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/*
* $Id: gwynlfit.c 24952 2022-08-26 15:24:56Z yeti-dn $
* Copyright (C) 2000-2003 Martin Siler.
* Copyright (C) 2004-2020 David Necas (Yeti), Petr Klapetek.
* E-mail: yeti@gwyddion.net, klapetek@gwyddion.net.
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor,
* Boston, MA 02110-1301, USA.
*/
#include "config.h"
#include <string.h>
#include <libgwyddion/gwymacros.h>
#include <libgwyddion/gwymath.h>
#include <libgwyddion/gwythreads.h>
#include <libgwyddion/gwynlfit.h>
#include "libgwyddion/gwyomp.h"
/* Side step constant for numerical differentiation in gwy_math_nlfit_derive()
*/
#define FitSqrtMachEps 1e-5
/* Constant for decision to stop fitting cycle due to relative difference
* in residual sum of squares between subsequent steps.
*/
#define EPS 1e-16
/* Lower symmetric part indexing */
/* i (row) MUST be greater or equal than j (column) */
#define SLi(a, i, j) a[(i)*((i) + 1)/2 + (j)]
typedef struct {
GwyNLFitter *fitter;
GwySetFractionFunc set_fraction;
GwySetMessageFunc set_message;
GwyNLFitIdxFunc func_idx;
GwyNLFitIdxDiffFunc diff_idx;
gboolean approx_geometric; /* Ignored. */
gint nparam;
} GwyNLFitterPrivate;
static void gwy_math_nlfit_init (GwyNLFitter *nlfit);
static gdouble gwy_math_nlfit_fit_real(GwyNLFitter *nlfit,
guint ndata,
const gdouble *x,
const gdouble *y,
const gdouble *weight,
guint nparam,
gdouble *param,
const gboolean *fixed_param,
const gint *link_map,
gpointer user_data);
static gdouble gwy_math_nlfit_residua (GwyNLFitFunc func,
GwyNLFitIdxFunc func_idx,
guint ndata,
const gdouble *x,
const gdouble *y,
const gdouble *weight,
guint nparam,
const gdouble *param,
gpointer user_data,
gdouble *resid,
gboolean *success);
static GwyNLFitterPrivate* find_private_data (GwyNLFitter *fitter,
gboolean do_create);
static void free_private_data (GwyNLFitter *fitter);
G_LOCK_DEFINE_STATIC(private_fitter_data);
static GList *private_fitter_data = NULL; /* Threads: protected by lock */
#if 0
GType
gwy_math_nlfit_get_type(void)
{
static GType nlfit_type = 0;
if (G_UNLIKELY(!nlfit_type)) {
nlfit_type = g_boxed_type_register_static("GwyMathNLFit",
(GBoxedCopyFunc)gwy_math_nlfit_copy,
(GBoxedFreeFunc)gwy_math_nlfit_free);
}
return nlfit_type;
}
#endif
/**
* gwy_math_nlfit_new:
* @func: The fitted function.
* @diff: The derivative of fitted function.
*
* Creates a new Marquardt-Levenberg nonlinear fitter for function with
* a real-valued independent variable.
*
* See gwy_math_nlfit_new_idx() for more complex scenarios.
*
* You can use gwy_math_nlfit_diff() computing the derivative numerically,
* when you do not know the derivatives explicitely. Since 2.46 passing %NULL
* as @diff has the same effect, i.e. the fitter will automatically use
* numerical differentiation.
*
* Returns: The newly created fitter.
**/
GwyNLFitter*
gwy_math_nlfit_new(GwyNLFitFunc func, GwyNLFitDerFunc diff)
{
GwyNLFitter *nlfit;
nlfit = g_new0(GwyNLFitter, 1);
gwy_math_nlfit_init(nlfit);
nlfit->fmarq = func;
nlfit->dmarq = diff ? diff : gwy_math_nlfit_diff;
return nlfit;
}
/**
* gwy_math_nlfit_new_idx:
* @func: The fitted function.
* @diff: The derivative of fitted function.
*
* Creates a new Marquardt-Levenberg nonlinear fitter for opaque indexed data.
*
* As only the data index is passed to the functions, using this interface
* permits fitting more complex functions. The abscissa can be arbitrary,
* for instance a vector, as it is not seen by the fitter. Similarly,
* vector-valued functions can be emulated by mapping tuples of indices to the
* vector components.
*
* You can pass %NULL as @diff to use automatically numerical differentiation
* when you do not know the derivatives explicitely. Note that this means you
* cannot use weighting. If you want weighting you need to pass your own
* @diff function that performs the weighting (it can utilise the
* gwy_math_nlfit_diff_idx() helper).
*
* Returns: The newly created fitter.
*
* Since: 2.46
**/
GwyNLFitter*
gwy_math_nlfit_new_idx(GwyNLFitIdxFunc func, GwyNLFitIdxDiffFunc diff)
{
GwyNLFitterPrivate *priv;
GwyNLFitter *nlfit;
nlfit = g_new0(GwyNLFitter, 1);
gwy_math_nlfit_init(nlfit);
priv = find_private_data(nlfit, TRUE);
priv->func_idx = func;
priv->diff_idx = diff;
return nlfit;
}
static void
gwy_math_nlfit_init(GwyNLFitter *nlfit)
{
nlfit->mfi = 1.0;
nlfit->mdec = 0.4;
nlfit->minc = 10.0;
nlfit->mtol = 1e-6;
nlfit->maxiter = 100;
nlfit->eval = FALSE;
nlfit->dispersion = -1;
nlfit->covar = NULL;
}
/**
* gwy_math_nlfit_free:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
*
* Completely frees a Marquardt-Levenberg nonlinear fitter.
**/
void
gwy_math_nlfit_free(GwyNLFitter *nlfit)
{
free_private_data(nlfit);
g_free(nlfit->covar);
nlfit->covar = NULL;
g_free(nlfit);
}
/**
* gwy_math_nlfit_copy:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
*
* Creates a copy of a nonlinear least squares fitter.
