This file is indexed.

/usr/share/octave/packages/optim-1.4.1/private/__lm_svd__.m is in octave-optim 1.4.1-2.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
## Copyright (C) 1992-1994 Richard Shrager
## Copyright (C) 1992-1994 Arthur Jutan
## Copyright (C) 1992-1994 Ray Muzic
## Copyright (C) 2010-2013 Olaf Till <i7tiol@t-online.de>
##
## 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 3 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, see <http://www.gnu.org/licenses/>.

function [p, resid, cvg, outp] = __lm_svd__ (F, pin, hook)

  ## This is a backend for optimization. This code was originally
  ## contained in leasqr.m, which is now a frontend.

  ## some backend specific defaults
  fract_prec_default = 0;
  max_fract_step_default = Inf;

  n = length (pin);

  ## passed constraints
  mc = hook.mc; # matrix of linear constraints
  vc = hook.vc; # vector of linear constraints
  f_cstr = hook.f_cstr; # function of all constraints
  df_cstr = hook.df_cstr; # function of derivatives of all constraints
  n_gencstr = hook.n_gencstr; # number of non-linear constraints
  eq_idx = hook.eq_idx; # logical index of equality constraints in all
                                # constraints
  lbound = hook.lbound; # bounds, subset of linear inequality
  ubound = hook.ubound; # constraints in mc and vc

  ## passed values of constraints for initial parameters
  pin_cstr = hook.pin_cstr;

  ## passed return value of F for initial parameters
  f_pin = hook.f_pin;

  ## passed derivative of residual function
  dfdp = hook.dfdp;

  ## passed function for complementary pivoting
  cpiv = hook.cpiv;

  ## passed options
  maxstep = hook.max_fract_change;
  maxstep(isna (maxstep)) = max_fract_step_default;
  pprec = hook.fract_prec;
  pprec(isna (pprec)) = fract_prec_default;
  ## keep absolute precision positive for non-null relative precision;
  ## arbitrary value, added to parameters before multiplying with
  ## relative precision
  add_pprec = zeros (n, 1);
  add_pprec(pprec > 0) = sqrt (eps);
  ##
  stol = hook.TolFun;
  niter = hook.MaxIter;
  if (isempty (niter)) niter = 20; endif
  wt = hook.weights;
  fixed = hook.fixed;
  verbose = strcmp (hook.Display, "iter");
  user_interaction = hook.user_interaction;

  ## only preliminary, for testing
  if (isfield (hook, "testing"))
    testing = hook.testing;
  else
    testing = false;
  endif
  if (isfield (hook, "new_s"))
    new_s = hook.new_s;
  else
    new_s = false;
  endif

  ## some useful variables derived from passed variables
  n_lcstr = size (vc, 1);
  have_constraints_except_bounds = ...
      n_lcstr + n_gencstr > ...
      sum (lbound ~= -Inf) + sum (ubound ~= Inf);
  wtl = wt(:);

  nz = 20 * eps; # This is arbitrary. Constraint function will be
                                # regarded as <= zero if less than nz.

  ## backend-specific checking of options and constraints
  if (have_constraints_except_bounds)
    if (any (pin_cstr.inequ.lin_except_bounds < 0) || ...
        (n_gencstr > 0 && any (pin_cstr.inequ.gen < 0)))
      warning ("initial parameters violate inequality constraints");
    endif
    if (any (abs (pin_cstr.equ.lin) >= nz) || ...
        (n_gencstr > 0 && any (abs (pin_cstr.equ.gen) >= nz)))
      warning ("initial parameters violate equality constraints");
    endif
  endif
  idx = lbound == ubound;
  if (any (idx))
    warning ("lower and upper bounds identical for some parameters, fixing the respective parameters");
    fixed(idx) = true;
  endif
  if (all (fixed))
    error ("no free parameters");
  endif
  lidx = pin < lbound;
  uidx = pin > ubound;
  if (any (lidx | uidx) && have_constraints_except_bounds)
    warning ("initial parameters outside bounds, not corrected since other constraints are given");
  else
    if (any (lidx))
      warning ("some initial parameters set to lower bound");
      pin(lidx, 1) = lbound(lidx, 1);
    endif
    if (any (uidx))
      warning ("some initial parameters set to upper bound");
      pin(uidx, 1) = ubound(uidx, 1);
    endif
  endif
  if (n_gencstr > 0 && any (~isinf (maxstep)))
    warning ("setting both a maximum fractional step change of parameters and general constraints may result in inefficiency and failure");
  endif

