double d;
double Clock;
Atom* pLeft;
Atom* pRight;
unsigned* uLeft;
unsigned* uRight;
int CPU = 1;
int Success = 0;
int CALLvalue = 0;
b = Birth(Common, Object->Natoms);
d = Death(Common, Object->Natoms);
for ( Clock = -log(Randouble(Rand)) / (b + d) ;
Clock < TIMESTEP ;
Clock += -log(Randouble(Rand)) / (b + d) )
{
n = Object->Natoms;
if ( (b + d) * Randouble(Rand) > b )
{
// Death: Natoms-1 or Natoms
del = Rangrid(Rand, Object->Natoms);
CopyLabel(xLabel, FindAtom(del, Link)->Label, Ndim);
CALL( Delete1(del, &L1, NULL, Common, Object, Link) ) CPU += 1;
}
else
{
// Birth: Natoms or Natoms+1
CALL( SafeCube(Common, Object) )
RanLabel(xLabel, Ndim, Rand);
if ( FindHere(xLabel, Link) )
continue;
LabeltoCube(Object, xLabel, Common);
CALL( Try1(&L1, Common, Object) ) CPU += 1;
if ( CALLvalue == 0 ) // abort if location rejected by user
continue;
}
L0 = Object->Lhood;
// Neighbours of selected position
if ( !(pLeft = FindLeft (xLabel, Link)) ) pLeft = EndLink(Link);
if ( !(pRight = FindRight(xLabel, Link)) ) pRight = BeginLink(Link);
uLeft = pLeft ? pLeft->Label : NULL;
uRight = pRight ? pRight->Label : NULL;
// Prepare to move
Ltry = (MaxAtoms == MinAtoms) ? cool * L1 : PLUS(cool * L0, cool * L1);
accept = Ltry + log(Randouble(Rand));
RanLabel(Origin, Ndim, Rand);
for ( jbits = Nbits * Ndim; jbits >= 0; jbits -= 1 )
{
// Slice sampling for optional atom
NewLabel(xTry, xLabel, Origin, Ndim, jbits, Nbits, Rand);
if ( Object->Natoms && Outside(xTry, uLeft, uRight, Ndim) )
continue;
LabeltoCube(Object, xTry, Common);
CALL( Try1(&L1, Common, Object) ) CPU += 1;
if ( CALLvalue == 0 ) // abort if location rejected by user
continue;
Ltry = (MaxAtoms == MinAtoms) ? cool * L1 : PLUS(cool * L0, cool * L1);
if ( Ltry >= accept )
break;
}
// Birth/Death/Move
if ( log(Randouble(Rand)) < cool * L1 - Ltry )
{
CALL( Insert1(Common, Object, Link) ) CPU += 1;
}
// Update event rates
b = Birth(Common, Object->Natoms);
d = Death(Common, Object->Natoms);
if ( (MaxAtoms != MinAtoms && Object->Natoms != n)
|| (MaxAtoms == MinAtoms && jbits > 0) ) ++ Success;
}
Exit:
Oper->CPU = CPU;
Oper->Success = Success;
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: LifeStory2 Parallel engine #4
//
// Purpose: LifeStory MCMC diffusion engine
//
// Birth/Move/Death for two adjacent atoms. Explores all space.
// Success defined as birth or death if this is allowed,
// else as movement.
//
// History: JS 2 Jan 2002 - 8 Feb 2003
//-----------------------------------------------------------------------------
static
int LifeStory2( // O 0, or -ve error
OperStr* Oper, // I O operation
CommonStr* Common, // I(O) general information
ObjectStr* Objects, // I O ENSEMBLE of objects
Node* Links) // I O linked lists of labels
{
// Sampling interval: each atom is investigated about TIMESTEP times
static const double TIMESTEP = 2.0000;
int Ndim = Common->Ndim;
double cool = Common->cool;
int Nbits = Common->Nbits;
int MinAtoms = Common->MinAtoms;
int MaxAtoms = Common->MaxAtoms;
ObjectStr* Object = &Objects[Oper->i];
Node* Link = &Links [Oper->i];
unsigned* xLabel = Object->xLabel;
unsigned* yLabel = Object->yLabel;
unsigned* xOrigin = Object->xOrigin;
unsigned* yOrigin = Object->yOrigin;
unsigned* xTry = Object->xTry;
unsigned* yTry = Object->yTry;
unsigned* Rand = Object->Rand;
int del;
int n;
int jbits;
double accept;
double Ltry;
double L1;
double L2;
double b;
double d;
double Clock;
Atom* pAtom;
Atom* pLeft;
Atom* pRight;
unsigned* uLeft;
unsigned* uRight;
int CPU = 1;
int Success = 0;
int CALLvalue = 0;
b = Birth(Common, Object->Natoms);
d = Death(Common, Object->Natoms);
for ( Clock = -log(Randouble(Rand)) / (b + d) ;
Clock < TIMESTEP ;
Clock += -log(Randouble(Rand)) / (b + d) )
{
n = Object->Natoms;
if ( (b + d) * Randouble(Rand) > b )
{
// Death: Natoms-1 or Natoms
L2 = Object->Lhood;
del = Rangrid(Rand, Object->Natoms);
CopyLabel(xLabel, FindAtom(del, Link)->Label, Ndim);
CALL( Delete1(del, NULL, NULL, Common, Object, Link) ) CPU += 1;
}
else
{
// Birth: Natoms or Natoms+1
RanLabel(xLabel, Ndim, Rand);
if ( FindHere(xLabel, Link) )
continue;
LabeltoCube(Object, xLabel, Common);
CALL( Try1(&L2, Common, Object) ) CPU += 1;
if ( CALLvalue == 0 ) //must abort here if location rejected by user
continue;
CALL( SafeCube(Common, Object) )
}
// Kill stimulation neighbour
if ( Rangrid(Rand, 2) )
{
if ( !(pAtom = FindLeft(xLabel, Link)) ) pAtom = EndLink(Link);
}
else
{
if ( !(pAtom = FindRight(xLabel, Link)) ) pAtom = BeginLink(Link);
}
del = Storage(pAtom);
CALL( Delete1(del, &L1, &L2, Common, Object, Link) ) CPU += 1;
Ltry = (MaxAtoms == MinAtoms) ? cool * L2 : PLUS(cool * L1, cool * L2);
// Neighbours of selected pair
CubetoLabel(yLabel, Object, Common);
if ( !(pLeft = FindLeft (yLabel, Link)) ) pLeft = EndLink(Link);
if ( !(pRight = FindRight(yLabel, Link)) ) pRight = BeginLink(Link);
uLeft = pLeft ? pLeft->Label : NULL;
uRight = pRight ? pRight->Label : NULL;
// Prepare to move
accept = Ltry + log(Randouble(Rand));
RanLabel(xOrigin, Ndim, Rand);
RanLabel(yOrigin, Ndim, Rand);
for ( jbits = Nbits * Ndim; jbits >= 0; jbits -= 1 )
{
// Slice sampling for replacement atom and optional atom
NewLabel(xTry, xLabel, xOrigin, Ndim, jbits, Nbits, Rand);
if ( Object->Natoms && Outside(xTry, uLeft, uRight, Ndim) )
continue;
NewLabel(yTry, yLabel, yOrigin, Ndim, jbits, Nbits, Rand);
if ( CmpLabel(xTry, yTry, Ndim) == 0 )
continue;
if ( Object->Natoms && Outside(yTry, uLeft, uRight, Ndim) )
continue;
Object->Natoms++;
LabeltoCube(Object, xTry, Common);
Object->Natoms--;
LabeltoCube(Object, yTry, Common);
CALL( Try2(&L1, &L2, Common, Object) ) CPU += 2;
if ( CALLvalue == 0 ) // abort if location rejected by user
continue;
Ltry = (MaxAtoms == MinAtoms) ? cool * L2 : PLUS(cool * L1, cool * L2);
if ( Ltry >= accept )
break;
}
// Birth/Death/Move
if ( log(Randouble(Rand)) < cool * L2 - Ltry )
{
CALL( Insert2(Common, Object, Link) ) CPU += 2;
}
else
{
CALL( Insert1(Common, Object, Link) ) CPU += 1;
}
// Update event rates
b = Birth(Common, Object->Natoms);
d = Death(Common, Object->Natoms);
if ( (MaxAtoms != MinAtoms && Object->Natoms != n)
|| (MaxAtoms == MinAtoms && jbits > 0) ) ++ Success;
}
Exit:
Oper->CPU = CPU;
Oper->Success = Success;
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Chameleon1 Parallel engine #5
//
// Purpose: MCMC engine.
//
// Tries to move atoms from one object to another,
// WITHOUT geometrical exploration. Success defined as acceptance.
//
// ========X===============X==================X=========
// |
// |
// \|/
// ====X==============X====:=====X========X=============
//
// Note: ENSEMBLE should be at least 2, obviously.
//
// History: JS 31 Jan 2002 - 8 Feb 2003
//-----------------------------------------------------------------------------
static
int Chameleon1( // O 0 = op, or -ve error
OperStr* Oper, // I O operation
CommonStr* Common, // I(O) general information
ObjectStr* Objects, // I O ENSEMBLE of objects
Node* Links) // I O linked lists of labels
{
// Sampling interval: each atom is investigated about TIMESTEP times
static const double TIMESTEP = 1.0000;
double cool = Common->cool;
ObjectStr* iObject = &Objects[Oper->i];
ObjectStr* jObject = &Objects[Oper->j];
ObjectStr* kObject;
Node* iLink = &Links [Oper->i];
Node* jLink = &Links [Oper->j];
Node* kLink;
unsigned* Rand = iObject->Rand;
int del;
double accept;
double L1;
double Ltry;
double* swap;
double b;
double d;
double constant;
double Clock;
int CPU = 1;
int Success = 0;
int CALLvalue = 0;
b = Birth(Common, iObject->Natoms) * Death(Common, jObject->Natoms);
d = Death(Common, iObject->Natoms) * Birth(Common, jObject->Natoms);
if ( b + d <= 0.0 )
goto Exit;
constant = (iObject->Natoms + jObject->Natoms) / 2.0;
for ( Clock = -log(Randouble(Rand)) * constant / (b + d);
Clock <= TIMESTEP;
Clock += -log(Randouble(Rand)) * constant / (b + d) )
{
if ( Randouble(Rand) > b / (b + d) )
{
kObject = iObject;
iObject = jObject;
jObject = kObject;
kLink = iLink;
iLink = jLink;
jLink = kLink;
}
// Try atom j ---> i
CALL( SafeCube(Common, iObject) )
// Ensure deletion not already present in destination
del = Rangrid(Rand, jObject->Natoms);
if ( FindHere(FindAtom(del, jLink)->Label, iLink) )
continue;
// Delete from source
CALL( Delete1(del, &L1, NULL, Common, jObject, jLink) ) ++ CPU;
accept = cool * (L1 + iObject->Lhood) + log(Randouble(Rand));
// Try movement
SWAP(iObject->Cubes[iObject->Natoms],
jObject->Cubes[jObject->Natoms])
CALL( Try1(&Ltry, Common, iObject) ) ++ CPU;
Ltry = cool * (Ltry + jObject->Lhood);
// Reject?
if ( CALLvalue == 0 || Ltry < accept )
{
SWAP(iObject->Cubes[iObject->Natoms],
jObject->Cubes[jObject->Natoms])
CALL( Insert1(Common, jObject, jLink) ) ++ CPU;
}
// Accept?
else
{
++ Success;
CALL( Insert1(Common, iObject, iLink) ) ++ CPU;
}
b = Birth(Common, iObject->Natoms) * Death(Common, jObject->Natoms);
d = Death(Common, iObject->Natoms) * Birth(Common, jObject->Natoms);
}
Exit:
Oper->CPU = CPU;
Oper->Success = Success;
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Chameleon2 Parallel engine #6
//
// Purpose: MCMC engine.
//
// Method: Tries to exchange positions of nearby atoms in different objects,
// but does NOT explore all space. Success defined as acceptance.
//
// =====X=====:======X============X=======
// /|\ Select
// | |
// | |
// Exchange \|/
// ===========X===========X=======:=======
//
// For reasonable success rate, the exchanging atom is taken to be
// the left or right neighbour of the original atom, and hence
// "close".
//
// Note: ENSEMBLE should be at least 2, obviously.
//
// History: JS 31 Jan 2002 - 8 Feb 2003
//-----------------------------------------------------------------------------
static
int Chameleon2( // O 0 = op, or -ve error
OperStr* Oper, // I O operation
CommonStr* Common, // I(O) general information
ObjectStr* Objects, // I O ENSEMBLE of objects
Node * Links) // I O linked lists of labels
{
// Sampling interval: each pair is investigated about TIMESTEP times
static const double TIMESTEP = 0.5000;
double cool = Common->cool;
ObjectStr* iObject = &Objects[Oper->i];
ObjectStr* jObject = &Objects[Oper->j];
ObjectStr* kObject;
Node* iLink = &Links [Oper->i];
Node* jLink = &Links [Oper->j];
Node* kLink;
unsigned* Rand = iObject->Rand;
int iNatoms = iObject->Natoms;
int jNatoms = jObject->Natoms;
int iatom; // first object
Atom* iAtom; // first object
int jatom; // other object
Atom* jAtom; // other object
double accept;
double Ltry;
double L2;
double* swap;
int count;
int r;
int CPU = 1;
int Success = 0;
int CALLvalue = 0;
for ( count = 0; count <= (iNatoms + jNatoms) * TIMESTEP; count++ )
{
// Select random atom
r = Rangrid(Rand, iNatoms + jNatoms);
iatom = r;
if ( r >= iNatoms )
{
iatom = r - iNatoms;
kObject = iObject;
iObject = jObject;
jObject = kObject;
kLink = iLink;
iLink = jLink;
jLink = kLink;
r = iNatoms;
iNatoms = jNatoms;
jNatoms = r;
}
iAtom = FindAtom(iatom, iLink);
if ( FindHere(iAtom->Label, jLink) ) // must not be in other object
continue;
if ( Rangrid(Rand, 2) )
{
if ( !(jAtom = FindLeft(iAtom->Label, jLink)) )
jAtom = EndLink(jLink);
}
else
{
if ( !(jAtom = FindRight(iAtom->Label, jLink)) )
jAtom = BeginLink(jLink);
}
if ( FindHere(jAtom->Label, iLink) ) // must not be in other object
continue;
jatom = Storage(jAtom);
// Exchange coordinates
CALL( Delete1(iatom, &Ltry, NULL, Common, iObject, iLink) ) ++ CPU;
CALL( Delete1(jatom, &L2, NULL, Common, jObject, jLink) ) ++ CPU;
accept = cool * (Ltry + L2) + log(Randouble(Rand));
SWAP(iObject->Cubes[iObject->Natoms],
jObject->Cubes[jObject->Natoms])
CALL( Try1(&Ltry, Common, iObject) ) ++ CPU;
if ( CALLvalue > 0 )
{ // care with user rejections
CALL( Try1(&L2, Common, jObject) ) ++ CPU;
Ltry += L2;
}
// Reject?
if ( CALLvalue == 0 || cool * Ltry < accept )
SWAP(iObject->Cubes[iObject->Natoms],
jObject->Cubes[jObject->Natoms])
else ++ Success;
// Rebuild
CALL( Insert1(Common, iObject, iLink) ) ++ CPU;
CALL( Insert1(Common, jObject, jLink) ) ++ CPU;
}
Exit:
Oper->CPU = CPU;
Oper->Success = Success;
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Leapfrog1 Parallel engine #7
//
// Purpose: Geometrical MCMC engine.
//
// Method: Tries to move points by inverting w.r.t. a catalyst atom,
// but does NOT explore all space. Success defined as acceptance.
//
// old position catalyst new position
// x1 >-----------------0-----------------> x2
//
// old + new = 2 * catalyst
//
// For reasonable success rate, the catalyst is taken to be either
// the left or right neighbour of the original atom, and hence
// "close". For detailed balance, the new position must also have
// its right or left neighbour (respectively) being the centre,
// otherwise the trial is aborted. Because a Hilbert curve may find
// similarly close atoms in any quadrant, the efficiency is roughly
// 1 in MIN(2^Ndim, Natoms) tries .
//
// Note: ENSEMBLE should be at least 3, otherwise
// Leapfrog1 will not of itself expand the bubble of atoms.
//
// History: JS 2 Jan 2002 - 8 Feb 2003
//-----------------------------------------------------------------------------
static
int Leapfrog1( // O 0, or -ve error
OperStr* Oper, // I O operation
CommonStr* Common, // I(O) general information
ObjectStr* Objects, // I O ENSEMBLE of objects
Node* Links) // I O linked lists of labels
{
// Sampling interval: each atom is investigated about TIMESTEP times
static const double TIMESTEP = 1.0000;
int Ndim = Common->Ndim;
double cool = Common->cool;
ObjectStr* iObject = &Objects[Oper->i];
ObjectStr* jObject = &Objects[Oper->j];
Node* iLink = &Links [Oper->i];
Node* jLink = &Links [Oper->j];
unsigned* xTry = iObject->xTry;
unsigned* Rand = iObject->Rand;
int Natoms = iObject->Natoms;
int del; // selection
Atom* pAtom; // selection
double* cube; // selection
int left; // catalyst
Atom* pCentre; // catalyst
double* centre; // catalyst
double* trial;
double Ltry;
double accept;
double t;
double* swap;
int r;
int count;
int CPU = 1;
int Success = 0;
int CALLvalue = 0;
for ( count = 0; count <= Natoms * TIMESTEP; count++ )
{
// Select original atom
del = Rangrid(Rand, Natoms);
cube = iObject->Cubes[del];
pAtom = FindAtom(del, iLink);
// Select centre
left = Rangrid(Rand, 2);
if ( left ) // left-definite
{
pCentre = FindRight(pAtom->Label, jLink);
if ( ! pCentre ) pCentre = BeginLink(jLink);
pCentre = PrevAtom(pCentre);
if ( ! pCentre ) pCentre = EndLink(jLink);
}
else // right-definite
{
pCentre = FindLeft(pAtom->Label, jLink);
if ( ! pCentre ) pCentre = EndLink(jLink);
pCentre = NextAtom(pCentre);
if ( ! pCentre ) pCentre = BeginLink(jLink);
}
centre = jObject->Cubes[Storage(pCentre)];
// Invert original cube through neighbour
trial = iObject->Cubes[Natoms];
for ( r = 0; r < Ndim; r++ )
{
t = cube[r] - centre[r];
if ( t < 0.0 )
t += 1.0;
t = centre[r] - t;
if ( t < 0.0 )
t += 1.0;
trial[r] = t;
}
// Ensure not already present
CubetoLabel(xTry, iObject, Common);
if ( FindHere(xTry, iLink) )
continue;
// Ensure in range for detailed balance
if ( left ) // right-definite
{
pAtom = FindLeft(xTry, jLink);
if ( ! pAtom ) pAtom = EndLink(jLink);
pAtom = NextAtom(pAtom);
if ( ! pAtom ) pAtom = BeginLink(jLink);
}
else // left-definite
{
pAtom = FindRight(xTry, jLink);
if ( ! pAtom ) pAtom = BeginLink(jLink);
pAtom = PrevAtom(pAtom);
if ( ! pAtom ) pAtom = EndLink(jLink);
}
if ( pAtom != pCentre )
continue;
// Delete from source
CALL( Delete1(del, &Ltry, NULL, Common, iObject, iLink) ) ++ CPU;
accept = cool * Ltry + log(Randouble(Rand));
SWAP(iObject->Cubes[Natoms], iObject->Cubes[Natoms-1])
CALL( Try1(&Ltry, Common, iObject) ) ++ CPU;
// Reject?
if ( CALLvalue == 0 || cool * Ltry < accept )
SWAP(iObject->Cubes[Natoms], iObject->Cubes[Natoms-1])
else ++ Success;
// Rebuild
CALL( Insert1(Common, iObject, iLink) ) ++ CPU;
}
Exit:
Oper->CPU = CPU;
Oper->Success = Success;
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Leapfrog2 Parallel engine #8
//
// Purpose: Geometrical MCMC engine.