*
* This function is mostly usefil for language bindings.
*
* Returns: The newly created fitter.
*
* Since: 2.47
**/
GwyNLFitter*
gwy_math_nlfit_copy(GwyNLFitter *nlfit)
{
GwyNLFitter *copy = g_memdup(nlfit, sizeof(GwyNLFitter));
GwyNLFitterPrivate *priv;
gint n;
priv = find_private_data(nlfit, FALSE);
if (nlfit->covar) {
g_assert(priv);
n = priv->nparam;
copy->covar = g_memdup(nlfit->covar, n*(n+1)/2*sizeof(gdouble));
}
if (priv)
*find_private_data(copy, TRUE) = *priv;
return copy;
}
/**
* gwy_math_nlfit_fit:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
* @ndata: The number of data points in @x, @y.
* @x: Array of independent variable values.
* @y: Array of dependent variable values.
* @nparam: The nuber of parameters.
* @param: Array of parameters (of size @nparam). Note the parameters must
* be initialized to reasonably near values.
* @user_data: Pointer that will be passed to the function and derivative
* as @user_data.
*
* Performs a nonlinear fit of simple function on data.
*
* Returns: The final residual sum, a negative number in the case of failure.
**/
gdouble
gwy_math_nlfit_fit(GwyNLFitter *nlfit,
gint ndata,
const gdouble *x,
const gdouble *y,
gint nparam,
gdouble *param,
gpointer user_data)
{
return gwy_math_nlfit_fit_real(nlfit, ndata, x, y, NULL,
nparam, param, NULL, NULL, user_data);
}
/**
* gwy_math_nlfit_fit_full:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
* @ndata: The number of data points in @x, @y, @weight.
* @x: Array of independent variable values.
* @y: Array of dependent variable values.
* @weight: Array of weights associated to each data point (usually equal to
* inverse squares errors). Can be %NULL, unit weight is then used
* for all data.
* @nparam: The nuber of parameters.
* @param: Array of parameters (of size @nparam). Note the parameters must
* be initialized to reasonably near values.
* @fixed_param: Which parameters should be treated as fixed (set corresponding
* element to %TRUE for them). May be %NULL if all parameters
* are variable.
* @link_map: Map of linked parameters. One of linked parameters is master,
* Values in this array are indices of corresponding master
* parameter for each parameter (for independent parameters set
* @link_map[i] == i). May be %NULL if all parameter are
* independent.
* @user_data: Pointer that will be passed to the function and derivative
*
* Performs a nonlinear fit of simple function on data, allowing some fixed
* parameters.
*
* Initial values of linked (dependent) parameters are overwritten by master
* values, their @fixed_param property is ignored and master's property
* controls whether all are fixed or all variable.
*
* Returns: The final residual sum, a negative number in the case of failure.
**/
gdouble
gwy_math_nlfit_fit_full(GwyNLFitter *nlfit,
gint ndata,
const gdouble *x,
const gdouble *y,
const gdouble *weight,
gint nparam,
gdouble *param,
const gboolean *fixed_param,
const gint *link_map,
gpointer user_data)
{
return gwy_math_nlfit_fit_real(nlfit, ndata, x, y, weight,
nparam, param, fixed_param, link_map,
user_data);
}
/**
* gwy_math_nlfit_fit_idx:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
* @ndata: The number of data points in @x, @y, @weight.
* @nparam: The nuber of parameters.
* @param: Array of parameters (of size @nparam). Note the parameters must
* be initialized to reasonably near values.
* @user_data: Pointer that will be passed to the function and derivative
*
* Performs a nonlinear fit of function on opaque indexed data.
*
* Returns: The final residual sum, a negative number in the case of failure.
*
* Since: 2.46
**/
gdouble
gwy_math_nlfit_fit_idx(GwyNLFitter *nlfit,
guint ndata,
guint nparam,
gdouble *param,
gpointer user_data)
{
return gwy_math_nlfit_fit_real(nlfit, ndata, NULL, NULL, NULL,
nparam, param, NULL, NULL, user_data);
}
/**
* gwy_math_nlfit_fit_idx_full:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
* @ndata: The number of data points in @x, @y, @weight.
* @nparam: The nuber of parameters.
* @param: Array of parameters (of size @nparam). Note the parameters must
* be initialized to reasonably near values.
* @fixed_param: Which parameters should be treated as fixed (set corresponding
* element to %TRUE for them). May be %NULL if all parameters
* are variable.
* @link_map: Map of linked parameters. One of linked parameters is master,
* Values in this array are indices of corresponding master
* parameter for each parameter (for independent parameters set
* @link_map[i] == i). May be %NULL if all parameter are
* independent.
* @user_data: Pointer that will be passed to the function and derivative
*
* Performs a nonlinear fit of function on opaque indexed data, allowing some
* fixed parameters.
*
* Initial values of linked (dependent) parameters are overwritten by master
* values, their @fixed_param property is ignored and master's property
* controls whether all are fixed or all variable.
*
* Returns: The final residual sum, a negative number in the case of failure.
