void calc_variograms(
variogram_search_template_t * templ,
hard_data_t * data,
float * result_covariations,
int result_length,
int percentToUse)
{
int lag_count = templ->m_num_lags <= result_length
? templ->m_num_lags
: result_length;
lag_statistics_t * lag_stats = (lag_statistics_t *) calloc(lag_count, sizeof(lag_statistics_t));
for (int i = 0; i < lag_count; ++i)
{
lag_stats[i].m_cov_count = 0;
lag_stats[i].m_cov_sum = 0.0;
}
//lag_t * lags = (lag_t*) calloc(lag_count, sizeof(lag_t));
//init_lag_list(templ, lags, lag_count);
search_template_window_t window;
calc_search_template_window(templ, &window);
for (int i2 = window.m_min_i; i2 <= window.m_max_i; ++i2)
for (int j2 = window.m_min_j; j2 <= window.m_max_j; ++j2)
for (int k2 = window.m_min_k; k2 <= window.m_max_k; ++k2)
{
vector_t vec;
vec.m_data[0] = i2;
vec.m_data[1] = j2;
vec.m_data[2] = k2;
int doffset = get_offset(&vec, data->m_data_strides);
int moffset = get_offset(&vec, data->m_mask_strides);
if (is_in_tunnel(templ, &vec))
{
int x1, y1, z1;
float * dpx, * dpy, * dpz;
unsigned char * mpx, * mpy, *mpz;
for (z1 = 0, dpz = data->m_data, mpz = data->m_mask;
z1 < data->m_data_shape[2];
++z1, dpz += data->m_data_strides[2], mpz += data->m_mask_strides[2])
for (y1 = 0, dpy = dpz, mpy = mpz;
y1 < data->m_data_shape[1];
++y1, dpy += data->m_data_strides[1], mpy += data->m_mask_strides[1])
for (x1 = 0, dpx = dpy, mpx = mpy;
x1 < data->m_data_shape[0];
++x1, dpx += data->m_data_strides[0], mpx += data->m_mask_strides[0])
{
if (*mpx != 0)
//if (is_informed_nocheck(data, x1, y1, z1))
//if (is_informed(data, x1, y1, z1))
{
double v1 = *dpx;
//double v1 = get_value(data, x1, y1, z1);
int x = x1 + vec.m_data[0];
int y = y1 + vec.m_data[1];
int z = z1 + vec.m_data[2];
if (is_inside(data, x,y,z) && mpx[moffset])
//if (is_informed(data, x,y,z))
{
if ((rand() % 100) >= percentToUse)
continue;
double dist = calc_dist(&vec);
double v2 = dpx[doffset];
//double v2 = get_value(data, x, y, z);
double var = v1 - v2;
var = var*var;
update_lags(templ, lag_stats, lag_count, dist, var);
}
}
}
}
}
for (int i = 0; i < lag_count; ++i)
{
result_covariations[i] = lag_stats[i].m_cov_sum / lag_stats[i].m_cov_count / 2;
}
free(lag_stats);
//free(lags);
}
int gmx_rmsdist(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes the root mean square deviation of atom distances,",
"which has the advantage that no fit is needed like in standard RMS",
"deviation as computed by [gmx-rms].",
"The reference structure is taken from the structure file.",
"The RMSD at time t is calculated as the RMS",
"of the differences in distance between atom-pairs in the reference",
"structure and the structure at time t.[PAR]",
"[THISMODULE] can also produce matrices of the rms distances, rms distances",
"scaled with the mean distance and the mean distances and matrices with",
"NMR averaged distances (1/r^3 and 1/r^6 averaging). Finally, lists",
"of atom pairs with 1/r^3 and 1/r^6 averaged distance below the",
"maximum distance ([TT]-max[tt], which will default to 0.6 in this case)",
"can be generated, by default averaging over equivalent hydrogens",
"(all triplets of hydrogens named \\*[123]). Additionally a list of",
"equivalent atoms can be supplied ([TT]-equiv[tt]), each line containing",
"a set of equivalent atoms specified as residue number and name and",
"atom name; e.g.:[PAR]",
"[TT]HB* 3 SER HB1 3 SER HB2[tt][PAR]",
"Residue and atom names must exactly match those in the structure",
"file, including case. Specifying non-sequential atoms is undefined."
};
int i, teller;
real t;
t_topology top;
int ePBC;
t_atoms *atoms;
matrix box;
rvec *x;
FILE *fp;
t_trxstatus *status;
int isize, gnr = 0;
atom_id *index, *noe_index;
char *grpname;
real **d_r, **d, **dtot, **dtot2, **mean, **rms, **rmsc, *resnr;
real **dtot1_3 = NULL, **dtot1_6 = NULL;
real rmsnow, meanmax, rmsmax, rmscmax;
real max1_3, max1_6;
t_noe_gr *noe_gr = NULL;
t_noe **noe = NULL;
t_rgb rlo, rhi;
gmx_bool bRMS, bScale, bMean, bNOE, bNMR3, bNMR6, bNMR;
static int nlevels = 40;
static real scalemax = -1.0;
static gmx_bool bSumH = TRUE;
static gmx_bool bPBC = TRUE;
output_env_t oenv;
t_pargs pa[] = {
{ "-nlevels", FALSE, etINT, {&nlevels},
"Discretize RMS in this number of levels" },
{ "-max", FALSE, etREAL, {&scalemax},
"Maximum level in matrices" },
{ "-sumh", FALSE, etBOOL, {&bSumH},
"Average distance over equivalent hydrogens" },
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Use periodic boundary conditions when computing distances" }
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efDAT, "-equiv", "equiv", ffOPTRD },
{ efXVG, NULL, "distrmsd", ffWRITE },
{ efXPM, "-rms", "rmsdist", ffOPTWR },
{ efXPM, "-scl", "rmsscale", ffOPTWR },
{ efXPM, "-mean", "rmsmean", ffOPTWR },
{ efXPM, "-nmr3", "nmr3", ffOPTWR },
{ efXPM, "-nmr6", "nmr6", ffOPTWR },
{ efDAT, "-noe", "noe", ffOPTWR },
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
bRMS = opt2bSet("-rms", NFILE, fnm);
bScale = opt2bSet("-scl", NFILE, fnm);
bMean = opt2bSet("-mean", NFILE, fnm);
bNOE = opt2bSet("-noe", NFILE, fnm);
bNMR3 = opt2bSet("-nmr3", NFILE, fnm);
bNMR6 = opt2bSet("-nmr6", NFILE, fnm);
bNMR = bNMR3 || bNMR6 || bNOE;
max1_3 = 0;
max1_6 = 0;
/* check input */
if (bNOE && scalemax < 0)
{
scalemax = 0.6;
fprintf(stderr, "WARNING: using -noe without -max "
"makes no sense, setting -max to %g\n\n", scalemax);
}
/* get topology and index */
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, NULL, box, FALSE);
if (!bPBC)
{
ePBC = epbcNONE;
}
atoms = &(top.atoms);
get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
/* initialize arrays */
snew(d, isize);
snew(dtot, isize);
snew(dtot2, isize);
if (bNMR)
{
snew(dtot1_3, isize);
snew(dtot1_6, isize);
}
snew(mean, isize);
snew(rms, isize);
snew(rmsc, isize);
snew(d_r, isize);
snew(resnr, isize);
for (i = 0; (i < isize); i++)
{
snew(d[i], isize);
snew(dtot[i], isize);
snew(dtot2[i], isize);
if (bNMR)
{
snew(dtot1_3[i], isize);
snew(dtot1_6[i], isize);
}
snew(mean[i], isize);
snew(rms[i], isize);
snew(rmsc[i], isize);
snew(d_r[i], isize);
resnr[i] = i+1;
}
/*set box type*/
calc_dist(isize, index, x, ePBC, box, d_r);
sfree(x);
/*open output files*/
fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "RMS Deviation", "Time (ps)", "RMSD (nm)",
oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"of distances between %s atoms\"\n", grpname);
}
/*do a first step*/
read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
teller = 0;
do
{
calc_dist_tot(isize, index, x, ePBC, box, d, dtot, dtot2, bNMR, dtot1_3, dtot1_6);
rmsnow = rms_diff(isize, d, d_r);
fprintf(fp, "%g %g\n", t, rmsnow);
teller++;
}
while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
xvgrclose(fp);
close_trj(status);
calc_rms(isize, teller, dtot, dtot2, rms, &rmsmax, rmsc, &rmscmax, mean, &meanmax);
fprintf(stderr, "rmsmax = %g, rmscmax = %g\n", rmsmax, rmscmax);
if (bNMR)
{
calc_nmr(isize, teller, dtot1_3, dtot1_6, &max1_3, &max1_6);
}
if (scalemax > -1.0)
{
rmsmax = scalemax;
rmscmax = scalemax;
meanmax = scalemax;
max1_3 = scalemax;
max1_6 = scalemax;
}
if (bNOE)
{
/* make list of noe atom groups */
snew(noe_index, isize+1);
snew(noe_gr, isize);
gnr = analyze_noe_equivalent(opt2fn_null("-equiv", NFILE, fnm),
atoms, isize, index, bSumH, noe_index, noe_gr);
fprintf(stdout, "Found %d non-equivalent atom-groups in %d atoms\n",
gnr, isize);
/* make half matrix of of noe-group distances from atom distances */
snew(noe, gnr);
for (i = 0; i < gnr; i++)
{
snew(noe[i], gnr);
}
calc_noe(isize, noe_index, dtot1_3, dtot1_6, gnr, noe);
}
rlo.r = 1.0, rlo.g = 1.0, rlo.b = 1.0;
rhi.r = 0.0, rhi.g = 0.0, rhi.b = 0.0;
if (bRMS)
{
write_xpm(opt2FILE("-rms", NFILE, fnm, "w"), 0,
"RMS of distance", "RMS (nm)", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, rms, 0.0, rmsmax, rlo, rhi, &nlevels);
}
if (bScale)
{
write_xpm(opt2FILE("-scl", NFILE, fnm, "w"), 0,
"Relative RMS", "RMS", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, rmsc, 0.0, rmscmax, rlo, rhi, &nlevels);
}
if (bMean)
{
write_xpm(opt2FILE("-mean", NFILE, fnm, "w"), 0,
"Mean Distance", "Distance (nm)", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, mean, 0.0, meanmax, rlo, rhi, &nlevels);
}
if (bNMR3)
{
write_xpm(opt2FILE("-nmr3", NFILE, fnm, "w"), 0, "1/r^3 averaged distances",
"Distance (nm)", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, dtot1_3, 0.0, max1_3, rlo, rhi, &nlevels);
}
if (bNMR6)
{
write_xpm(opt2FILE("-nmr6", NFILE, fnm, "w"), 0, "1/r^6 averaged distances",
"Distance (nm)", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, dtot1_6, 0.0, max1_6, rlo, rhi, &nlevels);
}
if (bNOE)
{
write_noe(opt2FILE("-noe", NFILE, fnm, "w"), gnr, noe, noe_gr, scalemax);
}
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);
return 0;
}
void dist_plot(const char *fn, const char *afile, const char *dfile,
const char *nfile, const char *rfile, const char *xfile,
real rcut, gmx_bool bMat, t_atoms *atoms,
int ng, atom_id *index[], int gnx[], char *grpn[], gmx_bool bSplit,
gmx_bool bMin, int nres, atom_id *residue, gmx_bool bPBC, int ePBC,
gmx_bool bGroup, gmx_bool bEachResEachTime, gmx_bool bPrintResName,
const output_env_t oenv)
{
FILE *atm, *dist, *num;
t_trxstatus *trxout;
char buf[256];
