/*----------------------------------------------------------------------
Parameters:
Description:
----------------------------------------------------------------------*/
MRI_SURFACE *
center_brain(MRI_SURFACE *mris_src, MRI_SURFACE *mris_dst) {
int fno, vno ;
FACE *face ;
VERTEX *vdst;
float x, y, z, x0, y0, z0 ;
if (!mris_dst)
mris_dst = MRISclone(mris_src) ;
x0 = y0 = z0 = 0 ; /* silly compiler warning */
for (fno = 0 ; fno < mris_src->nfaces ; fno++) {
face = &mris_dst->faces[fno] ;
if (face->ripflag)
continue ;
x = mris_dst->vertices[face->v[0]].x;
y = mris_dst->vertices[face->v[0]].y;
z = mris_dst->vertices[face->v[0]].z;
x += mris_dst->vertices[face->v[1]].x;
y += mris_dst->vertices[face->v[1]].y;
z += mris_dst->vertices[face->v[1]].z;
x += mris_dst->vertices[face->v[2]].x;
y += mris_dst->vertices[face->v[2]].y;
z += mris_dst->vertices[face->v[2]].z;
x /= face->area;
y/= face->area;
z/= face->area;
x0 += x;
y0 += y;
z0 += z;
}
x0 /= mris_dst->total_area ;
y0 /= mris_dst->total_area ;
z0 /= mris_dst->total_area ;
for (vno = 0 ; vno < mris_src->nvertices ; vno++) {
vdst = &mris_dst->vertices[vno] ;
if (vdst->ripflag)
continue ;
vdst->x -= x0 ;
vdst->y -= y0 ;
vdst->z -= z0 ;
}
mris_dst->xctr = mris_dst->yctr = mris_dst->zctr = 0 ;
return(mris_dst) ;
}
MRI_SURFACE *
MRISprojectOntoTranslatedSphere(MRI_SURFACE *mris_src, MRI_SURFACE *mris_dst, double r,
double x0, double y0, double z0) {
VERTEX *v;
int vno ;
double x, y, z, d, dx, dy, dz, dist, total_dist, x2, y2, z2 ;
if (FZERO(r))
r = DEFAULT_RADIUS ;
if (!mris_dst)
mris_dst = MRISclone(mris_src) ;
if ((mris_dst->status != MRIS_SPHERE) &&
(mris_dst->status != MRIS_PARAMETERIZED_SPHERE))
MRIScenter(mris_dst, mris_dst) ;
mris_dst->radius = r ;
for (total_dist = vno = 0 ; vno < mris_dst->nvertices ; vno++) {
v = &mris_dst->vertices[vno];
if (v->ripflag) /* shouldn't happen */
continue ;
if (vno == 118009) {
DiagBreak() ;
}
x = ((double)v->x);
y = ((double)v->y);
z = ((double)v->z);
x2 = x*x ;
y2 = y*y ;
z2 = z*z ;
dist = sqrt(x2+y2+z2) ;
if (FZERO(dist))
d = 0 ;
else
d = 1 - r / dist ;
dx = d*x ;
dy = d*y;
dz = d*z;
v->x = x-dx ;
v->y = y-dy;
v->z = z-dz;
if (!finite(v->x) || !finite(v->y) || !finite(v->z))
DiagBreak() ;
/* if ((Gdiag & DIAG_SHOW) && DIAG_VERBOSE_ON)*/
{
dist = sqrt((double)(dx*dx+dy*dy+dz*dz));
total_dist += dist;
}
#if 1
x = (double)v->x;
y = (double)v->y;
z = (double)v->z;
x2 = x*x ;
y2 = y*y ;
z2 = z*z ;
dist = sqrt(x2+y2+z2) ;
#endif
}
for (total_dist = vno = 0 ; vno < mris_dst->nvertices ; vno++) {
v = &mris_dst->vertices[vno];
if (v->ripflag) /* shouldn't happen */
continue ;
v->x += x0 ;
v->y += y0 ;
v->z += z0 ;
}
if ((Gdiag & DIAG_SHOW) && DIAG_VERBOSE_ON)
fprintf(stdout, "sphere_project: total dist = %f\n",total_dist);
MRISupdateEllipsoidSurface(mris_dst) ;
mris_dst->status = mris_src->status == MRIS_PARAMETERIZED_SPHERE ?