*
* Since: 2.46
**/
gdouble
gwy_math_nlfit_fit_idx_full(GwyNLFitter *nlfit,
guint ndata,
guint nparam,
gdouble *param,
const gboolean *fixed_param,
const gint *link_map,
gpointer user_data)
{
return gwy_math_nlfit_fit_real(nlfit, ndata, NULL, NULL, NULL,
nparam, param, fixed_param, link_map,
user_data);
}
static gdouble
gwy_math_nlfit_fit_real(GwyNLFitter *nlfit,
guint ndata,
const gdouble *x,
const gdouble *y,
const gdouble *weight,
guint nparam,
gdouble *param,
const gboolean *fixed_param,
const gint *link_map,
gpointer user_data)
{
GwyNLFitterPrivate *priv;
GwySetFractionFunc set_fraction = NULL;
GwySetMessageFunc set_message = NULL;
GwyNLFitFunc func;
GwyNLFitDerFunc diff;
GwyNLFitIdxFunc func_idx;
GwyNLFitIdxDiffFunc diff_idx;
gdouble mlambda = 1e-4;
gdouble sumr_new, sumr_best = G_MAXDOUBLE;
gdouble *v = NULL, *xr = NULL, *w = NULL,
*saveparam = NULL, *origparam = NULL, *resid = NULL,
*a = NULL, *save_a = NULL, *covar = NULL, **storage = NULL,
*param_best = NULL;
guint *var_param_id = NULL, *lmap = NULL;
gboolean *fixed = NULL;
guint covar_size;
guint i, j;
guint n_var_param;
guint nthreads = gwy_omp_max_threads();
guint miter = 0;
gint unimproved = 0;
gboolean end = FALSE;
g_return_val_if_fail(nlfit, -1.0);
g_return_val_if_fail(param || !nparam, -1.0); /* handle zero nparam later */
priv = find_private_data(nlfit, TRUE);
set_fraction = priv->set_fraction;
set_message = priv->set_message;
priv->nparam = 0;
func = nlfit->fmarq;
diff = nlfit->dmarq;
func_idx = priv->func_idx;
diff_idx = priv->diff_idx;
GWY_FREE(nlfit->covar);
nlfit->dispersion = -1.0;
if (ndata < nparam)
return -1.0;
g_return_val_if_fail((x && y && func && diff) || func_idx, -1.0);
g_return_val_if_fail(!func_idx || (!x && !y && !weight && !func), -1.0);
if (set_message)
set_message(_("Fitting..."));
if (set_fraction)
set_fraction(0.0);
/* Calculate square roots of weights because they are easily split into
* the expressions. The indexed interface already does it right. */
if (weight) {
w = g_new(gdouble, ndata);
for (i = 0; i < ndata; i++)
w[i] = sqrt(fmax(weight[i], 0.0));
}
/* Use defaults for param specials, if not specified */
if (!link_map) {
lmap = g_new(gint, nparam);
for (i = 0; i < nparam; i++)
lmap[i] = i;
link_map = lmap;
}
/* Sync slave param values with master */
origparam = g_memdup(param, nparam*sizeof(gdouble));
for (i = 0; i < nparam; i++) {
if (link_map[i] != i)
param[i] = param[link_map[i]];
}
if (nparam == 0)
goto fail;
resid = g_new(gdouble, ndata);
param_best = g_memdup(param, nparam*sizeof(gdouble));
sumr_new = gwy_math_nlfit_residua(func, func_idx, ndata, x, y, w,
nparam, param, user_data, resid,
&nlfit->eval);
gwy_debug("initial sumr %.16g", sumr_new);
if (!nlfit->eval) {
g_warning("Initial residua evaluation failed");
sumr_best = -1.0;
goto fail;
}
if (set_fraction && !set_fraction(1.0/(nlfit->maxiter + 1))) {
gwy_debug("cancelled");
nlfit->eval = FALSE;
sumr_best = -2.0;
goto fail;
}
/* find non-fixed parameters and map all -> non-fixed */
n_var_param = 0;
var_param_id = g_new(guint, nparam);
for (i = 0; i < nparam; i++) {
if (fixed_param && fixed_param[link_map[i]])
var_param_id[i] = G_MAXUINT;
else {
if (link_map[i] == i) {
var_param_id[i] = n_var_param;
n_var_param++;
}
}
gwy_debug("var_param_id[%d] = %d", i, var_param_id[i]);
}
/* assign master var_param_id to slaves in second pass, as it may have
* higher id than slave */
for (i = 0; i < nparam; i++) {
if (link_map[i] != i)
var_param_id[i] = var_param_id[link_map[i]];
}
if (!n_var_param)
goto fail;
/* Resolve which params are fixed, taking links into account. We
* cannot modify fixed_param, so create a new array. */
if (!fixed_param)
fixed = NULL;
else {
fixed = g_new0(gboolean, nparam);
for (i = 0; i < nparam; i++)
fixed[i] = fixed_param[link_map[i]];
}
covar_size = n_var_param*(n_var_param + 1)/2;
/* Allocate separate memory block for each thread's data. */
storage = g_new0(gdouble*, nthreads);
for (i = 0; i < nthreads; i++)
storage[i] = g_new(gdouble, n_var_param + covar_size + nparam);
v = storage[0];
a = v + n_var_param;
/* At a + covar_size starts is der[], but we never need in the global
* scope. */
xr = g_new(gdouble, n_var_param);
saveparam = g_new(gdouble, nparam);
save_a = g_new(gdouble, covar_size);
/* The actual minizmation */
do {
gboolean is_pos_def = FALSE;
gboolean first_pass = TRUE;
guint count = 0;
gboolean eval = TRUE;
if (unimproved == 0) {
mlambda *= nlfit->mdec;
sumr_best = sumr_new;