char **leg;
real t, dmin, dmax, **mindres = NULL, **maxdres = NULL;
int nmin, nmax;
t_trxstatus *status;
int i = -1, j, k, natoms;
int min1, min2, max1, max2, min1r, min2r, max1r, max2r;
atom_id oindex[2];
rvec *x0;
matrix box;
t_trxframe frout;
gmx_bool bFirst;
FILE *respertime = NULL;
if ((natoms = read_first_x(oenv, &status, fn, &t, &x0, box)) == 0)
{
gmx_fatal(FARGS, "Could not read coordinates from statusfile\n");
}
sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
dist = xvgropen(dfile, buf, output_env_get_time_label(oenv), "Distance (nm)", oenv);
sprintf(buf, "Number of Contacts %s %g nm", bMin ? "<" : ">", rcut);
num = nfile ? xvgropen(nfile, buf, output_env_get_time_label(oenv), "Number", oenv) : NULL;
atm = afile ? ffopen(afile, "w") : NULL;
trxout = xfile ? open_trx(xfile, "w") : NULL;
if (bMat)
{
if (ng == 1)
{
snew(leg, 1);
sprintf(buf, "Internal in %s", grpn[0]);
leg[0] = strdup(buf);
xvgr_legend(dist, 0, (const char**)leg, oenv);
if (num)
{
xvgr_legend(num, 0, (const char**)leg, oenv);
}
}
else
{
snew(leg, (ng*(ng-1))/2);
for (i = j = 0; (i < ng-1); i++)
{
for (k = i+1; (k < ng); k++, j++)
{
sprintf(buf, "%s-%s", grpn[i], grpn[k]);
leg[j] = strdup(buf);
}
}
xvgr_legend(dist, j, (const char**)leg, oenv);
if (num)
{
xvgr_legend(num, j, (const char**)leg, oenv);
}
}
}
else
{
snew(leg, ng-1);
for (i = 0; (i < ng-1); i++)
{
sprintf(buf, "%s-%s", grpn[0], grpn[i+1]);
leg[i] = strdup(buf);
}
xvgr_legend(dist, ng-1, (const char**)leg, oenv);
if (num)
{
xvgr_legend(num, ng-1, (const char**)leg, oenv);
}
}
if (bEachResEachTime)
{
sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
respertime = xvgropen(rfile, buf, output_env_get_time_label(oenv), "Distance (nm)", oenv);
xvgr_legend(respertime, ng-1, (const char**)leg, oenv);
if (bPrintResName)
{
fprintf(respertime, "# ");
}
for (j = 0; j < nres; j++)
{
fprintf(respertime, "%s%d ", *(atoms->resinfo[atoms->atom[index[0][residue[j]]].resind].name), atoms->atom[index[0][residue[j]]].resind);
}
fprintf(respertime, "\n");
}
j = 0;
if (nres)
{
snew(mindres, ng-1);
snew(maxdres, ng-1);
for (i = 1; i < ng; i++)
{
snew(mindres[i-1], nres);
snew(maxdres[i-1], nres);
for (j = 0; j < nres; j++)
{
mindres[i-1][j] = 1e6;
}
/* maxdres[*][*] is already 0 */
}
}
bFirst = TRUE;
do
{
if (bSplit && !bFirst && abs(t/output_env_get_time_factor(oenv)) < 1e-5)
{
fprintf(dist, "&\n");
if (num)
{
fprintf(num, "&\n");
}
if (atm)
{
fprintf(atm, "&\n");
}
}
fprintf(dist, "%12e", output_env_conv_time(oenv, t));
if (num)
{
fprintf(num, "%12e", output_env_conv_time(oenv, t));
}
if (bMat)
{
if (ng == 1)
{
calc_dist(rcut, bPBC, ePBC, box, x0, gnx[0], gnx[0], index[0], index[0], bGroup,
&dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
fprintf(dist, " %12e", bMin ? dmin : dmax);
if (num)
{
fprintf(num, " %8d", bMin ? nmin : nmax);
}
}
else
{
for (i = 0; (i < ng-1); i++)
{
for (k = i+1; (k < ng); k++)
{
calc_dist(rcut, bPBC, ePBC, box, x0, gnx[i], gnx[k], index[i], index[k],
bGroup, &dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
fprintf(dist, " %12e", bMin ? dmin : dmax);
if (num)
{
fprintf(num, " %8d", bMin ? nmin : nmax);
}
}
}
}
}
else
{
for (i = 1; (i < ng); i++)
{
calc_dist(rcut, bPBC, ePBC, box, x0, gnx[0], gnx[i], index[0], index[i], bGroup,
&dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
fprintf(dist, " %12e", bMin ? dmin : dmax);
if (num)
{
fprintf(num, " %8d", bMin ? nmin : nmax);
}
if (nres)
{
for (j = 0; j < nres; j++)
{
calc_dist(rcut, bPBC, ePBC, box, x0, residue[j+1]-residue[j], gnx[i],
&(index[0][residue[j]]), index[i], bGroup,
&dmin, &dmax, &nmin, &nmax, &min1r, &min2r, &max1r, &max2r);
mindres[i-1][j] = min(mindres[i-1][j], dmin);
maxdres[i-1][j] = max(maxdres[i-1][j], dmax);
}
}
}
}
fprintf(dist, "\n");
if (num)
{
fprintf(num, "\n");
}
if ( (bMin ? min1 : max1) != -1)
{
if (atm)
{
fprintf(atm, "%12e %12d %12d\n",
output_env_conv_time(oenv, t), 1+(bMin ? min1 : max1),
1+(bMin ? min2 : max2));
}
}
if (trxout)
{
oindex[0] = bMin ? min1 : max1;
oindex[1] = bMin ? min2 : max2;
write_trx(trxout, 2, oindex, atoms, i, t, box, x0, NULL, NULL);
}
bFirst = FALSE;
/*dmin should be minimum distance for residue and group*/
if (bEachResEachTime)
{
fprintf(respertime, "%12e", t);
for (i = 1; i < ng; i++)
{
for (j = 0; j < nres; j++)
{
fprintf(respertime, " %7g", bMin ? mindres[i-1][j] : maxdres[i-1][j]);
/*reset distances for next time point*/
mindres[i-1][j] = 1e6;
maxdres[i-1][j] = 0;
}
}
fprintf(respertime, "\n");
}
}
while (read_next_x(oenv, status, &t, x0, box));
close_trj(status);
ffclose(dist);
if (num)
{
ffclose(num);
}
if (atm)
{
ffclose(atm);
}
if (trxout)
{
close_trx(trxout);
}
if (nres && !bEachResEachTime)
{
FILE *res;
sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
res = xvgropen(rfile, buf, "Residue (#)", "Distance (nm)", oenv);
xvgr_legend(res, ng-1, (const char**)leg, oenv);
for (j = 0; j < nres; j++)
{
fprintf(res, "%4d", j+1);
for (i = 1; i < ng; i++)
{
fprintf(res, " %7g", bMin ? mindres[i-1][j] : maxdres[i-1][j]);
}
fprintf(res, "\n");
}
}
sfree(x0);
}
void
pml_hybrid(
const float *data, int dy, int dt, int dx,
const float *center, const float *theta,
float *recon, int ngridx, int ngridy, int num_iter,
const float *reg_pars)
{
float *gridx = (float *)malloc((ngridx+1)*sizeof(float));
float *gridy = (float *)malloc((ngridy+1)*sizeof(float));
float *coordx = (float *)malloc((ngridy+1)*sizeof(float));
float *coordy = (float *)malloc((ngridx+1)*sizeof(float));
float *ax = (float *)malloc((ngridx+ngridy)*sizeof(float));
float *ay = (float *)malloc((ngridx+ngridy)*sizeof(float));
float *bx = (float *)malloc((ngridx+ngridy)*sizeof(float));
float *by = (float *)malloc((ngridx+ngridy)*sizeof(float));
float *coorx = (float *)malloc((ngridx+ngridy)*sizeof(float));
float *coory = (float *)malloc((ngridx+ngridy)*sizeof(float));
float *dist = (float *)malloc((ngridx+ngridy)*sizeof(float));
int *indi = (int *)malloc((ngridx+ngridy)*sizeof(int));
assert(coordx != NULL && coordy != NULL &&
ax != NULL && ay != NULL && by != NULL && bx != NULL &&
coorx != NULL && coory != NULL && dist != NULL && indi != NULL);
int s, p, d, i, m, n, q;
int quadrant;
float theta_p, sin_p, cos_p;
float mov, xi, yi;
int asize, bsize, csize;
float *simdata;
float upd;
int ind_data, ind_recon;
float *sum_dist;
float sum_dist2;
float *E, *F, *G;
int ind0, ind1, indg[8];
float totalwg, wg[8], mg[8], rg[8], gammag[8];
for (i=0; i<num_iter; i++)
{
simdata = (float *)calloc((dt*dy*dx), sizeof(float));
// For each slice
for (s=0; s<dy; s++)
{
preprocessing(ngridx, ngridy, dx, center[s],
&mov, gridx, gridy); // Outputs: mov, gridx, gridy
sum_dist = (float *)calloc((ngridx*ngridy), sizeof(float));
E = (float *)calloc((ngridx*ngridy), sizeof(float));
F = (float *)calloc((ngridx*ngridy), sizeof(float));
G = (float *)calloc((ngridx*ngridy), sizeof(float));
// For each projection angle
for (p=0; p<dt; p++)
{
// Calculate the sin and cos values
// of the projection angle and find
// at which quadrant on the cartesian grid.
theta_p = fmod(theta[p], 2*M_PI);
quadrant = calc_quadrant(theta_p);
sin_p = sinf(theta_p);
cos_p = cosf(theta_p);
// For each detector pixel
for (d=0; d<dx; d++)
{
// Calculate coordinates
xi = -ngridx-ngridy;
yi = (1-dx)/2.0+d+mov;
calc_coords(
ngridx, ngridy, xi, yi, sin_p, cos_p, gridx, gridy,
coordx, coordy);
// Merge the (coordx, gridy) and (gridx, coordy)
trim_coords(
ngridx, ngridy, coordx, coordy, gridx, gridy,
&asize, ax, ay, &bsize, bx, by);
// Sort the array of intersection points (ax, ay) and
// (bx, by). The new sorted intersection points are
// stored in (coorx, coory). Total number of points
// are csize.
sort_intersections(
quadrant, asize, ax, ay, bsize, bx, by,
&csize, coorx, coory);
// Calculate the distances (dist) between the
// intersection points (coorx, coory). Find the
// indices of the pixels on the reconstruction grid.
calc_dist(
ngridx, ngridy, csize, coorx, coory,
indi, dist);
// Calculate simdata
calc_simdata(s, p, d, ngridx, ngridy, dt, dx,
csize, indi, dist, recon,
simdata); // Output: simdata
// Calculate dist*dist
sum_dist2 = 0.0;
for (n=0; n<csize-1; n++)
{
sum_dist2 += dist[n]*dist[n];
sum_dist[indi[n]] += dist[n];
}
// Update
if (sum_dist2 != 0.0)
{
ind_data = d+p*dx+s*dt*dx;
ind_recon = s*ngridx*ngridy;
upd = data[ind_data]/simdata[ind_data];
for (n=0; n<csize-1; n++)
{
E[indi[n]] -= recon[indi[n]+ind_recon]*upd*dist[n];
}
}
}
}
// Weights for inner neighborhoods.
totalwg = 4+4/sqrt(2);
wg[0] = 1/totalwg;
wg[1] = 1/totalwg;
wg[2] = 1/totalwg;
wg[3] = 1/totalwg;
wg[4] = 1/sqrt(2)/totalwg;
wg[5] = 1/sqrt(2)/totalwg;
wg[6] = 1/sqrt(2)/totalwg;
wg[7] = 1/sqrt(2)/totalwg;
// (inner region)
for (n = 1; n < ngridx-1; n++) {
for (m = 1; m < ngridy-1; m++) {
ind0 = m + n*ngridy;
ind1 = ind0 + s*ngridx*ngridy;
indg[0] = ind1+1;
indg[1] = ind1-1;
indg[2] = ind1+ngridy;
indg[3] = ind1-ngridy;
indg[4] = ind1+ngridy+1;
indg[5] = ind1+ngridy-1;
indg[6] = ind1-ngridy+1;
indg[7] = ind1-ngridy-1;
for (q = 0; q < 8; q++) {
mg[q] = recon[ind1]+recon[indg[q]];
rg[q] = recon[ind1]-recon[indg[q]];
gammag[q] = 1/(1+fabs(rg[q]/reg_pars[1]));
F[ind0] += 2*reg_pars[0]*wg[q]*gammag[q];
G[ind0] -= 2*reg_pars[0]*wg[q]*gammag[q]*mg[q];
}
}
}
// Weights for edges.