MRIS_PARAMETERIZED_SPHERE : MRIS_SPHERE ;
return(mris_dst) ;
}
/*-------------------------------------------------------------*/
int main(int argc, char *argv[])
{
int nargs;
int source_is_label = 0;
int source_is_path = 0;
int err = 0;
FILE* fp = NULL;
nargs = handle_version_option
(argc, argv,
"$Id: mri_path2label.c,v 1.23 2011/03/02 00:04:23 nicks Exp $",
"$Name: $");
if(nargs && argc - nargs == 1) exit (0);
argc -= nargs;
Progname = argv[0] ;
argc --;
argv++;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
if (argc == 0) usage_exit();
parse_commandline(argc, argv);
check_options();
if (checkoptsonly) return(0);
if(!label_to_path && !path_to_label) {
err = guess_file_type (source_file, &source_is_path, &source_is_label);
if (err) {
printf ("ERROR: Couldn't determine source file type.\n");
exit (1);
}
if(source_is_path) path_to_label = 1;
if(source_is_label) label_to_path = 1;
}
if (dest_file) {
fp = fopen (dest_file, "w");
if (NULL == fp) {
printf ("ERROR: Couldn't open dest file for writing.\n");
exit (1);
}
fclose (fp);
}
if(connect){
// Still under construction
printf("Connecting vertices in path\n");
int stat=connect_path(source_file, dest_file, subject, hemi) ;
exit(stat);
}
if(fill){
// Still under construction
printf("Filling vertices in path\n");
int stat=fill_path(source_file, dest_file, subject, hemi, fillseed) ;
exit(stat);
}
if(con_and_fill){
// Still under construction
printf("Connecting and Filling vertices in path\n");
int stat=
con_and_fill_path(source_file, dest_file, subject, hemi, fillseed) ;
exit(stat);
}
if(con_and_fillx){
int stat=1;
if (con_and_fillx_fname) {
// open file containing the list of fillseeds and path/label files
FILE* fp2 = fopen (con_and_fillx_fname, "r");
if (NULL == fp2) {
printf ("ERROR: Couldn't open file %s for reading.\n",
con_and_fillx_fname);
exit (1);
}
printf("Reading %s\n",surfacefname);
MRIS* mris = MRISread(surfacefname);
if(mris == NULL) exit(1);
size_t n=2000;
char tmpstr[2000];
char* tmps = &tmpstr[0];
while (0 < getline(&tmps,&n,fp2)) {
char srcfn[2000];
char dstfn[2000];
//printf("%s\n",tmpstr);
if (sscanf(tmpstr,"%d %s %s",&fillseed,srcfn,dstfn) > 0) {
printf("Connecting and filling vertices in path at fillseed %d\n",
fillseed);
MRIS* mrisclone = MRISclone(mris);
stat = con_and_fill_pathy (srcfn, dstfn, mrisclone, fillseed) ;
if (stat) break;
}
}
}
else {
printf("Connecting and filling vertices in path at fillseed %d\n",
fillseed);
stat=con_and_fill_pathx
(source_file, dest_file, surfacefname, fillseed) ;
}
exit(stat);
}
printf ("INFO: Converting %s\n", source_file);
printf ("INFO: to %s\n", dest_file);
if(path_to_label) printf ("INFO: Path to label\n");
else printf ("INFO: Label to path\n");
printf ("\n");
if (single_path) printf ("INFO: Converting a single path\n");
if (single_path) {
if(path_to_label) convert_single_path_to_label(source_file, dest_file);
else if (label_to_path) convert_single_label_to_path
(source_file, dest_file);
} else {
if (path_to_label) convert_path_to_label (source_file, dest_file);
else if (label_to_path) convert_label_to_path (source_file, dest_file);
}
return 0;
}
