/* --------------------------------------------------------------
regio_read_xfm() - reads a transform. If the file ends in .xfm,
then the last three lines are read, and the last line of the
transform is set to 0 0 0 1. Otherwise, the last four lines
are read. Blank lines at the end will defeat it. This should
be able to read tlas properly.
-------------------------------------------------------------- */
int regio_read_xfm(char *xfmfile, MATRIX **R)
{
char *ext, *fileinfo;
int err = 0;
ext = fio_extension(xfmfile);
if (strcmp(ext,"xfm") == 0)
{
err = regio_read_mincxfm(xfmfile,R,&fileinfo);
free(fileinfo);
}
else
err = regio_read_xfm4(xfmfile,R);
free(ext);
return(err);
}
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) ;
}