totalwg = 3+2/sqrt(2);
wg[0] = 1/totalwg;
wg[1] = 1/totalwg;
wg[2] = 1/totalwg;
wg[3] = 1/sqrt(2)/totalwg;
wg[4] = 1/sqrt(2)/totalwg;
// (top)
for (m = 1; m < ngridy-1; m++) {
ind0 = m;
ind1 = ind0 + s*ngridx*ngridy;
indg[0] = ind1+1;
indg[1] = ind1-1;
indg[2] = ind1+ngridy;
indg[3] = ind1+ngridy+1;
indg[4] = ind1+ngridy-1;
for (q = 0; q < 5; q++) {
mg[q] = recon[ind1]+recon[indg[q]];
rg[q] = recon[ind1]-recon[indg[q]];
gammag[q] = 1/(1+fabs(rg[q]/reg_pars[1]));
F[ind0] += 2*reg_pars[0]*wg[q]*gammag[q];
G[ind0] -= 2*reg_pars[0]*wg[q]*gammag[q]*mg[q];
}
}
// (bottom)
for (m = 1; m < ngridy-1; m++) {
ind0 = m + (ngridx-1)*ngridy;
ind1 = ind0 + s*ngridx*ngridy;
indg[0] = ind1+1;
indg[1] = ind1-1;
indg[2] = ind1-ngridy;
indg[3] = ind1-ngridy+1;
indg[4] = ind1-ngridy-1;
for (q = 0; q < 5; q++) {
mg[q] = recon[ind1]+recon[indg[q]];
rg[q] = recon[ind1]-recon[indg[q]];
gammag[q] = 1/(1+fabs(rg[q]/reg_pars[1]));
F[ind0] += 2*reg_pars[0]*wg[q]*gammag[q];
G[ind0] -= 2*reg_pars[0]*wg[q]*gammag[q]*mg[q];
}
}
// (left)
for (n = 1; n < ngridx-1; n++) {
ind0 = n*ngridy;
ind1 = ind0 + s*ngridx*ngridy;
indg[0] = ind1+1;
indg[1] = ind1+ngridy;
indg[2] = ind1-ngridy;
indg[3] = ind1+ngridy+1;
indg[4] = ind1-ngridy+1;
for (q = 0; q < 5; q++) {
mg[q] = recon[ind1]+recon[indg[q]];
rg[q] = recon[ind1]-recon[indg[q]];
gammag[q] = 1/(1+fabs(rg[q]/reg_pars[1]));
F[ind0] += 2*reg_pars[0]*wg[q]*gammag[q];
G[ind0] -= 2*reg_pars[0]*wg[q]*gammag[q]*mg[q];
}
}
// (right)
for (n = 1; n < ngridx-1; n++) {
ind0 = (ngridy-1) + n*ngridy;
ind1 = ind0 + s*ngridx*ngridy;
indg[0] = ind1-1;
indg[1] = ind1+ngridy;
indg[2] = ind1-ngridy;
indg[3] = ind1+ngridy-1;
indg[4] = ind1-ngridy-1;
for (q = 0; q < 5; q++) {
mg[q] = recon[ind1]+recon[indg[q]];
rg[q] = recon[ind1]-recon[indg[q]];
gammag[q] = 1/(1+fabs(rg[q]/reg_pars[1]));
F[ind0] += 2*reg_pars[0]*wg[q]*gammag[q];
G[ind0] -= 2*reg_pars[0]*wg[q]*gammag[q]*mg[q];
}
}
// Weights for corners.
totalwg = 2+1/sqrt(2);
wg[0] = 1/totalwg;
wg[1] = 1/totalwg;
wg[2] = 1/sqrt(2)/totalwg;
// (top-left)
ind0 = 0;
ind1 = ind0 + s*ngridx*ngridy;
indg[0] = ind1+1;
indg[1] = ind1+ngridy;
indg[2] = ind1+ngridy+1;
for (q = 0; q < 3; q++) {
mg[q] = recon[ind1]+recon[indg[q]];
rg[q] = recon[ind1]-recon[indg[q]];
gammag[q] = 1/(1+fabs(rg[q]/reg_pars[1]));
F[ind0] += 2*reg_pars[0]*wg[q]*gammag[q];
G[ind0] -= 2*reg_pars[0]*wg[q]*gammag[q]*mg[q];
}
// (top-right)
ind0 = (ngridy-1);
ind1 = ind0 + s*ngridx*ngridy;
indg[0] = ind1-1;
indg[1] = ind1+ngridy;
indg[2] = ind1+ngridy-1;
for (q = 0; q < 3; q++) {
mg[q] = recon[ind1]+recon[indg[q]];
rg[q] = recon[ind1]-recon[indg[q]];
gammag[q] = 1/(1+fabs(rg[q]/reg_pars[1]));
F[ind0] += 2*reg_pars[0]*wg[q]*gammag[q];
G[ind0] -= 2*reg_pars[0]*wg[q]*gammag[q]*mg[q];
}
// (bottom-left)
ind0 = (ngridx-1)*ngridy;
ind1 = ind0 + s*ngridx*ngridy;
indg[0] = ind1+1;
indg[1] = ind1-ngridy;
indg[2] = ind1-ngridy+1;
for (q = 0; q < 3; q++) {
mg[q] = recon[ind1]+recon[indg[q]];
rg[q] = recon[ind1]-recon[indg[q]];
gammag[q] = 1/(1+fabs(rg[q]/reg_pars[1]));
F[ind0] += 2*reg_pars[0]*wg[q]*gammag[q];
G[ind0] -= 2*reg_pars[0]*wg[q]*gammag[q]*mg[q];
}
// (bottom-right)
ind0 = (ngridy-1) + (ngridx-1)*ngridy;
ind1 = ind0 + s*ngridx*ngridy;
indg[0] = ind1-1;
indg[1] = ind1-ngridy;
indg[2] = ind1-ngridy-1;
for (q = 0; q < 3; q++) {
mg[q] = recon[ind1]+recon[indg[q]];
rg[q] = recon[ind1]-recon[indg[q]];
gammag[q] = 1/(1+fabs(rg[q]/reg_pars[1]));
F[ind0] += 2*reg_pars[0]*wg[q]*gammag[q];
G[ind0] -= 2*reg_pars[0]*wg[q]*gammag[q]*mg[q];
}
q = 0;
for (n = 0; n < ngridx*ngridy; n++) {
G[q] += sum_dist[n];
q++;
}
for (n = 0; n < ngridx; n++) {
for (m = 0; m < ngridy; m++) {
q = m + n*ngridy;
if (F[q] != 0.0) {
ind0 = q + s*ngridx*ngridy;
recon[ind0] = (-G[q]+sqrt(G[q]*G[q]-8*E[q]*F[q]))/(4*F[q]);
}
}
}
free(sum_dist);
free(E);
free(F);
free(G);
}
free(simdata);
}
free(gridx);
free(gridy);
free(coordx);
free(coordy);
free(ax);
free(ay);
free(bx);
free(by);
free(coorx);
free(coory);
free(dist);
free(indi);
}
void
art(const float* data, int dy, int dt, int dx, const float* center,
const float* theta, float* recon, int ngridx, int ngridy, int num_iter)
{
float* gridx = (float*) malloc((ngridx + 1) * sizeof(float));
float* gridy = (float*) malloc((ngridy + 1) * sizeof(float));
float* coordx = (float*) malloc((ngridy + 1) * sizeof(float));
float* coordy = (float*) malloc((ngridx + 1) * sizeof(float));
float* ax = (float*) malloc((ngridx + ngridy) * sizeof(float));
float* ay = (float*) malloc((ngridx + ngridy) * sizeof(float));
float* bx = (float*) malloc((ngridx + ngridy) * sizeof(float));
float* by = (float*) malloc((ngridx + ngridy) * sizeof(float));
float* coorx = (float*) malloc((ngridx + ngridy) * sizeof(float));
float* coory = (float*) malloc((ngridx + ngridy) * sizeof(float));
float* dist = (float*) malloc((ngridx + ngridy) * sizeof(float));
int* indi = (int*) malloc((ngridx + ngridy) * sizeof(int));
float* simdata = (float*) malloc((dy * dt * dx) * sizeof(float));
assert(coordx != NULL && coordy != NULL && ax != NULL && ay != NULL &&
by != NULL && bx != NULL && coorx != NULL && coory != NULL &&
dist != NULL && indi != NULL && simdata != NULL);
int s, p, d, i, n;
int quadrant;
float theta_p, sin_p, cos_p;
float mov, xi, yi;
int asize, bsize, csize;
float upd;
int ind_data, ind_recon;
for(i = 0; i < num_iter; i++)
{
// initialize simdata to zero
memset(simdata, 0, dy * dt * dx * sizeof(float));
preprocessing(ngridx, ngridy, dx, center[0], &mov, gridx,
gridy); // Outputs: mov, gridx, gridy
// For each projection angle
for(p = 0; p < dt; p++)
{
// Calculate the sin and cos values
// of the projection angle and find
// at which quadrant on the cartesian grid.
theta_p = fmodf(theta[p], 2.0f * (float) M_PI);
quadrant = calc_quadrant(theta_p);
sin_p = sinf(theta_p);
cos_p = cosf(theta_p);
// For each detector pixel
for(d = 0; d < dx; d++)
{
// Calculate coordinates
xi = -ngridx - ngridy;
yi = 0.5f * (1 - dx) + d + mov;
calc_coords(ngridx, ngridy, xi, yi, sin_p, cos_p, gridx, gridy,
coordx, coordy);
// Merge the (coordx, gridy) and (gridx, coordy)
trim_coords(ngridx, ngridy, coordx, coordy, gridx, gridy,
&asize, ax, ay, &bsize, bx, by);
// Sort the array of intersection points (ax, ay) and
// (bx, by). The new sorted intersection points are
// stored in (coorx, coory). Total number of points
// are csize.
sort_intersections(quadrant, asize, ax, ay, bsize, bx, by,
&csize, coorx, coory);
// Calculate the distances (dist) between the
// intersection points (coorx, coory). Find the
// indices of the pixels on the reconstruction grid.
calc_dist(ngridx, ngridy, csize, coorx, coory, indi, dist);
// Calculate dist*dist
float sum_dist2 = 0.0f;
for(n = 0; n < csize - 1; n++)
{
sum_dist2 += dist[n] * dist[n];
}
if(sum_dist2 != 0.0f)
{
// For each slice
for(s = 0; s < dy; s++)
{
// Calculate simdata
calc_simdata(s, p, d, ngridx, ngridy, dt, dx, csize,
indi, dist, recon,
simdata); // Output: simdata
// Update
ind_data = d + p * dx + s * dt * dx;
ind_recon = s * ngridx * ngridy;
upd = (data[ind_data] - simdata[ind_data]) / sum_dist2;
for(n = 0; n < csize - 1; n++)
{
recon[indi[n] + ind_recon] += upd * dist[n];
}
}
}
}
}
}
free(gridx);
free(gridy);
free(coordx);
free(coordy);
free(ax);
free(ay);
free(bx);
free(by);
free(coorx);
free(coory);
free(dist);
free(indi);
free(simdata);
}
void do_coupling(FILE *log,const output_env_t oenv,int nfile,
const t_filenm fnm[], t_coupl_rec *tcr,real t,
int step,real ener[], t_forcerec *fr,t_inputrec *ir,
gmx_bool bMaster, t_mdatoms *md,t_idef *idef,real mu_aver,int nmols,
t_commrec *cr,matrix box,tensor virial,
tensor pres,rvec mu_tot,
rvec x[],rvec f[],gmx_bool bDoIt)
{
#define enm2Debye 48.0321
#define d2e(x) (x)/enm2Debye
#define enm2kjmol(x) (x)*0.0143952 /* = 2.0*4.0*M_PI*EPSILON0 */
static real *f6,*f12,*fa,*fb,*fc,*fq;
static gmx_bool bFirst = TRUE;
int i,j,ati,atj,atnr2,type,ftype;
real deviation[eoObsNR],prdev[eoObsNR],epot0,dist,rmsf;
real ff6,ff12,ffa,ffb,ffc,ffq,factor,dt,mu_ind;
real Epol,Eintern,Virial,muabs,xiH=-1,xiS=-1,xi6,xi12;
rvec fmol[2];
gmx_bool bTest,bPrint;
t_coupl_LJ *tclj;
t_coupl_BU *tcbu;
t_coupl_Q *tcq;
t_coupl_iparams *tip;
atnr2 = idef->atnr * idef->atnr;
if (bFirst) {
if (PAR(cr))
fprintf(log,"GCT: this is parallel\n");
else
fprintf(log,"GCT: this is not parallel\n");
fflush(log);
snew(f6, atnr2);
snew(f12,atnr2);
snew(fa, atnr2);
snew(fb, atnr2);
snew(fc, atnr2);
snew(fq, idef->atnr);
if (tcr->bVirial) {
int nrdf = 0;
real TTT = 0;
real Vol = det(box);
for(i=0; (i<ir->opts.ngtc); i++) {
nrdf += ir->opts.nrdf[i];
TTT += ir->opts.nrdf[i]*ir->opts.ref_t[i];
}
TTT /= nrdf;
/* Calculate reference virial from reference temperature and pressure */
tcr->ref_value[eoVir] = 0.5*BOLTZ*nrdf*TTT - (3.0/2.0)*
Vol*tcr->ref_value[eoPres];
fprintf(log,"GCT: TTT = %g, nrdf = %d, vir0 = %g, Vol = %g\n",
TTT,nrdf,tcr->ref_value[eoVir],Vol);
fflush(log);
}
bFirst = FALSE;
}
bPrint = MASTER(cr) && do_per_step(step,ir->nstlog);
dt = ir->delta_t;
/* Initiate coupling to the reference pressure and temperature to start
* coupling slowly.