//
// Method: Tries to move points by reflecting between catalyst atoms,
// but does NOT explore all space. Success defined as acceptance.
//
// Lcatalyst old position
// /
// /
// /
// new position Rcatalyst
//
// old + new = Lcatalyst + Rcatalyst
//
// For reasonable success rate, the catalysts are taken to be
// the left and right neighbours of the original atom, and hence
// "close". For detailed balance, the new position must also have
// its left and right neighbours (respectively) being the catalysts,
// otherwise the trial is aborted. Because a Hilbert curve may find
// similarly close atoms in any quadrant, the efficiency is roughly
// 1 in MIN(2^Ndim, Natoms) tries .
//
// Note: ENSEMBLE should be at least 4, otherwise
// Leapfrog2 will not of itself expand the bubble of atoms.
//
// History: JS 2 Jan 2002 - 8 Feb 2003
//-----------------------------------------------------------------------------
static
int Leapfrog2( // O 0, or -ve error
OperStr* Oper, // I O operation
CommonStr* Common, // I(O) general information
ObjectStr* Objects, // I O ENSEMBLE of objects
Node* Links) // I O linked lists of labels
{
// Sampling interval: each atom is investigated about TIMESTEP times
static const double TIMESTEP = 1.0000;
int Ndim = Common->Ndim;
double cool = Common->cool;
ObjectStr* iObject = &Objects[Oper->i];
ObjectStr* jObject = &Objects[Oper->j];
ObjectStr* kObject = &Objects[Oper->k];
Node* iLink = &Links [Oper->i];
Node* jLink = &Links [Oper->j];
Node* kLink = &Links [Oper->k];
unsigned* xTry = iObject->xTry;
unsigned* Rand = iObject->Rand;
int Natoms = iObject->Natoms;
int del; // selection
Atom* pAtom; // selection
double* cube; // selection
double* left; // left catalyst
Atom* pLeft; // left catalyst
double* right; // right catalyst
Atom* pRight; // right catalyst
double* trial;
double Ltry;
double accept;
double t;
double* swap;
int r;
int count;
int CPU = 1;
int Success = 0;
int CALLvalue = 0;
for ( count = 0; count <= Natoms * TIMESTEP; count++ )
{
// Select original atom
del = Rangrid(Rand, Natoms);
cube = iObject->Cubes[del];
pAtom = FindAtom(del, iLink);
// Left-definite and Right-definite neighbours
pLeft = FindRight(pAtom->Label, jLink);
if ( ! pLeft ) pLeft = BeginLink(jLink);
pLeft = PrevAtom(pLeft);
if ( ! pLeft ) pLeft = EndLink(jLink);
left = jObject->Cubes[Storage(pLeft)];
pRight = FindLeft(pAtom->Label, kLink);
if ( ! pRight ) pRight = EndLink(kLink);
pRight = NextAtom(pRight);
if ( ! pRight ) pRight = BeginLink(kLink);
right = kObject->Cubes[Storage(pRight)];
// Invert original cube through centre
trial = iObject->Cubes[Natoms];
for ( r = 0; r < Ndim; r++ )
{
t = cube[r] - left[r];
if ( t < 0.0 )
t += 1.0;
t = right[r] - t;
if ( t < 0.0 )
t += 1.0;
trial[r] = t;
}
// Ensure not already present
CubetoLabel(xTry, iObject, Common);
if ( FindHere(xTry, iLink) )
continue;
// Ensure same neighbours for detailed balance
pAtom = FindRight(xTry, jLink);
if ( ! pAtom ) pAtom = BeginLink(jLink);
pAtom = PrevAtom(pAtom);
if ( ! pAtom ) pAtom = EndLink(jLink);
if ( pAtom != pLeft )
continue;
pAtom = FindLeft(xTry, kLink);
if ( ! pAtom ) pAtom = EndLink(kLink);
pAtom = NextAtom(pAtom);
if ( ! pAtom ) pAtom = BeginLink(kLink);
if ( pAtom != pRight )
continue;
// Delete from source
CALL( Delete1(del, &Ltry, NULL, Common, iObject, iLink) ) ++ CPU;
accept = cool * Ltry + log(Randouble(Rand));
SWAP(iObject->Cubes[Natoms], iObject->Cubes[Natoms-1])
CALL( Try1(&Ltry, Common, iObject) ) ++ CPU;
// Reject?
if ( CALLvalue == 0 || cool * Ltry < accept )
SWAP(iObject->Cubes[Natoms], iObject->Cubes[Natoms-1])
else ++ Success;
// Rebuild
CALL( Insert1(Common, iObject, iLink) ) ++ CPU;
}
Exit:
Oper->CPU = CPU;
Oper->Success = Success;
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: GuidedWalk Parallel engine #9
//
// Purpose: Geometrical MCMC engine.
//
// Method: Tries to offset atoms along a line parallel to the displacement
// vector between two neighbours from other objects.
// ________________________
// | |
// | .|
// | ... |
// | .. |
// | ... |
// | o. |
// | o.o |
// | ooo |
// | oX | X = original point
// | o.. R | R = catalyst
// |.. | L = catalyst
// | L | Line parallel to R-L
// |________________________|
// Points "o" of line have same Hilbert neighbours L and R as have X
// so these destinations are in detailed balance with X.
//
// It is likely (but not guaranteed) that a starting set of atom
// positions is capable of exploring the full space, but the number
// of atoms is constant, so not explored.
//
// Catalysts L and R are taken to be the left and right neighbours
// of the original atom X, drawn from other object(s).
// The line spans unit change in its most rapidly varying coordinate
// and has 2^32 constituent points. The phase of the original point
// X along the line is random. Trial positions are chosen by slice
// sampling along the line, so there will nearly always be movement.
//
// Hopefully, the cloud of neighbours of X from different objects
// follows the local shape of where X may lie, in which case the
// engine can fill out "unmeasured" directions exponentially fast.
//
// Note: ENSEMBLE should be at least 2 and Ndim should also be at least 2.
//
// History: JS 14 Jan 2003, 8 Feb 2002, 19 Jul 2003
//-----------------------------------------------------------------------------
static
int GuidedWalk( // O 0, or -ve error
OperStr* Oper, // I O operation
CommonStr* Common, // I(O) general information
ObjectStr* Objects, // I O ENSEMBLE of objects
Node* Links) // I O linked lists of labels
{
// Sampling interval: each atom is investigated about TIMESTEP times
static const double TIMESTEP = 1.0000;
static const double Z = (unsigned)(-1) + 1.0; // 2^32
int Ndim = Common->Ndim;
double cool = Common->cool;
unsigned* offset = Common->offset;
ObjectStr* iObject = &Objects[Oper->i];
ObjectStr* jObject = &Objects[Oper->j];
ObjectStr* kObject = &Objects[Oper->k];
Node* iLink = &Links [Oper->i];
Node* jLink = &Links [Oper->j];
Node* kLink = &Links [Oper->k];
unsigned* xTry = iObject->xTry;
unsigned* xLabel = iObject->xLabel;
unsigned* yLabel = iObject->yLabel;
unsigned* Rand = iObject->Rand;
int Natoms = iObject->Natoms;
int del; // selection
Atom* pAtom; // selection
double* cube; // old location
double* arrow; // displacement arrow
double* trial; // new location
double* left; // left catalyst
double* right; // right catalyst
Atom* pLeft; // left catalyst
Atom* pRight; // right catalyst
double Ltry; // likelihood
double accept; // acceptance level
double t; // temporary
double* swap; // exchange coordinates
int r; // coordinate index
int m; // dominant index of arrow
unsigned arc; // length along displacement arrow
unsigned old; // old position on displacement arrow
unsigned origin; // arbitrary for slice sampling
unsigned mask; // bits for slice sampling
unsigned* jLeft; // left boundary for object j
unsigned* jRight; // right boundary for object j
unsigned* kLeft; // left boundary for object k
unsigned* kRight; // right boundary for object k
int count; // # atoms investigated
int CPU = 1;
int Success = 0;
int CALLvalue = 0;
#undef STAIRCASE
#define STAIRCASE(i,s) ((arrow[i] >= 0.0) ? (unsigned)( s * arrow[i] ) \
: (unsigned)0 - (unsigned)((0-s) * arrow[i]))
arrow = jObject->Cubes[NumAtoms(jLink)];
for ( count = 0; count <= Natoms * TIMESTEP; count++ )
{
// Select original atom
del = Rangrid(Rand, Natoms);
pAtom = FindAtom(del, iLink);
CopyLabel(xLabel, pAtom->Label, Ndim);
// Neighbours
if ( !(pLeft = FindLeft (xLabel, jLink)) ) pLeft = EndLink(jLink);
if ( !(pRight = FindRight(xLabel, kLink)) ) pRight = BeginLink(kLink);
left = jObject->Cubes[Storage(pLeft)];
right = kObject->Cubes[Storage(pRight)];
if ( !(pAtom = NextAtom(pLeft)) ) pAtom = BeginLink(jLink);
jLeft = pLeft->Label;
jRight = pAtom->Label;
if ( !(pAtom = PrevAtom(pRight)) ) pAtom = EndLink(kLink);
kLeft = pAtom->Label;
kRight = pRight->Label;
// Displacement arrow
t = 0.0;
m = 0;
for ( r = 0; r < Ndim; r++ )
{
arrow[r] = right[r] - left[r];
if ( t < fabs(arrow[r]) )
{
t = fabs(arrow[r]);
m = r;
}
}
if ( t == 0.0 )
continue;
// Biggest reasonable slice-sampling mask
arc = (unsigned)(Z * t);
mask = 0;
do mask = mask + mask + 1;
while ( mask < arc );
// Normalised arrow
t = arrow[m];
for ( r = 0; r < Ndim; r++ )
arrow[r] /= t;
// Delete from source
CALL( Delete1(del, &Ltry, NULL, Common, iObject, iLink) ) ++ CPU;
accept = cool * Ltry + log(Randouble(Rand));
SWAP(iObject->Cubes[Natoms-1], iObject->Cubes[Natoms])
cube = iObject->Cubes[Natoms];
trial = iObject->Cubes[Natoms-1];
// Project original cube by displacement vector
for ( r = 0; r < Ndim; r++ )
xLabel[r] = (unsigned)(Z * cube[r]);
xLabel[m] -= offset[m];
old = xLabel[m];
for ( r = 0; r < Ndim; r++ )
xLabel[r] -= STAIRCASE(r, old);
origin = Ranint(Rand);
do
{
mask >>= 1;
arc = ((old - origin) ^ (Ranint(Rand) & mask)) + origin;
for ( r = 0; r < Ndim; r++ )
yLabel[r] = xLabel[r] + STAIRCASE(r, arc);
yLabel[m] += offset[m];
for ( r = 0; r < Ndim; r++ )
trial[r] = (0.5 + (double)yLabel[r]) / Z;
CubetoLabel(xTry, iObject, Common);
// Ensure same neighbours for detailed balance
if ( Outside(xTry, jLeft, jRight, Ndim)
|| Outside(xTry, kLeft, kRight, Ndim) || FindHere(xTry, iLink) )
continue;
CALL( Try1(&Ltry, Common, iObject) ) ++ CPU;
// Reject?
if ( CALLvalue > 0 && cool * Ltry >= accept )
break;
}
while ( mask );
// Rebuild: loop can only bottom out with trial = original cube
CALL( Insert1(Common, iObject, iLink) ) ++Success;
++ CPU;
}
Exit:
Oper->CPU = CPU;
Oper->Success = Success;
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: MCMCexit Parallel engine #10
//
// Purpose: Empty Links
//
// History: JS 16 Oct 2002, 1 Feb 2003
//-----------------------------------------------------------------------------
static
int MCMCexit( // O 0, or -ve error
OperStr* Oper, // I O operation
CommonStr* Common, // I general information
ObjectStr* Objects, //(I) ENSEMBLE of objects
Node* Links) // I O empty
{
Node* Link = &Links[Oper->i];
Atom* pAtom;
int CALLvalue = 0;
#if DEBUG // Check Cube/Link consistency
ObjectStr* Object = &Objects[Oper->i];
CALLvalue = Object->Natoms;
if ( NumAtoms(Link) != Object->Natoms )
return E_BAYESYS_DEBUG;
for ( Object->Natoms--; Object->Natoms >= 0; Object->Natoms-- )
{
CubetoLabel(Object->xTry, Object, Common);
if ( ! FindHere(Object->xTry, Link) )
return E_BAYESYS_DEBUG;
}
Object->Natoms = CALLvalue;
#endif
for ( pAtom = BeginLink(Link); pAtom; pAtom = BeginLink(Link) )
CALL( DelAtom(pAtom, Link) )
Exit:
return (Common && Objects) ? CALLvalue : CALLvalue; //avoid compiler whinge
}
//=============================================================================
//
// Event library for birth and death rates
//
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Birth
//
// Purpose: d(birth) / dtime
//
// History: JS 30 Sep 2002
//-----------------------------------------------------------------------------
static
double Birth( // O birth rate
CommonStr* Common, // I general information
int Natoms) // I # atoms
{
int MinAtoms = Common->MinAtoms;
int MaxAtoms = Common->MaxAtoms;
double Alpha = Common->Alpha;
double r; // birth rate
if ( MaxAtoms == MinAtoms )
r = 0.0;
else if ( Alpha == 0.0 ) // MaxAtoms=0 excluded as improper
r = (Natoms < MaxAtoms) ? Natoms + 1 - MinAtoms : 0;
else if ( Alpha > 0.0 )
{
r = Alpha;
if ( MaxAtoms )
r *= (double)(MaxAtoms - Natoms) / (MaxAtoms - MinAtoms);
}
else // Alpha < 0.0
{
r = (Natoms == MaxAtoms)
? 0.0
: (Natoms - MinAtoms + 1.0) * Alpha / (Alpha - 1.0);
}
return r;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Death
//
// Purpose: d(death) / dtime
//
// History: JS 30 Sep 2002
//-----------------------------------------------------------------------------
static
double Death( // O death rate
CommonStr* Common, // I general information
int Natoms) // I # atoms
{
int MinAtoms = Common->MinAtoms;
int MaxAtoms = Common->MaxAtoms;
if ( MaxAtoms == MinAtoms )
return 1.0;
else
return Natoms - MinAtoms;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: SafeCube
//
// Purpose: Ensure sufficient memory to add another atom into Object->Cubes
//
// History: JS 2 Jan 2002
//-----------------------------------------------------------------------------
static
int SafeCube( // O 0, or -ve allocation error
CommonStr* Common, // I info and workspace
ObjectStr* Object) // I O sample object
{
int Ndim = Common->Ndim;
int Valency = Common->Valency;
int Nsize = Ndim + Valency + 1;
int i, j, n;
int CALLvalue = 0;
if ( Ndim > 0 )
if ( Object->Natoms >= Object->Nstore - 1 )
{
n = Object->Natoms + Object->Natoms / 2 + 2;
REALLOC(Object->Cubes, n, double*)
for ( j = Object->Nstore; j < n; j++ )
{
Object->Cubes[j] = NULL; // (allows CALLOC to fail gracefully)
CALLOC(Object->Cubes[j], Nsize, double)
for ( i = 0; i < Nsize; i++ )
Object->Cubes[j][i] = 0.0;
}
Object->Nstore = n;
}
Exit:
return CALLvalue;
}
//=============================================================================
//
// Atom control
//
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Empty
//
// Purpose: Set empty object.
//
// History: JS 8 Feb 2002, 11 Oct 2003
//-----------------------------------------------------------------------------
static
int Empty( // O 0, or -ve error
CommonStr* Common, // I general information
ObjectStr* Object) // I O sample object
{
double Lhood;
int CALLvalue = 0;
CALL( UserEmpty(&Object->Lhood, Common, Object) )
if ( Common->Valency )
{
FluxEmpty(&Lhood, Common, Object);
Object->Lhood += Lhood;
}
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Try1
//
// Purpose: Try inserting one new atom from Object->Cubes[Object->Natoms],
// with NO update.
//
// History: JS 8 Feb 2002
//-----------------------------------------------------------------------------
static
int Try1( // O +ve = OK, 0 = DO NOT USE, -ve = error
double* Ltry, // O loglikelihood after adding trial atom
CommonStr* Common, // I general information
ObjectStr* Object) // I sample object
{
double Utry = 0.0;
double Ftry = 0.0;
int CALLvalue = 0;
CALL( UserTry1(&Utry, Common, Object) )
if ( Common->Valency )
CALL( FluxTry1(&Ftry, Common, Object) )
*Ltry = Object->Lhood + Utry + Ftry;
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Try2
//
// Purpose: Try inserting two new atoms from Object->Cubes[Object->Natoms]
// and Object->Cubes[Object->Natoms + 1], with NO update.
//
// History: JS 8 Feb 2002
//-----------------------------------------------------------------------------
static
int Try2( // O +ve = OK, 0 = DO NOT USE, -ve = error
double* Ltry1, // O loglikelihood after adding first trial atom
double* Ltry2, // O loglikelihood after adding both trial atoms
CommonStr* Common, // I general information
ObjectStr* Object) // I sample object
{
double Utry1 = 0.0;
double Ftry1 = 0.0;
double Utry2 = 0.0;
double Ftry2 = 0.0;
int CALLvalue = 0;
CALL( UserTry2(&Utry1, &Utry2, Common, Object) )
if ( Common->Valency )
CALL( FluxTry2(&Ftry1, &Ftry2, Common, Object) )
*Ltry1 = Object->Lhood + Utry1 + Ftry1;
*Ltry2 = Object->Lhood + Utry2 + Ftry2;
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Insert1
//
// Purpose: Insert one new atom from Object->Cubes[Object->Natoms],
// with full update.
//
// History: JS 2 Jan 2002, 8 Feb 2002
//-----------------------------------------------------------------------------
static
int Insert1( // O 0, or -ve error
CommonStr* Common, // I(O) general information
ObjectStr* Object, // I O sample object
Node* Link) // I O linked list of labels
{
Atom atom[1];
double dLhood;
int CALLvalue = 0;
atom->Label = Object->xTry;
CubetoLabel(atom->Label, Object, Common);
CALL( InsAtom(atom, Link) )
if ( ! CALLvalue )
return E_BAYESYS_SYSERR;
Object->Natoms ++;
CALL( UserInsert1(&dLhood, Common, Object) )
Object->Lhood += dLhood;
if ( Common->Valency )
{
CALL( FluxInsert1(&dLhood, Common, Object) )
Object->Lhood += dLhood;
}
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Insert2
//
// Purpose: Insert two new atoms from Object->Cubes[Object->Natoms] and
// Object->Cubes[Object->Natoms + 1], with full update.
//
// History: JS 2 Jan 2002, 8 Feb 2002
//-----------------------------------------------------------------------------
static
int Insert2( // O 0, or -ve error
CommonStr* Common, // I(O) general information
ObjectStr* Object, // I O sample object
Node* Link) // I O linked list of labels
{
Atom atom[1];
double dLhood;
int CALLvalue = 0;
atom->Label = Object->xTry;
CubetoLabel(atom->Label, Object, Common);
CALL( InsAtom(atom, Link) )
if ( ! CALLvalue )
return E_BAYESYS_SYSERR;
Object->Natoms ++;
CubetoLabel(atom->Label, Object, Common);
CALL( InsAtom(atom, Link) )
if ( ! CALLvalue )
return E_BAYESYS_SYSERR;
Object->Natoms ++;
CALL( UserInsert2(&dLhood, Common, Object) )
Object->Lhood += dLhood;
if ( Common->Valency )
{
CALL( FluxInsert2(&dLhood, Common, Object) )
Object->Lhood += dLhood;
}
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Delete1
//
// Purpose: Delete one old atom from Object->Cubes[del], with full update,
// and optional return of loglikelihoods after 1 or 2 re-insertions.
