void THD_load_tcat( THD_datablock *dblk )
{
int ivout , dd , iv ;
THD_3dim_dataset *dset_in , *dset_out ;
NI_str_array *sar ;
ENTRY("THD_load_tcat") ;
if( !ISVALID_DBLK(dblk) ) EXRETURN ;
dset_out = (THD_3dim_dataset *)dblk->parent ;
if( !ISVALID_DSET(dset_out) ) EXRETURN ;
sar = NI_decode_string_list( dset_out->tcat_list , "~" ) ;
if( sar == NULL ) EXRETURN ;
if( sar->num != dset_out->tcat_num ){ NI_delete_str_array(sar); EXRETURN; }
ivout = 0 ;
for( dd=0 ; dd < sar->num ; dd++ ){
dset_in = THD_open_dataset( sar->str[dd] ) ;
if( dset_in == NULL ){
NI_delete_str_array(sar) ; DSET_unload(dset_out) ;
EXRETURN ;
}
DSET_mallocize(dset_in) ; DSET_load(dset_in) ;
if( !DSET_LOADED(dset_in) ){
NI_delete_str_array(sar) ; DSET_unload(dset_out) ; DSET_delete(dset_in) ;
EXRETURN ;
}
for( iv=0 ; iv < DSET_NVALS(dset_in) ; iv++ ){
EDIT_substitute_brick( dset_out , ivout ,
DSET_BRICK_TYPE(dset_in,iv), DSET_ARRAY(dset_in,iv) );
mri_fix_data_pointer( NULL , DSET_BRICK(dset_in,iv) ) ;
EDIT_BRICK_FACTOR( dset_out , ivout , DSET_BRICK_FACTOR(dset_in,iv) ) ;
EDIT_BRICK_LABEL(dset_out, ivout,
DSET_BRICK_LABEL(dset_in, iv)); /* ZSS Aug. 27 2012 */
ivout++ ;
}
DSET_delete(dset_in) ;
}
NI_delete_str_array(sar) ; EXRETURN ;
}
THD_3dim_dataset * THD_open_tcat( char *dlist )
{
THD_3dim_dataset *dset_out , **dset_in ;
int ndset_in , dd , nerr , new_nvals, sb=0 ;
NI_str_array *sar ;
double angle=0.0;
char *dp, *dlocal = dlist; /* local dlist, in case it is altered */
ENTRY("THD_open_tcat") ;
if( dlocal == NULL || *dlocal == '\0' ) RETURN(NULL) ;
/* allow file list to be read from a file 23 Jul 2012 [rickr] */
if( ! strncmp(dlocal, "filelist:", 9) ) {
dlocal = AFNI_suck_file(dlocal+9) ;
if ( ! dlocal ) {
ERROR_message("THD_open_tcat: failed to open '%s' as filelist",
dlocal+9);
RETURN(NULL) ;
}
/* make it look more like expected */
for( dd=0, dp=dlocal; dd < strlen(dlocal); dd++, dp++ )
if( *dp == '\n' || *dp == '\r' ) *dp = ' ';
}
if( strchr(dlocal,' ') == NULL ){
dset_out = THD_open_dataset(dlocal) ; RETURN(dset_out) ;
}
sar = NI_decode_string_list( dlocal , "~" ) ;
if( sar == NULL ) RETURN(NULL) ;
ndset_in = sar->num ;
dset_in = (THD_3dim_dataset **)malloc(sizeof(THD_3dim_dataset *)*sar->num) ;
for( nerr=dd=0 ; dd < ndset_in ; dd++ ){
dset_in[dd] = THD_open_dataset( sar->str[dd] ) ;
if( dset_in[dd] == NULL ){
fprintf(stderr,"** THD_open_tcat: can't open dataset %s\n",sar->str[dd]) ;
nerr++ ;
}
}
if( nerr > 0 ){
for( dd=0 ; dd < ndset_in ; dd++ )
if( dset_in[dd] != NULL ) DSET_delete(dset_in[dd]) ;
free((void *)dset_in) ;
NI_delete_str_array(sar) ;
RETURN(NULL) ;
}
if( ndset_in == 1 ){
dset_out = dset_in[0] ;
free((void *)dset_in) ;
NI_delete_str_array(sar) ;
RETURN(dset_out) ;
}
(void)THD_check_for_duplicates( sar->num , sar->str , 1 ) ; /* 31 May 2007 */
for( nerr=0,dd=1 ; dd < ndset_in ; dd++ ){
if( DSET_NX(dset_in[0]) != DSET_NX(dset_in[dd]) ||
DSET_NY(dset_in[0]) != DSET_NY(dset_in[dd]) ||
DSET_NZ(dset_in[0]) != DSET_NZ(dset_in[dd]) ){
ERROR_message(
"THD_open_tcat: %s [%dx%dx%d] doesn't match %s [%dx%dx%d]\n",
sar->str[0] ,DSET_NX(dset_in[0]) ,
DSET_NY(dset_in[0]) ,DSET_NZ(dset_in[0]) ,
sar->str[dd],DSET_NX(dset_in[dd]),
DSET_NY(dset_in[dd]),DSET_NZ(dset_in[dd]) ) ;
nerr++ ;
} else {
if( !EQUIV_DATAXES(dset_in[dd]->daxes,dset_in[0]->daxes) ){
