void itoa( char arr[], int size, int val )
{
int i, max, dig, subval, loc;
for (i=0; i<size; i++ )
{
arr[i] = '\0';
}
for ( i=1; i<=2; i++ )
{
if (( val / myexp(i) ) == 0 )
{
max = i-1;
break;
}
}
subval = 0;
loc = 0;
for ( i=max; i>=0; i-- )
{
dig = 48 + ((val-subval) / myexp(i));
subval = (dig-48) * myexp(max);
arr[loc] = dig;
loc++;
}
return;
Exit(0);
}
static char* test_more()
{
mu_assert(in_delta(myexp(0.0), expect_myexp(0.0)));
mu_assert(in_delta(myexp(15.0), expect_myexp(15.0)));
mu_assert(in_delta(myexp(1.1), expect_myexp(1.1)));
mu_assert(in_delta(myexp(3.3), expect_myexp(3.3)));
mu_assert(in_delta(myexp(6.6), expect_myexp(6.6)));
return 0;
}
static char* test_example()
{
mu_assert(in_delta(myexp(1.0), 2.71828));
mu_assert(in_delta(myexp(2.0), 7.38906));
mu_assert(in_delta(myexp(3.0), 20.08554));
mu_assert(in_delta(myexp(4.0), 54.59815));
mu_assert(in_delta(myexp(5.0), 148.41316));
mu_assert(in_delta(myexp(6.0), 403.42879));
mu_assert(in_delta(myexp(7.0), 1096.63316));
mu_assert(in_delta(myexp(8.0), 2980.95799));
mu_assert(in_delta(myexp(9.0), 8103.08393));
mu_assert(in_delta(myexp(10.0), 22026.46579));
return 0;
}
/////////////////////////////////////////////////////////////////////////////
// //
// //
// MATH //
// //
// //
/////////////////////////////////////////////////////////////////////////////
double log_add (double x, double y)
{
if (x==LOG_ZERO)return y;
else if (y==LOG_ZERO)return x;
else if (x>=y)return x+mylog(1+exp(y-x));
else return y+mylog (1+myexp(x-y));
}
void main(void)
{
double x;
printf(" x myexp(x) exp(x)\n");
for (x = 0; x <= 40; x = x + 10){
printf("%5.1f%14.6g%14.6g\n", x, myexp(x), exp(x));
}
}
int main ( int argc, char ** argv ) {
for ( long double i = -20; i <= 20; i += 5 ) {
double mexp = ( double ) myexp ( i );
long double check = ( long double ) exp ( i );
long double er = ( long double ) err ( mexp, check );
printf ( "%+0.9Le %0.9e %0.9Le %0.15Le\n", i, mexp, check, er );
}
return 1;
}
int display_model (Hmm *H)//for debug only
{
FILE *fp;
UNPACK_HMM(H);
int a, b;
for (a=0; a<ns; a++)
{
for (b=0; b<ns; b++)
{
fprintf (stdout, "ST::%d -- ST::%d --> %.5f\n", a, b, myexp(M[a][b]));
}
for (b=ns; b<(ns+ne); b++)
{
fprintf (stdout, "ST::%d -- EM::%d --> %.5f\n", a, b-ns, myexp(M[a][b]));
}
}
return 1;
}
int main()
{
float x = 1.0;
float y1 =0.0, y2 = 0.0;
for (int i = 1; i <= 30; x+=.5, i++)
{
y1 = myexp(x);
y2 = expl(x);
float rel_error = abs((y2 - y1) / y2);
printf("%+0.9Le %0.9e %0.9Le %0.15Le\n", x, y1, y2, rel_error);
}
return 0;
}
real do_lmfit(int ndata, real c1[], real sig[], real dt, real x0[],
real begintimefit, real endtimefit, const output_env_t oenv,
gmx_bool bVerbose, int eFitFn, real fitparms[], int fix)
{
FILE *fp;
char buf[32];
int i, j, nparm, nfitpnts;
real integral, ttt;
real *parm, *dparm;
real *x, *y, *dy;
real ftol = 1e-4;
nparm = nfp_ffn[eFitFn];
if (debug)
{
fprintf(debug, "There are %d points to fit %d vars!\n", ndata, nparm);
fprintf(debug, "Fit to function %d from %g through %g, dt=%g\n",
eFitFn, begintimefit, endtimefit, dt);
}
snew(x, ndata);