*/
if (step == 0) {
for(i=0; (i<eoObsNR); i++)
tcr->av_value[i] = tcr->ref_value[i];
if ((tcr->ref_value[eoDipole]) != 0.0) {
mu_ind = mu_aver - d2e(tcr->ref_value[eoDipole]); /* in e nm */
Epol = mu_ind*mu_ind/(enm2kjmol(tcr->ref_value[eoPolarizability]));
tcr->av_value[eoEpot] -= Epol;
fprintf(log,"GCT: mu_aver = %g(D), mu_ind = %g(D), Epol = %g (kJ/mol)\n",
mu_aver*enm2Debye,mu_ind*enm2Debye,Epol);
}
}
/* We want to optimize the LJ params, usually to the Vaporization energy
* therefore we only count intermolecular degrees of freedom.
* Note that this is now optional. switch UseEinter to yes in your gct file
* if you want this.
*/
dist = calc_dist(log,x);
muabs = norm(mu_tot);
Eintern = Ecouple(tcr,ener)/nmols;
Virial = virial[XX][XX]+virial[YY][YY]+virial[ZZ][ZZ];
/*calc_force(md->nr,f,fmol);*/
clear_rvec(fmol[0]);
/* Use a memory of tcr->nmemory steps, so we actually couple to the
* average observable over the last tcr->nmemory steps. This may help
* in avoiding local minima in parameter space.
*/
set_act_value(tcr,eoPres, ener[F_PRES],step);
set_act_value(tcr,eoEpot, Eintern, step);
set_act_value(tcr,eoVir, Virial, step);
set_act_value(tcr,eoDist, dist, step);
set_act_value(tcr,eoMu, muabs, step);
set_act_value(tcr,eoFx, fmol[0][XX], step);
set_act_value(tcr,eoFy, fmol[0][YY], step);
set_act_value(tcr,eoFz, fmol[0][ZZ], step);
set_act_value(tcr,eoPx, pres[XX][XX],step);
set_act_value(tcr,eoPy, pres[YY][YY],step);
set_act_value(tcr,eoPz, pres[ZZ][ZZ],step);
epot0 = tcr->ref_value[eoEpot];
/* If dipole != 0.0 assume we want to use polarization corrected coupling */
if ((tcr->ref_value[eoDipole]) != 0.0) {
mu_ind = mu_aver - d2e(tcr->ref_value[eoDipole]); /* in e nm */
Epol = mu_ind*mu_ind/(enm2kjmol(tcr->ref_value[eoPolarizability]));
epot0 -= Epol;
if (debug) {
fprintf(debug,"mu_ind: %g (%g D) mu_aver: %g (%g D)\n",
mu_ind,mu_ind*enm2Debye,mu_aver,mu_aver*enm2Debye);
fprintf(debug,"Eref %g Epol %g Erunav %g Eact %g\n",
tcr->ref_value[eoEpot],Epol,tcr->av_value[eoEpot],
tcr->act_value[eoEpot]);
}
}
if (bPrint) {
pr_ff(tcr,t,idef,cr,nfile,fnm,oenv);
}
/* Calculate the deviation of average value from the target value */
for(i=0; (i<eoObsNR); i++) {
deviation[i] = calc_deviation(tcr->av_value[i],tcr->act_value[i],
tcr->ref_value[i]);
prdev[i] = tcr->ref_value[i] - tcr->act_value[i];
}
deviation[eoEpot] = calc_deviation(tcr->av_value[eoEpot],tcr->act_value[eoEpot],
epot0);
prdev[eoEpot] = epot0 - tcr->act_value[eoEpot];
if (bPrint)
pr_dev(tcr,t,prdev,cr,nfile,fnm,oenv);
/* First set all factors to 1 */
for(i=0; (i<atnr2); i++) {
f6[i] = f12[i] = fa[i] = fb[i] = fc[i] = 1.0;
}
for(i=0; (i<idef->atnr); i++)
fq[i] = 1.0;
/* Now compute the actual coupling compononents */
if (!fr->bBHAM) {
if (bDoIt) {
for(i=0; (i<tcr->nLJ); i++) {
tclj=&(tcr->tcLJ[i]);
ati=tclj->at_i;
atj=tclj->at_j;
ff6 = ff12 = 1.0;
if (tclj->eObs == eoForce) {
gmx_fatal(FARGS,"Hack code for this to work again ");
if (debug)
fprintf(debug,"Have computed derivatives: xiH = %g, xiS = %g\n",xiH,xiS);
if (ati == 1) {
/* Hydrogen */
ff12 += xiH;
}
else if (ati == 2) {
/* Shell */
ff12 += xiS;
}
else
gmx_fatal(FARGS,"No H, no Shell, edit code at %s, line %d\n",
__FILE__,__LINE__);
if (ff6 > 0)
set_factor_matrix(idef->atnr,f6, sqrt(ff6), ati,atj);
if (ff12 > 0)
set_factor_matrix(idef->atnr,f12,sqrt(ff12),ati,atj);
}
else {
if (debug)
fprintf(debug,"tcr->tcLJ[%d].xi_6 = %g, xi_12 = %g deviation = %g\n",i,
tclj->xi_6,tclj->xi_12,deviation[tclj->eObs]);
factor=deviation[tclj->eObs];
upd_f_value(log,idef->atnr,tclj->xi_6, dt,factor,f6, ati,atj);
upd_f_value(log,idef->atnr,tclj->xi_12,dt,factor,f12,ati,atj);
}
}
}
if (PAR(cr)) {
gprod(cr,atnr2,f6);
gprod(cr,atnr2,f12);
#ifdef DEBUGGCT
dump_fm(log,idef->atnr,f6,"f6");
dump_fm(log,idef->atnr,f12,"f12");
#endif
}
upd_nbfplj(log,fr->nbfp,idef->atnr,f6,f12,tcr->combrule);
/* Copy for printing */
for(i=0; (i<tcr->nLJ); i++) {
tclj=&(tcr->tcLJ[i]);
ati = tclj->at_i;
atj = tclj->at_j;
if (atj == -1)
{
atj = ati;
}
/* nbfp now includes the 6.0/12.0 derivative prefactors */
tclj->c6 = C6(fr->nbfp,fr->ntype,ati,atj)/6.0;
tclj->c12 = C12(fr->nbfp,fr->ntype,ati,atj)/12.0;
}
}
else {
if (bDoIt) {
for(i=0; (i<tcr->nBU); i++) {
tcbu = &(tcr->tcBU[i]);
factor = deviation[tcbu->eObs];
ati = tcbu->at_i;
atj = tcbu->at_j;
upd_f_value(log,idef->atnr,tcbu->xi_a,dt,factor,fa,ati,atj);
upd_f_value(log,idef->atnr,tcbu->xi_b,dt,factor,fb,ati,atj);
upd_f_value(log,idef->atnr,tcbu->xi_c,dt,factor,fc,ati,atj);
}
}
if (PAR(cr)) {
gprod(cr,atnr2,fa);
gprod(cr,atnr2,fb);
gprod(cr,atnr2,fc);
}
upd_nbfpbu(log,fr->nbfp,idef->atnr,fa,fb,fc);
/* Copy for printing */
for(i=0; (i<tcr->nBU); i++) {
tcbu=&(tcr->tcBU[i]);
ati = tcbu->at_i;
atj = tcbu->at_j;
if (atj == -1)
{
atj = ati;
}
/* nbfp now includes the 6.0 derivative prefactors */
tcbu->a = BHAMA(fr->nbfp,fr->ntype,ati,atj);
tcbu->b = BHAMB(fr->nbfp,fr->ntype,ati,atj);
tcbu->c = BHAMC(fr->nbfp,fr->ntype,ati,atj)/6.0;
if (debug)
fprintf(debug,"buck (type=%d) = %e, %e, %e\n",
tcbu->at_i,tcbu->a,tcbu->b,tcbu->c);
}
}
if (bDoIt) {
for(i=0; (i<tcr->nQ); i++) {
tcq=&(tcr->tcQ[i]);
if (tcq->xi_Q)
ffq = 1.0 + (dt/tcq->xi_Q) * deviation[tcq->eObs];
else
ffq = 1.0;
fq[tcq->at_i] *= ffq;
}
}
if (PAR(cr))
gprod(cr,idef->atnr,fq);
for(j=0; (j<md->nr); j++) {
md->chargeA[j] *= fq[md->typeA[j]];
}
for(i=0; (i<tcr->nQ); i++) {
tcq=&(tcr->tcQ[i]);
for(j=0; (j<md->nr); j++) {
if (md->typeA[j] == tcq->at_i) {
tcq->Q = md->chargeA[j];
break;
}
}
if (j == md->nr)
gmx_fatal(FARGS,"Coupling type %d not found",tcq->at_i);
}
for(i=0; (i<tcr->nIP); i++) {
tip = &(tcr->tIP[i]);
type = tip->type;
ftype = idef->functype[type];
factor = dt*deviation[tip->eObs];
switch(ftype) {
case F_BONDS:
if (tip->xi.harmonic.krA) idef->iparams[type].harmonic.krA *= (1+factor/tip->xi.harmonic.krA);
if (tip->xi.harmonic.rA) idef->iparams[type].harmonic.rA *= (1+factor/tip->xi.harmonic.rA);
break;
default:
break;
}
tip->iprint=idef->iparams[type];
}
}
int gmx_cluster(int argc,char *argv[])
{
static char *desc[] = {
"g_cluster can cluster structures with several different methods.",
"Distances between structures can be determined from a trajectory",
"or read from an XPM matrix file with the [TT]-dm[tt] option.",
"RMS deviation after fitting or RMS deviation of atom-pair distances",
"can be used to define the distance between structures.[PAR]",
"single linkage: add a structure to a cluster when its distance to any",
"element of the cluster is less than [TT]cutoff[tt].[PAR]",
"Jarvis Patrick: add a structure to a cluster when this structure",
"and a structure in the cluster have each other as neighbors and",
"they have a least [TT]P[tt] neighbors in common. The neighbors",
"of a structure are the M closest structures or all structures within",
"[TT]cutoff[tt].[PAR]",
"Monte Carlo: reorder the RMSD matrix using Monte Carlo.[PAR]",
"diagonalization: diagonalize the RMSD matrix.[PAR]"
"gromos: use algorithm as described in Daura [IT]et al.[it]",
"([IT]Angew. Chem. Int. Ed.[it] [BB]1999[bb], [IT]38[it], pp 236-240).",
"Count number of neighbors using cut-off, take structure with",
"largest number of neighbors with all its neighbors as cluster",
"and eleminate it from the pool of clusters. Repeat for remaining",
"structures in pool.[PAR]",
"When the clustering algorithm assigns each structure to exactly one",
"cluster (single linkage, Jarvis Patrick and gromos) and a trajectory",
"file is supplied, the structure with",
"the smallest average distance to the others or the average structure",
"or all structures for each cluster will be written to a trajectory",
"file. When writing all structures, separate numbered files are made",
"for each cluster.[PAR]"
"Two output files are always written:[BR]",
"[TT]-o[tt] writes the RMSD values in the upper left half of the matrix",
"and a graphical depiction of the clusters in the lower right half",
"When [TT]-minstruct[tt] = 1 the graphical depiction is black",
"when two structures are in the same cluster.",
"When [TT]-minstruct[tt] > 1 different colors will be used for each",
"cluster.[BR]",
"[TT]-g[tt] writes information on the options used and a detailed list",
"of all clusters and their members.[PAR]",
"Additionally, a number of optional output files can be written:[BR]",
"[TT]-dist[tt] writes the RMSD distribution.[BR]",
"[TT]-ev[tt] writes the eigenvectors of the RMSD matrix",
"diagonalization.[BR]",
"[TT]-sz[tt] writes the cluster sizes.[BR]",
"[TT]-tr[tt] writes a matrix of the number transitions between",
"cluster pairs.[BR]",
"[TT]-ntr[tt] writes the total number of transitions to or from",
"each cluster.[BR]",
"[TT]-clid[tt] writes the cluster number as a function of time.[BR]",
"[TT]-cl[tt] writes average (with option [TT]-av[tt]) or central",
"structure of each cluster or writes numbered files with cluster members",
"for a selected set of clusters (with option [TT]-wcl[tt], depends on",
"[TT]-nst[tt] and [TT]-rmsmin[tt]).[BR]",
};
FILE *fp,*log;
int i,i1,i2,j,nf,nrms;
matrix box;
rvec *xtps,*usextps,*x1,**xx=NULL;
char *fn,*trx_out_fn;
t_clusters clust;
t_mat *rms;
real *eigval;
t_topology top;
int ePBC;
t_atoms useatoms;
t_matrix *readmat;
real *tmp;
int isize=0,ifsize=0,iosize=0;