WARNING_message(
"THD_open_tcat: %s grid mismatch with %s\n",
sar->str[0] , sar->str[dd] ) ; /* don't increment nerr! */
}
angle = dset_obliquity_angle_diff(dset_in[dd], dset_in[0], -1.0);
if (angle > 0.0) {
WARNING_message(
"dataset %s has an obliquity difference of %f degress with %s\n",
dset_in[dd] ,
angle, dset_in[0] );
}
}
}
if( nerr > 0 ){
for( dd=0 ; dd < ndset_in ; dd++ )
if( dset_in[dd] != NULL ) DSET_delete(dset_in[dd]) ;
free((void *)dset_in) ;
NI_delete_str_array(sar) ;
RETURN(NULL) ;
}
/*-- Check for type problems ZSS: Aug 27 2012 --*/
for (nerr=0,dd=0; dd < ndset_in ; dd++) {
for (sb=0; sb < DSET_NVALS(dset_in[dd]); ++sb) {
if ( DSET_BRICK_TYPE(dset_in[0],0) !=
DSET_BRICK_TYPE(dset_in[dd],sb) ) {
++nerr;
}
}
}
if (nerr > 0) { /* don't die, just complain */
WARNING_message(
"Command-line catenated dataset has %d sub-bricks that differ \n"
" in data type from the first sub-brick of the first set.\n"
" Mme Irma sees potential for grief if you go down that path. \n"
" Use 3dinfo -datum on each input to understand why this is happening.\n"
" You can use 3dcalc's -datum option to rewrite the dataset with \n"
" all sub-bricks set to the same type then start over.\n\n",
nerr);
nerr=0;
}
/*-- OK, start making new dataset --*/
new_nvals = 0 ;
for( dd=0 ; dd < ndset_in ; dd++ )
new_nvals += DSET_NVALS(dset_in[dd]) ;
for( dd=0 ; dd < ndset_in ; dd++ )
if( DSET_TIMESTEP(dset_in[dd]) > 0.0 ) break ; /* 1st 3D+time */
if( dd == ndset_in ) dd = 0 ;
dset_out = EDIT_empty_copy( dset_in[dd] ) ;
/* since this is basically an input dataset, set the storage_mode
* to match 27 Jul 2010 [rickr] */
if( DSET_ONDISK(dset_out) && IS_VALID_NON_AFNI_DSET(dset_in[dd]) )
THD_set_storage_mode(dset_out, dset_in[dd]->dblk->diskptr->storage_mode);
EDIT_dset_items( dset_out ,
ADN_prefix , "tcat" ,
ADN_func_type , ISANAT(dset_in[dd]) ? ANAT_EPI_TYPE
: FUNC_FIM_TYPE ,
ADN_ntt , new_nvals ,
ADN_nvals , new_nvals ,
ADN_none ) ;
DSET_mallocize( dset_out ) ;
/* check if we have a valid time axis; if not, make one up */
if( DSET_TIMESTEP(dset_out) <= 0.0f ){
float TR=1.0f , torg=0.0f , tdur=0.0f ;
int tunits=UNITS_SEC_TYPE ;
EDIT_dset_items( dset_out ,
ADN_tunits , tunits ,
ADN_ttdel , TR ,
ADN_ttorg , torg ,
ADN_ttdur , tdur ,
ADN_none ) ;
}
dset_out->tcat_list = strdup( dlocal ) ;
dset_out->tcat_num = ndset_in ;
dset_out->tcat_len = (int *)malloc(sizeof(int)*ndset_in) ;
for( dd=0 ; dd < ndset_in ; dd++ ){
dset_out->tcat_len[dd] = DSET_NVALS(dset_in[dd]) ;
DSET_delete(dset_in[dd]) ;
}
free((void *)dset_in) ;
NI_delete_str_array(sar) ;
#if 0
fprintf(stderr,"THD_open_tcat('%s'):",dset_out->tcat_list);
for(dd=0;dd<ndset_in;dd++)fprintf(stderr," %d",dset_out->tcat_len[dd]);
fprintf(stderr,"\n");
#endif
RETURN(dset_out) ;
}
int THD_datablock_from_atr( THD_datablock *dblk, char *dirname, char *headname )
{
THD_diskptr *dkptr ;
ATR_int *atr_rank , *atr_dimen , *atr_scene , *atr_btype ;
ATR_float *atr_flt ;
ATR_string *atr_labs ;
int ii , view_type , func_type , dset_type ,
nx,ny,nz,nvox , nvals , ibr,typ ;
Boolean ok ;
char prefix[THD_MAX_NAME]="Unknown" ;
MRI_IMAGE *qim ;
int brick_ccode ;
char name[666] ;
ENTRY("THD_datablock_from_atr") ;
if( dblk == NULL || dblk->natr <= 0 ) RETURN(0) ; /* bad input */
dkptr = dblk->diskptr ;
/*-- get relevant attributes: rank, dimensions, view_type & func_type --*/