snew(y, ndata);
snew(dy, ndata);
j = 0;
for (i = 0; i < ndata; i++)
{
ttt = x0 ? x0[i] : dt*i;
if (ttt >= begintimefit && ttt <= endtimefit)
{
x[j] = ttt;
y[j] = c1[i];
/* mrqmin does not like sig to be zero */
if (sig[i] < 1.0e-7)
{
dy[j] = 1.0e-7;
}
else
{
dy[j] = sig[i];
}
if (debug)
{
fprintf(debug, "j= %d, i= %d, x= %g, y= %g, dy= %g\n",
j, i, x[j], y[j], dy[j]);
}
j++;
}
}
nfitpnts = j;
integral = 0;
if (nfitpnts < nparm)
{
fprintf(stderr, "Not enough data points for fitting!\n");
}
else
{
snew(parm, nparm);
snew(dparm, nparm);
if (fitparms)
{
for (i = 0; (i < nparm); i++)
{
parm[i] = fitparms[i];
}
}
if (!lmfit_exp(nfitpnts, x, y, dy, ftol, parm, dparm, bVerbose, eFitFn, fix))
{
fprintf(stderr, "Fit failed!\n");
}
else if (nparm <= 3)
{
/* Compute the integral from begintimefit */
if (nparm == 3)
{
integral = (parm[0]*myexp(begintimefit, parm[1], parm[0]) +
parm[2]*myexp(begintimefit, 1-parm[1], parm[2]));
}
else if (nparm == 2)
{
integral = parm[0]*myexp(begintimefit, parm[1], parm[0]);
}
else if (nparm == 1)
{
integral = parm[0]*myexp(begintimefit, 1, parm[0]);
}
else
{
gmx_fatal(FARGS, "nparm = %d in file %s, line %d",
nparm, __FILE__, __LINE__);
}
/* Generate THE output */
if (bVerbose)
{
fprintf(stderr, "FIT: # points used in fit is: %d\n", nfitpnts);
fprintf(stderr, "FIT: %21s%21s%21s\n",
"parm0 ", "parm1 (ps) ", "parm2 (ps) ");
fprintf(stderr, "FIT: ------------------------------------------------------------\n");
fprintf(stderr, "FIT: %8.3g +/- %8.3g%9.4g +/- %8.3g%8.3g +/- %8.3g\n",
parm[0], dparm[0], parm[1], dparm[1], parm[2], dparm[2]);
fprintf(stderr, "FIT: Integral (calc with fitted function) from %g ps to inf. is: %g\n",
begintimefit, integral);
sprintf(buf, "test%d.xvg", nfitpnts);
fp = xvgropen(buf, "C(t) + Fit to C(t)", "Time (ps)", "C(t)", oenv);
fprintf(fp, "# parm0 = %g, parm1 = %g, parm2 = %g\n",
parm[0], parm[1], parm[2]);
for (j = 0; (j < nfitpnts); j++)
{
ttt = x0 ? x0[j] : dt*j;
fprintf(fp, "%10.5e %10.5e %10.5e\n",
ttt, c1[j], fit_function(eFitFn, parm, ttt));
}
xvgrclose(fp);
}
}
if (fitparms)
{
for (i = 0; (i < nparm); i++)
{
fitparms[i] = parm[i];
}
}
sfree(parm);
sfree(dparm);
}
sfree(x);
sfree(y);
sfree(dy);
return integral;
}
real do_lmfit(int ndata, real c1[], real sig[], real dt, real *x0,
real begintimefit, real endtimefit, const gmx_output_env_t *oenv,
gmx_bool bVerbose, int eFitFn, double fitparms[], int fix,
const char *fn_fitted)
{
FILE *fp;
int i, j, nfitpnts;
double integral, ttt;
double *x, *y, *dy;
if (0 != fix)
{
fprintf(stderr, "Using fixed parameters in curve fitting is temporarily not working.\n");
}
if (debug)
{
fprintf(debug, "There are %d points to fit %d vars!\n", ndata, effnNparams(eFitFn));
fprintf(debug, "Fit to function %d from %g through %g, dt=%g\n",
eFitFn, begintimefit, endtimefit, dt);
}
snew(x, ndata);
snew(y, ndata);
snew(dy, ndata);
j = 0;
for (i = 0; i < ndata; i++)
{
ttt = x0 ? x0[i] : dt*i;
if (ttt >= begintimefit && ttt <= endtimefit)
{
x[j] = ttt;
y[j] = c1[i];
if (NULL == sig)
{
// No weighting if all values are divided by 1.