//
// History: JS 2 Jan 2002, 8 Feb 2003
//-----------------------------------------------------------------------------
static
int Delete1( // O 0, or -ve error
int del, // I serial # for deletion
double* L1, // (O) loglikelihood after deletion then 1 insertion
double* L2, // (O) loglikelihood after deletion then 2 insertions
CommonStr* Common, // I general information
ObjectStr* Object, // I O sample object
Node* Link) // I O linked list of labels
{
Atom* pAtom;
double* swap;
double dLhood;
int CALLvalue = 0;
if ( L1 )
*L1 = Object->Lhood;
pAtom = FindAtom(del, Link);
CALL( DelAtom(pAtom, Link) )
Object->Natoms --;
SWAP(Object->Cubes[del], Object->Cubes[Object->Natoms])
if ( Common->Valency )
{
CALL( FluxDelete1(&dLhood, Common, Object) )
Object->Lhood += dLhood;
}
CALL( UserDelete1(&dLhood, Common, Object) )
Object->Lhood += dLhood;
if ( L1 && Common->Valency )
{
if ( L2 )
CALL( Try2(L1, L2, Common, Object) )
else
CALL( Try1(L1, Common, Object) )
}
Exit:
return CALLvalue;
}
//=============================================================================
//
// Label library for multi-bit labels
// Label is multi-bit integer stored as vector of unsigned, [0] high.
//
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Topology
//
// Purpose: Set "hypercube axes to extended-integer label" mapping,
// preserving a degree of locality.
//
// Mapping scales each coordinate is to an unsigned integer plus random
// offset, reduced to range [0,2^32) by wraparound continuity.
// Then either
// Simple raster in random order, in which successive dimensions
// take precedence.
// or
// Space-filling Hilbert curve in random orientation
// (usually the preferred choice).
//
// History: JS 2 Jan 2002, 16 Oct 2002
//-----------------------------------------------------------------------------
static
void Topology(
CommonStr* Common) // I O workspace
{
int Ndim = Common->Ndim; // I # dimensions
int* permute = Common->permute; // O permutation
unsigned* offset = Common->offset; // O random
unsigned* Rand = Common->Rand; // I O random generator state
if ( Ndim <= 0 )
return;
RanLabel(offset, Ndim, Rand);
Ranperm(Rand, Ndim, permute);
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: CubetoLabel
//
// Purpose: Translate hypercube axes to extended-integer label.
// Inverse of LabeltoCube.
//
// History: JS 25 April 2001, 2 Jan 2002, 16 Oct 2002
//-----------------------------------------------------------------------------
static
void CubetoLabel(
unsigned* Label, // O extended-integer label [Ndim]
ObjectStr* Object, // I object containing input cube
CommonStr* Common) // I general information
{
static const double Z = (unsigned)(-1) + 1.0; // 2^32
int method = Common->Method; // I mapping switch
int Ndim = Common->Ndim; // I # dimensions
int Nbits = Common->Nbits; // I # bits per word
int* permute = Common->permute; // I permutation
unsigned* offset = Common->offset; // I random
unsigned* work = Object->work; // (O) workspace
double* Cube = Object->Cubes[Object->Natoms]; // I hypercube[Ndim]
int i;
if ( Ndim <= 0 )
return;
for ( i = 0; i < Ndim; i++ ) // Read from "double" in (0,1)
work[i] = (unsigned)(Z * fmod(fabs(Cube[permute[i]]), 1.)) + offset[i];
if ( method & 1 )
AxestoLine(Label, work, Nbits, Ndim); // Hilbert curve
else
for ( i = 0; i < Ndim; i++ ) // Simple raster
Label[i] = work[i];
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: LabeltoCube
//
// Purpose: Translate extended-integer label to hypercube axes.
// Inverse of CubetoLabel.
//
// History: JS 25 April 2001, 2 Jan 2002, 6 Jan 2002, 16 Oct 2002
//-----------------------------------------------------------------------------
static
void LabeltoCube(
ObjectStr* Object, // O object containing output cube
unsigned* Label, // I extended-integer label [Ndim]
CommonStr* Common) // I(O) workspace
{
static const double Z = (unsigned)(-1) + 1.0; // 2^32
int method = Common->Method; // I mapping switch
int Ndim = Common->Ndim; // I # dimensions
int Nbits = Common->Nbits; // I # bits per word
int* permute = Common->permute; // I permutation
unsigned* offset = Common->offset; // I random
unsigned* work = Object->work; // (O) workspace
double* Cube = Object->Cubes[Object->Natoms]; // O hypercube[Ndim]
unsigned temp;
int i;
if ( Ndim <= 0 )
return;
if ( method & 1 )
LinetoAxes(work, Label, Nbits, Ndim); // Hilbert curve
else
for ( i = 0; i < Ndim; i++ ) // Simple raster
work[i] = Label[i];
for ( i = 0; i < Ndim; i++ )
{
temp = work[i] - offset[i]; // force unsigned arith here
Cube[permute[i]] = (temp + 0.5) / Z; // Write to "double" in (0,1)
}
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: RanLabel
//
// Purpose: Set r = random
//
// History: JS 25 Apr 2001
//-----------------------------------------------------------------------------
static
void RanLabel(
unsigned* r, // O value [Ndim]
int Ndim, // I dimension
unsigned* Rand) // I O random generator state
{
int j;
for ( j = 0; j < Ndim; j++ )
r[j] = Ranint(Rand);
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: CopyLabel
//
// Purpose: Set w = u
//
// History: JS 28 Jan 2002
//-----------------------------------------------------------------------------
static
void CopyLabel(
unsigned* w, // O w = u [Ndim]
unsigned* u, // I can be overwritten [Ndim]
int Ndim) // I dimension
{
int i;
for ( i = 0; i < Ndim; i++ )
{
w[i] = u[i];
}
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: NewLabel
//
// Purpose: Set New = ((Old - Origin) ^ Random) + Origin
// nbits nbits nbits rbits nbits
//
// History: JS 2 Jan, 12 Jan 2002
//-----------------------------------------------------------------------------
static
void NewLabel(
unsigned* New, // O new label [Ndim]
unsigned* Old, // I old label [Ndim]
unsigned* Origin, // I random origin [Ndim]
int Ndim, // I dimension
int rbits, // I # low-order bits to be randomised
int Nbits, // I # bits per word (nbits = Ndim * Nbits)
unsigned* Rand) // I O random generator state
{
int shift;
int i;
if ( rbits < 1 )
{
for ( i = 0; i < Ndim; i++ )
New[i] = Old[i];
}
else
{
SubLabel(New, Old, Origin, Ndim);
shift = Nbits - 1 - (rbits - 1) % Nbits;
i = Ndim - 1 - (rbits - 1) / Nbits;
New[i] = New[i] ^ ((unsigned)Ranint(Rand) >> shift);
for ( i++; i < Ndim; i++ )
New[i] = New[i] ^ (unsigned)Ranint(Rand);
AddLabel(New, New, Origin, Ndim);
}
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Outside
//
// Purpose: Is point strictly inside interval, or is it outside or on edge?
// Interval [Left,Right] may wraparound.
//
// History: JS 2 Jan 2002
//-----------------------------------------------------------------------------
static
int Outside( // O 0 = strictly inside, 1 = outside or on edge
unsigned* Where, // I where is this point? [Ndim]
unsigned* Left, // I left edge [Ndim]
unsigned* Right, // I right edge [Ndim]
int Ndim) // I dimension
{
if ( CmpLabel(Right, Left, Ndim) > 0 ) // [0...Left........Right....2^32-1]
{ // .inside.
if ( (CmpLabel(Where, Left, Ndim) <= 0)
|| (CmpLabel(Where, Right, Ndim) >= 0) )
return 1;
}
else // [0........Right....Left...2^32-1]
{ // .inside. .inside.
if ( (CmpLabel(Where, Left, Ndim) <= 0)
&& (CmpLabel(Where, Right, Ndim) >= 0) )
return 1;
}
return 0;
}
//=============================================================================
//
// MassInf procedures
//
// MAIN
// ______|_______
// | |
// | BayeSys3 |
// |______________|
// | |
// | |
// | |_______________________________________________
// | | MassInf |
// | | FluxEmpty | |
// | | FluxTry1 ,FluxTry2 | FluxAlloc, FluxInit |
// | | FluxInsert1,FluxInsert2 | FluxCalib0,FluxCalib |
// | | FluxDelete1 | FluxFree |
// | |_________________________|______________________|
// | |
// | |
// ____________|___________________|_______
// | USER |
// | UserMonitor | |
// | UserEmpty | |
// | UserTry1 ,UserTry2 | UserFoot |
// | UserInsert1,UserInsert2 | |
// | UserDelete1 | |
// |_________________________|______________|
//=============================================================================
//
// MassInf ancillary library
//
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: FluxAlloc
//
// Purpose: Allocate memory for MassInf
//
// History: JS 10 Feb 2003, 15 Aug 2003
//-----------------------------------------------------------------------------
static
int FluxAlloc( // O 0, or -ve error
CommonStr* Common, // I general info
ObjectStr* Objects) // I O allocate memory
{
int ENSEMBLE = Common->ENSEMBLE;
int MassInf = Common->MassInf;
int Valency = Common->Valency;
int Ndata = Common->Ndata;
int k;
int CALLvalue = 0;
Common->Counts = NULL;
if ( MassInf >= 100 )
CALLOC(Common->Counts, Ndata, int)
for ( k = 0; k < ENSEMBLE; k++ )
{
Objects[k].Mock = NULL;
Objects[k].g1 = NULL;
Objects[k].g2 = NULL;
Objects[k].A11 = NULL;
Objects[k].A12 = NULL;
Objects[k].A22 = NULL;
Objects[k].Xindex = NULL;
Objects[k].nbits = NULL;
Objects[k].nbitx = NULL;
Objects[k].ibits = NULL;
Objects[k].ibitx = NULL;
Objects[k].zbits = NULL;
Objects[k].zbitx = NULL;
Objects[k].Foot = NULL;
Objects[k].flags = NULL;
CALLOC(Objects[k].Mock, Ndata, double)
CALLOC(Objects[k].g1, Valency, double)
CALLOC(Objects[k].g2, Valency, double)
CALLOC(Objects[k].A11, Valency, double)
CALLOC(Objects[k].A12, Valency, double)
CALLOC(Objects[k].A22, Valency, double)
CALLOC(Objects[k].Xindex, Valency, int)
CALLOC(Objects[k].nbits, Valency, int)
CALLOC(Objects[k].nbitx, Valency, int)
if ( k == 0 || PARALLEL )
{
CALLOC(Objects[k].ibits, Ndata, int)
CALLOC(Objects[k].ibitx, Ndata, int)
CALLOC(Objects[k].zbits, Ndata, double)
CALLOC(Objects[k].zbitx, Ndata, double)
CALLOC(Objects[k].Foot , Ndata, double)
CALLOC(Objects[k].flags, Ndata, int)
}
else
{
Objects[k].ibits = Objects[0].ibits;
Objects[k].ibitx = Objects[0].ibitx;
Objects[k].zbits = Objects[0].zbits;
Objects[k].zbitx = Objects[0].zbitx;
Objects[k].Foot = Objects[0].Foot;
Objects[k].flags = Objects[0].flags;
}
}
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: FluxInit
//
// Purpose: Initialise system for MassInf
//
// History: JS 10 Feb 2003
//-----------------------------------------------------------------------------
static
int FluxInit( // O 0, or -ve error
CommonStr* Common, // I general info
ObjectStr* Objects) // I O initialise object info
{
int ENSEMBLE = Common->ENSEMBLE;
int Ndata = Common->Ndata;
int j, k;
for ( k = 0; k < ENSEMBLE; k++ )
for ( j = 0; j < Ndata; j++ )
{
Objects[k].flags[j] = -1;
Objects[k].Foot[j] = 0.0;
}
return 0;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: FluxCalib0
//
// Purpose: Set internal hyperparameters
// FluxUnit0 in Common and FluxUnit in Objects.
//
// History: JS 1 Feb 2003, 11 Jul 2003, 12 Aug 2003, 20 Aug 2003
// 12 Sep 2003
//-----------------------------------------------------------------------------
static
int FluxCalib0( // O 0, or -ve error
CommonStr* Common, // I O set hyperparameters
ObjectStr* Objects, // O set hyperparameters
Node* Links) // (O) empty on exit
{
int ENSEMBLE = Common->ENSEMBLE; // I # objects
int MassInf = Common->MassInf; // I type of data
int Ndata = Common->Ndata; // I # data
double* Data = Common->Data; // I data [Ndata]
double* Acc = Common->Acc; // I accuracies [Ndata]
double* Mock = Objects->Mock; // (O) mock data [Ndata]
int* Counts = Common->Counts; // (O) (Poisson data) [Ndata]
int N = 12; // adequate # samples
double Datanorm = 0.0; // ||data||
double Mocknorm = 0.0; // ||mockdata||
OperStr Operations[1]; // set prior
int i, k; // counter
int CALLvalue = 0;
// Poisson Counts = 0 at cool=0
if ( MassInf >= 100 )
for ( k = 0; k < Ndata; k++ )
Counts[k] = 0;
// Common parameter(s) from preliminary peek at data, if necessary
if ( Common->FluxUnit0 == 0.0 )
{
Objects->FluxUnit = 1.0; // Preliminary flux unit
Operations->engine = 0; // SetPrior
Operations->iType = -1;
Operations->i = 0;
Operations->jType = 0;
Operations->kType = 0;
if ( MassInf >= 100 ) // Poisson
{
for ( i = 0; i < Ndata; i++ )
Datanorm += Data[i] + Acc[i];
for ( k = 0; k < N; k++ )
{
CALL( DoOperations(Operations, Common, Objects, Links, 1) )
for ( i = 0; i < Ndata; i++ )
Mocknorm += Mock[i] + Acc[i];
}
Mocknorm /= N;
}
else // Gaussian
{
for ( i = 0; i < Ndata; i++ )
Datanorm += Data[i] * Acc[i] * Acc[i] * Data[i];
Datanorm = sqrt(Datanorm);
for ( k = 0; k < N; k++ )
{
CALL( DoOperations(Operations, Common, Objects, Links, 1) )
for ( i = 0; i < Ndata; i++ )
Mocknorm += Mock[i] * Acc[i] * Acc[i] * Mock[i];
}
Mocknorm = sqrt(Mocknorm / N);
}
Common->FluxUnit0 = -( (Datanorm > 0.0 && Mocknorm > 0.0)
? Datanorm / Mocknorm : 1.0 );
}
// Object parameters
if ( Common->FluxUnit0 > 0.0 )
for ( k = 0; k < ENSEMBLE; k++ )
Objects[k].FluxUnit = Common->FluxUnit0;
else
for ( k = 0; k < ENSEMBLE; k++ )
Objects[k].FluxUnit = Ran1posX(Objects[k].Rand,
1.0 / (-Common->FluxUnit0), 0.0);
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: FluxCalib
//
// Purpose: Reset after cooling.
//
// Common Counts = (int)(cool * Poisson data)
//
// Object FluxUnit q = mean prior flux per atom
// sampled according to
// Pr(q | F*,Data) ~ Prior(q) Likelihood(Data | qF*)
// where
// Prior(q) ~ q exp(-q/q0), q0 = prior hyperparameter
// F* = Mock/q = current mock signal as generated from unit q=1
//
// History: JS 2 Jan 2002 - 20 Aug 2003
//-----------------------------------------------------------------------------
static
void FluxCalib(
CommonStr* Common, // I read hyperparameters
ObjectStr* Object) // I O reset hyperparameters
{
int MassInf = Common->MassInf; // I type of data
double cool = Common->cool; // I Annealing parameter
double q0 = Common->FluxUnit0; // I Prior hyperparameter
int Ndim = Common->Ndim; // I # coordinates
int Valency = Common->Valency; // I # fluxes
int Ndata = Common->Ndata; // I # data
double* Data = Common->Data; // I data [Ndata]
double* Acc = Common->Acc; // I accuracies [Ndata]
int* Counts = Common->Counts; // (O) (Poisson data) [Ndata]
double* Mock = Object->Mock; // I O mock data [Ndata]
int Natoms = Object->Natoms; // I # atoms
double q = Object->FluxUnit; // I flux unit: F*=Mock/q
double* Flux; // fluxes [Valency]
double a; // autoscaled accuracy
double FF; // Mock.Acc.Acc.Mock
double FD; // Mock.Acc.Acc.Data
double g; // gradient F*.Acc.Acc.Data
double A; // curvature F*.Acc.Acc.F*
double s; // rescale by (new q)/(old q)
int i, j; // counters
// Poisson data ?
if ( MassInf >= 100 )
{
a = 0.5 + cool * (Data[0] + Acc[0]);
Counts[0] = (int)a;
for ( i = 1; i < Ndata; i++ )
{
a += cool * (Data[i] + Acc[i]) - Counts[i-1];
Counts[i] = (int)a;
}
}
// New flux unit
FF = FD = 0.0;
for ( i = 0; i < Ndata; i++ )
{
if ( MassInf >= 100 ) // Poisson (approx is OK here)
{
FF += Mock[i] * Mock[i] / (Data[i] + Acc[i]);
FD += Mock[i] * Data[i] / (Data[i] + Acc[i]);
}
else // Gaussian
{
FF += Mock[i] * Acc[i] * Acc[i] * Mock[i];
FD += Mock[i] * Acc[i] * Acc[i] * Data[i];
}
}
g = cool * FD / q;
A = cool * FF / (q * q);
if ( q0 <= 0.0 )
Object->FluxUnit = Ran1posX(Object->Rand, 1.0 / fabs(q0) - g, A);
// Rescale observables
s = Object->FluxUnit / q;
for ( i = 0; i < Ndata; i++ )
Mock[i] *= s;
for ( i = 0; i < Natoms; i++ )
{
Flux = Object->Cubes[i] + Ndim;
for ( j = 0; j < Valency; j++ )
Flux[j] *= s;
}
Object->Lhood = (MassInf >= 100 )
? PoissLhood(Ndata, Mock, Data, Acc)
: GaussLhood(Ndata, Mock, Data, Acc);
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: FluxFree
//
// Purpose: Free memory for MassInf
//
// History: JS 10 Feb 2003
//-----------------------------------------------------------------------------
static
void FluxFree(
CommonStr* Common, // I general info
ObjectStr* Objects) // I(O) free memory
{
int ENSEMBLE = Common->ENSEMBLE;
int MassInf = Common->MassInf;
int k; // object counter
for ( k = 0; k < ENSEMBLE; k++ )
{
if ( k == 0 || PARALLEL )
{
FREE(Objects[k].flags)
FREE(Objects[k].Foot)
FREE(Objects[k].zbitx)
FREE(Objects[k].zbits)
FREE(Objects[k].ibitx)
FREE(Objects[k].ibits)
}
FREE(Objects[k].nbitx)
FREE(Objects[k].nbits)
FREE(Objects[k].Xindex)
FREE(Objects[k].A22)
FREE(Objects[k].A12)
FREE(Objects[k].A11)
FREE(Objects[k].g2)
FREE(Objects[k].g1)
FREE(Objects[k].Mock)
}
if ( MassInf >= 100 )
FREE(Common->Counts)
}
//=============================================================================
//
// MassInf outer procedures
//
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: FluxEmpty
//
// Purpose: Set Lhood = logLikelihood(fluxes) from Data, for empty sample
// with 0 atoms in Object, and initialise its other information.
//
// Lhood := log L(empty)
//
// The number 0 has already been placed in Object->Natoms.
//
// History: JS 21 Mar 2002, 3 Oct 2002, 18 Aug 2003
//-----------------------------------------------------------------------------
static
void FluxEmpty(
double* Lhood, // O loglikelihood
CommonStr* Common, // I O general information
ObjectStr* Object) // I(O) sample object
{
int MassInf = Common->MassInf; // MassInf switches
int Ndata = Common->Ndata; // I # data
double* Data = Common->Data; // I Data [Ndata]
double* Acc = Common->Acc; // I Accuracies [Ndata]
double* Mock = Object->Mock; // O Mock data [Ndata]
int k; // data counter
for ( k = 0; k < Ndata; k++ )
Mock[k] = 0.0;
*Lhood = (MassInf >= 100)
? PoissLhood(Ndata, Mock, Data, Acc)
: GaussLhood(Ndata, Mock, Data, Acc);
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: FluxTry1
//
// Purpose: d(logLikelihood(fluxes)) after supposedly adding one new atom
// to Object, without any side effects on it.