gwy_assign(param_best, param, nparam);
/* J'J and J'r computation */
#ifdef _OPENMP
#pragma omp parallel if(gwy_threads_are_enabled()) default(none) \
reduction(&&:eval) \
private(i,j) \
shared(diff_idx,func_idx,diff,func,user_data,param,nparam,fixed,link_map,var_param_id,ndata,covar_size,n_var_param,x,w,storage,resid)
#endif
{
guint ifrom = gwy_omp_chunk_start(ndata);
guint ito = gwy_omp_chunk_end(ndata);
guint tid = gwy_omp_thread_num();
gdouble *tv = storage[tid];
gdouble *ta = tv + n_var_param;
gdouble *der = ta + covar_size;
gboolean eeval = TRUE;
gwy_clear(ta, covar_size);
gwy_clear(tv, n_var_param);
for (i = ifrom; i < ito; i++) {
if (diff_idx) {
diff_idx(i, param, fixed, func_idx, user_data, der,
&eeval);
}
else if (diff) {
diff(x[i], nparam, param, fixed, func, user_data, der,
&eeval);
}
else {
gwy_math_nlfit_diff_idx(i, nparam, param, fixed,
func_idx, user_data, der,
&eeval);
}
if (!eeval)
break;
/* This should be done only for the real-function
* interface; but that is also the only case when @w can be
* non-NULL. */
if (w) {
for (j = 0; j < nparam; j++)
der[j] *= w[i];
}
/* Accumulate derivatives by slave parameters in master. */
for (j = 0; j < nparam; j++) {
if (link_map[j] != j)
der[link_map[j]] += der[j];
}
/* Accumulate the Hessian and gradient. */
for (j = 0; j < nparam; j++) {
guint jid, diag, k;
/* Only variable master parameters matter */
if ((jid = var_param_id[j]) == G_MAXUINT
|| link_map[j] != j)
continue;
diag = jid*(jid + 1)/2;
/* for J'r */
tv[jid] += der[j] * resid[i];
for (k = 0; k <= j; k++) { /* for J'J */
gint kid = var_param_id[k];
if (kid != G_MAXUINT)
ta[diag + kid] += der[j] * der[k];
}
}
}
eval = eeval;
}
nlfit->eval = eval;
for (i = 1; i < nthreads; i++) {
gdouble *st0 = storage[0], *sti = storage[i];
for (j = 0; j < n_var_param + covar_size; j++)
st0[j] += sti[j];
}
if (nlfit->eval) {
gwy_assign(save_a, a, covar_size);
gwy_assign(saveparam, param, nparam);
}
else {
gwy_debug("eval failed.");
sumr_best = -1.0;
break;
}
}
while (!is_pos_def) {
if (!first_pass)
gwy_assign(a, save_a, covar_size);
else
first_pass = FALSE;
for (j = 0; j < n_var_param; j++) {
/* Add diagonal elements */
guint diag = j*(j + 3)/2;
/* This used to be there. But it breaks the scaling because
* mfi is just a number while a[] elements scale with the
* param derivatives.
* a[diag] = save_a[diag]*(1.0 + mlambda) + nlfit->mfi*mlambda;
*/
if (G_UNLIKELY(save_a[diag] == 0.0))
a[diag] = nlfit->mfi*mlambda;
else
a[diag] = save_a[diag]*(1.0 + mlambda);
xr[j] = -v[j];
}
/* Choleski decompoation J'J in A*/
is_pos_def = gwy_math_choleski_decompose(n_var_param, a);
if (!is_pos_def) {
/* Increase lambda */
mlambda *= nlfit->minc;
if (mlambda == 0.0)
mlambda = nlfit->mtol;
}
}
gwy_math_choleski_solve(n_var_param, a, xr);
/* Move master params along the solved gradient */
for (i = 0; i < nparam; i++) {
if (var_param_id[i] == G_MAXUINT || link_map[i] != i)
continue;
param[i] = saveparam[i] + xr[var_param_id[i]];
if (fabs(param[i] - saveparam[i]) == 0)
count++;
}
/* Sync slave params with master */
for (i = 0; i < nparam; i++) {
if (var_param_id[i] != G_MAXUINT && link_map[i] != i)
param[i] = param[link_map[i]];
}
if (count == n_var_param)
break;
/* See what the new residua is. */
sumr_new = gwy_math_nlfit_residua(func, func_idx, ndata, x, y, w,
nparam, param, user_data, resid,
&nlfit->eval);
/* Catch failed evaluation even if it's not reported. */
if (gwy_isinf(sumr_new) || gwy_isnan(sumr_new)) {
gwy_debug("Inf/NaN encountered");
nlfit->eval = FALSE;
sumr_best = -1.0;
break;
}
/* Good, we've finished */
gwy_debug("sumr change %.16g -> %.16g (%g)",
sumr_best, sumr_new, (sumr_new - sumr_best)/sumr_best);
if (sumr_new == 0
|| (miter > 2 && fabs((sumr_best - sumr_new)/sumr_best) < EPS)) {
gwy_debug("reached zero residuum or converged");
end = TRUE;
}
/* Overshoot, increase lambda */
if (!nlfit->eval || sumr_new >= sumr_best) {
mlambda *= nlfit->minc;
if (mlambda == 0.0)
mlambda = nlfit->mtol;
unimproved++;
}
else
unimproved = 0;
if (unimproved >= 12) {
gwy_debug("lack of improvement");
break;
}
if (++miter >= nlfit->maxiter) {
gwy_debug("maxiter reached");
break;
}
if (set_fraction && !set_fraction((gdouble)miter/nlfit->maxiter)) {
gwy_debug("cancelled");
nlfit->eval = FALSE;
sumr_best = -2.0;
break;
}
} while (!end);
gwy_assign(param, param_best, nparam);
/* Parameter errors computation */
if (nlfit->eval) {
gboolean eeval;
/* Fix the case of exactly zero derivatives.