atom_id *index=NULL, *fitidx, *outidx;
char *grpname;
real rmsd,**d1,**d2,*time,time_invfac,*mass=NULL;
char buf[STRLEN],buf1[80],title[STRLEN];
bool bAnalyze,bUseRmsdCut,bJP_RMSD=FALSE,bReadMat,bReadTraj;
int method,ncluster=0;
static char *methodname[] = {
NULL, "linkage", "jarvis-patrick","monte-carlo",
"diagonalization", "gromos", NULL
};
enum { m_null, m_linkage, m_jarvis_patrick,
m_monte_carlo, m_diagonalize, m_gromos, m_nr };
/* Set colors for plotting: white = zero RMS, black = maximum */
static t_rgb rlo_top = { 1.0, 1.0, 1.0 };
static t_rgb rhi_top = { 0.0, 0.0, 0.0 };
static t_rgb rlo_bot = { 1.0, 1.0, 1.0 };
static t_rgb rhi_bot = { 0.0, 0.0, 1.0 };
static int nlevels=40,skip=1;
static real scalemax=-1.0,rmsdcut=0.1,rmsmin=0.0;
static bool bRMSdist=FALSE,bBinary=FALSE,bAverage=FALSE,bFit=TRUE;
static int niter=10000,seed=1993,write_ncl=0,write_nst=1,minstruct=1;
static real kT=1e-3;
static int M=10,P=3;
t_pargs pa[] = {
{ "-dista", FALSE, etBOOL, {&bRMSdist},
"Use RMSD of distances instead of RMS deviation" },
{ "-nlevels",FALSE,etINT, {&nlevels},
"Discretize RMSD matrix in # levels" },
{ "-cutoff",FALSE, etREAL, {&rmsdcut},
"RMSD cut-off (nm) for two structures to be neighbor" },
{ "-fit", FALSE, etBOOL, {&bFit},
"Use least squares fitting before RMSD calculation" },
{ "-max", FALSE, etREAL, {&scalemax},
"Maximum level in RMSD matrix" },
{ "-skip", FALSE, etINT, {&skip},
"Only analyze every nr-th frame" },
{ "-av", FALSE, etBOOL, {&bAverage},
"Write average iso middle structure for each cluster" },
{ "-wcl", FALSE, etINT, {&write_ncl},
"Write all structures for first # clusters to numbered files" },
{ "-nst", FALSE, etINT, {&write_nst},
"Only write all structures if more than # per cluster" },
{ "-rmsmin",FALSE, etREAL, {&rmsmin},
"minimum rms difference with rest of cluster for writing structures" },
{ "-method",FALSE, etENUM, {methodname},
"Method for cluster determination" },
{ "-minstruct", FALSE, etINT, {&minstruct},
"Minimum number of structures in cluster for coloring in the xpm file" },
{ "-binary",FALSE, etBOOL, {&bBinary},
"Treat the RMSD matrix as consisting of 0 and 1, where the cut-off "
"is given by -cutoff" },
{ "-M", FALSE, etINT, {&M},
"Number of nearest neighbors considered for Jarvis-Patrick algorithm, "
"0 is use cutoff" },
{ "-P", FALSE, etINT, {&P},
"Number of identical nearest neighbors required to form a cluster" },
{ "-seed", FALSE, etINT, {&seed},
"Random number seed for Monte Carlo clustering algorithm" },
{ "-niter", FALSE, etINT, {&niter},
"Number of iterations for MC" },
{ "-kT", FALSE, etREAL, {&kT},
"Boltzmann weighting factor for Monte Carlo optimization "
"(zero turns off uphill steps)" }
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffOPTRD },
{ efTPS, "-s", NULL, ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXPM, "-dm", "rmsd", ffOPTRD },
{ efXPM, "-o", "rmsd-clust", ffWRITE },
{ efLOG, "-g", "cluster", ffWRITE },
{ efXVG, "-dist", "rmsd-dist", ffOPTWR },
{ efXVG, "-ev", "rmsd-eig", ffOPTWR },
{ efXVG, "-sz", "clust-size", ffOPTWR},
{ efXPM, "-tr", "clust-trans",ffOPTWR},
{ efXVG, "-ntr", "clust-trans",ffOPTWR},
{ efXVG, "-clid", "clust-id.xvg",ffOPTWR},
{ efTRX, "-cl", "clusters.pdb", ffOPTWR }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
/* parse options */
bReadMat = opt2bSet("-dm",NFILE,fnm);
bReadTraj = opt2bSet("-f",NFILE,fnm) || !bReadMat;
if ( opt2parg_bSet("-av",asize(pa),pa) ||
opt2parg_bSet("-wcl",asize(pa),pa) ||
opt2parg_bSet("-nst",asize(pa),pa) ||
opt2parg_bSet("-rmsmin",asize(pa),pa) ||
opt2bSet("-cl",NFILE,fnm) )
trx_out_fn = opt2fn("-cl",NFILE,fnm);
else
trx_out_fn = NULL;
if (bReadMat && time_factor()!=1) {
fprintf(stderr,
"\nWarning: assuming the time unit in %s is %s\n",
opt2fn("-dm",NFILE,fnm),time_unit());
}
if (trx_out_fn && !bReadTraj)
fprintf(stderr,"\nWarning: "
"cannot write cluster structures without reading trajectory\n"
" ignoring option -cl %s\n", trx_out_fn);
method=1;
while ( method < m_nr && strcasecmp(methodname[0], methodname[method])!=0 )
method++;
if (method == m_nr)
gmx_fatal(FARGS,"Invalid method");
bAnalyze = (method == m_linkage || method == m_jarvis_patrick ||
method == m_gromos );
/* Open log file */
log = ftp2FILE(efLOG,NFILE,fnm,"w");
fprintf(stderr,"Using %s method for clustering\n",methodname[0]);
fprintf(log,"Using %s method for clustering\n",methodname[0]);
/* check input and write parameters to log file */
bUseRmsdCut = FALSE;
if (method == m_jarvis_patrick) {
bJP_RMSD = (M == 0) || opt2parg_bSet("-cutoff",asize(pa),pa);
if ((M<0) || (M == 1))
gmx_fatal(FARGS,"M (%d) must be 0 or larger than 1",M);
if (M < 2) {
sprintf(buf1,"Will use P=%d and RMSD cutoff (%g)",P,rmsdcut);
bUseRmsdCut = TRUE;
} else {
if (P >= M)
gmx_fatal(FARGS,"Number of neighbors required (P) must be less than M");
if (bJP_RMSD) {
sprintf(buf1,"Will use P=%d, M=%d and RMSD cutoff (%g)",P,M,rmsdcut);
bUseRmsdCut = TRUE;
} else
sprintf(buf1,"Will use P=%d, M=%d",P,M);
}
ffprintf1(stderr,log,buf,"%s for determining the neighbors\n\n",buf1);
} else /* method != m_jarvis */
bUseRmsdCut = ( bBinary || method == m_linkage || method == m_gromos );
if (bUseRmsdCut && method != m_jarvis_patrick)
fprintf(log,"Using RMSD cutoff %g nm\n",rmsdcut);
if ( method==m_monte_carlo )
fprintf(log,"Using %d iterations\n",niter);
if (skip < 1)
gmx_fatal(FARGS,"skip (%d) should be >= 1",skip);
/* get input */
if (bReadTraj) {
/* don't read mass-database as masses (and top) are not used */
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),buf,&top,&ePBC,&xtps,NULL,box,
bAnalyze);
fprintf(stderr,"\nSelect group for least squares fit%s:\n",
bReadMat?"":" and RMSD calculation");
get_index(&(top.atoms),ftp2fn_null(efNDX,NFILE,fnm),
1,&ifsize,&fitidx,&grpname);
if (trx_out_fn) {
fprintf(stderr,"\nSelect group for output:\n");
get_index(&(top.atoms),ftp2fn_null(efNDX,NFILE,fnm),
1,&iosize,&outidx,&grpname);
/* merge and convert both index groups: */
/* first copy outidx to index. let outidx refer to elements in index */
snew(index,iosize);
isize = iosize;
for(i=0; i<iosize; i++) {
index[i]=outidx[i];
outidx[i]=i;
}
/* now lookup elements from fitidx in index, add them if necessary
and also let fitidx refer to elements in index */
for(i=0; i<ifsize; i++) {
j=0;
while (j<isize && index[j]!=fitidx[i])
j++;
if (j>=isize) {
/* slow this way, but doesn't matter much */
isize++;
srenew(index,isize);
}
index[j]=fitidx[i];
fitidx[i]=j;
}
} else { /* !trx_out_fn */
isize = ifsize;
snew(index, isize);
for(i=0; i<ifsize; i++) {
index[i]=fitidx[i];
fitidx[i]=i;
}
}
}
/* Initiate arrays */
snew(d1,isize);
snew(d2,isize);
for(i=0; (i<isize); i++) {
snew(d1[i],isize);
snew(d2[i],isize);
}
if (bReadTraj) {
/* Loop over first coordinate file */
fn = opt2fn("-f",NFILE,fnm);
xx = read_whole_trj(fn,isize,index,skip,&nf,&time);
convert_times(nf, time);
if (!bRMSdist || bAnalyze) {
/* Center all frames on zero */
snew(mass,isize);
for(i=0; i<ifsize; i++)
mass[fitidx[i]] = top.atoms.atom[index[fitidx[i]]].m;
if (bFit)
for(i=0; i<nf; i++)
reset_x(ifsize,fitidx,isize,NULL,xx[i],mass);
}
}
if (bReadMat) {
fprintf(stderr,"Reading rms distance matrix ");
read_xpm_matrix(opt2fn("-dm",NFILE,fnm),&readmat);
fprintf(stderr,"\n");
if (readmat[0].nx != readmat[0].ny)
gmx_fatal(FARGS,"Matrix (%dx%d) is not square",
readmat[0].nx,readmat[0].ny);
if (bReadTraj && bAnalyze && (readmat[0].nx != nf))
gmx_fatal(FARGS,"Matrix size (%dx%d) does not match the number of "
"frames (%d)",readmat[0].nx,readmat[0].ny,nf);
nf = readmat[0].nx;
sfree(time);
time = readmat[0].axis_x;
time_invfac = time_invfactor();
for(i=0; i<nf; i++)
time[i] *= time_invfac;
rms = init_mat(readmat[0].nx,method == m_diagonalize);
convert_mat(&(readmat[0]),rms);
nlevels = readmat[0].nmap;
} else { /* !bReadMat */
rms = init_mat(nf,method == m_diagonalize);
nrms = (nf*(nf-1))/2;
if (!bRMSdist) {
fprintf(stderr,"Computing %dx%d RMS deviation matrix\n",nf,nf);
snew(x1,isize);
for(i1=0; (i1<nf); i1++) {
for(i2=i1+1; (i2<nf); i2++) {
for(i=0; i<isize; i++)
copy_rvec(xx[i1][i],x1[i]);
if (bFit)
do_fit(isize,mass,xx[i2],x1);
rmsd = rmsdev(isize,mass,xx[i2],x1);
set_mat_entry(rms,i1,i2,rmsd);
}
nrms -= (nf-i1-1);
fprintf(stderr,"\r# RMSD calculations left: %d ",nrms);
}
} else { /* bRMSdist */
fprintf(stderr,"Computing %dx%d RMS distance deviation matrix\n",nf,nf);
for(i1=0; (i1<nf); i1++) {
calc_dist(isize,xx[i1],d1);
for(i2=i1+1; (i2<nf); i2++) {
calc_dist(isize,xx[i2],d2);
set_mat_entry(rms,i1,i2,rms_dist(isize,d1,d2));
}
nrms -= (nf-i1-1);
fprintf(stderr,"\r# RMSD calculations left: %d ",nrms);
}
}
fprintf(stderr,"\n\n");
}
ffprintf2(stderr,log,buf,"The RMSD ranges from %g to %g nm\n",
rms->minrms,rms->maxrms);
ffprintf1(stderr,log,buf,"Average RMSD is %g\n",2*rms->sumrms/(nf*(nf-1)));
ffprintf1(stderr,log,buf,"Number of structures for matrix %d\n",nf);
ffprintf1(stderr,log,buf,"Energy of the matrix is %g nm\n",mat_energy(rms));
if (bUseRmsdCut && (rmsdcut < rms->minrms || rmsdcut > rms->maxrms) )
fprintf(stderr,"WARNING: rmsd cutoff %g is outside range of rmsd values "
"%g to %g\n",rmsdcut,rms->minrms,rms->maxrms);
if (bAnalyze && (rmsmin < rms->minrms) )
fprintf(stderr,"WARNING: rmsd minimum %g is below lowest rmsd value %g\n",