dy[j] = 1;
}
else
{
dy[j] = std::max(1.0e-7, (double)sig[i]);
}
if (debug)
{
fprintf(debug, "j= %d, i= %d, x= %g, y= %g, dy=%g, ttt=%g\n",
j, i, x[j], y[j], dy[j], ttt);
}
j++;
}
}
nfitpnts = j;
integral = 0;
if (nfitpnts < effnNparams(eFitFn))
{
fprintf(stderr, "Not enough (%d) data points for fitting, dt = %g!\n",
nfitpnts, dt);
}
else
{
gmx_bool bSuccess;
if (bVerbose)
{
print_chi2_params(stdout, eFitFn, fitparms, "initial", nfitpnts, x, y);
}
initiate_fit_params(eFitFn, fitparms);
bSuccess = lmfit_exp(nfitpnts, x, y, dy, fitparms, bVerbose, eFitFn, fix);
extract_fit_params(eFitFn, fitparms);
if (!bSuccess)
{
fprintf(stderr, "Fit failed!\n");
}
else
{
if (bVerbose)
{
print_chi2_params(stdout, eFitFn, fitparms, "final", nfitpnts, x, y);
}
switch (eFitFn)
{
case effnEXP1:
integral = fitparms[0]*myexp(begintimefit, 1, fitparms[0]);
break;
case effnEXP2:
integral = fitparms[0]*myexp(begintimefit, fitparms[1], fitparms[0]);
break;
case effnEXPEXP:
integral = (fitparms[0]*myexp(begintimefit, fitparms[1], fitparms[0]) +
fitparms[2]*myexp(begintimefit, 1-fitparms[1], fitparms[2]));
break;
case effnEXP5:
case effnEXP7:
case effnEXP9:
integral = 0;
for (i = 0; (i < (effnNparams(eFitFn)-1)/2); i++)
{
integral += fitparms[2*i]*myexp(begintimefit, fitparms[2*i+1], fitparms[2*i]);
}
break;
default:
/* Do numerical integration */
integral = 0;
for (i = 0; (i < nfitpnts-1); i++)
{
double y0 = lmcurves[eFitFn](x[i], fitparms);
double y1 = lmcurves[eFitFn](x[i+1], fitparms);
integral += (x[i+1]-x[i])*(y1+y0)*0.5;
}
break;
}
if (bVerbose)
{
printf("FIT: Integral of fitted function: %g\n", integral);
if ((effnEXP5 == eFitFn) || (effnEXP7 == eFitFn) || (effnEXP9 == eFitFn))
{
printf("FIT: Note that the constant term is not taken into account when computing integral.\n");
}
}
/* Generate debug output */
if (NULL != fn_fitted)
{
fp = xvgropen(fn_fitted, "Data + Fit", "Time (ps)",
"Data (t)", oenv);
for (i = 0; (i < effnNparams(eFitFn)); i++)
{
fprintf(fp, "# fitparms[%d] = %g\n", i, fitparms[i]);
}
for (j = 0; (j < nfitpnts); j++)
{
real ttt = x0 ? x0[j] : dt*j;
fprintf(fp, "%10.5e %10.5e %10.5e\n",
x[j], y[j], (lmcurves[eFitFn])(ttt, fitparms));
}
xvgrclose(fp);
}
}
}
sfree(x);
sfree(y);
sfree(dy);
return integral;
}
static void
do_curses(struct varnish_stats *VSL_stats, int delay, const char *fields)
{
struct varnish_stats copy;
struct varnish_stats seen;
intmax_t ju;
struct timeval tv;
double tt, lt, hit, miss, ratio, up;
double a1, a2, a3;
unsigned n1, n2, n3;
time_t rt;
int ch, line;
memset(©, 0, sizeof copy);
memset(&seen, 0, sizeof seen);
a1 = a2 = a3 = 0.0;
n1 = n2 = n3 = 0;
initscr();
raw();
noecho();
nonl();
intrflush(stdscr, FALSE);
curs_set(0);
erase();
lt = 0;
while (1) {
gettimeofday(&tv, NULL);
tt = tv.tv_usec * 1e-6 + tv.tv_sec;
lt = tt - lt;
rt = tv.tv_sec - VSL_stats->start_time;
up = rt;
mvprintw(0, 0, "%*s", COLS - 1, VSL_Name());
mvprintw(0, 0, "%d+%02d:%02d:%02d", rt / 86400,
