/*----------------------------------------------------------------------
Parameters:
Description:
----------------------------------------------------------------------*/
static double
MRISannotArea(MRI_SURFACE *mris, int label) {
int vno, annotation ;
VERTEX *v ;
double area ;
annotation = index_to_annotation(label) ;
for (area = 0.0, vno = 0 ; vno < mris->nvertices ; vno++) {
v = &mris->vertices[vno] ;
if (v->ripflag)
continue ;
if (v->annotation == annotation)
area += v->area ;
}
return(area) ;
}
static int
translate_indices_to_annotations(MRI_SURFACE *mris, char *translation_fname) {
int vno ;
VERTEX *v ;
read_named_annotation_table(translation_fname) ;
for (vno = 0 ; vno < mris->nvertices ; vno++) {
v = &mris->vertices[vno] ;
if (v->ripflag)
continue ;
v->annotation = index_to_annotation((int)v->val) ;
if (v->annotation == -1)
v->annotation = (unknown_label > 0) ? unknown_label : 0 ;
}
return(NO_ERROR) ;
}
/*----------------------------------------------------------------------
Parameters:
Description:
----------------------------------------------------------------------*/
int
main(int argc, char *argv[]) {
char **av, *subject_name, *cp, *hemi,
*surf_name, *annot_name, fname[STRLEN], *name ;
int ac, nargs, msec, minutes, label, seconds, i ;
double area, total_area ;
struct timeb start ;
MRIS *mris ;
FILE *log_fp ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mris_compute_overlap.c,v 1.6 2011/03/02 00:04:30 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
TimerStart(&start) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 3)
usage_exit(1) ;
subject_name = argv[1] ;
hemi = argv[2] ;
surf_name = argv[3] ;
annot_name = argv[4] ;
if (strlen(sdir) == 0) {
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit
(ERROR_BADPARM,
"%s: SUBJECTS_DIR not defined in env or cmd line",
Progname) ;
strcpy(sdir, cp) ;
}
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject_name, hemi, surf_name) ;
mris = MRISread(fname) ;
if (!mris)
ErrorExit
(ERROR_NOFILE,
"%s: could not read surface from %s",
Progname,fname) ;
MRIScomputeMetricProperties(mris) ;
#if 0
if (in_label >= 0)
MRIreplaceValues(mri, mri, in_label, out_label) ;
#endif
if (compute_pct)
total_area = mris->total_area ;
else
total_area = 1 ;
if (MRISreadAnnotation(mris, annot_name) != NO_ERROR)
ErrorExit
(ERROR_NOFILE,
"%s: could not read annot file %s",
Progname, annot_name) ;
for (i = 5 ; i < argc ; i++) {
label = atoi(argv[i]) ;
name = annotation_to_name(index_to_annotation(label), NULL) ;
printf("processing label %s (%d)...\n", name, label) ;
area = MRISannotArea(mris, label) ;
if (log_fname) {
char fname[STRLEN] ;
sprintf(fname, log_fname, label) ;
printf("logging to %s...\n", fname) ;
log_fp = fopen(fname, "a+") ;
if (!log_fp)
ErrorExit(ERROR_BADFILE, "%s: could not open %s for writing",
Progname, fname) ;
} else
log_fp = NULL ;
if (compute_pct) {
printf("%2.3f mm^2 in label %d (%s), "
"%%%2.6f of total cortical area (%2.2f)\n",
area, label, name,
100.0*(float)area/(float)total_area,
total_area) ;
if (log_fp) {
fprintf(log_fp,"%2.6f\n", 100.0*area/(float)total_area) ;
fclose(log_fp) ;
}
} else {
printf("%2.0f mm^2 in label %s (%d)\n", area, name, label) ;
if (log_fp) {
fprintf(log_fp,"%f\n", area) ;
fclose(log_fp) ;
}
}
}