  ## fill constant fields of hook for derivative-functions; some fields
  ## may be backend-specific
  dfdp_hook.fixed = fixed; # this may be handled by the frontend, but
                                # the backend still may add to it

  ## set up for iterations
  ##
  p = pin;
  f = f_pin; fbest=f; pbest=p;
  m = prod (size (f));
  r = wt .* f;
  r = r(:);
  if (~isreal (r)) error ("weighted residuals are not real"); endif
  ss = r.' * r;
  sbest=ss;
  chgprev=Inf*ones(n,1);
  cvg=0;
  epsLlast=1;
  epstab=[.1, 1, 1e2, 1e4, 1e6];
  ac_idx = true (n_lcstr + n_gencstr, 1); # all constraints
  nc_idx = false (n_lcstr + n_gencstr, 1); # none of all constraints
  gc_idx = cat (1, false (n_lcstr, 1), true (n_gencstr, 1)); # gen. constr.
  lc_idx = ~gc_idx;

  if (([stop, outp.user_interaction] = ...
       __do_user_interaction__ (user_interaction, p,
                                struct ("iteration", 0,
                                        "residual", f),
                                "init")))
    outp.niter = 0;
    resid = f;
    cvg = -1;
    return;
  endif

  ## do iterations
  ##
  for iter = 1:niter
    deb_printf (testing, "\nstart outer iteration\n");
    v_cstr = f_cstr (p, ac_idx);
    ## index of active constraints
    c_act =  v_cstr < nz | eq_idx; # equality constraints might be
                                # violated at start
    if (any (c_act))
      if (n_gencstr > 0)
        ## full gradient is needed later
        dct = df_cstr (p, ac_idx, ...
                       setfield (dfdp_hook, "f", v_cstr));
        dct(:, fixed) = 0; # for user supplied dfdp; necessary?
        dcat = dct(c_act, :);
      else
        dcat = df_cstr (p, c_act, ...
                        setfield (dfdp_hook, "f", v_cstr));
        dcat(:, fixed) = 0; # for user supplied dfdp; necessary?
      endif
      dca = dcat.';
    endif
    nrm = zeros (1, n);
    pprev=pbest;
    prt = dfdp (p, setfield (dfdp_hook, "f", fbest(:)));
    prt(:, fixed) = 0; # for user supplied dfdp; necessary?
    r = wt .* -fbest;
    r = r(:);
    if (~isreal (r)) error ("weighted residuals are not real"); endif
    sprev=sbest;
    sgoal=(1-stol)*sprev;
    msk = ~fixed;
    prt(:, msk) = prt(:, msk) .* wtl(:, ones (1, sum (msk)));
    nrm(msk) = sumsq (prt(:, msk), 1);
    msk = nrm > 0;
    nrm(msk) = 1 ./ sqrt (nrm(msk));
    prt = prt .* nrm(ones (1, m), :);
    nrm = nrm.';
    [prt,s,v]=svd(prt,0);
    s=diag(s);
    g = prt.' * r;
    for jjj=1:length(epstab)
      deb_printf (testing, "\nstart inner iteration\n");
      epsL = max(epsLlast*epstab(jjj),1e-7);
      ## printf ("epsL: %e\n", epsL); # for testing