// cool
// dLtry := (1/cool) DELTA log INTEGRAL dPrior(z) L(...,x,z)
//
// The new atom x has already been placed after the last location
// of the Atoms list, at Object->Cubes[ Object->Natoms ].
//
// History: JS 21 Mar 2002, 3 Oct 2002, 12 Aug 2003, 18 Aug 2003
//-----------------------------------------------------------------------------
static
int FluxTry1( // O +ve = OK, 0 = DO NOT USE, -ve = error abort
double* dLtry, // O d(logLikelihood) from inserting one atom
CommonStr* Common, // I general information
ObjectStr* Object) // I sample object (DO NOT UPDATE Object info)
{
int MassInf = Common->MassInf; // MassInf switches
int Valency = Common->Valency; // # fluxes per atom
double ProbON = Common->ProbON; // Pr(individual flux != 0)
double cool = Common->cool; // Annealing parameter
double* Data = Common->Data; // Data [Ndata]
double* Acc = Common->Acc; // Accuracies [Ndata]
int* Counts = Common->Counts; // Annealed Poisson counts [Ndata]
double* Mock = Object->Mock; // Mock data [Ndata]
double* g1 = Object->g1; // grad chisquared [Valency]
double* A11 = Object->A11; // grad grad chisquared [Valency]
double q = Object->FluxUnit; // Unit of flux
int* nbits = Object->nbits; // # fragments [Valency]
int* ibits = Object->ibits; // Fragment positions [<=Ndata]
double* zbits = Object->zbits; // Fragment quantities [<=Ndata]
int* flags = Object->flags; // flags for overlap [Ndata]
double* Cube; // Position of new atom [Ndim]
int code;
int CALLvalue = 0;
*dLtry = 0.0; // default output
// Footprint
Cube = Object->Cubes[Object->Natoms];
CALL( AtomBits(Cube, Common, ibits, zbits, nbits, flags) )
if ( CALLvalue == 0 )
goto Exit;
code = CALLvalue;
// Gaussian
if ( MassInf < 100 )
{
// Construct quadratic chisquared
SetGrad1(Mock, Data, Acc, Valency, nbits, ibits, zbits, g1, A11);
// Marginal likelihood
*dLtry = GaussTry1(MassInf, cool, q, ProbON, Valency, g1, A11);
}
// Poisson
else
CALL( PoissTry1(MassInf, cool, q, ProbON, Mock, Data, Acc, Counts,
Valency, nbits, ibits, zbits, dLtry) )
return code;
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: FluxTry2
//
// Purpose: d(logLikelihood(fluxes)) after supposedly adding one, then
// two new atoms to Object, without any side effects on it.
//
// cool
// dLtry1 := (1/cool) DELTA log INTEGRAL dPrior(z1) L(...,x1,z1)
// cool
// dLtry2 := (1/cool) DELTA log INTEGRAL dPrior(z1,z2) L(...,x1,z1,x2,z2)
//
// The new atoms x1,x2 have already been put after the last location
// of the Atoms list, at Object->Cubes[ Object->Natoms ] and
// at Object->Cubes[ Object->Natoms + 1 ].
//
// History: JS 21 Mar 2002, 3 Oct 2002, 12 Aug 2003, 18 Aug 2003
//-----------------------------------------------------------------------------
static
int FluxTry2( // O +ve = OK, 0 = DO NOT USE, -ve = error abort
double* dLtry1, // O d(logLikelihood) from inserting first atom
double* dLtry2, // O d(logLikelihood) from inserting both atoms
CommonStr* Common, // I general information
ObjectStr* Object) // I sample object (DO NOT UPDATE Object info)
{
int MassInf = Common->MassInf; // MassInf switches
int Valency = Common->Valency; // # fluxes per atom
double ProbON = Common->ProbON; // Pr(individual flux != 0)
double cool = Common->cool; // Annealing parameter
double* Data = Common->Data; // Data [Ndata]
double* Acc = Common->Acc; // Accuracies [Ndata]
int* Counts = Common->Counts; // Annealed Poisson counts [Ndata]
double* Mock = Object->Mock; // Mock data [Ndata]
double* Foot = Object->Foot; // Footprint workspace (=0) [Ndata]
int* flags = Object->flags; // Valency identifiers (-1) [Ndata]
double* g1 = Object->g1; // grad chisquared [Valency]
double* g2 = Object->g2; // grad chisquared [Valency]
double* A11 = Object->A11; // grad grad chisquared [Valency]
double* A12 = Object->A12; // grad grad chisquared [Valency]
double* A22 = Object->A22; // grad grad chisquared [Valency]
int* Xindex = Object->Xindex; // index to crossterms [Valency]
double q = Object->FluxUnit; // Unit of flux
int* nbits = Object->nbits; // # fragments [Valency]
int* nbitx = Object->nbitx; // # fragments [Valency]
int* ibits = Object->ibits; // Fragment positions [<=Ndata]
int* ibitx = Object->ibitx; // Fragment positions [<=Ndata]
double* zbits = Object->zbits; // Fragment quantities [<=Ndata]
double* zbitx = Object->zbitx; // Fragment quantities [<=Ndata]
double* Cube1; // Position of new atom [Ndim]
double* Cube2; // Position of new atom [Ndim]
int code;
int CALLvalue = 0;
*dLtry1 = *dLtry2 = 0.0; // default output
// Footprints
Cube1 = Object->Cubes[Object->Natoms];
Cube2 = Object->Cubes[Object->Natoms + 1];
CALL( AtomBits(Cube1, Common, ibits, zbits, nbits, flags) )
if ( CALLvalue == 0 )
goto Exit;
CALL( AtomBits(Cube2, Common, ibitx, zbitx, nbitx, flags) )
if ( CALLvalue == 0 )
goto Exit;
code = CALLvalue;
SetIndex(Valency, nbits, ibits, nbitx, ibitx, flags, Xindex);
// Gaussian
if ( MassInf < 100 )
{
// Construct quadratic chisquared
SetGrad2(Mock, Data, Acc, Foot, Valency,
nbits, ibits, zbits, nbitx, ibitx, zbitx,
g1, g2, A11, A12, A22, Xindex);
// Marginal likelihoods
GaussTry2(MassInf, cool, q, ProbON, Valency,
g1, g2, A11, A12, A22, Xindex, dLtry1, dLtry2);
}
// Poisson
else
CALL( PoissTry2(MassInf, cool, q, ProbON, Mock, Data, Acc, Counts, Foot,
Valency, nbits, ibits, zbits, nbitx, ibitx, zbitx,
Xindex, dLtry1, dLtry2) )
return code;
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: FluxInsert1
//
// Purpose: Insert 1 new atom with fluxes into Object, keeping it up-to-date,
// and set d(loglikelihood(fluxes)).
// cool
// Sample z from Prior(z) L(...,x,z)
//
// and set dL := DELTA logL(...,x,z) at the sampled z.
//
// The new atom x has already been placed in the last location of
// the updated Atoms list, at Object->Cubes[ Object->Natoms - 1 ].
//
// History: JS 21 Mar 2002, 3 Oct 2002, 12 Aug 2003, 18 Aug 2003
//-----------------------------------------------------------------------------
static
int FluxInsert1( // O 0, or -ve return code
double* dL, // O d(loglikelihood(fluxes))
CommonStr* Common, // I O general information
ObjectStr* Object) // I O updated sample object
{
int MassInf = Common->MassInf; // MassInf switches
int Ndim = Common->Ndim; // dimension
int Valency = Common->Valency; // # fluxes per atom
double ProbON = Common->ProbON; // Pr(individual flux != 0)
double cool = Common->cool; // Annealing parameter
double* Data = Common->Data; // Data [Ndata]
double* Acc = Common->Acc; // Accuracies [Ndata]
int* Counts = Common->Counts; // Annealed Poisson counts [Ndata]
double* Mock = Object->Mock; // Mock data [Ndata]
int* flags = Object->flags; // Valency identifiers (-1) [Ndata]
double* g1 = Object->g1; // grad chisquared [Valency]
double* A11 = Object->A11; // grad grad chisquared [Valency]
int reset = Object->reset; // Reset inserted MassInf fluxes?
double q = Object->FluxUnit; // Unit of flux
unsigned* Rand = Object->Rand; // Random generator
int* nbits = Object->nbits; // # fragments [Valency]
int* ibits = Object->ibits; // Fragment positions [<=Ndata]
double* zbits = Object->zbits; // Fragment quantities [<=Ndata]
double* Cube; // Position of new atom [Ndim]
double* Flux; // Flux of new atom [Valency]
int CALLvalue = 0;
*dL = 0.0; // default output
// Footprint
Cube = Object->Cubes[Object->Natoms - 1];
Flux = Cube + Ndim;
CALL( AtomBits(Cube, Common, ibits, zbits, nbits, flags) )
if ( CALLvalue == 0 )
return E_BAYESYS_SYSERR;
CALL( Overlap1(nbits, ibits, flags, Valency) ) // Abort?
// Gaussian
if ( MassInf < 100 )
{
// Construct quadratic chisquared
SetGrad1(Mock, Data, Acc, Valency, nbits, ibits, zbits, g1, A11);
// Optionally reset Flux
if ( reset )
GaussInsert1(MassInf, Rand, cool, q, ProbON, Valency,
g1, A11, Flux);
// Modify Lhood
*dL = GaussLhood1(Valency, Flux, g1, A11, +1);
}
// Poisson
else
{
if ( reset )
CALL( PoissInsert1(MassInf, Rand, cool, q, ProbON, Mock, Data, Acc,
Counts, Valency, nbits, ibits, zbits, Flux) )
*dL = PoissLhood1(Mock, Data, Acc,
Valency, nbits, ibits, zbits, Flux, +1);
}
// Modify mock data
InsBits(Mock, Flux, nbits, ibits, zbits, Valency);
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: FluxInsert2
//
// Purpose: Insert 2 new atoms with fluxes into Object, keeping it up-to-date
// and set d(loglikelihood(fluxes)).
// cool
// Sample z1,z2 from Prior(z1,z2) L(...,x1,z1,x2,z2)
//
// and set dL := DELTA logL(...,x1,z1,x2,z2) at the sampled z1,z2.
//
// The new atoms x1,x2 have already been put in the last locations
// of the updated Atoms list at Object->Cubes[ Object->Natoms - 2 ]
// and at Object->Cubes[ Object->Natoms - 1 ]
//
// History: JS 21 Mar 2002, 3 Oct 2002, 12 Aug 2003, 18 Aug 2003
//-----------------------------------------------------------------------------
static
int FluxInsert2( // O 0, or -ve return code
double* dL, // O d(loglikelihood(fluxes))
CommonStr* Common, // I O general information
ObjectStr* Object) // I O updated sample object
{
int MassInf = Common->MassInf; // MassInf switches
int Ndim = Common->Ndim; // dimension
int Valency = Common->Valency; // # fluxes per atom
double ProbON = Common->ProbON; // Pr(individual flux != 0)
double cool = Common->cool; // Annealing parameter
double* Data = Common->Data; // Data [Ndata]
double* Acc = Common->Acc; // Accuracies [Ndata]
int* Counts = Common->Counts; // Annealed Poisson counts [Ndata]
double* Mock = Object->Mock; // Mock data [Ndata]
double* Foot = Object->Foot; // Footprint workspace (=0) [Ndata]
int* flags = Object->flags; // Valency identifiers (=-1)[Ndata]
double* g1 = Object->g1; // grad chisquared [Valency]
double* g2 = Object->g2; // grad chisquared [Valency]
double* A11 = Object->A11; // grad grad chisquared [Valency]
double* A12 = Object->A12; // grad grad chisquared [Valency]
double* A22 = Object->A22; // grad grad chisquared [Valency]
int* Xindex = Object->Xindex; // index to crossterms [Valency]
double q = Object->FluxUnit; // Unit of flux
unsigned* Rand = Object->Rand; // Random generator state
int* nbits = Object->nbits; // # fragments [Valency]
int* nbitx = Object->nbitx; // # fragments [Valency]
int* ibits = Object->ibits; // Fragment positions [<=Ndata]
int* ibitx = Object->ibitx; // Fragment positions [<=Ndata]
double* zbits = Object->zbits; // Fragment quantities [<=Ndata]
double* zbitx = Object->zbitx; // Fragment quantities [<=Ndata]
double* Cube1; // Position of new atom [Ndim]
double* Cube2; // Position of new atom [Ndim]
double* Flux1; // Flux of new atom [Valency]
double* Flux2; // Flux of new atom [Valency]
int CALLvalue = 0;
*dL = 0.0; // default output
// Footprints
Cube1 = Object->Cubes[Object->Natoms - 1];
Cube2 = Object->Cubes[Object->Natoms - 2];
Flux1 = Cube1 + Ndim;
Flux2 = Cube2 + Ndim;
CALL( AtomBits(Cube2, Common, ibitx, zbitx, nbitx, flags) )
if ( CALLvalue == 0 )
return E_BAYESYS_SYSERR;
CALL( AtomBits(Cube1, Common, ibits, zbits, nbits, flags) )
if ( CALLvalue == 0 )
return E_BAYESYS_SYSERR;
CALL( Overlap2(nbits, ibits, nbitx, ibitx, flags, Xindex, Valency) )
// Gaussian
if ( MassInf < 100 )
{
// Construct quadratic chisquared
SetGrad2(Mock, Data, Acc, Foot, Valency,
nbits, ibits, zbits, nbitx, ibitx, zbitx,
g1, g2, A11, A12, A22, Xindex);
// Reset Fluxes
GaussInsert2(MassInf, Rand, cool, q, ProbON, Valency,
g1, g2, A11, A12, A22, Xindex, Flux1, Flux2);
// Modify Lhood
*dL = GaussLhood2(Valency, g1, g2, A11, A12, A22, Xindex, Flux1, Flux2);
}
// Poisson
else
{
CALL( PoissInsert2(MassInf, Rand, cool, q, ProbON,
Mock, Data, Acc, Counts, Foot,
Valency, nbits, ibits, zbits, nbitx, ibitx, zbitx,
Xindex, Flux1, Flux2) )
*dL = PoissLhood2(Mock, Data, Acc, Foot,
Valency, nbits, ibits, zbits, nbitx, ibitx, zbitx,
Xindex, Flux1, Flux2);
}
// Modify mock data
InsBits(Mock, Flux1, nbits, ibits, zbits, Valency);
InsBits(Mock, Flux2, nbitx, ibitx, zbitx, Valency);
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: FluxDelete1
//
// Purpose: Delete 1 old atom with fluxes from Object, keeping it up-to-date,
// and set d(loglikelihood(fluxes)).
//
// dL := d logL(...)
//
// The old atom has been placed after the last location of
// the updated Atoms list, at Object->Cubes[ Object->Natoms ].
//
// History: JS 21 Mar 2002, 3 Oct 2002, 12 Aug 2003, 18 Aug 2003
//-----------------------------------------------------------------------------
static
int FluxDelete1( // O 0, or -ve return code
double* dL, // O d(loglikelihood(fluxes))
CommonStr* Common, // I general information
ObjectStr* Object) // I O updated sample object
{
int MassInf = Common->MassInf; // MassInf switches
int Valency = Common->Valency; // # fluxes per atom
int Ndim = Common->Ndim; // dimension
double* Data = Common->Data; // Data [Ndata]
double* Acc = Common->Acc; // Accuracies [Ndata]
double* Mock = Object->Mock; // Mock data [Ndata]
double* g1 = Object->g1; // grad chisquared [Valency]
double* A11 = Object->A11; // grad grad chisquared [Valency]
int* nbits = Object->nbits; // # fragments [Valency]
int* ibits = Object->ibits; // Fragment positions [<=Ndata]
double* zbits = Object->zbits; // Fragment quantities [<=Ndata]
int* flags = Object->flags; // flags for overlap [Ndata]
double* Cube; // Position of new atom [Ndim]
double* Flux; // Flux of new atom [Valency]
int CALLvalue = 0;
*dL = 0.0; // default output
// Footprint
Cube = Object->Cubes[Object->Natoms];
Flux = Cube + Ndim;
CALL( AtomBits(Cube, Common, ibits, zbits, nbits, flags) )
// Gaussian
if ( MassInf < 100 )
{
// Construct quadratic chisquared
SetGrad1(Mock, Data, Acc, Valency, nbits, ibits, zbits, g1, A11);
// Modify Lhood
*dL = GaussLhood1(Valency, Flux, g1, A11, -1);
}
// Poisson
else
*dL = PoissLhood1(Mock, Data, Acc, Valency, nbits, ibits, zbits,
Flux, -1);
// Modify mock data
DelBits(Mock, Flux, nbits, ibits, zbits, Valency);
Exit:
return CALLvalue;
}
//=============================================================================
// MassInf application procedures for user Footprints
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: AtomBits
//
// Purpose: Wrapper for user's UserFoot, offering some protection against
// user writing unusable fragments:
// nbits[ Valency ] elements obey nbits[.] >= 0
// and SUM(nbits[.]) <= Ndata
// ibits[ SUM(nbits[.]) ] elements obey 0 <= ibits[.] < Ndata
// zbits[ SUM(nbits[.]) ]
//
// History: JS 21 Mar 2002, 3 Oct 2002, 12 Aug 2003
//-----------------------------------------------------------------------------
static
int AtomBits( // O +ve = OK
// 0 = DO NOT USE this position
// -ve = ERROR
double* Cube, // I Atom position
CommonStr* Common, // I Definition of footprint
int* ibits, // O Fragment coords on data, serially per valency
double* zbits, // O Fragment quantities, serially per valency
int* nbits, // O # fragments, for each valency
int* flags) //(I O) squash any un-necessary overlap from user
{
int Valency = Common->Valency;
int Ndata = Common->Ndata;
int i, j, k, n, v;
int CALLvalue = 0;
// Footprint from user
CALL( UserFoot(Cube, Common, ibits, zbits, nbits) )
i = j = k = n = 0;
for ( v = 0; v < Valency; v++ )
{
// Check for overwriting
if ( nbits[v] < 0 )
return E_MASSINF_NBITS;
n += nbits[v];
if ( n > Ndata )
return E_MASSINF_NBITS;
// Ignore any zeros and overlay any overlaps
for ( ; i < n; i++ )
if ( zbits[i] != 0.0 )
{
if ( ibits[i] < 0 || ibits[i] >= Ndata )
return E_MASSINF_RANGE;
if ( flags[ibits[i]] < 0 )
{
flags[ibits[i]] = j;
ibits[j] = ibits[i];
zbits[j] = zbits[i];
j++;
}
else
zbits[flags[ibits[i]]] += zbits[i];
}
nbits[v] = j - k;
for ( ; k < j; k++ )
flags[ibits[k]] = -1;
}
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Overlap1
//
// Purpose: Ensure (before inserting) that atom valencies do not overlap.
//
// Dot products of individual footprints must be diagonal, else
// error return.
// --------------------------
// | A11[0] . . . |
// | |
// | . A11[1] . . |
// | |
// | . . A11[2] . |
// | |
// | . . . A11[3] |
// --------------------------
// --> Valency
//
// History: JS 2 Jan 2002, 21 Mar 2002
//-----------------------------------------------------------------------------
static
int Overlap1( // O 0, or -ve user error
int* nbits, // I # fragments [Valency]
int* ibits, // I Fragment positions [<=Ndata]
int* flags, // I O Valency identifiers (-1) [Ndata]
int Valency) // I # fluxes per atom
{
int i; // bits counter
int k; // data counter
int v; // valency counter
int n; // bits limiter
// Check Atom valencies do not overlap by setting valency flags
i = n = 0;
for ( v = 0; v < Valency; v++ )
{
n += nbits[v];
for ( ; i < n; i++ )
{
k = ibits[i];
if ( flags[k] == -1 )
flags[k] = v;
else if ( flags[k] != v )
return E_MASSINF_OVERLAP;
}
}
// Reset flags = -1 (off)
for ( n--; n >= 0; n-- )
flags[ibits[n]] = -1;
return 0;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Overlap2
//
// Purpose: Ensure (before inserting) that valencies of two atoms do not
// wrongly overlap.