(rt % 86400) / 3600, (rt % 3600) / 60, rt % 60);
hit = VSL_stats->cache_hit - copy.cache_hit;
miss = VSL_stats->cache_miss - copy.cache_miss;
hit /= lt;
miss /= lt;
if (hit + miss != 0) {
ratio = hit / (hit + miss);
myexp(&a1, ratio, &n1, 10);
myexp(&a2, ratio, &n2, 100);
myexp(&a3, ratio, &n3, 1000);
}
mvprintw(1, 0, "Hitrate ratio: %8u %8u %8u", n1, n2, n3);
mvprintw(2, 0, "Hitrate avg: %8.4f %8.4f %8.4f", a1, a2, a3);
line = 3;
#define MAC_STAT(n, t, l, f, d) \
if ((fields == NULL || show_field( #n, fields )) && line < LINES) { \
ju = VSL_stats->n; \
if (ju == 0 && !seen.n) { \
} else if (f == 'a') { \
seen.n = 1; \
line++; \
mvprintw(line, 0, "%12ju %12.2f %12.2f %s\n", \
ju, (ju - (intmax_t)copy.n)/lt, ju / up, d); \
copy.n = ju; \
} else { \
seen.n = 1; \
line++; \
mvprintw(line, 0, "%12ju %12s %12s %s\n", \
ju, ". ", ". ", d); \
} \
}
#include "stat_field.h"
#undef MAC_STAT
lt = tt;
refresh();
timeout(delay * 1000);
switch ((ch = getch())) {
case ERR:
break;
#ifdef KEY_RESIZE
case KEY_RESIZE:
erase();
break;
#endif
case '\014': /* Ctrl-L */
case '\024': /* Ctrl-T */
redrawwin(stdscr);
refresh();
break;
case '\003': /* Ctrl-C */
raise(SIGINT);
break;
case '\032': /* Ctrl-Z */
raise(SIGTSTP);
break;
case '\021': /* Ctrl-Q */
case 'Q':
case 'q':
endwin();
exit(0);
case '0':
case '1':
case '2':
case '3':
case '4':
case '5':
case '6':
case '7':
case '8':
case '9':
delay = 1 << (ch - '0');
break;
default:
beep();
break;
}
}
}
double baum_welch(Hmm*H)
{
int k,b, l, i;
int pseudocount=0;
UNPACK_HMM(H);
if (isnan(H->P=backward(H)))return LOG_ZERO;
if (isnan(H->P=forward (H)))return LOG_ZERO;
for(k=0; k<ns; k++)
for (l=0; l<(ns+ne); l++)
NM[k][l]=LOG_ZERO;
for (k=0; k<ns; k++)
{
int ll=0;
while ((l=PST[k][ll++])!=-1)
{
for (i=1; i<L; i++)
{
double fo, ba, tr, em;
int symbol=S[i+1];
if (M[l][symbol]==LOG_ZERO){continue;}
fo=F[i][k];
ba=B[i+1][l];
tr=M[k][l];
em=M[l][symbol];
NM[k][l]=log_add(NM[k][l], log_multiply4(fo,tr,em,ba));
}
NM[k][l]=log_divide (NM[k][l],H->P);
}
}
//update emissions
for (k=0; k<ns; k++)
{
for (b=ns; b<(ns+ne);b++)
{
for (i=1; i<=L; i++)
{
if (S[i]==b)
{
NM[k][b]=log_add(NM[k][b], log_multiply2(F[i][k],B[i][k]));
}
}
NM[k][b]=log_divide(NM[k][b],H->P);
}
}
//modelL2count+psudocounts
for (k=0; k<ns; k++)
for (l=0; l<(ns+ne); l++)
NM[k][l]=myexp(NM[k][l])+pseudocount;
//update transitions
for (k=0; k<ns; k++)
{
double t=0,f=0;
for (l=0; l<ns; l++)
{
if (CM[k][l]==LOG_ZERO)t+=NM[k][l];
else f+=CM[k][l];
}
t/=(f==1)?1:(1-f);
for (l=0; l<ns; l++)
{
if (CM[k][l]==LOG_ZERO)NM[k][l]/=(t<DELTA)?1:t;
else NM[k][l]=CM[k][l];
}
}
//update emissions
for (k=0; k<ns; k++)
{
double t=0,f=0;
for (l=ns; l<(ns+ne); l++)
{
if (CM[k][l]==LOG_ZERO)t+=NM[k][l];
else f+=CM[k][l];
}
t/=(f==1)?1:(1-f);
for (l=ns; l<(ns+ne); l++)
{
if (CM[k][l]==LOG_ZERO)NM[k][l]/=(t<DELTA)?1:t;
else NM[k][l]=CM[k][l];
}
}
//moldel2modelL
for (k=0; k<ns; k++)
{
for (l=0; l<(ns+ne); l++)
{
M[k][l]=mylog(NM[k][l]);
}
}
return H->P;
}