      ## Usage of this "ser" later is equivalent to pre-multiplying the
      ## gradient with a positive-definit matrix, but not with a
      ## diagonal matrix, at epsL -> Inf; so there is a fallback to
      ## gradient descent, but not in general to descent for each
      ## gradient component. Using the commented-out "ser" ((1 / (1 +
      ## epsL^2)) * (1 ./ se + epsL * s)) would be equivalent to using
      ## Marquardts diagonal of the Hessian-approximation for epsL ->
      ## Inf, but currently this gives no advantages in tests, even with
      ## constraints.
### ser = 1 ./ sqrt((s.*s)+epsL);
      se = sqrt ((s.*s) + epsL);
      if (new_s)
        ## for testing
        ser = (1 / (1 + epsL^2)) * (1 ./ se + epsL * s);
      else
        ser = 1 ./ se;
      endif
      tp1 = (v * (g .* ser)) .* nrm;
      if (any (c_act))
        deb_printf (testing, "constraints are active:\n");
        deb_printf (testing, "%i\n", c_act);
        ## calculate chg by "quadratic programming"
        nrme= diag (nrm);
        ser2 = diag (ser .* ser);
        mfc1 = nrme * v * ser2 * v.' * nrme;
        tp2 = mfc1 * dca;
        a_eq_idx = eq_idx(c_act);
        [lb, bidx, ridx, tbl] = cpiv (dcat * tp1, dcat * tp2, a_eq_idx);
        chg = tp1 + tp2(:, bidx) * lb; # if a parameter is "fixed",
                                # the respective component of chg should
                                # be zero too, even here (with active
                                # constraints)
        deb_printf (testing, "change:\n");
        deb_printf (testing, "%e\n", chg);
        deb_printf (testing, "\n");
        ## indices for different types of constraints
        c_inact = ~c_act; # inactive constraints
        c_binding = nc_idx; 
        c_binding(c_act) = bidx; # constraints selected binding
        c_unbinding = nc_idx;
        c_unbinding(c_act) = ridx; # constraints unselected binding
        c_nonbinding = c_act & ~(c_binding | c_unbinding); # constraints
                                # selected non-binding
      else
        ## chg is the Levenberg/Marquardt step
        chg = tp1;
        ## indices for different types of constraints
        c_inact = ac_idx; # inactive constraints consist of all
                                # constraints
        c_binding = nc_idx;
        c_unbinding = nc_idx;
        c_nonbinding = nc_idx;
      endif
      ## apply constraints to step width (since this is a
      ## Levenberg/Marquardt algorithm, no line-search is performed
      ## here)
      k = 1;
      c_tp = c_inact(1:n_lcstr);
      mcit = mc(:, c_tp).';
      vci = vc(c_tp);
      hstep = mcit * chg;
      idx = hstep < 0;
      if (any (idx))
        k = min (1, min (- (vci(idx) + mcit(idx, :) * pprev) ./ ...
                         hstep(idx)));
      endif
      if (k < 1)
        deb_printf (testing, "stepwidth: linear constraints\n");
      endif
      if (n_gencstr > 0)
        c_tp = gc_idx & (c_nonbinding | c_inact);
        if (any (c_tp) && any (f_cstr (pprev + k * chg, c_tp) < 0))
          [k, fval, info] = ...
              fzero (@ (x) min (cat (1, ...
                                     f_cstr (pprev + x * chg, c_tp), ...
                                     k - x, ...
                                     ifelse (x < 0, -Inf, Inf))), ...
                     0);
          if (info ~= 1 || abs (fval) >= nz)
            error ("could not find stepwidth to satisfy inactive and non-binding general inequality constraints");
          endif
          deb_printf (testing, "general constraints limit stepwidth\n");
        endif
      endif
      chg = k * chg;

      if (any (gc_idx & c_binding)) # none selected binding =>
                                # none unselected binding
        deb_printf (testing, "general binding constraints must be regained:\n");
        ## regain binding constraints and one of the possibly active
        ## previously inactive or non-binding constraints
        ptp1 = pprev + chg;