//
// Dot products of individual footprints must be diagonal, and
// each valency of an atom can overlap with at most one valency
// of another, else error return.
//
// Atom1 Atom2
// -----------------------------------------------------
// | A11[0] . . . | . . A12[0] . | Xindex[0] = 2
// | | |
// | . A11[1] . . | . . . . | Xindex[1] off
// Atom1 | | |
// | . . A11[2] . | . . . . | Xindex[2] off
// | | |
// | . . . A11[3] | . A12[3] . . | Xindex[3] = 1
// |--------------------------|--------------------------|
// | . . . . | A22[0] . . . |
// | | |
// | . . . A12[3] | . A22[1] . . |
// Atom2 | | |
// | A12[0] . . . | . . A22[2] . |
// | | |
// | . . . . | . . . A22[3] |
// -----------------------------------------------------
// --> Valency -->Valency
//
// Cross-terms between the two atoms (at most 1 per row or column)
// are indexed by Xindex, as in this example with Valency = 4.
//
// History: JS 2 Jan 2002
//-----------------------------------------------------------------------------
static
int Overlap2( // O 0, or -ve user error
int* nbits, // I # fragments [Valency]
int* ibits, // I Fragment positions [<=Ndata]
int* nbitx, // I # fragments [Valency]
int* ibitx, // I Fragment positions [<=Ndata]
int* flags, // I O Valency identifiers (-1) [Ndata]
int* Xindex, // O index to cross-terms [Valency]
int Valency) // I # fluxes per atom
{
int i; // bits counter
int k; // data counter
int v1; // valency counter
int v2; // valency counter
int n1; // bits limiter
int n2; // bits limiter
int check; // crossterm checker
// Check Atom1 valencies do not overlap by setting valency flags
i = n1 = 0;
for ( v1 = 0; v1 < Valency; v1++ )
{
n1 += nbits[v1];
for ( ; i < n1; i++ )
{
k = ibits[i];
if ( flags[k] == -1 )
flags[k] = v1;
else if ( flags[k] != v1 )
return E_MASSINF_OVERLAP;
}
}
// Check no more than one Atom1 overlap with each Atom2 valency
i = n2 = 0;
for ( v2 = 0; v2 < Valency; v2++ )
{
check = -1;
n2 += nbitx[v2];
for ( ; i < n2; i++ )
{
k = ibitx[i];
if ( flags[k] != -1 )
{
if ( check == -1 )
check = flags[k];
else if ( check != flags[k] )
return E_MASSINF_OVERLAP;
}
}
}
// Reset flags = -1 (off)
for ( n1--; n1 >= 0; n1-- )
flags[ibits[n1]] = -1;
// Check Atom2 valencies do not overlap
i = n2 = 0;
for ( v2 = 0; v2 < Valency; v2++ )
{
n2 += nbitx[v2];
for ( ; i < n2; i++ )
{
k = ibitx[i];
if ( flags[k] == -1 )
flags[k] = v2;
else if ( flags[k] != v2 )
return E_MASSINF_OVERLAP;
}
}
// Check no more than one Atom2 overlap with each Atom1 valency
// Set Xindex[.] = Atom2 valency overlapping with Atom1 valency (-1 if none)
i = n1 = 0;
for ( v1 = 0; v1 < Valency; v1++ )
{
check = -1;
n1 += nbits[v1];
for ( ; i < n1; i++ )
{
k = ibits[i];
if ( flags[k] != -1 )
{
if ( check == -1 )
check = flags[k];
else if ( check != flags[k] )
return E_MASSINF_OVERLAP;
}
}
Xindex[v1] = check;
}
// Reset flags = -1 (off)
for ( n2--; n2 >= 0; n2-- )
flags[ibitx[n2]] = -1;
return 0;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: SetIndex
//
// Purpose: Set Xindex cross-terms between valencies.
//
// History: JS 18 Aug 2003 from SetGrad2
//-----------------------------------------------------------------------------
static
void SetIndex(
int Valency, // I # fluxes per atom
int* nbits, // I # fragments [Valency]
int* ibits, // I Fragment positions [<=Ndata]
int* nbitx, // I # fragments [Valency]
int* ibitx, // I Fragment positions [<=Ndata]
int* flags, // I O Valency identifiers (=-1) [Ndata]
int* Xindex) // O index to cross-terms [Valency]
{
int i; // bits counter
int k; // data counter
int v1; // valency counter
int v2; // valency counter
int m1; // bits limiter
int n1; // bits limiter
int n2; // bits limiter
// Set valency flags
i = n2 = 0;
for ( v2 = 0; v2 < Valency; v2++ )
{
n2 += nbitx[v2];
for ( ; i < n2; i++ )
flags[ibitx[i]] = v2;
}
// Set Xindex[.] = Atom2 valency overlapping with Atom1 valency (-1 if none)
m1 = n1 = 0;
for ( v1 = 0; v1 < Valency; v1++ )
{
Xindex[v1] = -1;
n1 += nbits[v1];
for ( i = m1; i < n1; i++ )
{
k = ibits[i];
if ( flags[k] >= 0 )
{
Xindex[v1] = flags[k];
break;
}
}
m1 += nbits[v1];
}
// Reset flags = -1 (off)
n2 = 0;
for ( v2 = 0; v2 < Valency; v2++ )
n2 += nbitx[v2];
for ( i = 0; i < n2; i++ )
flags[ibitx[i]] = -1;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: InsBits
//
// Purpose: Insert atom fluxes into mock data
//
// History: JS 2 Jan 2002
//-----------------------------------------------------------------------------
static
void InsBits(
double* Mock, // I O Mock data
double* Flux, // I fluxes [Valency]
int* nbit, // I # fragments [Valency]
int* ibit, // I fragment positions [<=Ndata]
double* zbit, // I fragment quantities [<=Ndata]
int Valency) // I # fluxes per atom
{
int i, v, n;
i = n = 0;
for ( v = 0; v < Valency; v++ )
{
n += nbit[v];
for ( ; i < n; i++ )
Mock[ibit[i]] += Flux[v] * zbit[i];
}
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: DelBits
//
// Purpose: Delete atom fluxes from mock data
//
// History: JS 2 Jan 2002
//-----------------------------------------------------------------------------
static
void DelBits(
double* Mock, // I O Mock data
double* Flux, // I fluxes [Valency]
int* nbit, // I # fragments [Valency]
int* ibit, // I fragment positions [<=Ndata]
double* zbit, // I fragment quantities [<=Ndata]
int Valency) // I # fluxes per atom
{
int i, v, n;
i = n = 0;
for ( v = 0; v < Valency; v++ )
{
n += nbit[v];
for ( ; i < n; i++ )
Mock[ibit[i]] -= Flux[v] * zbit[i];
}
}
//=============================================================================
// MassInf application procedures for quadratic chisquared
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: SetGrad1
//
// Purpose: Set quadratic coeffs for increment of logLikelihood from 1 atom,
// allowing for multiple Valency.
//
// d(Lhood) = - g1.Flux - Flux.A11.Flux / 2
//
// History: JS 2 Jan 2002
// 14 Aug 2003 Rely on no overlay in received bits
//-----------------------------------------------------------------------------
static
void SetGrad1(
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Accuracies [Ndata]
int Valency, // I # fluxes per atom
int* nbits, // I # fragments [Valency]
int* ibits, // I Fragment positions [<=Ndata]
double* zbits, // I Fragment quantities [<=Ndata]
double* g1, // O grad chisquared [Valency]
double* A11) // O grad grad chisquared [Valency]
{
int i; // bits counter
int k; // data counter
int v; // valency counter
int m; // bits limiter
int n; // bits limiter
double z; // local footprint
m = n = 0;
for ( v = 0; v < Valency; v++ )
{
g1[v] = A11[v] = 0.0;
n += nbits[v];
for ( i = m; i < n; i++ )
{
k = ibits[i];
z = zbits[i] * Acc[k];
g1[v] += z * Acc[k] * (Mock[k] - Data[k]);
A11[v] += z * z;
}
m += nbits[v];
}
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: SetGrad2
//
// Purpose: Set quadratic coeffs for increment of logLikelihood from 2 atoms,
// allowing for multiple Valency.
//
// d(Lhood) = - g1.Flux1 - g2.Flux2
// - (Flux1.A11.Flux1 + 2 Flux1.A12.Flux2 + Flux2.A22.Flux2) / 2
//
// History: JS 2 Jan 2002
// 18 Aug 2003 Rely on no overlay in received bits
//-----------------------------------------------------------------------------
static
void SetGrad2(
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Accuracies [Ndata]
double* Foot, // I O Footprint workspace (=0) [Ndata]
int Valency, // I # fluxes per atom
int* nbits, // I # fragments [Valency]
int* ibits, // I Fragment positions [<=Ndata]
double* zbits, // I Fragment quantities [<=Ndata]
int* nbitx, // I # fragments [Valency]
int* ibitx, // I Fragment positions [<=Ndata]
double* zbitx, // I Fragment quantities [<=Ndata]
double* g1, // O grad chisquared [Valency]
double* g2, // O grad chisquared [Valency]
double* A11, // O grad grad chisquared [Valency]
double* A12, // O grad grad chisquared [Valency]
double* A22, // O grad grad chisquared [Valency]
int* Xindex) // I index to cross-terms [Valency]
{
int i; // bits counter
int k; // data counter
int v1; // valency counter
int v2; // valency counter
int m1; // bits limiter
int n1; // bits limiter
int n2; // bits limiter
double z; // local flux
// For each Atom1 valency
m1 = n1 = 0;
for ( v1 = 0; v1 < Valency; v1++ )
{
g1[v1] = g2[v1] = A11[v1] = A12[v1] = A22[v1] = 0.0;
// Footprint
n1 += nbits[v1];
for ( i = m1; i < n1; i++ )
Foot[ibits[i]] = zbits[i];
// Index to cross term (if any)
if ( Xindex[v1] >= 0 )
{
i = 0;
for ( v2 = 0; v2 < Xindex[v1]; v2++ )
i += nbitx[v2];
n2 = i + nbitx[v2];
for ( ; i < n2; i++ )
{
k = ibitx[i];
A12[v1] += zbitx[i] * Acc[k] * Acc[k] * Foot[k];
}
}
// Diagonal term
for ( i = m1; i < n1; i++ )
{
k = ibits[i];
z = Foot[k] * Acc[k] * Acc[k];
g1[v1] += z * (Mock[k] - Data[k]);
A11[v1] += z * Foot[k];
Foot[k] = 0.0;
}
m1 += nbits[v1];
}
// For each Atom2 valency, diagonal term
i = n2 = 0;
for ( v2 = 0; v2 < Valency; v2++ )
{
n2 += nbitx[v2];
for ( ; i < n2; i++ )
{
k = ibitx[i];
z = zbitx[i] * Acc[k] * Acc[k];
g2[v2] += z * (Mock[k] - Data[k]);
A22[v2] += z * zbitx[i];
}
}
}
//=============================================================================
// MassInf application procedures for quadratic probabilities
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: GaussLhood
// -1 -chisquared/2
// Purpose: Set Lhood = log(L), L = Z e
//
// History: JS 18 Aug 2003
//-----------------------------------------------------------------------------
static
double GaussLhood( // O log(L)
int Ndata, // I # data
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc) // I Accuracies [Ndata]
{
static const double sqrt2pi = 2.50662827463100050240;
double C = 0.0;
double Lnorm = 0.0;
double temp;
int k;
for ( k = 0; k < Ndata; k++ )
{
if ( Acc[k] > 0.0 )
{
temp = Acc[k];
Lnorm += log(temp / sqrt2pi);
temp *= Mock[k] - Data[k];
C += temp * temp;
}
}
return Lnorm - C / 2.0;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: GaussTry1
//
// (1/cool) log INTEGRAL dPrior (Lhood / L0)^cool
//
// for entire atom with Gaussian likelihood
//
// History: JS 19 Jul 2003, 14 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
double GaussTry1( // O DELTA logL
int MassInf, // I MassInf prior
double cool, // I Annealing coefficient
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
int Valency, // I # fluxes per atom
double* g1, // I grad chisquared [Valency]
double* A11) // I grad grad chisquared [Valency]
{
double dL = 0.0;
int v;
for ( v = 0; v < Valency; v++ )
dL += Gauss1Marginal(MassInf, cool, q, ProbON, g1[v], A11[v]);
return dL;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: GaussTry2
//
// (1/cool) log INTEGRAL dPrior (Lhood / L0)^cool
//
// for two entire atoms with Gaussian likelihood
//
// History: JS 19 Jul 2003, 14 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
void GaussTry2(
int MassInf, // I MassInf prior
double cool, // I Annealing coefficient
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
int Valency, // I # fluxes per atom
double* g1, // I grad chisquared [Valency]
double* g2, // I grad chisquared [Valency]
double* A11, // I grad grad chisquared [Valency]
double* A12, // I grad grad chisquared [Valency]
double* A22, // I grad grad chisquared [Valency]
int* Xindex, // I index to cross-terms [Valency]
double* dLtry1, // O DELTA logL for first atom
double* dLtry2) // O DELTA logL for both atoms
{
int v1, v2;
*dLtry1 = *dLtry2 = 0.0;
// Trial Lhood increment
for ( v1 = 0; v1 < Valency; v1++ )
*dLtry1 += Gauss1Marginal(MassInf, cool, q, ProbON, g1[v1], A11[v1]);
// Trial Lhood increment
for ( v1 = 0; v1 < Valency; v1++ )
{
v2 = Xindex[v1];
if ( v2 >= 0 ) // pick up Atom1/Atom2 cross term...
*dLtry2 += Gauss2Marginal(MassInf, cool, q, ProbON,
g1[v1], g2[v2], A11[v1], A12[v1], A22[v2]);
else // ... or pick up lone Atom1
*dLtry2 += Gauss1Marginal(MassInf, cool, q, ProbON, g1[v1], A11[v1]);
}
for ( v2 = 0; v2 < Valency; v2++ )
{
for ( v1 = 0; v1 < Valency; v1++ )
if ( Xindex[v1] == v2 )
break;
if ( v1 == Valency ) // remaining lone Atom2
*dLtry2 += Gauss1Marginal(MassInf, cool, q, ProbON, g2[v2], A22[v2]);
}
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: GaussInsert1
//
// Sample fluxes from Prior * Lhood^cool
// for one entire atom with Gaussian likelihood
//
// History: JS 19 Jul 2003, 14 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
void GaussInsert1(
int MassInf, // I MassInf prior
Rand_t Rand, // I O random generator state
double cool, // I Annealing coefficient
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
int Valency, // I # fluxes per atom
double* g1, // I grad chisquared [Valency]
double* A11, // I grad grad chisquared [Valency]
double* Flux) // O fluxes [Valency]
{
int v;
for ( v = 0; v < Valency; v++ )
Flux[v] = Gauss1Sample(MassInf, Rand, cool, q, ProbON, g1[v], A11[v]);
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: GaussInsert2
//
// Sample fluxes from Prior * Lhood^cool
// for two entire atoms with Gaussian likelihood
//
// History: JS 19 Jul 2003, 14 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
void GaussInsert2(
int MassInf, // I MassInf prior
Rand_t Rand, // I O random generator state
double cool, // I Annealing coefficient
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
int Valency, // I # fluxes per atom
double* g1, // I grad chisquared [Valency]
double* g2, // I grad chisquared [Valency]
double* A11, // I grad grad chisquared [Valency]
double* A12, // I grad grad chisquared [Valency]
double* A22, // I grad grad chisquared [Valency]
int* Xindex, // I index to cross-terms [Valency]
double* Flux1, // O fluxes of atom1 [Valency]
double* Flux2) // O fluxes of atom2 [Valency]
{
int v1, v2;
for ( v1 = 0; v1 < Valency; v1++ )
{
v2 = Xindex[v1];
if ( v2 >= 0 )
Gauss2Sample(MassInf, Rand, cool, q, ProbON,
g1[v1], g2[v2], A11[v1], A12[v1], A22[v2],
&Flux1[v1], &Flux2[v2]);
else
Flux1[v1] = Gauss1Sample(MassInf, Rand, cool, q, ProbON,
g1[v1], A11[v1]);
}
for ( v2 = 0; v2 < Valency; v2++ )
{
for ( v1 = 0; v1 < Valency; v1++ )
if ( Xindex[v1] == v2 )
break;
if ( v1 == Valency )
Flux2[v2] = Gauss1Sample(MassInf, Rand, cool, q, ProbON,
g2[v2], A22[v2]);
}
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: GaussLhood1
//
// DELTA( log Lhood ) for inserting or deleting
// one entire atom with Gaussian likelihood
//
// History: JS 18 Aug 2003
//-----------------------------------------------------------------------------
static
double GaussLhood1(
int Valency, // I # fluxes per atom
double* Flux , // I fluxes [Valency]
double* g1, // I grad chisquared [Valency]