* XXX: Can we do something about the error then? */
gwy_assign(a, save_a, covar_size);
for (i = 0; i < n_var_param; i++) {
guint diag = i*(i + 3)/2;
if (a[diag] == 0.0)
save_a[diag] = 1.0;
}
/* If we fail just slightly, try again. */
eeval = gwy_math_choleski_invert(n_var_param, save_a);
if (!eeval) {
gwy_assign(save_a, a, covar_size);
for (i = 0; i < n_var_param; i++) {
guint diag = i*(i + 3)/2;
if (a[diag] == 0.0)
save_a[diag] = 1.0;
save_a[diag] *= 1.0001;
}
eeval = gwy_math_choleski_invert(n_var_param, save_a);
}
if (eeval) {
/* Stretch the matrix to span over fixed params too. This is
* actually a bit silly and callers may want to undo it later. */
nlfit->covar = covar = g_new(gdouble, nparam*(nparam + 1)/2);
for (i = 0; i < nparam; i++) {
gint iid = var_param_id[i];
for (j = 0; j < i; j++) {
gint jid = var_param_id[j];
if (iid < 0 || jid < 0)
SLi(covar, i, j) = 0.0; /* Fixed. */
else {
/* For linked params i > j does not ensure iid > jid. */
SLi(covar, i, j) = SLi(save_a,
MAX(iid, jid), MIN(iid, jid));
}
}
if (iid < 0)
SLi(covar, i, j) = 1.0;
else
SLi(covar, i, i) = SLi(save_a, iid, iid);
}
nlfit->dispersion = sumr_best/(ndata - n_var_param);
}
else {
/* XXX: else what? */
gwy_debug("cannot invert covariance matrix");
sumr_best = -1.0;
GWY_FREE(nlfit->covar);
}
}
for (i = 0; i < nparam; i++) {
if (gwy_isinf(param[i]) || gwy_isnan(param[i])) {
sumr_best = nlfit->dispersion = -1.0;
GWY_FREE(nlfit->covar);
gwy_assign(param, origparam, nparam);
gwy_debug("final params are Inf/NaN");
break;
}
}
if (nlfit->covar) {
priv->nparam = nparam;
covar = nlfit->covar;
for (i = 0; i < nparam*(nparam + 1)/2; i++) {
if (gwy_isinf(covar[i]) || gwy_isnan(covar[i])) {
priv->nparam = 0;
sumr_best = nlfit->dispersion = -1.0;
GWY_FREE(nlfit->covar);
gwy_assign(param, origparam, nparam);
gwy_debug("covariance matrix items are Inf/NaN");
break;
}
}
}
fail:
g_free(param_best);
g_free(origparam);
g_free(save_a);
if (storage) {
for (i = 0; i < nthreads; i++)
g_free(storage[i]);
g_free(storage);
}
g_free(saveparam);
g_free(xr);
g_free(fixed);
g_free(var_param_id);
g_free(resid);
g_free(w);
g_free(lmap);
return sumr_best;
}
/**
* gwy_math_nlfit_derive:
* @x: The value to compute the derivative at.
* @nparam: The nuber of parameters.
* @param: Array of parameters (of size @nparam).
* @fixed_param: Which parameters should be treated as fixed (corresponding
* entries are set to %TRUE).
* @func: The fitted function.
* @user_data: User data to be passed to @func.
* @der: Array where the put the result to.
* @success: Set to %TRUE if succeeds, %FALSE on failure.
*
* Numerically computes the partial derivatives of a function.
*
* This is a legacy name for function gwy_math_nlfit_diff().
**/
void
gwy_math_nlfit_derive(gdouble x,
gint nparam,
const gdouble *param,
const gboolean *fixed_param,
GwyNLFitFunc func,
gpointer user_data,
gdouble *diff,
gboolean *success)
{
return gwy_math_nlfit_diff(x, nparam, param, fixed_param, func, user_data,
diff, success);
}
/**
* gwy_math_nlfit_diff:
* @x: The value to compute the derivative at.
* @nparam: The nuber of parameters.
* @param: Array of parameters (of size @nparam).
* @fixed_param: Which parameters should be treated as fixed (corresponding
* entries are set to %TRUE).
* @func: The fitted function.
* @user_data: User data to be passed to @func.
* @der: Array where the put the result to.
* @success: Set to %TRUE if succeeds, %FALSE on failure.
*
* Numerically computes the partial derivatives of a function.
*
* Since: 2.46
**/
void
gwy_math_nlfit_diff(gdouble x,
gint nparam,
const gdouble *param,
const gboolean *fixed_param,
GwyNLFitFunc func,
gpointer user_data,
gdouble *der,
gboolean *success)
{
gdouble *param_tmp;
gdouble hj, left, right;
gint j;
param_tmp = g_newa(gdouble, nparam);
gwy_assign(param_tmp, param, nparam);
for (j = 0; j < nparam; j++) {
if (fixed_param && fixed_param[j]) {
der[j] = 0.0;
continue;
}
hj = fabs(param_tmp[j]) * FitSqrtMachEps;
if (hj == 0.0)
hj = FitSqrtMachEps;
param_tmp[j] -= hj;
left = func(x, nparam, param_tmp, user_data, success);
if (!*success)
return;
param_tmp[j] += 2 * hj;
right = func(x, nparam, param_tmp, user_data, success);
if (!*success)
return;
der[j] = (right - left)/2/hj;
param_tmp[j] = param[j];
}
}
/**
* gwy_math_nlfit_diff_idx:
* @i: Data index from the set {0, 1, 2, ..., ndata-1}.
* @nparam: The nuber of parameters.
* @param: Array of parameters (of size @nparam).
* @fixed_param: Which parameters should be treated as fixed (corresponding
* entries are set to %TRUE).
* @func: The fitted function.
* @user_data: User data to be passed to @func.
* @der: Array where the put the result to.
* @success: Set to %TRUE if succeeds, %FALSE on failure.
*
* Numerically computes the partial derivatives of an opaque function.
*
* This function cannot be passed as derivative calculation function to
* gwy_math_nlfit_new_idx() because it is not of the #GwyNLFitIdxDiffFunc.
* Just pass %NULL to gwy_math_nlfit_new_idx() if you want automatic
* numerical derivatives.
*
* You can employ this function in your own #GwyNLFitIdxDiffFunc function
* if you need to modify the derivatives somehow, for instance to apply
* weighting.