        tp = true;
        nt_nosuc = true;
        lim = 20;
        while (nt_nosuc && lim >= 0)
          deb_printf (testing, "starting from new value of p in regaining:\n");
          deb_printf (testing, "%e\n", ptp1);
          ## we keep d_p.' * inv (mfc1) * d_p minimal in each step of
          ## the inner loop; this is both sensible (this metric
          ## considers a guess of curvature of sum of squared residuals)
          ## and convenient (we have useful matrices available for it)
          c_tp0 = c_inact | c_nonbinding;
          c_tp1 = c_inact | (gc_idx & c_nonbinding);
          btbl = tbl(bidx, bidx);
          c_tp2 = c_binding;
          if (any (tp)) # if none before, does not get true again
            tp = f_cstr (ptp1, c_tp1) < nz;
            if (any (tp)) # could be less clumsy, but ml-compatibility..
              ## keep only the first true entry in tp
              tp(tp) = logical (cat (1, 1, zeros (sum (tp) - 1, 1)));
              ## supplement binding index with one (the first) getting
              ## binding in c_tp1
              c_tp2(c_tp1) = tp;
              ## gradient of this added constraint
              caddt = dct(c_tp2 & ~c_binding, :);
              cadd = caddt.';
              C = dct(c_binding, :) * mfc1 * cadd;
              Ct = C.';
              G = [btbl, btbl * C; ...
                   -Ct * btbl, caddt * mfc1 * cadd - Ct * btbl * C];
              btbl = gjp (G, size (G, 1));
            endif
          endif
          dcbt = dct(c_tp2, :);
          mfc = - mfc1 * dcbt.' * btbl;
          deb_printf (testing, "constraints to regain:\n");
          deb_printf (testing, "%i\n", c_tp2);

          ptp2 = ptp1;
          nt_niter_start = 100;
          nt_niter = nt_niter_start;
          while (nt_nosuc && nt_niter >= 0)
            hv = f_cstr (ptp2, c_tp2);
            if (all (abs (hv) < nz))
              nt_nosuc = false;
              chg = ptp2 - pprev;
            else
              ptp2 = ptp2 + mfc * hv; # step should be zero for each
                                # component for which the parameter is
                                # "fixed"
            endif
            nt_niter = nt_niter - 1;
          endwhile
          deb_printf (testing, "constraints after regaining:\n");
          deb_printf (testing, "%e\n", hv);
          if (nt_nosuc || ...
              any (abs (chg) > abs (pprev .* maxstep)) || ...
              any (f_cstr (ptp2, c_tp0) < -nz))
            if (nt_nosuc)
              deb_printf (testing, "regaining did not converge\n");
            else
              deb_printf (testing, "regaining violated type 3 and 4\n");
            endif
            nt_nosuc = true;
            ptp1 = (pprev + ptp1) / 2;
          endif
          if (~nt_nosuc)
            tp = f_cstr (ptp2, c_unbinding);
            if (any (tp) < 0) # again ml-compatibility clumsyness..
              [discarded, id] = min(tp);
              tid = find (ridx);
              id = tid(id); # index within active constraints
              unsuccessful_exchange = false;
              if (abs (tbl(id, id)) < nz) # Bard: not absolute value
                ## exchange this unselected binding constraint against a
                ## binding constraint, but not against an equality
                ## constraint
                tbidx = bidx & ~a_eq_idx;
                if (~any (tbidx))
                  unsuccessful_exchange = true;
                else
                  [discarded, idm] = max (abs (tbl(tbidx, id)));
                  tid = find (tbidx);
                  idm = tid(idm); # -> index within active constraints
                  tbl = gjp (tbl, idm);
                  bidx(idm) = false;
                  ridx(idm) = true;
                endif
              endif
              if (unsuccessful_exchange)
                ## It probably doesn't look good now; this desperate
                ## last attempt is not in the original algortithm, since
                ## that didn't account for equality constraints.
                ptp1 = (pprev + ptp1) / 2;
              else
                tbl = gjp (tbl, id);
                bidx(id) = true;
                ridx(id) = false;
                c_binding = nc_idx;
                c_binding(c_act) = bidx;
                c_unbinding = nc_idx;
                c_unbinding(c_act) = ridx;
              endif
              nt_nosuc = true;
              deb_printf (testing, "regaining violated type 2\n");
            endif
          endif
          if (~nt_nosuc)
            deb_printf (testing, "regaining successful, converged with %i iterations:\n", ...
            nt_niter_start - nt_niter);
            deb_printf (testing, "%e\n", ptp2);
          endif
          lim = lim - 1;
        endwhile
        if (nt_nosuc)
          error ("could not regain binding constraints");
        endif
      else
        ## check the maximal stepwidth and apply as necessary
        ochg=chg;
        idx = ~isinf(maxstep);
        limit = abs(maxstep(idx).*pprev(idx));
        chg(idx) = min(max(chg(idx),-limit),limit);
        if (verbose && any(ochg ~= chg))
          disp(['Change in parameter(s): ', ...
                sprintf("%d ",find(ochg ~= chg)), "maximal fractional stepwidth enforced"]);
        endif
      endif
      aprec = pprec .* (abs (pbest) + add_pprec);
      ## ss=scalar sum of squares=sum((wt.*f)^2).
      if (any(abs(chg) > 0.1*aprec))#---  # only worth evaluating
                                # function if there is some non-miniscule
                                # change
        ## In the code of the outer loop before the inner loop pbest is
        ## actually identical to p, since once they deviate, the outer
        ## loop will not be repeated. Though the inner loop can still be
        ## repeated in this case, pbest is not used in it. Since pprev
        ## is set from pbest in the outer loop before the inner loop, it
        ## is also identical to p up to here.
        p=chg+pprev;
        ## since the projection method may have slightly violated
        ## constraints due to inaccuracy, correct parameters to bounds
        ## --- but only if no further constraints are given, otherwise
        ## the inaccuracy in honoring them might increase by this
        skipped = false;
        if (~have_constraints_except_bounds)
          lidx = p < lbound;
          uidx = p > ubound;
          p(lidx, 1) = lbound(lidx, 1);
          p(uidx, 1) = ubound(uidx, 1);
          chg(lidx, 1) = p(lidx, 1) - pprev(lidx, 1);
          chg(uidx, 1) = p(uidx, 1) - pprev(uidx, 1);
        endif
        ##
        f = F (p);
        r = wt .* f;
        r = r(:);
        if (~isreal (r))
          error ("weighted residuals are not real");
        endif
        ss = r.' * r;
        deb_printf (testing, "tried parameters:\n");
        deb_printf (testing, "%.16e\n", p); 
        deb_printf (testing, "sbest: %.16e\n", sbest);
        deb_printf (testing, "sgoal: %.16e\n", sgoal);
        deb_printf (testing, "   ss: %.16e\n", ss);
        if (ss<sbest)
          pbest=p;
          fbest=f;
          sbest=ss;
        endif
        if (ss < sgoal) # <, not <=, since sgoal can be equal to sprev
                                # if TolFun <= eps
          break;
        endif
      else
        skipped = true;
        break;
      endif                          #---
    endfor
    ## printf ("epsL no.: %i\n", jjj); # for testing
    epsLlast = epsL;