double* A11, // I grad grad chisquared [Valency]
int flag) // I +1 = insert, -1 = delete
{
double dL = 0.0;
int v;
if ( flag > 0 )
for ( v = 0; v < Valency; v++ )
dL -= Flux[v] * (Flux[v] * A11[v] / 2.0 + g1[v]);
else
for ( v = 0; v < Valency; v++ )
dL -= Flux[v] * (Flux[v] * A11[v] / 2.0 - g1[v]);
return dL;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: GaussLhood2
//
// DELTA( log Lhood )
// for inserting two entire atoms with Gaussian likelihood
//
// History: JS 18 Aug 2003
//-----------------------------------------------------------------------------
static
double GaussLhood2(
int Valency, // I # fluxes per atom
double* g1, // I grad chisquared [Valency]
double* g2, // I grad chisquared [Valency]
double* A11, // I grad grad chisquared [Valency]
double* A12, // I grad grad chisquared [Valency]
double* A22, // I grad grad chisquared [Valency]
int* Xindex, // I index to cross-terms [Valency]
double* Flux1, // I fluxes of atom1 [Valency]
double* Flux2) // I fluxes of atom2 [Valency]
{
double dL = 0.0;
int v1, v2;
for ( v1 = 0; v1 < Valency; v1++ )
{
v2 = Xindex[v1];
if ( v2 >= 0 )
dL -= g1[v1] * Flux1[v1] + g2[v2] * Flux2[v2]
+ A11[v1] * Flux1[v1] * Flux1[v1] / 2.0
+ A12[v1] * Flux1[v1] * Flux2[v2]
+ A22[v2] * Flux2[v2] * Flux2[v2] / 2.0;
else
dL -= g1[v1] * Flux1[v1] + A11[v1] * Flux1[v1] * Flux1[v1] / 2.0;
}
for ( v2 = 0; v2 < Valency; v2++ )
{
for ( v1 = 0; v1 < Valency; v1++ )
if ( Xindex[v1] == v2 )
break;
if ( v1 == Valency )
dL -= g2[v2] * Flux2[v2] + A22[v2] * Flux2[v2] * Flux2[v2] / 2.0;
}
return dL;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Gauss1Marginal
// -cool(g*z + A*z*z/2)
// (1/cool) log INTEGRAL dz Pr(z) e
//
// History: JS 19 Jul 2003, 18 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
double Gauss1Marginal( // O value, calculated OK even if cool=0
int MassInf, // I MassInf prior (0,1,2,3)
double cool, // I Annealing coefficient
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
double g, // I gradient
double A) // I curvature
{
double p;
double ProbOFF;
p = gauss1marginal(MassInf, cool, q, g, A);
if ( ProbON < 1.0 )
{
ProbOFF = 1.0 - ProbON;
if ( cool * cool * p * p < DBL_EPSILON )
p *= ProbON;
else
p = PLUS(log(ProbOFF), log(ProbON) + cool * p) / cool;
}
return p;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Gauss2Marginal
// -cool(g.x + x.A.x/2)
// (1/cool) log INTEGRAL dxdy Pr(x)Pr(y) e
//
// where g.x = g1*x + g2*y, x.A.x = A11*x*x + 2*A12*x*y + A22*y*y
//
// History: JS 19 Jul 2003, 18 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
double Gauss2Marginal( // O value, calculated OK even if cool=0
int MassInf, // I MassInf prior (0,1,2,3)
double cool, // I Annealing coefficient
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
double g1, // I gradient
double g2, // I gradient
double A11, // I curvature
double A12, // I curvature
double A22) // I curvature
{
double p1, p2, p12;
double ProbOFF;
p12 = gauss2marginal(MassInf, cool, q, g1, g2, A11, A12, A22);
if ( ProbON < 1.0 )
{
ProbOFF = 1.0 - ProbON;
p1 = gauss1marginal(MassInf, cool, q, g1, A11);
p2 = gauss1marginal(MassInf, cool, q, g2, A22);
if ( cool * cool * (p1*p1 + p2*p2 + p12*p12) < DBL_EPSILON )
{
p12 = ProbON * (ProbOFF * (p1 + p2) + ProbON * p12);
p1 *= ProbON;
}
else
{
p1 = PLUS(log(ProbOFF), log(ProbON) + cool * p1);
p2 = PLUS(log(ProbOFF) + cool * p2, log(ProbON) + cool * p12);
p12 = PLUS(log(ProbOFF) + p1, log(ProbON) + p2) / cool;
}
}
return p12;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Gauss1Sample
// -cool(g*z + A*z*z/2)
// Sample single flux z from Pr(z) e
//
// History: JS 19 Jul 2003, 18 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
double Gauss1Sample( // O flux z
int MassInf, // I MassInf prior (0,1,2,3)
Rand_t Rand, // I O random generator state
double cool, // I cooling parameter
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
double g, // I gradient
double A) // I curvature
{
double p, ProbOFF;
int k = 1;
if ( ProbON < 1.0 )
{
ProbOFF = 1.0 - ProbON;
p = log(ProbON) + cool * gauss1marginal(MassInf, cool, q, g, A);
if ( log(Randouble(Rand)) > p - PLUS(log(ProbOFF), p) )
k = 0;
}
return k ? gauss1sample(MassInf, Rand, cool, q, g, A) : 0.0;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Gauss2Sample
// -cool(g.x + x.A.x/2)
// Sample single fluxes (x,y) from Pr(x)Pr(y) e
// where g.x = g1*x + g2*y, x.A.x = A11*x*x + 2*A12*x*y + A22*y*y
//
// History: JS 19 Jul 2003, 18 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
void Gauss2Sample(
int MassInf, // I MassInf prior (0,1,2,3)
Rand_t Rand, // I O random generator state
double cool, // I cooling parameter
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
double g1, // I gradient
double g2, // I gradient
double A11, // I curvature
double A12, // I curvature
double A22, // I curvature
double* Flux1, // O flux
double* Flux2) // O flux
{
double p, p1, p2, p12, a, b, c, r, ProbOFF;
int k = 3;
*Flux1 = *Flux2 = 0.0;
if ( ProbON < 1.0 )
{
ProbOFF = 1.0 - ProbON;
p = log(ProbOFF) + log(ProbOFF);
p1 = log(ProbOFF) + log(ProbON)
+ cool * gauss1marginal(MassInf, cool, q, g1, A11);
p2 = log(ProbOFF) + log(ProbON)
+ cool * gauss1marginal(MassInf, cool, q, g2, A22);
p12 = log(ProbON) + log(ProbON)
+ cool * gauss2marginal(MassInf, cool, q, g1, g2, A11, A12, A22);
a = PLUS(p, p1);
b = PLUS(p2, p12);
c = PLUS(a, b);
p1 = exp(p1 - c);
p2 = exp(p2 - c);
p12 = exp(p12 - c);
r = Randouble(Rand);
if ( r < p12 )
k = 3;
else if ( r < p12 + p2 )
k = 2;
else if ( r < p12 + p2 + p1 )
k = 1;
else
k = 0;
}
if ( k == 1 )
*Flux1 = gauss1sample(MassInf, Rand, cool, q, g1, A11);
if ( k == 2 )
*Flux2 = gauss1sample(MassInf, Rand, cool, q, g2, A22);
if ( k == 3 )
gauss2sample(MassInf, Rand, cool, q, g1, g2, A11, A12, A22, Flux1, Flux2);
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: gauss1marginal
// -cool(g*z + A*z*z/2)
// (1/cool) log INTEGRAL dz Pr(z) e
//
// where z is non-zero flux
//
// History: JS 2 Jan 2002
// 19 Jul 2003 "switch" recoding
//-----------------------------------------------------------------------------
static
double gauss1marginal( // O value, calculated OK even if cool=0
int MassInf, // I Prior (0=monkeys,1=pos,2=posneg,3=gauss)
double cool, // I Annealing coefficient
double q, // I Flux unit
double g, // I gradient
double A) // I curvature
{
double t, pos, neg;
g *= q;
A *= q * q;
switch ( MassInf % 10 )
{
case 0:
return -(g + A / 2.0);
case 1:
t = cool * (fabs(g) + A);
if ( t * t > DBL_EPSILON )
return logerf(1.0 + cool * g, cool * A) / cool;
else
return -(g + A);
case 2:
t = cool * (cool * g * g + A);
if ( t * t > DBL_EPSILON )
{
pos = logerf(1.0 + cool * g, cool * A);
neg = logerf(1.0 - cool * g, cool * A);
return (log(0.5) + PLUS(pos, neg)) / cool;
}
else
return cool * g * g - A;
case 3:
t = cool * A;
if ( t * t > DBL_EPSILON )
t = log(1.0 + t) / cool;
else
t = A;
return 0.5 * (cool * g * g / (1.0 + cool * A) - t);
}
return 0.0; // calling error
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: gauss2marginal
// -cool(g.x + x.A.x/2)
// (1/cool) log INTEGRAL dxdy P(x)P(y) e
//
// where g.x = g1*x + g2*y, x.A.x = A11*x*x + 2*A12*x*y + A22*y*y
// and x,y are non-zero fluxes
//
// History: JS 2 Jan 2002
// 19 Jul 2003 "switch" recoding
//-----------------------------------------------------------------------------
static
double gauss2marginal( // O value, calculated OK even if cool=0
int MassInf, // I Prior (0=monkeys,1=pos,2=posneg,3=gauss)
double cool, // I Annealing coefficient
double q, // I Flux unit
double g1, // I gradient
double g2, // I gradient
double A11, // I curvature
double A12, // I curvature
double A22) // I curvature
{
double t, pospos, posneg, negpos, negneg, pos, neg, det, gBg;
g1 *= q;
g2 *= q;
A11 *= q * q;
A12 *= q * q;
A22 *= q * q;
t = sqrt(A11 * A22);
if ( A12 > t )
A12 = t;
if ( A12 < -t )
A12 = -t;
switch ( MassInf % 10 )
{
case 0:
return -(g1 + g2 + 0.5 * A11 + A12 + 0.5 * A22);
case 1:
t = cool * (fabs(g1) + fabs(g2) + A11 + A22);
if ( t * t > DBL_EPSILON )
return logerf2(1.0 + cool * g1, 1.0 + cool * g2,
cool * A11, cool * A12, cool * A22) / cool;
else
return -(g1 + g2 + A11 + A12 + A22);
case 2:
t = cool * (cool * (g1 * g1 + g2 * g2) + A11 + A22);
if ( t * t > DBL_EPSILON )
{
pospos = logerf2(1.0 + cool * g1, 1.0 + cool * g2,
cool * A11, cool * A12, cool * A22);
posneg = logerf2(1.0 + cool * g1, 1.0 - cool * g2,
cool * A11, cool * A12, cool * A22);
negpos = logerf2(1.0 - cool * g1, 1.0 + cool * g2,
cool * A11, cool * A12, cool * A22);
negneg = logerf2(1.0 - cool * g1, 1.0 - cool * g2,
cool * A11, cool * A12, cool * A22);
pos = PLUS(pospos, posneg);
neg = PLUS(negpos, negneg);
return (log(0.25) + PLUS(pos, neg)) / cool;
}
else
return cool * (g1 * g1 + g2 * g2) - (A11 + A12 + A22);
case 3:
t = cool * (A11 + A22);
det = A11 * A22 - A12 * A12;
if ( det < 0.0 )
det = 0.0;
det = 1.0 + t + cool * cool * det;
gBg = (g1 * g1 * (1.0 + cool * A22) - 2.0 * g1 * g2 * cool * A12
+ g2 * g2 * (1.0 + cool * A11)) / det;
if ( t * t > DBL_EPSILON )
t = log(det) / cool;
else
t = A11 + A22;
return 0.5 * (cool * gBg - t);
}
return 0.0; // calling error
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: gauss1sample
// -cool(g*z + A*z*z/2)
// Sample non-zero flux z from P(z) e
//
// History: JS 2 Jan 2002
// 17 Dec 2002 MassInf=3 debugged
// 19 Jul 2003 "switch" recoding
// 13 Aug 2003 q into output
//-----------------------------------------------------------------------------
static
double gauss1sample( // O flux z
int MassInf, // I Prior (0=monkeys,1=pos,2=posneg,3=gauss)
Rand_t Rand, // I O random generator state
double cool, // I cooling parameter
double q, // I Flux unit
double g, // I gradient
double A) // I curvature
{
g *= cool * q;
A *= cool * q * q;
switch ( MassInf % 10 )
{
case 0:
return q;
case 1:
return q * Ran1pos(Rand, g + 1.0, A);
case 2:
return q * Ran1posneg(Rand, g, 1.0, A);
case 3:
return q * Rangauss(Rand) / sqrt(1.0 + A) - g / (1.0 + A);
}
return 0.0; // calling error
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: gauss2sample
// -cool(g.x + x.A.x/2)
// Sample non-zero fluxes (x,y) from P(x)P(y) e
//
// where g.x = g1*x + g2*y, x.A.x = A11*x*x + 2*A12*x*y + A22*y*y
//
// History: JS 2 Jan 2002
// 19 Jul 2003 "switch" recoding
// 13 Aug 2003 q into output
//-----------------------------------------------------------------------------
static
void gauss2sample(
int MassInf, // I Prior (0=monkeys,1=pos,2=posneg,3=gauss)
Rand_t Rand, // I O random generator state
double cool, // I cooling parameter
double q, // I Flux unit
double g1, // I gradient
double g2, // I gradient
double A11, // I curvature
double A12, // I curvature
double A22, // I curvature
double* x, // O flux
double* y) // O flux
{
double t;
g1 *= cool * q;
g2 *= cool * q;
A11 *= cool * q * q;
A12 *= cool * q * q;
A22 *= cool * q * q;
t = sqrt(A11 * A22);
if ( A12 > t )
A12 = t;
if ( A12 < -t )
A12 = -t;
switch ( MassInf % 10 )
{
case 0:
*x = *y = 1.0;
break;
case 1:
Ran2pos(Rand, g1 + 1.0, g2 + 1.0, A11, A12, A22, x, y);
break;
case 2:
Ran2posneg(Rand, g1, g2, 1.0, 1.0, A11, A12, A22, x, y);
break;
case 3:
Ran2gauss(Rand, g1, g2, 1.0 + A11, A12, 1.0 + A22, x, y);
break;
default:
*x = *y = 0.0; // calling error
}
*x *= q;
*y *= q;
}
//=============================================================================
// MassInf application procedures for Poisson probabilities
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: PoissLhood
//
// Purpose: Set Lhood = log(L) where
//
// -(F+B) D+B
// L = PRODUCT e (F+B) / (D+B)!
//
// D = data, F = mock data, B = background > 0 wherever D+B > 0.
// Maximum likelihood is F = D, as wanted.
// For small F, L remains finite, so empty object is non-singular.
// For small B, L becomes exp(-F) F^D / D!, standard Poisson.
//
// History: JS 18 Aug 2003, 25 Oct 2003
//-----------------------------------------------------------------------------
static
double PoissLhood( // O log(L)
int Ndata, // I # data
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc) // I Background [Ndata]
{
double C = 0.0;
double D, F;
int k;
for ( k = 0; k < Ndata; k++ )
{
D = Data[k] + Acc[k];
F = Mock[k] + Acc[k];
if ( F > 0.0 ) // else D known to be 0 also
C += D * log(F) - F - logGamma(1.0 + D);
}
return C;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: PoissTry1
//
// (1/cool) log INTEGRAL dPrior (Lhood / L0)^cool
//
// for entire atom with Poisson likelihood
//
// History: JS 18 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
int PoissTry1( // O 0, or -ve error
int MassInf, // I 100=monkeys, 101=positive, add 10 for z=0
double cool, // I Annealing coefficient
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Background [Ndata]
int* Counts, // I Annealed data [Ndata]
int Valency, // I # fluxes per atom
int* nbits, // I # fragments [Valency]
int* ibits, // I Fragment positions [<=Ndata]
double* zbits, // I Fragment quantities [<=Ndata]
double* dLtry) // O (1/cool) INT dprior (L/L0)^cool
{
double dL = 0.0;
double t;
int k, v;
int CALLvalue = 0;
for ( k = v = 0; v < Valency; k += nbits[v++] )
{
CALL( Poiss1Marginal(MassInf, cool, q, ProbON, Mock, Data, Acc, Counts,
nbits[v], &ibits[k], &zbits[k], &t) )
dL += t;
}
*dLtry = dL;
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: PoissTry2
//
// (1/cool) log INTEGRAL dPrior (Lhood / L0)^cool
//
// for two entire atoms with Poisson likelihood
//
// History: JS 18 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
int PoissTry2( // O 0, or -ve error
int MassInf, // I 100=monkeys, 101=positive, add 10 for z=0
double cool, // I Annealing coefficient
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Background [Ndata]
int* Counts, // I Annealed data [Ndata]
double* Foot, //(I O) Footprint (=0) [Ndata]
int Valency, // I # fluxes per atom
int* nbits, // I # fragments [Valency]
int* ibits, // I Fragment positions [<=Ndata]
double* zbits, // I Fragment quantities [<=Ndata]
int* nbitx, // I # fragments [Valency]
int* ibitx, // I Fragment positions [<=Ndata]
double* zbitx, // I Fragment quantities [<=Ndata]
int* Xindex, // I index to cross terms [Valency]
double* dLtry1, // O (1/cool) INT dprior[1] (L/L0)^cool
double* dLtry2) // O (1/cool) INT dprior[2] (L/L0)^cool
{
double dL1, dL2, t1, t2;
int i, k1, k2, v1, v2;
int CALLvalue = 0;
dL1 = dL2 = 0.0;
// Trial Lhood increments
for ( k1 = v1 = 0; v1 < Valency; k1 += nbits[v1++] )
{
v2 = Xindex[v1];
if ( v2 >= 0 ) // pick up Atom1/Atom2 cross term...