rmsmin,rms->minrms);
if (bAnalyze && (rmsmin > rmsdcut) )
fprintf(stderr,"WARNING: rmsd minimum %g is above rmsd cutoff %g\n",
rmsmin,rmsdcut);
/* Plot the rmsd distribution */
rmsd_distribution(opt2fn("-dist",NFILE,fnm),rms);
if (bBinary) {
for(i1=0; (i1 < nf); i1++)
for(i2=0; (i2 < nf); i2++)
if (rms->mat[i1][i2] < rmsdcut)
rms->mat[i1][i2] = 0;
else
rms->mat[i1][i2] = 1;
}
snew(clust.cl,nf);
switch (method) {
case m_linkage:
/* Now sort the matrix and write it out again */
gather(rms,rmsdcut,&clust);
break;
case m_diagonalize:
/* Do a diagonalization */
snew(eigval,nf);
snew(tmp,nf*nf);
memcpy(tmp,rms->mat[0],nf*nf*sizeof(real));
eigensolver(tmp,nf,0,nf,eigval,rms->mat[0]);
sfree(tmp);
fp = xvgropen(opt2fn("-ev",NFILE,fnm),"RMSD matrix Eigenvalues",
"Eigenvector index","Eigenvalues (nm\\S2\\N)");
for(i=0; (i<nf); i++)
fprintf(fp,"%10d %10g\n",i,eigval[i]);
ffclose(fp);
break;
case m_monte_carlo:
mc_optimize(log,rms,niter,&seed,kT);
swap_mat(rms);
reset_index(rms);
break;
case m_jarvis_patrick:
jarvis_patrick(rms->nn,rms->mat,M,P,bJP_RMSD ? rmsdcut : -1,&clust);
break;
case m_gromos:
gromos(rms->nn,rms->mat,rmsdcut,&clust);
break;
default:
gmx_fatal(FARGS,"DEATH HORROR unknown method \"%s\"",methodname[0]);
}
if (method == m_monte_carlo || method == m_diagonalize)
fprintf(stderr,"Energy of the matrix after clustering is %g nm\n",
mat_energy(rms));
if (bAnalyze) {
if (minstruct > 1) {
ncluster = plot_clusters(nf,rms->mat,&clust,nlevels,minstruct);
} else {
mark_clusters(nf,rms->mat,rms->maxrms,&clust);
}
init_t_atoms(&useatoms,isize,FALSE);
snew(usextps, isize);
useatoms.resname=top.atoms.resname;
for(i=0; i<isize; i++) {
useatoms.atomname[i]=top.atoms.atomname[index[i]];
useatoms.atom[i].resnr=top.atoms.atom[index[i]].resnr;
useatoms.nres=max(useatoms.nres,useatoms.atom[i].resnr+1);
copy_rvec(xtps[index[i]],usextps[i]);
}
useatoms.nr=isize;
analyze_clusters(nf,&clust,rms->mat,isize,&useatoms,usextps,mass,xx,time,
ifsize,fitidx,iosize,outidx,
bReadTraj?trx_out_fn:NULL,
opt2fn_null("-sz",NFILE,fnm),
opt2fn_null("-tr",NFILE,fnm),
opt2fn_null("-ntr",NFILE,fnm),
opt2fn_null("-clid",NFILE,fnm),
bAverage, write_ncl, write_nst, rmsmin, bFit, log,
rlo_bot,rhi_bot);
}
ffclose(log);
if (bBinary && !bAnalyze)
/* Make the clustering visible */
for(i2=0; (i2 < nf); i2++)
for(i1=i2+1; (i1 < nf); i1++)
if (rms->mat[i1][i2])
rms->mat[i1][i2] = rms->maxrms;
fp = opt2FILE("-o",NFILE,fnm,"w");
fprintf(stderr,"Writing rms distance/clustering matrix ");
if (bReadMat) {
write_xpm(fp,0,readmat[0].title,readmat[0].legend,readmat[0].label_x,
readmat[0].label_y,nf,nf,readmat[0].axis_x,readmat[0].axis_y,
rms->mat,0.0,rms->maxrms,rlo_top,rhi_top,&nlevels);
}
else {
sprintf(buf,"Time (%s)",time_unit());
sprintf(title,"RMS%sDeviation / Cluster Index",
bRMSdist ? " Distance " : " ");
if (minstruct > 1) {
write_xpm_split(fp,0,title,"RMSD (nm)",buf,buf,
nf,nf,time,time,rms->mat,0.0,rms->maxrms,&nlevels,
rlo_top,rhi_top,0.0,(real) ncluster,
&ncluster,TRUE,rlo_bot,rhi_bot);
} else {
write_xpm(fp,0,title,"RMSD (nm)",buf,buf,
nf,nf,time,time,rms->mat,0.0,rms->maxrms,
rlo_top,rhi_top,&nlevels);
}
}
fprintf(stderr,"\n");
ffclose(fp);
/* now show what we've done */
do_view(opt2fn("-o",NFILE,fnm),"-nxy");
do_view(opt2fn_null("-sz",NFILE,fnm),"-nxy");
if (method == m_diagonalize)
do_view(opt2fn_null("-ev",NFILE,fnm),"-nxy");
do_view(opt2fn("-dist",NFILE,fnm),"-nxy");
if (bAnalyze) {
do_view(opt2fn_null("-tr",NFILE,fnm),"-nxy");
do_view(opt2fn_null("-ntr",NFILE,fnm),"-nxy");
do_view(opt2fn_null("-clid",NFILE,fnm),"-nxy");
}
/* Thank the user for her patience */
thanx(stderr);
return 0;
}
void geocacheMenu(void)
{
int pressedKey = mySwitch.checkKeypad();
switch (menuState)
{
case MENU0:
tft.fillScreen(ST7735_BLACK);
setCursorTFT(0,0);
tft.print(menuHeader);
setCursorTFT(1,0);
tft.setTextColor(ST7735_WHITE,ST7735_BLUE);
tft.print(monGPSLocn);
setCursorTFT(2,0);
tft.setTextColor(ST7735_WHITE,ST7735_BLACK);
tft.print(monGPSClk);
setCursorTFT(3,0);
tft.print(downldWays);
setCursorTFT(4,0);
tft.print(goToWaypts);
setCursorTFT(5,0);
tft.print(setActWays);
setCursorTFT(6,0);
tft.print(showWaypts);
menuState = MENU0B;
break;
case MENU0B:
if (pressedKey != NOKEY)
{
if ((pressedKey == SELECT) || (pressedKey == RIGHT))
{
tft.fillScreen(ST7735_BLACK);
setCursorTFT(0,0);
tft.setTextColor(ST7735_WHITE,ST7735_BLUE);
tft.print(monGPSLocn);
tft.setTextColor(ST7735_WHITE,ST7735_BLACK);
clearLine(1);
clearLine(2);
clearLine(3);
clearLine(4);
clearLine(5);
clearLine(6);
menuState = MENU0C;
}
else if (pressedKey == DOWN)
menuState = MENU1;
}
break;
case MENU0C:
if (pressedKey != NOKEY)
menuState = MENU0;
readGPS();
break;
case MENU1:
tft.fillScreen(ST7735_BLACK);
setCursorTFT(0,0);
tft.print(menuHeader);
setCursorTFT(1,0);
tft.print(monGPSLocn);
setCursorTFT(2,0);
tft.setTextColor(ST7735_WHITE,ST7735_BLUE);
tft.print(monGPSClk);
tft.setTextColor(ST7735_WHITE,ST7735_BLACK);
setCursorTFT(3,0);
tft.print(downldWays);
setCursorTFT(4,0);
tft.print(goToWaypts);
setCursorTFT(5,0);
tft.print(setActWays);
setCursorTFT(6,0);
tft.print(showWaypts);
menuState = MENU1B;
break;
case MENU1B:
if (pressedKey != NOKEY)
{
if ((pressedKey == SELECT) || (pressedKey == RIGHT))
{
clearLine(0);
tft.setTextColor(ST7735_WHITE,ST7735_BLUE);
tft.print(monGPSClk);
tft.setTextColor(ST7735_WHITE,ST7735_BLACK);
clearLine(1);
clearLine(2);
clearLine(3);
clearLine(4);
clearLine(5);
clearLine(6);
menuState = MENU1C;
}
else if (pressedKey == UP)
menuState = MENU0;
else if (pressedKey == DOWN)
menuState = MENU2;
}
break;
case MENU1C:
if (pressedKey != NOKEY)
{
tft.fillScreen(ST7735_BLACK);
menuState = MENU1;
}
GPSClock();
break;
case MENU2:
tft.fillScreen(ST7735_BLACK);
setCursorTFT(0,0);
tft.print(menuHeader);
setCursorTFT(1,0);
tft.print(monGPSLocn);
setCursorTFT(2,0);
tft.print(monGPSClk);
setCursorTFT(3,0);
tft.setTextColor(ST7735_WHITE,ST7735_BLUE);
tft.print(downldWays);
tft.setTextColor(ST7735_WHITE,ST7735_BLACK);
setCursorTFT(4,0);
tft.print(goToWaypts);
setCursorTFT(5,0);
tft.print(setActWays);
setCursorTFT(6,0);
tft.print(showWaypts);
menuState = MENU2B;
break;
case MENU2B:
{
int charIn;
if (pressedKey != NOKEY)
{
if ((pressedKey == SELECT) || (pressedKey == RIGHT))
{
rxCount = 0;
clearLine(2);
clearLine(3);
clearLine(4);
clearLine(5);
clearLine(6);
clearLine(1);
tft.setTextColor(ST7735_WHITE,ST7735_BLUE);
tft.print(downldWays);
tft.setTextColor(ST7735_WHITE,ST7735_BLACK);
setCursorTFT(2,0);
menuState = MENU2C;
while (Serial.available()) // flush the serial read port
charIn = Serial.read();
Serial.println("<DL>"); // signals host that it's time to load waypoints
}
else if (pressedKey == UP)
menuState = MENU1;
else if (pressedKey == DOWN)
menuState = MENU3;
}
}
break;
case MENU2C:
{
int charIn;
int errorCode;
if (Serial.available())
{
charIn = Serial.read();
if (charIn == '\n')
{
tft.print(".");
rxBuffer[rxCount] = 0;
errorCode = parseRxBuffer();
if (errorCode == -1)
{
clearLine(2);
tft.print("Error: Missing equal");
}
else if (errorCode == -2)
{
clearLine(2);
tft.print("Error: Bad waypt num");
}
rxCount = 0;
Serial.write('A');
if ((rxBuffer[0] == '1') && (rxBuffer[1]=='9'))
{
clearLine(3);
tft.print("Download Completed ");
EEPROM_writeAnything(0, myStoreVals);
Serial.println("</SERIN>"); // signals host that it's time to load waypoints
delay(2000); // 2 second message
menuState = MENU2;
}
}
else
{
rxBuffer[rxCount++] = charIn;
}
}
if (pressedKey == UP)
{
Serial.println("</DL>"); // signals host that it's time to load waypoints
clearLine(2);
tft.print("Download Terminated ");
delay(2000); // 2 second message
menuState = MENU2;
}
}
break;
case MENU3:
tft.fillScreen(ST7735_BLACK);
setCursorTFT(0,0);
tft.print(menuHeader);
setCursorTFT(1,0);
tft.print(monGPSLocn);
setCursorTFT(2,0);
tft.print(monGPSClk);
setCursorTFT(3,0);
tft.print(downldWays);
setCursorTFT(4,0);
tft.setTextColor(ST7735_WHITE,ST7735_BLUE);
tft.print(goToWaypts);
tft.setTextColor(ST7735_WHITE,ST7735_BLACK);
setCursorTFT(5,0);
tft.print(setActWays);
setCursorTFT(6,0);
tft.print(showWaypts);
menuState = MENU3B;
break;
case MENU3B:
if (pressedKey != NOKEY)
{
if ((pressedKey == SELECT) || (pressedKey == RIGHT))
{
quietReadGPS();
delay(500);
menuState = MENU3C;
}
else if (pressedKey == UP)
menuState = MENU2;
else if (pressedKey == DOWN)
menuState = MENU4;
}
break;
case MENU3C:
tft.fillScreen(ST7735_BLACK);
tft.drawCircle(64,110,45,ST7735_WHITE);
setCursorTFT(0,0);
tft.print(menuHeader);
setCursorTFT(1,0);
tft.print("Going to Waypoint ");
setCursorTFT(1,18);
tft.print(currentWayPoint, DEC);
setCursorTFT(2,0);
tft.print("Bearing =");
setCursorTFT(3,0);
tft.print("Distance =");
setCursorTFT(4,0);
tft.print("Direction =");
setCursorTFT(5,0);
tft.print("Satellites =");
quietReadGPS();
setCursorTFT(2,10);
tft.print(" ");
setCursorTFT(2,10);
bearing = calc_bearing(fLat2,fLon2,myStoreVals.lats[currentWayPoint],myStoreVals.lons[currentWayPoint]);
tft.print(bearing);
lastLat = fLat2;
setCursorTFT(3,11);
tft.print(" ");
setCursorTFT(3,11);
tft.print(calc_dist(fLat2,fLon2,myStoreVals.lats[currentWayPoint],myStoreVals.lons[currentWayPoint]));
lastLon = fLon2;
setCursorTFT(4,12);
tft.print(GPS.angle-bearing);
lastAngle = GPS.angle;
