int
main(int argc, char *argv[])
{
char **av ;
int ac, nargs ;
MRI *mri=NULL ;
char *xform_fname=NULL, *in_fname=NULL, *out_fname=NULL ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_add_xform_to_header.c,v 1.12 2011/03/02 00:04:13 nicks Exp $",
"$Name: $");
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
if (argc == 1)
{
usage_exit();
}
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 2)
{
ErrorExit(ERROR_BADPARM, "%s: no transform name specified", Progname) ;
}
xform_fname = argv[1] ;
if (argc < 3)
{
ErrorExit(ERROR_BADPARM, "%s: no input name specified", Progname) ;
}
in_fname = argv[2] ;
if (argc < 4)
{
out_fname = in_fname ;
}
else
{
out_fname = argv[3] ;
}
if (verbose)
{
fprintf(stderr, "reading from %s...", in_fname) ;
}
// we have two cases, in_fname is just a directory name or .mgz
if (fio_IsDirectory(in_fname))
{
mri = MRIreadInfo(in_fname) ; // must be old COR volume
}
else if (fio_FileExistsReadable(in_fname))
{
char *ext = fio_extension(in_fname);
if (ext==0)
{
ErrorExit(ERROR_BADPARM, "%s: no extension found", Progname) ;
}
printf("INFO: extension is %s\n", ext);
if (strcmp(ext, "mgz")==0 || strcmp(ext, "mgh")==0)
{
mri = MRIread(in_fname); // mgh or mgz
}
else
{
ErrorExit(ERROR_BADPARM,
"%s: currently only .mgz or .mgh saves transform name",
Progname) ;
}
}
if (!mri)
ErrorExit(ERROR_NO_FILE, "%s: could not open source file %s",
Progname, in_fname) ;
if (! CopyNameOnly)
{
// why do we need to load the transform at this time
// mri is removed anyway???? -- good point, added -s for noload
if (input_transform_file(xform_fname, &mri->transform) != OK)
ErrorPrintf(ERROR_NO_MEMORY,
"%s: could not read xform file '%s'\n",
Progname, xform_fname);
// my guess is just to verify the validity of the transform?
mri->linear_transform = get_linear_transform_ptr(&mri->transform) ;
mri->inverse_linear_transform =
get_inverse_linear_transform_ptr(&mri->transform) ;
mri->free_transform = 1 ;
}
strcpy(mri->transform_fname, xform_fname) ;
if (verbose)
{
fprintf(stderr, "done.\nwriting to %s...", out_fname) ;
}
// this writes COR-.info only
if (fio_IsDirectory(out_fname))
{
MRIwriteInfo(mri, out_fname) ;
}
else
{
MRIwrite(mri, out_fname); // currently only mgh format write xform info
}
if (verbose)
{
fprintf(stderr, "done.\n") ;
}
MRIfree(&mri) ;
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;
}