{
for ( k2 = i = 0; i < v2; k2 += nbitx[i++] ) ;
CALL( Poiss2Marginal(MassInf, cool, q, ProbON,
Mock, Data, Acc, Counts, Foot,
nbits[v1], &ibits[k1], &zbits[k1],
nbitx[v2], &ibitx[k2], &zbitx[k2],
&t1, &t2) )
dL2 += t2;
}
else // ... or pick up lone Atom1
{
Poiss1Marginal(MassInf, cool, q, ProbON, Mock, Data, Acc, Counts,
nbits[v1], &ibits[k1], &zbits[k1], &t1);
dL2 += t1;
}
dL1 += t1;
}
for ( k2 = v2 = 0; v2 < Valency; k2 += nbitx[v2++] )
{
for ( v1 = 0; v1 < Valency; v1++ )
if ( Xindex[v1] == v2 )
break;
if ( v1 == Valency ) // remaining lone Atom2
{
Poiss1Marginal(MassInf, cool, q, ProbON, Mock, Data, Acc, Counts,
nbitx[v2], &ibitx[k2], &zbitx[k2], &t2);
dL2 += t2;
}
}
*dLtry1 = dL1;
*dLtry2 = dL2;
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: PoissInsert1
//
// Sample fluxes from Prior * Lhood^cool
// for one entire atom with Poisson likelihood
//
// History: JS 18 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
int PoissInsert1( // O 0, or -ve error
int MassInf, // I 100=monkeys, 101=positive, add 10 for z=0
Rand_t Rand, // I O Random generator state
double cool, // I Annealing coefficient
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Background [Ndata]
int* Counts, // I Annealed data [Ndata]
int Valency, // I # fluxes per atom
int* nbits, // I # fragments [Valency]
int* ibits, // I Fragment positions [<=Ndata]
double* zbits, // I Fragment quantities [<=Ndata]
double* Flux) // O Sample fluxes [Valency]
{
int k, v;
int CALLvalue = 0;
for ( k = v = 0; v < Valency; k += nbits[v++] )
CALL( Poiss1Sample(MassInf, Rand, cool, q, ProbON, Mock, Data, Acc,
Counts, nbits[v], &ibits[k], &zbits[k], &Flux[v]) )
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: PoissInsert2
//
// Sample fluxes from Prior * Lhood^cool
// for two entire atoms with Poisson likelihood
//
// History: JS 18 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
int PoissInsert2( // O 0, or -ve error
int MassInf, // I 100=monkeys, 101=positive, add 10 for z=0
Rand_t Rand, // I O Random generator state
double cool, // I Annealing coefficient
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Background [Ndata]
int* Counts, // I Annealed data [Ndata]
double* Foot, //(I O) Footprint (=0) [Ndata]
int Valency, // I # fluxes per atom
int* nbits, // I # fragments [Valency]
int* ibits, // I Fragment positions [<=Ndata]
double* zbits, // I Fragment quantities [<=Ndata]
int* nbitx, // I # fragments [Valency]
int* ibitx, // I Fragment positions [<=Ndata]
double* zbitx, // I Fragment quantities [<=Ndata]
int* Xindex, // I Index to cross-terms [Valency]
double* Flux1, // O Fluxes of 1st atom [Valency]
double* Flux2) // O Fluxes of 2nd atom [Valency]
{
int i, k1, k2, v1, v2;
int CALLvalue = 0;
for ( k1 = v1 = 0; v1 < Valency; k1 += nbits[v1++] )
{
v2 = Xindex[v1];
if ( v2 >= 0 )
{
for ( k2 = i = 0; i < v2; k2 += nbitx[i++] ) ;
CALL( Poiss2Sample(MassInf, Rand, cool, q, ProbON,
Mock, Data, Acc, Counts, Foot,
nbits[v1], &ibits[k1], &zbits[k1],
nbitx[v2], &ibitx[k2], &zbitx[k2],
&Flux1[v1], &Flux2[v2]) )
}
else
CALL( Poiss1Sample(MassInf, Rand, cool, q, ProbON,
Mock, Data, Acc, Counts,
nbits[v1], &ibits[k1], &zbits[k1], &Flux1[v1]) )
}
for ( k2 = v2 = 0; v2 < Valency; k2 += nbitx[v2++] )
{
for ( v1 = 0; v1 < Valency; v1++ )
if ( Xindex[v1] == v2 )
break;
if ( v1 == Valency )
CALL( Poiss1Sample(MassInf, Rand, cool, q, ProbON,
Mock, Data, Acc, Counts,
nbitx[v2], &ibitx[k2], &zbitx[k2], &Flux2[v2]) )
}
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: PoissLhood1
//
// DELTA( log Lhood ) for inserting or deleting
// one entire atom with Poisson likelihood
//
// History: JS 18 Aug 2003
//-----------------------------------------------------------------------------
static
double PoissLhood1(// O DELTA(logL)
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Background [Ndata]
int Valency, // I # fluxes per atom
int* nbits, // I # fragments [Valency]
int* ibits, // I Fragment positions [<=Ndata]
double* zbits, // I Fragment quantities [<=Ndata]
double* Flux, // I Fluxes of atom [Valency]
int flag) // I +1 = insert, -1 = delete
{
double dL = 0.0;
int k, v;
if ( flag < 0 )
for ( v = 0; v < Valency; v++ )
Flux[v] = -Flux[v];
for ( k = v = 0; v < Valency; k += nbits[v++] )
dL += poiss1lhood(Flux[v], Mock, Data, Acc,
nbits[v], &ibits[k], &zbits[k]);
if ( flag < 0 )
for ( v = 0; v < Valency; v++ )
Flux[v] = -Flux[v];
return dL;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: PoissLhood2
//
// DELTA( log Lhood )
// for inserting two entire atoms with Poisson likelihood
//
// History: JS 18 Aug 2003
//-----------------------------------------------------------------------------
static
double PoissLhood2(// O DELTA(logL)
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Background [Ndata]
double* Foot, //(I O) Footprint (=0) [Ndata]
int Valency, // I # fluxes per atom
int* nbits, // I # fragments [Valency]
int* ibits, // I Fragment positions [<=Ndata]
double* zbits, // I Fragment quantities [<=Ndata]
int* nbitx, // I # fragments [Valency]
int* ibitx, // I Fragment positions [<=Ndata]
double* zbitx, // I Fragment quantities [<=Ndata]
int* Xindex, // I index to cross-terms [Valency]
double* Flux1, // I Fluxes of 1st atom [Valency]
double* Flux2) // I Fluxes of 2nd atom [Valency]
{
double dL = 0.0;
double t1, t2;
int i, k1, k2, v1, v2;
for ( k1 = v1 = 0; v1 < Valency; k1 += nbits[v1++] )
{
v2 = Xindex[v1];
if ( v2 >= 0 )
{
for ( k2 = i = 0; i < v2; k2 += nbitx[i++] ) ;
poiss2lhood(Flux1[v1], Flux2[v2], Mock, Data, Acc, Foot,
nbits[v1], &ibits[k1], &zbits[k1],
nbitx[v2], &ibitx[k2], &zbitx[k2], &t1, &t2);
dL += t2;
}
else
dL += poiss1lhood(Flux1[v1], Mock, Data, Acc,
nbits[v1], &ibits[k1], &zbits[k1]);
}
for ( k2 = v2 = 0; v2 < Valency; k2 += nbitx[v2++] )
{
for ( v1 = 0; v1 < Valency; v1++ )
if ( Xindex[v1] == v2 )
break;
if ( v1 == Valency )
dL += poiss1lhood(Flux2[v2], Mock, Data, Acc,
nbitx[v2], &ibitx[k2], &zbitx[k2]);
}
return dL;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Poiss1Marginal
//
// infinity -cool*R*z Counts
// (1/cool) log INTEGRAL dz Pr(z) e ( 1 + z * R/(Mock+Acc) )
// z=0
//
// Counts are integer approximations to cooled data, cool*(Data+Acc)
//
// History: JS 18 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
int Poiss1Marginal(// O 0, or -ve error
int MassInf, // I 100=monkeys, 101=positive, add 10 for z=0
double cool, // I Annealing coefficient
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Background [Ndata]
int* Counts, // I Annealed data [Ndata]
int nbits, // I # fragments
int* ibits, // I Fragment positions [nbits]
double* zbits, // I Fragment quantities R [nbits]
double* dLtry) // O (1/cool) INT dprior (L/L0)^cool
{
double p;
double ProbOFF;
int CALLvalue = 0;
CALL( Poisson1(MassInf, NULL, cool, q, Mock, Data, Acc, Counts,
nbits, ibits, zbits, &p) )
if ( ProbON < 1.0 )
{
ProbOFF = 1.0 - ProbON;
if ( cool * cool * p * p < DBL_EPSILON )
p *= ProbON;
else
p = PLUS(log(ProbOFF), log(ProbON) + cool * p) / cool;
}
Exit:
*dLtry = p;
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Poiss2Marginal
//
//
// infinity -cool*R*x Counts
// (1/cool) log INTEGRAL dx Pr(x) e ( 1 + x * R/(Mock+Acc) )
// x=0
// and
// infinity -cool*u Counts
// (1/cool) log INTEGRAL dxdy Pr(x)Pr(y) e ( 1 + u/(Mock+Acc) )
// x,y = 0
//
// where u = R*x + S*y,
// Counts are integer approximations to cooled data, cool*(Data+Acc)
//
// History: JS 18 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
int Poiss2Marginal(// O 0, or -ve error
int MassInf, // I 100=monkeys, 101=positive, add 10 for z=0
double cool, // I Annealing coefficient
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Background [Ndata]
int* Counts, // I Annealed data [Ndata]
double* Foot, //(I O) Footprint (=0) [Ndata]
int nbits, // I # fragments
int* ibits, // I Fragment positions [nbits]
double* zbits, // I Fragment quantities R [nbits]
int nbitx, // I # fragments
int* ibitx, // I Fragment positions [nbitx]
double* zbitx, // I Fragment quantities S [nbitx]
double* dLtry1, // O (1/cool) INT dprior[1] (L/L0)^cool
double* dLtry2) // O (1/cool) INT dprior[2] (L/L0)^cool
{
double p1, p2, p12;
double ProbOFF;
int CALLvalue = 0;
CALL( Poisson2(MassInf, NULL, cool, q, Mock, Data, Acc, Counts, Foot,
nbits, ibits, zbits, nbitx, ibitx, zbitx, &p1, &p12) )
if ( ProbON < 1.0 )
{
ProbOFF = 1.0 - ProbON;
CALL( Poisson1(MassInf, NULL, cool, q, Mock, Data, Acc, Counts,
nbitx, ibitx, zbitx, &p2) )
if ( cool * cool * (p1*p1 + p2*p2 + p12*p12) < DBL_EPSILON )
{
p12 = ProbON * (ProbOFF * (p1 + p2) + ProbON * p12);
p1 *= ProbON;
}
else
{
p1 = PLUS(log(ProbOFF), log(ProbON) + cool * p1);
p2 = PLUS(log(ProbOFF) + cool * p2, log(ProbON) + cool * p12);
p12 = PLUS(log(ProbOFF) + p1, log(ProbON) + p2) / cool;
}
}
Exit:
*dLtry1 = p1;
*dLtry2 = p12;
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Poiss1Sample
//
// Sample flux z from
// -cool*R*z Counts
// Pr(z) e ( 1 + z * R/(Mock+Acc) )
//
// Counts are integer approximations to cooled data, cool*(Data+Acc)
//
// History: JS 18 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
int Poiss1Sample( // O 0, or -ve error
int MassInf, // I 100=monkeys, 101=positive, add 10 for z=0
Rand_t Rand, // I O Random generator state
double cool, // I Annealing coefficient
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Background [Ndata]
int* Counts, // I Annealed data [Ndata]
int nbits, // I # fragments
int* ibits, // I Fragment positions [nbits]
double* zbits, // I Fragment quantities R [nbits]
double* Flux) // O Sample flux z
{
double p, ProbOFF;
int k = 1;
int CALLvalue = 0;
*Flux = 0.0;
if ( ProbON < 1.0 )
{
ProbOFF = 1.0 - ProbON;
CALL( Poisson1(MassInf, NULL, cool, q, Mock, Data, Acc, Counts,
nbits, ibits, zbits, &p) )
p = log(ProbON) + cool * p;
if ( log(Randouble(Rand)) > p - PLUS(log(ProbOFF), p) )
k = 0;
}
if ( k )
CALL( Poisson1(MassInf, Rand, cool, q, Mock, Data, Acc, Counts,
nbits, ibits, zbits, Flux) )
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Poiss2Sample
//
// Sample single fluxes x,y from
// -cool*(R*x+S*y) Counts
// Pr(x)Pr(y) e ( 1 + (R*x+S*y)/(Mock+Acc) )
//
// Counts are integer approximations to cooled data, cool*(Data+Acc)
//
// History: JS 18 Aug 2003, 12 Sep 2003
//-----------------------------------------------------------------------------
static
int Poiss2Sample( // O 0, or -ve error
int MassInf, // I 100=monkeys, 101=positive, add 10 for z=0
Rand_t Rand, // I O Random generator state
double cool, // I Annealing coefficient
double q, // I Flux unit
double ProbON, // I Pr(individual flux != 0)
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Background [Ndata]
int* Counts, // I Annealed data [Ndata]
double* Foot, //(I O) Footprint (=0) [Ndata]
int nbits, // I # fragments
int* ibits, // I Fragment positions [nbits]
double* zbits, // I Fragment quantities R [nbits]
int nbitx, // I # fragments
int* ibitx, // I Fragment positions [nbitx]
double* zbitx, // I Fragment quantities S [nbitx]
double* Flux1, // O Flux x of 1st atom
double* Flux2) // O Flux y of 2nd atom
{
double p, p1, p2, p12, a, b, c, r, ProbOFF;
int k = 3;
int CALLvalue = 0;
*Flux1 = *Flux2 = 0.0;
if ( ProbON < 1.0 )
{
ProbOFF = 1.0 - ProbON;
CALL( Poisson2(MassInf, NULL, cool, q, Mock, Data, Acc, Counts,
Foot, nbits, ibits, zbits, nbitx, ibitx, zbitx,
&p1, &p12) )
CALL( Poisson1(MassInf, NULL, cool, q, Mock, Data, Acc, Counts,
nbits, ibits, zbits, &p2) )
p = log(ProbOFF) + log(ProbOFF);
p1 = log(ProbOFF) + log(ProbON) + cool * p1;
p2 = log(ProbOFF) + log(ProbON) + cool * p2;
p12 = log(ProbON) + log(ProbON) + cool * p12;
a = PLUS(p, p1);
b = PLUS(p2, p12);
c = PLUS(a, b);
p1 = exp(p1 - c);
p2 = exp(p2 - c);
p12 = exp(p12 - c);
r = Randouble(Rand);
if ( r < p12 )
k = 3;
else if ( r < p12 + p2 )
k = 2;
else if ( r < p12 + p2 + p1 )
k = 1;
else
k = 0;
}
if ( k == 1 )
CALL( Poisson1(MassInf, Rand, cool, q, Mock, Data, Acc, Counts,
nbits, ibits, zbits, Flux1) )
if ( k == 2 )
CALL( Poisson1(MassInf, Rand, cool, q, Mock, Data, Acc, Counts,
nbitx, ibitx, zbitx, Flux2) )
if ( k == 3 )
CALL( Poisson2(MassInf, Rand, cool, q, Mock, Data, Acc, Counts, Foot,
nbits, ibits, zbits, nbitx, ibitx, zbitx, Flux1, Flux2) )
Exit:
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Poisson1
//
// EITHER EVALUATE
// infinity -cool*R*z Counts
// (1/cool) log INTEGRAL dz P(z) e ( 1 + z * R/(Mock+Acc) )
// z=0
// OR SAMPLE FLUX z from
// -cool*R*z Counts
// Posterior = P(z) e ( 1 + z * R/(Mock+Acc) )
//
// Counts are integer approximations to cooled data, cool*(Data+Acc)
//
// History: JS 18 Aug 2003
//-----------------------------------------------------------------------------
static
int Poisson1( // O 0, or -ve error
int MassInf, // I 100=monkeys, 101=positive
Rand_t Rand, //(I) NULL is trial dL, else z for insertion
double cool, // I Annealing coefficient
double q, // I Flux unit
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Background [Ndata]
int* Counts, // I Annealed data [Ndata]
int nbits, // I # fragments
int* ibits, // I Fragment positions [nbits]
double* zbits, // I Fragment quantities [nbits]
double* result) // O if "try", dLtry = (1/cool) INT dprior (L/L0)^cool
// else "insert", z = random flux
{
int npoly; // # Counts covered by "bits"
double* poly = NULL; // polynomial from "bits" [0..npoly]
double scale; // dimensional scaling for Footprint
double sum; // polynomial normalisation
double r; // random limit
double t; // temporary
int i; // counter for "bits"
int j; // counter for Counts
int k; // counter for polynomial
int CALLvalue = 0;
// MONKEYS
if ( MassInf % 10 == 0 )
{
// "try"............................
if ( ! Rand )
*result = poiss1lhood(q, Mock, Data, Acc, nbits, ibits, zbits);
// "insert".........................
else
*result = q;
}
// POSITIVE
if ( MassInf % 10 == 1 )
{
// Dimensional scaling
t = 0.0;
for ( i = 0; i < nbits; i++ )
t += zbits[i];
// Special case of cool = 0
if ( cool * cool < DBL_EPSILON )
{
// "try"............................
if ( ! Rand )
*result = - q * t;
// "insert".........................
else
*result = - q * log(Randouble(Rand));
}
else
// General case
{
scale = 1.0 / q + cool * t;
// Get polynomial size from integer-approximated annealed Counts
npoly = 0;
for ( i = 0; i < nbits; i++ )
npoly += Counts[ibits[i]];
CALLOC(poly, 1 + npoly, double)
for ( i = 0; i <= npoly; i++ )
poly[i] = 0.0;
// Set polynomial, normalised against overflow as exp(s)*poly with SUM(poly)=1
sum = 0.0;
npoly = 0;
poly[0] = 1.0;
for ( i = 0; i < nbits; i++ )
{
t = zbits[i] / ((Mock[ibits[i]] + Acc[ibits[i]]) * scale);
for ( j = Counts[ibits[i]]; j > 0; j-- )
{
r = poly[0];
for ( k = ++npoly; k > 0; k-- )
r += poly[k] += t * poly[k-1] * k;
sum += log(r);
r = 1.0 / r;
for ( k = 0; k <= npoly; k++ )
poly[k] *= r;
}
}
// "try"............................
if ( ! Rand )
*result = (sum - log(q * scale)) / cool;
// "insert".........................
else
{
// Sample k from poly
r = Randouble(Rand);
t = 0.0;
for ( k = 0; k < npoly; k++ ) // k=npoly is last case
if ( (t += poly[k]) >= r )
break;
// Sample z from Gamma
*result = Rangamma(Rand, k + 1.0) / scale;
}
FREE(poly);
}
}
Exit:
FREE(poly);
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Poisson2
//
// EITHER EVALUATE
// infinity -cool*R*x Counts
// (1/cool) log INTEGRAL dx P(x) e ( 1 + x * R/(Mock+Acc) )
// x=0
// and
// infinity -cool*u Counts
// (1/cool) log INTEGRAL dxdy P(x)P(y) e ( 1 + u/(Mock+Acc) )
// x,y = 0
// OR SAMPLE FLUX x from
// -cool*R*x Counts
// Posterior = P(x) e ( 1 + x * R/(Mock+Acc) )
// and x,y from
// -cool*u Counts
// Posterior = P(x)P(y) e ( 1 + u/(Mock+Acc) )
// WHERE u = R*x + S*y.
// Counts are integer approximations to cooled data, cool*(Data+Acc)
//
// History: JS 18 Aug 2003
//-----------------------------------------------------------------------------
static
int Poisson2( // O 0, or -ve error
int MassInf, // I 100=monkeys, 101=positive
Rand_t Rand, //(I) NULL is trial dL1 dL2, else (x,y) flux for insertion
double cool, // I Annealing coefficient
double q, // I Flux unit
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Background [Ndata]
int* Counts, // I Annealed data [Ndata]
double* Foot, //(I O) Footprint (=0) [Ndata]
int nbits, // I # fragments
int* ibits, // I Fragment positions [nbits]
double* zbits, // I Fragment quantities [nbits]
int nbitx, // I # fragments
int* ibitx, // I Fragment positions [nbitx]
double* zbitx, // I Fragment quantities [nbitx]
double* result1, // O if "try" dLtry1 = (1/cool) INT dprior[1] (L/L0)^cool
// for "bits" only, else x = 1st random flux
double* result2) // O if "try" dLtry2 = (1/cool) INT dprior[2] (L/L0)^cool
// for "bits" and "bitx", else y = 2nd random flux
{
static const double BIG = DBL_MAX * DBL_EPSILON;
int npoly1; // # Counts covered by "bits" but not "bitx"
int npoly2; // # Counts covered by "bitx" but not "bits"
int npoly0; // # Counts covered by both "bits" and "bitx"
double* poly1 = NULL; // polynomial from "bits" [0...npoly1]
double* poly2 = NULL; // polynomial from "bitx" [0...npoly2]
double** poly0 = NULL; // polynomial from both [i][j] (i+j=0...npoly0)
double scale1; // dimensional scaling for "bits" Footprint
double scale2; // dimensional scaling for "bitx" Footprint
double s1; // normalisation of poly1
double s2; // normalisation of poly2
double s0; // normalisation of poly0
double r; // random limit
double t1; // build-up of poly1 and poly0
double t2; // build-up of poly2 and poly0
double sum1; // summation over "bits"
double sum2; // summation over "bitx"
double weight; // row or column weighting of poly0
double t; // temporary
double x; // temporary
double y; // temporary
int i; // index for "bits" (and general)
int j; // index for "bitx"
int m; // 1st index of poly0
int n; // 2nd index of poly0
int k; // temporary
int CALLvalue = 0;
// MONKEYS
if ( MassInf % 10 == 0 )
{
// "try"............................
if ( ! Rand )
poiss2lhood(q, q, Mock, Data, Acc, Foot,
nbits, ibits, zbits, nbitx, ibitx, zbitx,
result1, result2);
// "insert".........................
else
*result1 = *result2 = q;
}
// POSITIVE
if ( MassInf % 10 == 1 )
{
// Dimensional scaling
t1 = t2 = 0.0;
for ( i = 0; i < nbits; i++ )
t1 += zbits[i];
for ( j = 0; j < nbitx; j++ )
t2 += zbitx[j];
// Special case of cool = 0
if ( cool * cool < DBL_EPSILON )
{
// "try"............................
if ( ! Rand )
{
*result1 = -q * t1;
*result2 = -q * (t1 + t2);
}
// "insert".........................
else
{
*result1 = - q * log(Randouble(Rand));
*result2 = - q * log(Randouble(Rand));
}
}
else
// General case
{
scale1 = 1.0 / q + cool * t1;
scale2 = 1.0 / q + cool * t2;
// Get polynomial sizes from integer-approximated annealed Counts
npoly0 = npoly1 = npoly2 = 0;
for ( j = 0; j < nbitx; j++ )
Foot[ibitx[j]] = 1.0;
for ( i = 0; i < nbits; i++ )
{
k = ibits[i];
if ( Foot[k] != 0.0 )
{
npoly0 += Counts[k];
Foot[k] = 0.0;
}
else
npoly1 += Counts[k];
}
for ( j = 0; j < nbitx; j++ )
{
k = ibitx[j];
if ( Foot[k] != 0.0 )
{
npoly2 += Counts[k];
Foot[k] = 0.0;
}
}
// Assign polynomials
CALLOC(poly1, 1 + npoly1, double)
CALLOC(poly2, 1 + npoly2, double)
CALLOC(poly0, 1 + npoly0, double*)
CALLOC(poly0[0], (1 + npoly0) * (2 + npoly0) / 2, double)
for ( i = 1; i <= npoly0; i++ )
poly0[i] = poly0[i-1] + 2 + npoly0 - i;
for ( i = 0; i <= npoly1; i++ )
poly1[i] = 0.0;
for ( i = 0; i <= npoly2; i++ )
poly2[i] = 0.0;
for ( i = 0; i <= npoly0; i++ )
for ( j = 0; i + j <= npoly0; j++ )
poly0[i][j] = 0.0;
poly1[0] = poly2[0] = poly0[0][0] = 1.0;
s1 = s2 = s0 = 0.0;
// Set polynomials, normalised against overflow as exp(s)*poly with SUM(poly)=1
npoly0 = npoly1 = npoly2 = 0;
for ( j = 0; j < nbitx; j++ )
Foot[ibitx[j]] = zbitx[j];
for ( i = 0; i < nbits; i++ )
{
k = ibits[i];
t1 = zbits[i] / ((Mock[k] + Acc[k]) * scale1);
if ( Foot[k] != 0.0 )
{
t2 = Foot[k] / ((Mock[k] + Acc[k]) * scale2);
for ( j = Counts[k]; j > 0; j-- )
{
r = poly0[0][0];
for ( n = ++npoly0; n > 0; n-- )
{
r += poly0[n][0] += t1 * poly0[n-1][0] * n;
for ( m = 1; m < n; m++ )
r += poly0[n-m][m]
+= t1 * poly0[n-m-1][m] * (n - m)
+ t2 * poly0[n-m][m-1] * m;
r += poly0[0][m] += t2 * poly0[0][m-1] * m;
}
s0 += log(r);
r = 1.0 / r;
for ( n = 0; n <= npoly0; n++ )
for ( m = 0; m + n <= npoly0; m++ )
poly0[n][m] *= r;
}
Foot[k] = 0.0;
}
else
{
for ( j = Counts[k]; j > 0; j-- )
{
r = poly1[0];
for ( m = ++npoly1; m > 0; m-- )
r += poly1[m] += t1 * poly1[m-1] * m;
s1 += log(r);
r = 1.0 / r;
for ( m = 0; m <= npoly1; m++ )
poly1[m] *= r;
}
}
}
for ( j = 0; j < nbitx; j++ )
{
k = ibitx[j];
if ( Foot[k] != 0.0 )
{
t2 = zbitx[j] / ((Mock[k] + Acc[k]) * scale2);
for ( i = Counts[k]; i > 0; i-- )
{
r = poly2[0];
for ( m = ++npoly2; m > 0; m-- )
r += poly2[m] += t2 * poly2[m-1] * m;
s2 += log(r);
r = 1.0 / r;
for ( m = 0; m <= npoly2; m++ )
poly2[m] *= r;
}
Foot[k] = 0.0;
}
}
// Weight poly0 rows by SUM[k=0..npoly1] poly1[k] (k+i)!/k!i!