lastBearing = bearing;
setCursorTFT(5,13);
tft.print(GPS.satellites);
lastSats = GPS.satellites;
menuState = MENU3D;
break;
case MENU3D:
{
if (pressedKey != NOKEY)
{
menuState = MENU3;
break;
}
if (quietReadGPS() != 0)
{
break;
}
float distCalc = calc_dist(fLat2,fLon2,myStoreVals.lats[currentWayPoint],myStoreVals.lons[currentWayPoint]);
bearing = calc_bearing(fLat2,fLon2,myStoreVals.lats[currentWayPoint],myStoreVals.lons[currentWayPoint]);
if ((fLat2 != lastLat) || (fLon2 != lastLon))
{
setCursorTFT(2,10);
tft.print(" ");
setCursorTFT(2,10);
tft.print(bearing);
setCursorTFT(3,11);
tft.print(" ");
setCursorTFT(3,11);
tft.print(distCalc);
lastLat = fLat2;
lastLon = fLon2;
}
if ((GPS.angle != lastAngle) || (bearing != lastBearing))
{
setCursorTFT(4,12);
tft.print(" ");
setCursorTFT(4,12);
tft.print(GPS.angle-bearing);
drawVector(GPS.angle-bearing);
lastAngle = GPS.angle;
lastBearing = bearing;
}
if (lastSats != GPS.satellites)
{
setCursorTFT(5,13);
tft.print(GPS.satellites);
tft.print(" ");
}
}
break;
case MENU4:
tft.fillScreen(ST7735_BLACK);
setCursorTFT(0,0);
tft.print(menuHeader);
setCursorTFT(1,0);
tft.print(monGPSLocn);
setCursorTFT(2,0);
tft.print(monGPSClk);
setCursorTFT(3,0);
tft.print(downldWays);
setCursorTFT(4,0);
tft.print(goToWaypts);
setCursorTFT(5,0);
tft.setTextColor(ST7735_WHITE,ST7735_BLUE);
tft.print(setActWays);
tft.setTextColor(ST7735_WHITE,ST7735_BLACK);
setCursorTFT(6,0);
tft.print(showWaypts);
menuState = MENU4B;
break;
case MENU4B:
if (pressedKey != NOKEY)
{
if ((pressedKey == SELECT) || (pressedKey == RIGHT))
{
tft.fillScreen(ST7735_BLACK);
setCursorTFT(0,0);
tft.setTextColor(ST7735_WHITE,ST7735_BLUE);
tft.print(setActWays);
tft.setTextColor(ST7735_WHITE,ST7735_BLACK);
setCursorTFT(1,0);
tft.print(currentWayPoint, DEC);
menuState = MENU4C;
}
else if (pressedKey == UP)
{
menuState = MENU3;
}
else if (pressedKey == DOWN)
{
menuState = MENU5;
}
}
break;
case MENU4C:
{
if (pressedKey != NOKEY)
{
switch(pressedKey)
{
case SELECT:
myStoreVals.myCurrentWayPoint = currentWayPoint;
EEPROM_writeAnything(0, myStoreVals);
menuState = MENU4;
break;
case UP:
if (currentWayPoint < 19)
currentWayPoint++;
delay(250);
break;
case DOWN:
if (currentWayPoint > 0)
currentWayPoint--;
delay(250);
break;
}
clearLine(1);
tft.print(currentWayPoint, DEC);
}
}
break;
case MENU5:
tft.fillScreen(ST7735_BLACK);
setCursorTFT(0,0);
tft.print(menuHeader);
setCursorTFT(1,0);
tft.print(monGPSLocn);
setCursorTFT(2,0);
tft.print(monGPSClk);
setCursorTFT(3,0);
tft.print(downldWays);
setCursorTFT(4,0);
tft.print(goToWaypts);
setCursorTFT(5,0);
tft.print(setActWays);
setCursorTFT(6,0);
tft.setTextColor(ST7735_WHITE,ST7735_BLUE);
tft.print(showWaypts);
tft.setTextColor(ST7735_WHITE,ST7735_BLACK);
menuState = MENU5B;
break;
case MENU5B:
if (pressedKey != NOKEY)
{
if ((pressedKey == SELECT) || (pressedKey == RIGHT))
{
tft.fillScreen(ST7735_BLACK);
setCursorTFT(0,0);
tft.setTextColor(ST7735_WHITE,ST7735_BLUE);
tft.print(showWaypts);
tft.setTextColor(ST7735_WHITE,ST7735_BLACK);
for (int row = 0; row < 15; row++)
{
setCursorTFT(row+1,0);
tft.print(row);
tft.print(",");
tft.print(myStoreVals.lats[row],4);
tft.print(",");
tft.print(myStoreVals.lons[row],4);
}
menuState = MENU5C;
}
else if (pressedKey == UP)
{
menuState = MENU4;
}
}
break;
case MENU5C:
{
if (pressedKey != NOKEY)
{
switch(pressedKey)
{
case SELECT:
case UP:
tft.fillScreen(ST7735_BLACK);
menuState = MENU5;
break;
}
}
break;
}
}
}
int gmx_saltbr(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] plots the distance between all combination of charged groups",
"as a function of time. The groups are combined in different ways.",
"A minimum distance can be given (i.e. a cut-off), such that groups",
"that are never closer than that distance will not be plotted.[PAR]",
"Output will be in a number of fixed filenames, [TT]min-min.xvg[tt], [TT]plus-min.xvg[tt]",
"and [TT]plus-plus.xvg[tt], or files for every individual ion pair if the [TT]-sep[tt]",
"option is selected. In this case, files are named as [TT]sb-(Resname)(Resnr)-(Atomnr)[tt].",
"There may be [BB]many[bb] such files."
};
static gmx_bool bSep = FALSE;
static real truncate = 1000.0;
t_pargs pa[] = {
{ "-t", FALSE, etREAL, {&truncate},
"Groups that are never closer than this distance are not plotted" },
{ "-sep", FALSE, etBOOL, {&bSep},
"Use separate files for each interaction (may be MANY)" }
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPR, NULL, NULL, ffREAD },
};
#define NFILE asize(fnm)
FILE *out[3], *fp;
static const char *title[3] = {
"Distance between positively charged groups",
"Distance between negatively charged groups",
"Distance between oppositely charged groups"
};
static const char *fn[3] = {
"plus-plus.xvg",
"min-min.xvg",
"plus-min.xvg"
};
int nset[3] = {0, 0, 0};
t_topology *top;
int ePBC;
char *buf;
t_trxstatus *status;
int i, j, k, m, nnn, teller, ncg;
real t, *time, qi, qj;
t_charge *cg;
real ***cgdist;
int **nWithin;
t_pbc pbc;
rvec *x;
matrix box;
gmx_output_env_t *oenv;
if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
cg = mk_charge(&top->atoms, &(top->cgs), &ncg);
snew(cgdist, ncg);
snew(nWithin, ncg);
for (i = 0; (i < ncg); i++)
{
snew(cgdist[i], ncg);
snew(nWithin[i], ncg);
}
read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
teller = 0;
time = NULL;
do
{
srenew(time, teller+1);
time[teller] = t;
set_pbc(&pbc, ePBC, box);
for (i = 0; (i < ncg); i++)
{
for (j = i+1; (j < ncg); j++)
{
srenew(cgdist[i][j], teller+1);
cgdist[i][j][teller] =
calc_dist(&pbc, x, &(top->cgs), cg[i].cg, cg[j].cg);
if (cgdist[i][j][teller] < truncate)
{
nWithin[i][j] = 1;
}
}
}
teller++;
}
while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
close_trj(status);
if (bSep)
{
snew(buf, 256);
for (i = 0; (i < ncg); i++)
{
for (j = i+1; (j < ncg); j++)
{
if (nWithin[i][j])
{
sprintf(buf, "sb-%s:%s.xvg", cg[i].label, cg[j].label);
fp = xvgropen(buf, buf, "Time (ps)", "Distance (nm)", oenv);
for (k = 0; (k < teller); k++)
{
fprintf(fp, "%10g %10g\n", time[k], cgdist[i][j][k]);
}
xvgrclose(fp);
}
}
}
sfree(buf);
}
else
{
for (m = 0; (m < 3); m++)
{
out[m] = xvgropen(fn[m], title[m], "Time (ps)", "Distance (nm)", oenv);
}
snew(buf, 256);
for (i = 0; (i < ncg); i++)
{
qi = cg[i].q;
for (j = i+1; (j < ncg); j++)
{
qj = cg[j].q;
if (nWithin[i][j])
{
sprintf(buf, "%s:%s", cg[i].label, cg[j].label);
if (qi*qj < 0)
{
nnn = 2;
}
else if (qi+qj > 0)
{
nnn = 0;
}
else
{
nnn = 1;
}
if (nset[nnn] == 0)
{
xvgr_legend(out[nnn], 1, (const char**)&buf, oenv);
}
else
{
if (output_env_get_xvg_format(oenv) == exvgXMGR)
{
fprintf(out[nnn], "@ legend string %d \"%s\"\n", nset[nnn], buf);
}
else if (output_env_get_xvg_format(oenv) == exvgXMGRACE)
{
fprintf(out[nnn], "@ s%d legend \"%s\"\n", nset[nnn], buf);
}
}
nset[nnn]++;
nWithin[i][j] = nnn+1;
}
}
}
for (k = 0; (k < teller); k++)
{
for (m = 0; (m < 3); m++)
{
fprintf(out[m], "%10g", time[k]);
}
for (i = 0; (i < ncg); i++)
{
for (j = i+1; (j < ncg); j++)
{
nnn = nWithin[i][j];
if (nnn > 0)
{
fprintf(out[nnn-1], " %10g", cgdist[i][j][k]);
}
}
}
for (m = 0; (m < 3); m++)
{
fprintf(out[m], "\n");
}
}
for (m = 0; (m < 3); m++)
{
xvgrclose(out[m]);
if (nset[m] == 0)
{
remove(fn[m]);
}
}
}
return 0;
}
float calc_radius(struct halo *h, struct halo *p) {
struct halo *p2 = find_parent_at_scale(h->scale, p);
if (!p2) p2 = find_earliest_parent(p);
if (!p2) return 0;
return calc_dist(h, p2);
}
char current_location(int* position)
{
// int buffer to hold blob data
unsigned int buffer[12];
// read wii camera blob data into int buffer
m_wii_read(buffer);
// star points
int x1 = (int)buffer[0];
int y1 = (int)buffer[1];
int x2 = (int)buffer[3];
int y2 = (int)buffer[4];
int x3 = (int)buffer[6];
int y3 = (int)buffer[7];
int x4 = (int)buffer[9];
int y4 = (int)buffer[10];
// array of points
int x_points[4] = {x1, x2, x3, x4};
int y_points[4] = {y1, y2, y3, y4};
// lose star case
int i;
for(i = 0; i<=4;i++)
{
if (x_points[i]==1023 && y_points[i]==1023)
{
x_points[i] = NaN;
y_points[i] = NaN;
}
}
// calculate all possible distances
int d12 = calc_dist(x_points[0], y_points[0], x_points[1], y_points[1]);
int d13 = calc_dist(x_points[0], y_points[0], x_points[2], y_points[2]);
int d14 = calc_dist(x_points[0], y_points[0], x_points[3], y_points[3]);
int d23 = calc_dist(x_points[1], y_points[1], x_points[2], y_points[2]);
int d24 = calc_dist(x_points[1], y_points[1], x_points[3], y_points[3]);
int d34 = calc_dist(x_points[2], y_points[2], x_points[3], y_points[3]);
// store all distances in an array
int all_distances[6] = {d12,d13,d14,d23,d24,d34};
// store all pair
int all_pairs[6][2] = {{0,1},{0,2},{0,3},{1,2},{1,3},{2,3}};
// index and value of max and min distance
int max_dat[2];
int min_dat[2];
// find min and max arrays
max_array(all_distances, 6, max_dat);
min_array(all_distances, 6, min_dat);
// index of max and min points
int max_index = max_dat[1];
int max = max_dat[0];
int min_index = min_dat[1];
// array of pair indicies
int long_pair[2] = {all_pairs[max_index][0], all_pairs[max_index][1]};
int short_pair[2] = {all_pairs[min_index][0], all_pairs[min_index][1]};
int top_point[2];
int bottom_point[2];
// finds top and bottom points
if (long_pair[0] == short_pair[0] || long_pair[0] == short_pair[1])