    hook.plot_cmd (f);

    if (([stop, outp.user_interaction] = ...
         __do_user_interaction__ (user_interaction, p,
                                  struct ("iteration", iter,
                                          "residual", f),
                                  "iter")))
      outp.niter = iter;
      resid = f;
      cvg = -1;
      return;
    endif
    if (skipped)
      cvg = 2;
      break;
    endif
    if (ss < eps) # in this case ss == sbest
      cvg = 3; # there is no more suitable flag for this
      break;
    endif
    if (ss >= sgoal) # >=, not >, since sgoal can be equal to sprev if
                                # TolFun <= eps
      cvg = 3;
      break;
    endif
    aprec = pprec .* (abs (pbest) + add_pprec);
    ## [aprec, chg, chgprev]
    if (all(abs(chg) <= aprec) && all(abs(chgprev) <= aprec))
      cvg = 2;
      if (verbose)
        fprintf("Parameter changes converged to specified precision\n");
      endif
      break;
    else
      chgprev=chg;
    endif
  endfor

  ## set further return values
  ##
  p = pbest;
  resid = fbest;
  outp.niter = iter;

  if (([stop, outp.user_interaction] = ...
       __do_user_interaction__ (user_interaction, pbest,
                                struct ("iteration", iter,
                                        "residual", fbest),
                                "done")))
    cvg = -1;
  endif

endfunction

function deb_printf (do_printf, varargin)

  ## for testing

  if (do_printf)
    printf (varargin{:})
  endif

endfunction