void shape_initialize(Shape * shape) {
vector_initialize(&shape->bounds_min);
vector_initialize(&shape->bounds_max);
for (size_t i = 0; i < shape->count; ++i)
update_bounds_min_max(shape, shape->points[i]);
}
int main( int argc , char *argv[] )
{
MRI_IMAGE *inim , *outim ; float *iv ;
int iarg , ii,jj , nreg , ntime , *tau=NULL , rnum ;
NI_element *nelmat=NULL ; char *matname=NULL ;
MTYPE rhomax=0.7 , bmax=0.7 ; int rhonum=7 , bnum=14 ;
char *cgl , *rst ;
matrix X ; vector y ;
float cput ;
reml_collection *rrcol ;
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf(
"Usage: 1dREMLfit [option] file.1D\n"
"Least squares fit with REML estimation of the ARMA(1,1) noise.\n"
"\n"
"Options (the first one is mandatory)\n"
"------------------------------------\n"
" -matrix mmm = Read the matrix 'mmm', which should have been\n"
" output from 3dDeconvolve via the '-x1D' option.\n"
" -MAXrho rm = Set the max allowed rho parameter to 'rm' (default=0.7).\n"
" -Nrho nr = Use 'nr' values for the rho parameter (default=7).\n"
" -MAXb bm = Set max allow MA b parameter to 'bm' (default=0.7).\n"
" -Nb nb = Use 'nb' values for the b parameter (default=7).\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
iarg = 1 ;
while( iarg < argc && argv[iarg][0] == '-' ){
/** rho and del params **/
if( strcmp(argv[iarg],"-MAXrho") == 0 ){
rhomax = (MTYPE)strtod(argv[++iarg],NULL) ;
if( rhomax < 0.3 ) rhomax = 0.3 ;
else if( rhomax > 0.9 ) rhomax = 0.9 ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-Nrho") == 0 ){
rhonum = (int)strtod(argv[++iarg],NULL) ;
if( rhonum < 2 ) rhonum = 2 ;
else if( rhonum > 20 ) rhonum = 20 ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-MAXb") == 0 ){
bmax = (MTYPE)strtod(argv[++iarg],NULL) ;
if( bmax < 0.3 ) bmax = 0.3 ;
else if( bmax > 0.9 ) bmax = 0.9 ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-Nb") == 0 ){
bnum = (int)strtod(argv[++iarg],NULL) ;
if( bnum < 2 ) bnum = 2 ;
else if( bnum > 20 ) bnum = 20 ;
iarg++ ; continue ;
}
/** -matrix **/
if( strcmp(argv[iarg],"-matrix") == 0 ){
if( nelmat != NULL ) ERROR_exit("More than 1 -matrix option!");
nelmat = NI_read_element_fromfile( argv[++iarg] ) ; /* read NIML file */
matname = argv[iarg];
if( nelmat == NULL ){ /* try to read as a 1D file */
MRI_IMAGE *nim ; float *nar ;
nim = mri_read_1D(argv[iarg]) ;
if( nim != NULL ){ /* construct a minimal NIML element */
nelmat = NI_new_data_element( "matrix" , nim->nx ) ;
nar = MRI_FLOAT_PTR(nim) ;
for( jj=0 ; jj < nim->ny ; jj++ )
NI_add_column( nelmat , NI_FLOAT , nar + nim->nx*jj ) ;
mri_free(nim) ;
}
}
if( nelmat == NULL || nelmat->type != NI_ELEMENT_TYPE )
ERROR_exit("Can't process -matrix file!");
iarg++ ; continue ;
}
ERROR_exit("Unknown option '%s'",argv[iarg]) ;
}
if( iarg >= argc ) ERROR_exit("No 1D file on command line?!") ;
inim = mri_read_1D( argv[iarg] ) ;
if( inim == NULL ) ERROR_exit("Can't read 1D file %s",argv[iarg]) ;
nreg = nelmat->vec_num ;
ntime = nelmat->vec_len ;
if( ntime != inim->nx )
ERROR_exit("matrix vectors are %d long but input 1D file is %d long",
ntime,inim->nx) ;
cgl = NI_get_attribute( nelmat , "GoodList" ) ;
if( cgl != NULL ){
int Ngoodlist,*goodlist , Nruns,*runs ;
NI_int_array *giar ;
giar = NI_decode_int_list( cgl , ";," ) ;
if( giar == NULL || giar->num < ntime )
ERROR_exit("-matrix 'GoodList' badly formatted?") ;
Ngoodlist = giar->num ; goodlist = giar->ar ;
rst = NI_get_attribute( nelmat , "RunStart" ) ;
if( rst != NULL ){
NI_int_array *riar = NI_decode_int_list( rst , ";,") ;
if( riar == NULL ) ERROR_exit("-matrix 'RunStart' badly formatted?") ;
Nruns = riar->num ; runs = riar->ar ;
} else {
Nruns = 1 ; runs = calloc(sizeof(int),1) ;
}
rnum = 0 ; tau = (int *)malloc(sizeof(int)*ntime) ;
for( ii=0 ; ii < ntime ; ii++ ){
jj = goodlist[ii] ;
for( ; rnum+1 < Nruns && jj >= runs[rnum+1] ; rnum++ ) ; /*nada*/
tau[ii] = jj + 10000*rnum ;
}
}
matrix_initialize( &X ) ;
matrix_create( ntime , nreg , &X ) ;
if( nelmat->vec_typ[0] == NI_FLOAT ){
float *cd ;
for( jj=0 ; jj < nreg ; jj++ ){
cd = (float *)nelmat->vec[jj] ;
for( ii=0 ; ii < ntime ; ii++ ) X.elts[ii][jj] = (MTYPE)cd[ii] ;
}
} else if( nelmat->vec_typ[0] == NI_DOUBLE ){
double *cd ;
for( jj=0 ; jj < nreg ; jj++ ){
cd = (double *)nelmat->vec[jj] ;
for( ii=0 ; ii < ntime ; ii++ ) X.elts[ii][jj] = (MTYPE)cd[ii] ;
}
} else {
ERROR_exit("-matrix file stored will illegal data type!?") ;
}
cput = COX_cpu_time() ;
rrcol = REML_setup( &X , tau , rhonum,rhomax,bnum,bmax ) ;
if( rrcol == NULL ) ERROR_exit("REML setup fails?" ) ;
cput = COX_cpu_time() - cput ;
INFO_message("REML setup: rows=%d cols=%d %d cases CPU=%.2f",
ntime,nreg,rrcol->nset,cput) ;
cput = COX_cpu_time() ;
vector_initialize( &y ) ; vector_create_noinit( ntime , &y ) ;
for( jj=0 ; jj < inim->ny ; jj++ ){
iv = MRI_FLOAT_PTR(inim) + ntime*jj ;
for( ii=0 ; ii < ntime ; ii++ ) y.elts[ii] = (MTYPE)iv[ii] ;
(void)REML_find_best_case( &y , rrcol ) ;
INFO_message(
"Vector #%d: best_rho=%.2f best_b=%.2f best_lam=%.2f best_ssq=%g olsq_ssq=%g",
jj, REML_best_rho, REML_best_bb, REML_best_lam, REML_best_ssq, REML_olsq_ssq ) ;
}
cput = COX_cpu_time() - cput ;
INFO_message("REML fitting: CPU=%.2f",cput) ;
exit(0) ;
}
static void __attribute__((constructor)) initialize_client_list()
{
vector_initialize(&client_list, 32);
}