{
top_point[0] = x_points[long_pair[0]];
top_point[1] = y_points[long_pair[0]];
bottom_point[0] = x_points[long_pair[1]];
bottom_point[1] = y_points[long_pair[1]];
}
else
{
top_point[0] =x_points[long_pair[1]];
top_point[1] =y_points[long_pair[1]];
bottom_point[0] =x_points[long_pair[0]];
bottom_point[1] =y_points[long_pair[0]];
}
// calculate center of rink
double x_center = ((double)top_point[0] + (double)bottom_point[0])/2;
double y_center = ((double)top_point[1] + (double)bottom_point[1])/2;
//double theta = acos(y_unit);
double x_diff = (double)top_point[0] - x_center;
double y_diff =(double)top_point[1] - y_center;
// calculate position of camera relative to camera coordinate axes
double camera_x = 512;
double camera_y = 384;
// calculate angle theta
double theta = atan2(x_diff, y_diff);
// rotated points
float rotated_x = ((((camera_x-x_center)*cos(theta)) + ((camera_y-y_center)*-sin(theta))) + camera_x) - camera_x;
float rotated_y = ((((camera_x-x_center)*sin(theta)) + ((camera_y-y_center)*cos(theta))) + camera_y) - camera_y;
// position and angle relative to rink axes
position[0] = (int) (29*(rotated_x))/max;
position[1] = (int) (29*(rotated_y))/max;
position[2] = (int) (theta*(180/M_PI));
return 1;
}
int main(int argc, char** argv)
{
int height ,width ,step ,channels;
int same, lighter;
float thresh;
uchar *dataB, *dataG, *dataR, *dataGray, *dataD;
uchar b1, g1, r1, b2, g2, r2;
int w = 3;
int th = 50;
int idx1, idx2;
cv::Mat img = cv::imread(argv[1]);
height = img.rows;
width = img.cols;
cv::namedWindow("Image0", cv::WINDOW_NORMAL);
cv::Mat textImg(1000, 1200, CV_8UC1, cv::Scalar(255));
cv::putText(textImg, "Original Image:", cv::Point(400, 500), cv::FONT_HERSHEY_SIMPLEX, 2, cv::Scalar(0, 0, 0));
//cv::imshow("Image0", textImg);
//cv::waitKey();
//cv::imshow("Image0", img);
//cv::waitKey();
textImg.setTo(cv::Scalar(255, 255, 255));
cv::putText(textImg, "Next: Apply SUSAN algorithm to detect edge and cross.", cv::Point(200, 500), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
cv::putText(textImg, "Press any key to continue...", cv::Point(400, 600), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
//cv::imshow("Image0", textImg);
//cv::waitKey();
std::vector<cv::Mat> imgChannels;
cv::split(img, imgChannels);
cv::Mat dstSusan(height, width, CV_8UC1, cv::Scalar(0));
cv::Mat grayImg(height, width, CV_8UC1, cv::Scalar(0));
step = imgChannels[0].step[0];
dataB = imgChannels[0].data;
dataG = imgChannels[1].data;
dataR = imgChannels[2].data;
dataGray = grayImg.data;
dataD= dstSusan.data;
for (int x = w; x < width-w; x++)
{
for (int y = w; y < height-w; y++)
{
same = 0;
idx1 = x + y * step;
b1 = dataB[idx1];
g1 = dataG[idx1];
r1 = dataR[idx1];
for (int u = 0; u < w+1; u++)
{
for (int v = 0; v < w+1; v++)
{
if (u + v == 0)
{
continue;
}
idx2 = (x+u) + (y+v) * step;
b2 = dataB[idx2];
g2 = dataG[idx2];
r2 = dataR[idx2];
if (calc_dist(b1, g1, r1, b1, g2, r2) < th)
{
same += 1;
}
idx2 = (x-u) + (y+v) * step;
b2 = dataB[idx2];
g2 = dataG[idx2];
r2 = dataR[idx2];
if (u != 0 && calc_dist(b1, g1, r1, b1, g2, r2) < th)
{
same += 1;
}
idx2 = (x+u) + (y-v) * step;
b2 = dataB[idx2];
g2 = dataG[idx2];
r2 = dataR[idx2];
if (v != 0 && calc_dist(b1, g1, r1, b1, g2, r2) < th)
{
same += 1;
}
idx2 = (x-u) + (y-v) * step;
b2 = dataB[idx2];
g2 = dataG[idx2];
r2 = dataR[idx2];
if (u != 0 && v != 0 && calc_dist(b1, g1, r1, b1, g2, r2) < th)
{
same += 1;
}
}
}
dataD[idx1] = uchar(255.0 * float(same) / ((2*w+1) * (2*w+1) - 1));
if (dataD[idx1] < 128)
{
dataD[idx1] = 255;
}
else
{
dataD[idx1] = 0;
}
}
}
//cv::imshow("Image0", dstSusan);
cv::imwrite("outimg_1.jpg", dstSusan);
textImg.setTo(cv::Scalar(255, 255, 255));
cv::putText(textImg, "Next: Apply Hough algorithm to detect lines.", cv::Point(300, 500), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
cv::putText(textImg, "Press any key to continue...", cv::Point(400, 600), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
//cv::waitKey();
//cv::imshow("Image0", textImg);
//cv::waitKey();
//Hough line detection
std::vector<cv::Vec4i> lines;
HoughLinesP(dstSusan, lines, 1, CV_PI/180, 80, 500, 20);
double thetaSum = 0.0;
int thetaNum = 0;
double theta;
for(size_t i = 0; i < lines.size(); i++)
{
cv::Vec4i l = lines[i];
cv::line(img, cv::Point(l[0], l[1]), cv::Point(l[2], l[3]), cv::Scalar(186,88,255), 1, CV_AA);
if (l[0] == l[2])
{
theta = CV_PI / 2;
}
else
{
theta = std::atan(-double(l[3]-l[1]) / (l[2] - l[0]));
}
if (theta >= -CV_PI / 4 && theta <= CV_PI / 4)
{
thetaSum += theta;
thetaNum += 1;
}
}
theta = -thetaSum / thetaNum * 180 / CV_PI;
//cv::imshow("Image0", img);
cv::imwrite("outimg_2.jpg", img);
//cv::waitKey();
textImg.setTo(cv::Scalar(255, 255, 255));
std::ostringstream textStr;
textStr << "Find " << lines.size() << " lines.";
cv::putText(textImg, textStr.str(), cv::Point(500, 400), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
textStr.str(std::string());
textStr.clear();
textStr << "Rotating angle is " << theta << " degree.";
cv::putText(textImg, textStr.str(), cv::Point(350, 500), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
cv::putText(textImg, "Next: Rotating the image.", cv::Point(400, 600), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
cv::putText(textImg, "Press any key to continue...", cv::Point(400, 700), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
//cv::imshow("Image0", textImg);
//cv::waitKey();
img.release();
img = cv::imread(argv[1]);
imgChannels[0].release();
imgChannels[1].release();
imgChannels[2].release();
imgChannels.clear();
cv::Mat rotateImg(height, width, CV_8UC3);
cv::Point2f center;
center.x = float(width / 2.0 + 0.5);
center.y = float(height / 2.0 + 0.5);
cv::Mat affineMat = getRotationMatrix2D(center, theta, 1);
cv::warpAffine(img,rotateImg, affineMat, cv::Size(width, height), CV_INTER_LINEAR+CV_WARP_FILL_OUTLIERS);
//cv::imshow("Image0", rotateImg);
cv::imwrite("outimg_3.jpg", rotateImg);
//cv::waitKey();
textImg.setTo(cv::Scalar(255, 255, 255));
cv::putText(textImg, "Next: Transform the image to gray scale.", cv::Point(300, 500), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
cv::putText(textImg, "Press any key to continue...", cv::Point(400, 600), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
//cv::imshow("Image0", textImg);
//cv::waitKey();
cv::split(rotateImg, imgChannels);
dataB = imgChannels[0].data;
dataG = imgChannels[1].data;
dataR = imgChannels[2].data;
step = imgChannels[0].step[0];
//imgChannels[2].setTo(cv::Scalar(0));
for (int x = 0; x < rotateImg.cols; x++)
{
for (int y = 0; y < rotateImg.rows; y++)
{
int idx = x + y * step;
if (dataB[idx] < dataG[idx] && dataB[idx] < dataR[idx])
{
dataG[idx] = dataB[idx];
dataR[idx] = dataB[idx];
}
if (dataG[idx] < dataB[idx] && dataG[idx] < dataR[idx])
{
dataB[idx] = dataG[idx];
dataR[idx] = dataG[idx];
}
if (dataR[idx] < dataB[idx] && dataR[idx] < dataG[idx])
{
dataB[idx] = dataR[idx];
dataG[idx] = dataR[idx];
}
}
}
cv::Mat filterRedImg(rotateImg.rows, rotateImg.cols, CV_8UC3, cv::Scalar::all(255));
cv::merge(imgChannels, filterRedImg);
cv::cvtColor(filterRedImg, grayImg, CV_BGR2GRAY);
//cv::imshow("Image0", grayImg);
cv::imwrite("outimg_4.jpg", grayImg);
//cv::waitKey();
textImg.setTo(cv::Scalar(255, 255, 255));
cv::putText(textImg, "Next: Clean the noise.", cv::Point(450, 500), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
cv::putText(textImg, "Press any key to continue...", cv::Point(400, 600), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
//cv::imshow("Image0", textImg);
//cv::waitKey();
step = grayImg.step[0];
for (int x = 0; x < width; x++)
{
for (int y = 0; y < height; y++)
{
int idx = x + y * step;
if (grayImg.data[idx] > 100)
//if(!is_gray(dataB[idx], dataG[idx], dataR[idx]))
{
grayImg.data[idx] = 255;
}
}
}
//cv::imshow("Image0", grayImg);
cv::imwrite("outimg_5.jpg", grayImg);
//cv::waitKey();
textImg.setTo(cv::Scalar(255, 255, 255));
cv::putText(textImg, "Next: Digitizing the curves.", cv::Point(400, 500), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
cv::putText(textImg, "Press any key to continue...", cv::Point(400, 600), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
//cv::imshow("Image0", textImg);
//cv::waitKey();
cv::Mat newImg(height, width, CV_8UC3, cv::Scalar::all(255));
SegmentFactory segFactory = SegmentFactory(0);
std::vector<Segment *> segments;
segFactory.makeSegments(grayImg, segments);
std::vector<Segment *>::iterator itr;
for (itr = segments.begin(); itr != segments.end(); itr++)
{
Segment *seg = *itr;
std::vector<SegmentLine *>::iterator itr_l;
for (itr_l = seg->m_lines.begin(); itr_l != seg->m_lines.end(); itr_l++)
{
SegmentLine *line = *itr_l;
cv::line(newImg, cv::Point(line->m_x1, line->m_y1), cv::Point(line->m_x2, line->m_y2), cv::Scalar(186,88,255), 1, CV_AA);
std::cout << line->m_x1 << ", " << line->m_y1 << ", " << line->m_x2 << ", " << line->m_y2 << std::endl;
}
}
//cv::imshow("Image0", newImg);
cv::imwrite("outimg_6.jpg", newImg);
//cv::waitKey();
textImg.setTo(cv::Scalar(255, 255, 255));
cv::putText(textImg, "Done.", cv::Point(550, 500), cv::FONT_HERSHEY_SIMPLEX, 1, cv::Scalar(0, 255, 255));
//cv::imshow("Image0", textImg);
//cv::waitKey();
return 0;
}