*
* Since: 2.46
**/
void
gwy_math_nlfit_diff_idx(guint i,
gint nparam,
const gdouble *param,
const gboolean *fixed_param,
GwyNLFitIdxFunc func,
gpointer user_data,
gdouble *der,
gboolean *success)
{
gdouble *param_tmp;
gdouble hj, left, right;
gint j;
param_tmp = g_newa(gdouble, nparam);
gwy_assign(param_tmp, param, nparam);
for (j = 0; j < nparam; j++) {
if (fixed_param && fixed_param[j]) {
der[j] = 0.0;
continue;
}
hj = fabs(param_tmp[j]) * FitSqrtMachEps;
if (hj == 0.0)
hj = FitSqrtMachEps;
param_tmp[j] -= hj;
left = func(i, param_tmp, user_data, success);
if (!*success)
return;
param_tmp[j] += 2 * hj;
right = func(i, param_tmp, user_data, success);
if (!*success)
return;
der[j] = (right - left)/2/hj;
param_tmp[j] = param[j];
}
}
/* NB: we apply weighting to to resid[]. */
static gdouble
gwy_math_nlfit_residua(GwyNLFitFunc func,
GwyNLFitIdxFunc func_idx,
guint ndata,
const gdouble *x,
const gdouble *y,
const gdouble *weight,
guint nparam,
const gdouble *param,
gpointer user_data,
gdouble *resid,
gboolean *success)
{
gdouble s = 0.0;
gboolean ok = TRUE;
g_return_val_if_fail(func || func_idx, -1.0);
if (func_idx) {
#ifdef _OPENMP
#pragma omp parallel if(gwy_threads_are_enabled()) default(none) \
reduction(+:s) reduction(&&:ok) \
shared(func_idx,ndata,resid,param,user_data)
#endif
{
guint ifrom = gwy_omp_chunk_start(ndata);
guint ito = gwy_omp_chunk_end(ndata);
guint i;
for (i = ifrom; i < ito; i++) {
gboolean ook;
resid[i] = func_idx(i, param, user_data, &ook);
s += resid[i] * resid[i];
if (!ook) {
ok = FALSE;
break;
}
}
}
}
else {
#ifdef _OPENMP
#pragma omp parallel if(gwy_threads_are_enabled()) default(none) \
reduction(+:s) reduction(&&:ok) \
shared(func,x,y,ndata,resid,weight,nparam,param,user_data)
#endif
{
guint ifrom = gwy_omp_chunk_start(ndata);
guint ito = gwy_omp_chunk_end(ndata);
guint i;
for (i = ifrom; i < ito; i++) {
gboolean ook;
resid[i] = func(x[i], nparam, param, user_data, &ook) - y[i];
if (weight)
resid[i] *= weight[i];
s += resid[i] * resid[i];
if (!ook) {
ok = FALSE;
break;
}
}
}
}
*success = ok;
return s;
}
/**
* gwy_math_nlfit_get_max_iterations:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
*
* Returns the maximum number of iterations of nonlinear fitter @nlfit.
*
* Returns: The maximum number of iterations.
**/
gint
gwy_math_nlfit_get_max_iterations(GwyNLFitter *nlfit)
{
return nlfit->maxiter;
}
/**
* gwy_math_nlfit_set_max_iterations:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
* @maxiter: The maximum number of iterations.
*
* Sets the maximum number of iterations for nonlinear fitter @nlfit.
**/
void
gwy_math_nlfit_set_max_iterations(GwyNLFitter *nlfit,
gint maxiter)
{
g_return_if_fail(maxiter > 0);
nlfit->maxiter = maxiter;
}
/**
* gwy_math_nlfit_get_approx_geometric:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
*
* Reports if a non-linear fitter performs approximately orthogonal fitting.
*
* This function does not do anything useful.
*
* Returns: %TRUE if the fitting is approximately orthogonal; %FALSE for
* ordinary least squares.
*
* Since: 2.47
**/
gboolean
gwy_math_nlfit_get_approx_geometric(GwyNLFitter *nlfit)
{
GwyNLFitterPrivate *priv;
priv = find_private_data(nlfit, FALSE);
return priv && priv->approx_geometric;
}
/**
* gwy_math_nlfit_set_approx_geometric:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
* @setting: %TRUE to approximately orthogonal (geometrical) fitting.
*
* Sets a non-linear fitter to perform ordinary or approximately orthogonal
* fitting.
*
* This function does not do anything useful. Since 2.56 it is no-op.
*
* Since: 2.47
**/
void
gwy_math_nlfit_set_approx_geometric(GwyNLFitter *nlfit,
gboolean setting)
{
GwyNLFitterPrivate *priv;
priv = find_private_data(nlfit, TRUE);
priv->approx_geometric = setting;
}
/**
* gwy_math_nlfit_succeeded:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
*
* Obtains the status of the last fitting.
*
* Fitting failure can be (and usually should be) also determined by checking
* for negative return value of gwy_math_nlfit_fit() or
* gwy_math_nlfit_fit_full(). This function allows to test it later.
*
* Returns: %TRUE if the last fitting suceeded, %FALSE if it failed.
*
* Since: 2.7
**/
gboolean
gwy_math_nlfit_succeeded(GwyNLFitter *nlfit)
{
if ((!nlfit->covar && nlfit->dispersion >= 0.0)
|| (nlfit->covar && nlfit->dispersion < 0.0)) {
g_warning("Covar and dispersion do not agree on whether the fit "
"was successful.");
return FALSE;
}
return nlfit->covar != NULL;
}
/**
* gwy_math_nlfit_get_sigma:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
* @par: Parameter index.
*
* Returns the standard deviation of parameter number @par.
*
* This function makes sense only after a successful fit and for a free
* parameter.
*
* Returns: The SD of @par-th parameter.
**/
gdouble
gwy_math_nlfit_get_sigma(GwyNLFitter *nlfit, gint par)
{
g_return_val_if_fail(nlfit->covar, G_MAXDOUBLE);
return sqrt(nlfit->dispersion * SLi(nlfit->covar, par, par));
}
/**
* gwy_math_nlfit_get_dispersion:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
*
* Returns the residual sum divided by the number of degrees of freedom.