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
if (DIAG_VERBOSE_ON)
printf("area calculation took %d minutes and %d seconds.\n",
minutes, seconds) ;
exit(0) ;
return(0) ;
}
/*---------------------------------------------------------------*/
int main(int argc, char *argv[]) {
int nargs, nthlabel, n, vtxno, ano, index, nunhit;
nargs = handle_version_option (argc, argv, vcid, "$Name: stable5 $");
if (nargs && argc - nargs == 1) exit (0);
argc -= nargs;
cmdline = argv2cmdline(argc,argv);
uname(&uts);
getcwd(cwd,2000);
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);
dump_options(stdout);
// Make sure subject exists
sprintf(tmpstr,"%s/%s",SUBJECTS_DIR,subject);
if (!fio_IsDirectory(tmpstr)) {
printf("ERROR: cannot find %s\n",tmpstr);
exit(1);
}
if(AnnotPath == NULL){
// Get path to annot, make sure it does not exist
sprintf(tmpstr,"%s/%s/label/%s.%s.annot",
SUBJECTS_DIR,subject,hemi,AnnotName);
if (fio_FileExistsReadable(tmpstr)) {
printf("ERROR: %s already exists\n",tmpstr);
exit(1);
}
AnnotPath = strcpyalloc(tmpstr);
}
// Read the surf
sprintf(tmpstr,"%s/%s/surf/%s.orig",SUBJECTS_DIR,subject,hemi);
printf("Loading %s\n",tmpstr);
mris = MRISread(tmpstr);
if (mris == NULL) exit(1);
// Set up color table
set_atable_from_ctable(ctab);
mris->ct = ctab;
// Set up something to keep track of nhits
nhits = MRIalloc(mris->nvertices,1,1,MRI_INT);
// Set up something to keep track of max stat for that vertex
if (maxstatwinner) maxstat = MRIalloc(mris->nvertices,1,1,MRI_FLOAT);
// Go thru each label
for (nthlabel = 0; nthlabel < nlabels; nthlabel ++) {
label = LabelRead(subject,LabelFiles[nthlabel]);
if (label == NULL) {
printf("ERROR: reading %s\n",LabelFiles[nthlabel]);
exit(1);
}
index = nthlabel;
if (MapUnhitToUnknown) index ++;
ano = index_to_annotation(index);
printf("%2d %2d %s\n",index,ano,index_to_name(index));
for (n = 0; n < label->n_points; n++) {
vtxno = label->lv[n].vno;
if (vtxno < 0 || vtxno > mris->nvertices) {
printf("ERROR: %s, n=%d, vertex %d out of range\n",
LabelFiles[nthlabel],n,vtxno);
exit(1);
}
if(DoLabelThresh && label->lv[n].stat < LabelThresh) continue;
if (maxstatwinner) {
float stat = MRIgetVoxVal(maxstat,vtxno,0,0,0);
if (label->lv[n].stat < stat) {
if (verbose) {
printf("Keeping prior label for vtxno %d "
"(old_stat=%f > this_stat=%f)\n",
vtxno,stat,label->lv[n].stat);
}
continue;
}
MRIsetVoxVal(maxstat,vtxno,0,0,0,label->lv[n].stat);
}
if (verbose) {
if (MRIgetVoxVal(nhits,vtxno,0,0,0) > 0) {
printf
("WARNING: vertex %d maps to multiple labels! (overwriting)\n",
vtxno);
}
}
MRIsetVoxVal(nhits,vtxno,0,0,0,MRIgetVoxVal(nhits,vtxno,0,0,0)+1);
mris->vertices[vtxno].annotation = ano;
//printf("%5d %2d %2d %s\n",vtxno,segid,ano,index_to_name(segid));
} // label ponts
LabelFree(&label);
}// Label
nunhit = 0;
if (MapUnhitToUnknown) {
printf("Mapping unhit to unknown\n");
for (vtxno = 0; vtxno < mris->nvertices; vtxno++) {
if (MRIgetVoxVal(nhits,vtxno,0,0,0) == 0) {
ano = index_to_annotation(0);
mris->vertices[vtxno].annotation = ano;
nunhit ++;
}
}
printf("Found %d unhit vertices\n",nunhit);
}
if (dilate_label_name)
{
dilate_label_into_unknown(mris, dilate_label_annot) ;
}
printf("Writing annot to %s\n",AnnotPath);
MRISwriteAnnotation(mris, AnnotPath);
if (NHitsFile != NULL) MRIwrite(nhits,NHitsFile);
return 0;
}