// Get sum1 (usable for dL1)
sum1 = 0.0;
for ( i = 0; i <= npoly0; i++ )
{
weight = 0.0;
x = 1.0;
for ( k = 0; k <= npoly1; k++ )
{
weight += x * poly1[k];
x *= 1.0 + i / (k + 1.0);
if ( x > BIG )
return E_MASSINF_COUNTS; // incipient overflow
}
for ( j = 0; i + j <= npoly0; j++ )
poly0[i][j] *= weight;
sum1 += poly0[i][0];
}
// Weight poly0 columns by SUM[k=0..npoly2] poly2[k] (k+j)!/k!j!
// Get sum2 (usable for dL2)
sum2 = 0.0;
for ( j = 0; j <= npoly0; j++ )
{
weight = 0.0;
x = 1.0 / sum1; // overflow safety
for ( k = 0; k <= npoly2; k++ )
{
weight += x * poly2[k];
x *= 1.0 + j / (k + 1.0);
if ( x > BIG )
return E_MASSINF_COUNTS; // incipient overflow
}
for ( i = 0; i + j <= npoly0; i++ )
sum2 += poly0[i][j] *= weight;
}
// "try"............................
if ( ! Rand )
{
*result1 = (s0 + s1 + log(sum1 / (q * scale1))) / cool;
*result2 = (s0 + s1 + s2 + log(sum1 / (q * scale1))
+ log(sum2 / (q * scale2))) / cool;
}
// "insert".........................
else
{
// Sample i,j from poly0
r = sum2 * Randouble(Rand);
t = 0.0;
for ( i = 0; i <= npoly0; i++ )
{
for ( j = 0; i + j <= npoly0; j++ )
if ( (t += poly0[i][j]) >= r )
break;
if ( t >= r )
break;
}
if ( i > npoly0 ) i = j = 0; // extra protection
// Sample m from poly1
t = 0.0;
x = y = 1.0;
for ( m = 0; m <= npoly1; m++ )
{
t += poly1[m] *= x;
x *= 1.0 + i / y;
y += 1.0;
}
t *= Randouble(Rand);
for ( m = 0; m < npoly1; m++ ) // m=npoly1 is last case
if ( (t -= poly1[m]) <= 0.0 )
break;
// Sample n from poly2
t = 0.0;
x = y = 1.0;
for ( n = 0; n <= npoly2; n++ )
{
t += poly2[n] *= x;
x *= 1.0 + j / y;
y += 1.0;
}
t *= Randouble(Rand);
for ( n = 0; n < npoly2; n++ ) // n=npoly2 is last case
if ( (t -= poly2[n]) <= 0.0 )
break;
// Sample x,y from Gamma
*result1 = Rangamma(Rand, m + i + 1.0) / scale1;
*result2 = Rangamma(Rand, n + j + 1.0) / scale2;
}
}
}
Exit:
if ( poly0 )
FREE(poly0[0])
FREE(poly0)
FREE(poly2)
FREE(poly1)
return CALLvalue;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: poiss1lhood
// -R*z Data+Acc
// Contribution log(e (1 + R*z/(Mock+Acc)) )
//
// to DELTA(logL) from single flux.
//
// History: JS 18 Aug 2003
//-----------------------------------------------------------------------------
static
double poiss1lhood(// O DELTA(logL)
double Flux, // I Flux z of atom
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Background [Ndata]
int nbits, // I # fragments
int* ibits, // I Fragment positions [nbits]
double* zbits) // I Fragment quantities R [nbits]
{
double dL = 0.0;
int i, k;
for ( i = 0; i < nbits; i++ )
{
k = ibits[i];
dL += (Data[k] + Acc[k]) * log(1.0 + Flux * zbits[i] / (Mock[k] + Acc[k]))
- Flux * zbits[i];
}
return dL;
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: poiss2lhood
// -R*x Data+Acc
// Contributions log(e (1 + R*x/(Mock+Acc)) )
//
// -(R*x+S*y) Data+Acc
// and log(e (1 + (R*x+S*y)/(Mock+Acc)) )
//
// to DELTA(logL) from one, and from two, single fluxes.
//
// History: JS 18 Aug 2003
//-----------------------------------------------------------------------------
static
void poiss2lhood(
double Flux1, // I Flux x for "bits"
double Flux2, // I Flux y for "bitx"
double* Mock, // I Mock data [Ndata]
double* Data, // I Data [Ndata]
double* Acc, // I Background [Ndata]
double* Foot, //(I O) Footprint (=0) [Ndata]
int nbits, // I # fragments
int* ibits, // I Fragment positions [nbits]
double* zbits, // I Fragment quantities R [nbits]
int nbitx, // I # fragments
int* ibitx, // I Fragment positions [nbitx]
double* zbitx, // I Fragment quantities S [nbitx]
double* dL1, // O DELTA(logL) for x only
double* dL2) // O DELTA(logL) for x and y
{
double sum1, sum2, t;
int i, k;
for ( i = 0; i < nbitx; i++ )
Foot[ibitx[i]] = zbitx[i];
sum1 = sum2 = 0.0;
for ( i = 0; i < nbits; i++ )
{
k = ibits[i];
sum1 -= Flux1 * zbits[i];
sum2 -= Flux1 * zbits[i];
t = (Data[k] + Acc[k]) * log(1.0 + Flux1 * zbits[i] / (Mock[k] + Acc[k]));
sum1 += t;
if ( Foot[k] == 0.0 )
sum2 += t;
else
{
t = Flux1 * zbits[i] + Flux2 * Foot[k];
sum2 += (Data[k] + Acc[k]) * log(1.0 + t / (Mock[k] + Acc[k]));
Foot[k] = 0.0;
}
}
for ( i = 0; i < nbitx; i++ )
{
k = ibitx[i];
sum2 -= Flux2 * zbitx[i];
if ( Foot[k] != 0.0 )
{
sum2 += (Data[k] + Acc[k])
* log(1.0 + Flux2 * Foot[k] / (Mock[k] + Acc[k]));
Foot[k] = 0.0;
}
}
*dL1 = sum1;
*dL2 = sum2;
}
#if PARALLEL
//=============================================================================
// PARALLEL code replacing DoOperations procedure in BayeSys3
// History: Do Kester / John Skilling 4 Nov 2002, 10 Feb 2003
//=============================================================================
#define THREADS
#define FLOWCHECK 0 // debugging aid
#define E_FLOWCHECK -230 // parallel flow error
#ifdef THREADS
#include <pthread.h>
#define pthread_create( a, b, c, d ) \
pthread_create( a, b, (void*(*)(void*))c, (void*)d )
#else
#define pthread_t char // not used
#define pthread_create( a, b, c, d ) if( a ) c( d ) // avoid compiler whinge
#define pthread_join( a, b ) // null statement
#endif
typedef struct // COLLECTED PARAMETERS
{
OperStr* Operations; // all operations
CommonStr* Common; // general information
ObjectStr* Objects; // all objects
Node* Links; // all linked lists
int op; // current operation #
int status; // 0 = idle, 1 = active, 2 = finished, -ve = error
} WorkStr;
#if FLOWCHECK
#include <stdio.h>
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: PrintStart
// Development diagnostics for start of operation
//-----------------------------------------------------------------------------
static void PrintStart(int slave, WorkStr* Work)
{
CommonStr* Common = Work[slave].Common;
ObjectStr* Objects = Work[slave].Objects;
OperStr* Oper = &Work[slave].Operations[Work[slave].op];
int i, flag;
printf("+ oper%4d on%2d ", Work[slave].op, slave);
for ( i = 0; i < Common->ENSEMBLE; i++ )
{
if ( (Oper->kType == +1 && Oper->k == i)
|| (Oper->jType == +1 && Oper->j == i)
|| (Oper->iType == +1 && Oper->i == i) )
printf(" r");
else if ( (Oper->kType == -1 && Oper->k == i)
|| (Oper->jType == -1 && Oper->j == i)
|| (Oper->iType == -1 && Oper->i == i) )
printf(" w");
else if ( Objects[i].flowcheck )
printf(" |");
else
printf(" .");
}
printf(" ");
flag = 0;
for ( i = 1; i <= PARALLEL; i++ )
{
if ( Work[i].status == 0 ) printf(".");
if ( Work[i].status == 1 ) printf("#");
if ( Work[i].status == 2 ) printf("-");
if ( Work[i].status ) flag++;
}
printf("%2d\n", flag);
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: PrintFinish
// Development diagnostics for finish of operation
//-----------------------------------------------------------------------------
static void PrintFinish(int slave, WorkStr* Work)
{
CommonStr* Common = Work[slave].Common;
ObjectStr* Objects = Work[slave].Objects;
OperStr* Oper = &Work[slave].Operations[Work[slave].op];
int i;
printf("- oper%4d on%2d ", Work[slave].op, slave);
for ( i = 0; i < Common->ENSEMBLE; i++ )
{
if ( (Oper->kType == +1 && Oper->k == i)
|| (Oper->jType == +1 && Oper->j == i)
|| (Oper->iType == +1 && Oper->i == i) )
printf(" R");
else if ( (Oper->kType == -1 && Oper->k == i)
|| (Oper->jType == -1 && Oper->j == i)
|| (Oper->iType == -1 && Oper->i == i) )
printf(" W");
else if ( Objects[i].flowcheck )
printf(" |");
else
printf(" .");
}
printf(" ");
for ( i = 1; i <= PARALLEL; i++ )
{
if ( Work[i].status == 0 ) printf(".");
if ( Work[i].status == 1 ) printf("#");
if ( Work[i].status == 2 ) printf("-");
}
printf("\n");
}
#endif
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: Do1oper
// Controller for Do1operation
// Report return state in Slave->status
//-----------------------------------------------------------------------------
static void Do1oper( WorkStr* Slave)
{
CommonStr* Common = Slave->Common; // general information
ObjectStr* Objects = Slave->Objects; // ENSEMBLE of samples
Node* Links = Slave->Links; // linked lists of labels
OperStr* Operations = Slave->Operations; // all operations
int op = Slave->op; // this operation
int CALLvalue;
CALLvalue = Do1operation(Operations, Common, Objects, Links, op);
Slave->status = 2; // finished
if ( CALLvalue < 0 )
Slave->status = CALLvalue; // error state
}
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// Function: DoOperations
// Control operation of batch of parallelisable engine calls
//-----------------------------------------------------------------------------
static int DoOperations( // O 0, or -ve error
OperStr* Operations, // I O all operations
CommonStr* Common, // I O general information
ObjectStr* Objects, // I O ENSEMBLE of samples
Node* Links, // I O linked lists of labels
int nOper) // I # operations
{
int ENSEMBLE = Common->ENSEMBLE; // # objects
OperStr* Oper; // & individual operation
int op; // operation choice
int remain; // # operations still unfinished
int slave; // processor id
int m; // object counter
WorkStr Work [1+PARALLEL]; // Only this many threads...
pthread_t threads[1+PARALLEL]; // ...possible at one time
int* r = NULL;
int* w = NULL;
int CALLvalue = 0;
time_t start, end;
// Initialisations
for ( slave = 1; slave <= PARALLEL; slave++ )
{
Work[slave].Operations = Operations;
Work[slave].Common = Common;
Work[slave].Objects = Objects;
Work[slave].Links = Links;
Work[slave].op = -1;
Work[slave].status = 0;
}
CALLOC(r, ENSEMBLE, int)
CALLOC(w, ENSEMBLE, int)
// Set usable ranges Early <= clock <= Late of start/end counts for each object
// clock increments at each start and each finish (start even, finish odd).
// clock= 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
// Write---Read----Write---Read----Read----Read----Read----Write---Write
// <---any overlapping order--->
// Early= 0 2 4 6 6 6 6 14 16
// Late = 0 2 4 12 12 12 12 14 16
for ( m = 0; m < ENSEMBLE; m++ )
{
w[m] = -2;
r[m] = 0;
}
for ( op = 0; op < nOper; op++ )
{
Oper = &Operations[op];
if ( Oper->iType )
{
m = Oper->i;
Oper->iEarly = (Oper->iType == -1) ? (w[m] = r[m]) : w[m] + 2;
r[m] += 2;
}
if ( Oper->jType )
{
m = Oper->j;
Oper->jEarly = (Oper->jType == -1) ? (w[m] = r[m]) : w[m] + 2;
r[m] += 2;
}
if ( Oper->kType )
{
m = Oper->k;
Oper->kEarly = (Oper->kType == -1) ? (w[m] = r[m]) : w[m] + 2;
r[m] += 2;
}
}
for ( m = 0; m < ENSEMBLE; m++ )
{
w[m] = r[m];
r[m] -= 2;
}
for ( op = nOper - 1; op >= 0; op-- )
{
Oper = &Operations[op];
if ( Oper->iType )
{
m = Oper->i;
Oper->iLate = (Oper->iType == -1) ? (w[m] = r[m]) : w[m] - 2;
r[m] -= 2;
}
if ( Oper->jType )
{
m = Oper->j;
Oper->jLate = (Oper->jType == -1) ? (w[m] = r[m]) : w[m] - 2;
r[m] -= 2;
}
if ( Oper->kType )
{
m = Oper->k;
Oper->kLate = (Oper->kType == -1) ? (w[m] = r[m]) : w[m] - 2;
r[m] -= 2;
}
}
#if FLOWCHECK
// Optional flowchart checks
for ( m = 0; m < ENSEMBLE; m++ )
Objects[m].flowcheck = 0;
#endif
// Operation counts
for ( m = 0; m < ENSEMBLE; m++ )
Objects[m].clock = 0;
// Operations not done (invalid processor #)
for ( op = 0; op < nOper; op++ )
Operations[op].slave = -1;
// Slaves idle
for ( slave = 1; slave <= PARALLEL; slave++ )
Work[slave].status = 0;
// Counter
remain = nOper;
printf("%d operations to do\n", nOper);
time(&start);
// Cycle round the slaves
for ( slave = 1; remain; slave = 1 + (slave % PARALLEL) )
{
// Keep monitoring slaves
if ( Work[slave].status < 0 ) // Error state
{
CALLvalue = Work[slave].status;
goto Exit;
}
if ( Work[slave].status == 2 ) // This slave finished, remove flags
{
pthread_join( threads[slave], NULL ); // **JOIN** slave
Work[slave].status = 0;
op = Work[slave].op;
Oper = &Operations[op];
// Update operation count
if ( Oper->iType ) Objects[Oper->i].clock ++;
if ( Oper->jType ) Objects[Oper->j].clock ++;
if ( Oper->kType ) Objects[Oper->k].clock ++;
remain --;
#if FLOWCHECK
// Optional status checks
if ( Oper->iType == -1 )
{
if ( Objects[Oper->i].flowcheck != -1 )
{
CALLvalue = E_FLOWCHECK;
goto Exit;
}
Objects[Oper->i].flowcheck = 0;
}
if ( Oper->iType == +1 )
{
if ( Objects[Oper->i].flowcheck <= 0 )
{
CALLvalue = E_FLOWCHECK;
goto Exit;
}
Objects[Oper->i].flowcheck --;
}
if ( Oper->jType == -1 )
{
if ( Objects[Oper->j].flowcheck != -1 )
{
CALLvalue = E_FLOWCHECK;
goto Exit;
}
Objects[Oper->j].flowcheck = 0;
}
if ( Oper->jType == +1 )
{
if ( Objects[Oper->j].flowcheck <= 0 )
{
CALLvalue = E_FLOWCHECK;
goto Exit;
}
Objects[Oper->j].flowcheck --;
}
if ( Oper->kType == -1 )
{
if ( Objects[Oper->k].flowcheck != -1 )
{
CALLvalue = E_FLOWCHECK;
goto Exit;
}
Objects[Oper->k].flowcheck = 0;
}
if ( Oper->kType == +1 )
{
if ( Objects[Oper->k].flowcheck <= 0 )
{
CALLvalue = E_FLOWCHECK;
goto Exit;
}
Objects[Oper->k].flowcheck --;
}
PrintFinish(slave, Work);
#endif
}
if ( Work[slave].status )
continue; // This slave is not free. Else...
// Seek usable operation
for ( op = 0; op < nOper; op++ )
{
Oper = &Operations[op];
// Already done?
if ( Oper->slave >= 0 )
continue;
// Out of range?
if ( Oper->iType )
if ( Objects[Oper->i].clock < Oper->iEarly
|| Objects[Oper->i].clock > Oper->iLate ) continue;
if ( Oper->jType )
if ( Objects[Oper->j].clock < Oper->jEarly
|| Objects[Oper->j].clock > Oper->jLate ) continue;
if ( Oper->kType )
if ( Objects[Oper->k].clock < Oper->kEarly
|| Objects[Oper->k].clock > Oper->kLate ) continue;
// Handshake slave<-->operation
Oper->slave = slave;
Work[slave].op = op;
// Slave now active
Work[slave].status = 1;
// Update operation count
if ( Oper->iType ) Objects[Oper->i].clock ++;
if ( Oper->jType ) Objects[Oper->j].clock ++;
if ( Oper->kType ) Objects[Oper->k].clock ++;
#if FLOWCHECK
// Optional flowchart checks
if ( Oper->iType == -1 )
{
if ( Objects[Oper->i].flowcheck != 0 )
{
CALLvalue = E_FLOWCHECK;
goto Exit;
}
Objects[Oper->i].flowcheck = -1;
}
if ( Oper->iType == +1 )
{
if ( Objects[Oper->i].flowcheck < 0 )
{
CALLvalue = E_FLOWCHECK;
goto Exit;
}
Objects[Oper->i].flowcheck ++;
}
if ( Oper->jType == -1 )
{
if ( Objects[Oper->j].flowcheck != 0 )
{
CALLvalue = E_FLOWCHECK;
goto Exit;
}
Objects[Oper->j].flowcheck = -1;
}
if ( Oper->jType == +1 )
{
if ( Objects[Oper->j].flowcheck < 0 )
{
CALLvalue = E_FLOWCHECK;
goto Exit;
}
Objects[Oper->j].flowcheck ++;
}
if ( Oper->kType == -1 )
{
if ( Objects[Oper->k].flowcheck != 0 )
{
CALLvalue = E_FLOWCHECK;
goto Exit;
}
Objects[Oper->k].flowcheck = -1;
}
if ( Oper->kType == +1 )
{
if ( Objects[Oper->k].flowcheck < 0 )
{
CALLvalue = E_FLOWCHECK;
goto Exit;
}
Objects[Oper->k].flowcheck ++;
}
PrintStart(slave, Work);
#endif
// Do usable operation. A free processor is guaranteed. **CREATE** slave.
pthread_create( &threads[slave], NULL, Do1oper, &Work[slave] );
break;
}
}
Exit:
time(&end);
printf( "%d operations done in %lf\n", nOper, difftime(&end, &start));
FREE(w)
FREE(r)
return CALLvalue;
}
#endif
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