*
* This function can be used only after a successful fit.
*
* Returns: The dispersion.
**/
gdouble
gwy_math_nlfit_get_dispersion(GwyNLFitter *nlfit)
{
g_return_val_if_fail(nlfit->covar, G_MAXDOUBLE);
return nlfit->dispersion;
}
/**
* gwy_math_nlfit_get_nparam:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
*
* Gets the number of parameters of a nonlinear fitter.
*
* The number of parameters determines the size of covariance matrix obtained
* by gwy_math_nlfit_get_covar() and valid arguments for
* gwy_math_nlfit_get_correlations().
*
* Returns: The number of parameters for the last fit. If the last fit was not
* successful zero is returned.
*
* Since: 2.47
**/
gint
gwy_math_nlfit_get_nparam(GwyNLFitter *nlfit)
{
GwyNLFitterPrivate *priv;
priv = find_private_data(nlfit, FALSE);
return priv ? priv->nparam : 0;
}
/**
* gwy_math_nlfit_get_eval:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
*
* Gets the state of a nonlinear fitter.
*
* Returns: %TRUE if the last fit succeeded, %FALSE if it failed.
*
* Since: 2.47
**/
gboolean
gwy_math_nlfit_get_eval(GwyNLFitter *nlfit)
{
return nlfit->eval;
}
/**
* gwy_math_nlfit_get_covar:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
*
* Gets the covariance matrix of a nonlinear fitter.
*
* The returned matrix may be only used between fits. Any fitting can free and
* reallocate it.
*
* Returns: The covariance matrix, as lower triangular matrix, owned by the
* fitter. The return value will be %NULL if the last fit did not
* succeed.
*
* Since: 2.47
**/
const gdouble*
gwy_math_nlfit_get_covar(GwyNLFitter *nlfit)
{
return nlfit->covar;
}
/**
* gwy_math_nlfit_get_correlations:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
* @par1: First parameter index.
* @par2: Second parameter index.
*
* Returns the correlation coefficient between @par1-th and @par2-th parameter.
*
* This function can be used only after a successful fit.
*
* Returns: The correlation coefficient.
**/
gdouble
gwy_math_nlfit_get_correlations(GwyNLFitter *nlfit, gint par1, gint par2)
{
gdouble t;
g_return_val_if_fail(nlfit->covar, G_MAXDOUBLE);
if (par1 == par2)
return 1.0;
GWY_ORDER(gint, par2, par1);
t = SLi(nlfit->covar, par1, par1) * SLi(nlfit->covar, par2, par2);
if (t == 0) {
g_warning("Zero element in covar matrix");
return G_MAXDOUBLE;
}
return SLi(nlfit->covar, par1, par2)/sqrt(t);
}
/**
* gwy_math_nlfit_set_callbacks:
* @nlfit: A Marquardt-Levenberg nonlinear fitter.
* @set_fraction: Function that sets fraction to output (or %NULL).
* @set_message: Function that sets message to output (or %NULL).
*
* Sets callbacks reporting a non-linear least squares fitter progress.
*
* Since: 2.46
**/
void
gwy_math_nlfit_set_callbacks(GwyNLFitter *fitter,
GwySetFractionFunc set_fraction,
GwySetMessageFunc set_message)
{
GwyNLFitterPrivate *priv;
priv = find_private_data(fitter, TRUE);
priv->set_fraction = set_fraction;
priv->set_message = set_message;
}
static GwyNLFitterPrivate*
find_private_data(GwyNLFitter *fitter, gboolean do_create)
{
GwyNLFitterPrivate *priv;
GList *l;
G_LOCK(private_fitter_data);
for (l = private_fitter_data; l; l = g_list_next(l)) {
priv = (GwyNLFitterPrivate*)l->data;
if (priv->fitter == fitter) {
G_UNLOCK(private_fitter_data);
return priv;
}
}
if (!do_create) {
G_UNLOCK(private_fitter_data);
return NULL;
}
priv = g_new0(GwyNLFitterPrivate, 1);
priv->fitter = fitter;
private_fitter_data = g_list_prepend(private_fitter_data, priv);
G_UNLOCK(private_fitter_data);
return priv;
}
static void
free_private_data(GwyNLFitter *fitter)
{
GwyNLFitterPrivate *priv;
GList *l;
G_LOCK(private_fitter_data);
for (l = private_fitter_data; l; l = g_list_next(l)) {
priv = (GwyNLFitterPrivate*)l->data;
if (priv->fitter == fitter) {
private_fitter_data = g_list_delete_link(private_fitter_data, l);
g_free(priv);
break;
}
}
G_UNLOCK(private_fitter_data);
}
/**
* gwy_math_nlfit_map_free_params:
* @fixed_param: Which parameters are fixed.
* @n: Length of @fixed_param array.
* @id_map: Parameter id map to fill.
*
* Creates a map from free parameter ids to all-parameter ids.
*
* This is a helper function for reduction of full parameter vectors and
* covariance matrices to only free parameters.
*
* The array @id_map must at least as many elements as there are free
* parameters. However, it is usually better to just pass an array of size @n
* because the number of free parameters is what this function calculates.
*
* Returns: The number of free parameters. This is the number of ids filled
* in @id_map.
*
* Since: 2.50
**/
gint
gwy_math_nlfit_map_free_params(const gboolean *fixed_param,
gint n,
gint *id_map)
{
gint i, j;
if (!n)
return 0;
g_return_val_if_fail(fixed_param, 0);
g_return_val_if_fail(id_map, 0);
for (i = j = 0; i < n; i++) {
if (!fixed_param[i])
id_map[j++] = i;
}
return j;
}
/************************** Documentation ****************************/
/**
* SECTION:gwynlfit
* @title: GwyNLFitter
* @short_description: Marquardt-Levenberg nonlinear least square fitter
* @see_also: #GwyNLFitPreset
*
* A new Marquardt-Levenberg nonlinear least square fitter can be created with
* gwy_math_nlfit_new(), specifying the function to fit (as #GwyNLFitFunc) and
* its derivative (as #GwyNLFitDerFunc). For functions for whose analytic
* derivative is not available or very impractical, gwy_math_nlfit_derive()
* (computing the derivative numerically) can be used instead.
*
* A fitter can be then repeatedly used on different data either in
* gwy_math_nlfit_fit(), or gwy_math_nlfit_fit_full() when there are some
* fixed or linked parameters. Arbitrary additional (non-fitting) parameters
* can be passed to the fited function in @user_data.
*
* After a successfull fit additional fit information can be obtained with
* gwy_math_nlfit_get_dispersion(), gwy_math_nlfit_get_correlations(),
* gwy_math_nlfit_get_sigma(). Note these functions may be used only after a
* successfull fit. When a fitter is no longer needed, it should be freed with
* gwy_math_nlfit_free().
*
* Several common functions are also available as fitting presets that can be
* fitted with gwy_nlfit_preset_fit(). See #GwyNLFitPreset for details.
**/
/**
* GwyNLFitFunc:
* @x: The value to compute the function at.
* @nparam: The number of parameters (size of @param).
* @param: Parameters.
* @user_data: User data as passed to gwy_math_nlfit_fit().
* @success: Set to %TRUE if succeeds, %FALSE on failure.
*
* Fitting function type for real-valued independent variables.
*
* Returns: The function value at @x.
*/
/**
* GwyNLFitDerFunc:
* @x: x-data as passed to gwy_math_nlfit_fit().
* @nparam: The number of parameters (size of @param).
* @param: Parameters.
* @fixed_param: Which parameters should be treated as fixed (corresponding
* entries are set to %TRUE).
* @func: The fitted function.
* @user_data: User data as passed to gwy_math_nlfit_fit().
* @der: Array where the @nparam partial derivatives by each parameter are
* to be stored. Derivatives by fixed parameters are ignored so the
* function may set corresponding elements or not, whichever is more
* convenient.
* @success: Set to %TRUE if succeeds, %FALSE on failure.
*
* Fitting function partial derivative type for real-valued independent
* variables.
*/
/**
* GwyNLFitIdxFunc:
* @i: Data index from the set {0, 1, 2, ..., ndata-1}.
* @param: Parameters.
* @user_data: User data as passed to gwy_math_nlfit_fit().
* @success: Set to %TRUE if succeeds, %FALSE on failure.
*
* Fitting function type for opaque indexed data.
*
* Note that unlike #GwyNLFitFunc which returns just the function value this
* function must return the <emphasis>difference</emphasis> between the
* function value and fitted data value (that is function minus data point).
* When opaque data are fitted the fitter does not know what the data values
* are.
*
* The function must take care of weighting. The difference should be
* multiplied by the inverse of the (unsquared) estimated error of the
* @i-th data point. Not multiplying by anything correspond to using the
* default unit weights.
*
* Returns: Difference between the function value and data in the @i-th data
* point.
*
* Since: 2.46
**/
/**
* GwyNLFitIdxDiffFunc:
* @i: Data index from the set {0, 1, 2, ..., ndata-1}.
* @param: Parameters.
* @fixed_param: Which parameters should be treated as fixed (corresponding
* entries are set to %TRUE). It may be %NULL is no parameters
* are fixed. The function must set derivatives by fixed
* parameters to zero.
* @func: The fitted function.
* @user_data: User data as passed to gwy_math_nlfit_fit().
* @der: Array where the @nparam partial derivatives by each parameter are
* to be stored. Derivatives by fixed parameters are ignored so the
* function may set corresponding elements or not, whichever is more
* convenient.
* @success: Set to %TRUE if succeeds, %FALSE on failure.
*
* Fitting function partial derivatives type for opaque indexed data.
*
* The function must take care of weighting. The derivatives should be
* multiplied by the inverse of the (unsquared) estimated error of the
* @i-th data point. Not multiplying by anything correspond to using the
* default unit weights.
*
* Since: 2.46
**/
/**
* GwyNLFitter:
* @fmarq: Evaluates the fitted function.
* @dmarq: Evaluates derivatives of the fitted function.
* @maxiter: Maximum number of iteration.
* @eval: %TRUE if last evaluation succeeded.
* @covar: Covariance matrix (set upon successful fit).
* @dispersion: Mean residual sum of squares per point, set to -1 on failure.
* @mfi: Lambda parameter is multiplied by it. Probably keep at 1.
* @mdec: Decrease of lambda parameter after an unsuccessful step.
* @minc: Increase of lambda parameter after a successful step.
* @mtol: If lambda parameter becomes zero it is set to this value.
*
* Non-linear least-squares fitter.
*
* The fields should be considered private.
*
* Use gwy_math_nlfit_get_eval(), gwy_math_nlfit_get_covar() and
* gwy_math_nlfit_get_dispersion() and gwy_math_nlfit_succeeded() to examine
* the fitter state.
*
* Use gwy_math_nlfit_set_max_iterations() to set the maximum iteration.
*
* In rare occasions you might want modify @mdec or @minc. The rest is better
* left untouched.
*/
/**
* GwyNLFitParamFlags:
* @GWY_NLFIT_PARAM_ANGLE: Parameter is an angle. It is defined in radians and
* unitless but you may wish to convert it from/to
* degrees in the user interface. It is consdered
* periodic and always reduced to the range [0, 2π).
* @GWY_NLFIT_PARAM_ABSVAL: Parameter is a width or distance that is by
* definition positive. Only its absolute value
* matters and it is always made non-negative.
*
* Type of fitting parameter properties.
*
* Since: 2.47
**/
/* vim: set cin et ts=4 sw=4 cino=>1s,e0,n0,f0,{0,}0,^0,\:1s,=0,g1s,h0,t0,+1s,c3,(0,u0 : */
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