atr_rank = THD_find_int_atr( dblk , ATRNAME_DATASET_RANK ) ;
atr_dimen = THD_find_int_atr( dblk , ATRNAME_DATASET_DIMENSIONS ) ;
atr_scene = THD_find_int_atr( dblk , ATRNAME_SCENE_TYPE ) ;
/*-- missing an attribute ==> quit now --*/
if( atr_rank == NULL || atr_dimen == NULL || atr_scene == NULL ) RETURN(0) ;
/*-- load type codes from SCENE attribute --*/
STATUS("loading *_type from SCENE") ;
view_type = atr_scene->in[0] ;
func_type = atr_scene->in[1] ;
dset_type = atr_scene->in[2] ;
/*-- load other values from attributes into relevant places --*/
ok = True ;
nvox = 1 ;
STATUS("loading from RANK") ;
dkptr->rank = atr_rank->in[0] ; /* N.B.: rank isn't used much */
dkptr->nvals = dblk->nvals = nvals = atr_rank->in[1] ; /* but nvals is used */
STATUS("loading from DIMENSIONS") ;
for( ii=0 ; ii < dkptr->rank ; ii++ ){
dkptr->dimsizes[ii] = atr_dimen->in[ii] ;
ok = ( ok && dkptr->dimsizes[ii] >= 1 ) ;
nvox *= dkptr->dimsizes[ii] ;
}
#if 0
if( PRINT_TRACING ){
char str[256] ;
sprintf(str,"rank=%d nvals=%d dim[0]=%d dim[1]=%d dim[2]=%d nvox=%d",
dkptr->rank , dkptr->nvals ,
dkptr->dimsizes[0] , dkptr->dimsizes[1] , dkptr->dimsizes[2] , nvox ) ;
STATUS(str) ;
}
#endif
if( !ok || nvals < 1 ||
dkptr->rank < THD_MIN_RANK || dkptr->rank > THD_MAX_RANK ){
STATUS("bad rank!!??") ;
RETURN(0) ;
}
/*-- create the storage filenames --*/
STATUS("creating storage filenames") ;
if( headname != NULL && strchr(headname,'+') != NULL ){
FILENAME_TO_PREFIX(headname,prefix) ;
THD_init_diskptr_names( dkptr, dirname,NULL,prefix , view_type , True ) ;
} else {
if( headname != NULL ) MCW_strncpy(prefix,headname,THD_MAX_NAME) ;
THD_init_diskptr_names( dkptr, dirname,NULL,prefix , view_type , True ) ;
}
/*-- determine if the BRIK file exists --*/
STATUS("checking if .BRIK file exists") ;
brick_ccode = COMPRESS_filecode(dkptr->brick_name) ;
if (dkptr->storage_mode == STORAGE_UNDEFINED) { /* ZSS: Oct. 2011
the next line was being called all the time before */
if( brick_ccode != COMPRESS_NOFILE )
dkptr->storage_mode = STORAGE_BY_BRICK ; /* a .BRIK file */
}
/*-- if VOLUME_FILENAMES attribute exists, make it so [20 Jun 2002] --*/
if( headname != NULL && dkptr->storage_mode == STORAGE_UNDEFINED ){
atr_labs = THD_find_string_atr(dblk,"VOLUME_FILENAMES") ;
if( atr_labs != NULL ){
dkptr->storage_mode = STORAGE_BY_VOLUMES ;
dblk->malloc_type = DATABLOCK_MEM_MALLOC ;
}
}
/*-- now set the memory allocation codes, etc. --*/
dblk->brick_fac = (float *) XtMalloc( sizeof(float) * nvals ) ;
for( ibr=0 ; ibr < nvals ; ibr++ ) dblk->brick_fac[ibr] = 0.0 ;
/* scaling factors from short type to float type, if nonzero */
if( !AFNI_yesenv("AFNI_IGNORE_BRICK_FLTFAC") ){
atr_flt = THD_find_float_atr( dblk , ATRNAME_BRICK_FLTFAC ) ;
if( atr_flt != NULL ){
for( ibr=0 ; ibr < nvals && ibr < atr_flt->nfl ; ibr++ )
dblk->brick_fac[ibr] = atr_flt->fl[ibr] ;
}
}
/** Now create an empty shell of the "brick" == the data structure
that will hold all the voxel data. Note that all datablocks
will have a brick, even if they never actually contain data
themselves (are only warp-on-demand).
If the BRICK_TYPES input attribute doesn't exist, then all
sub-bricks are shorts. This makes the code work with old-style
datasets, which were always made up of shorts.
**/
atr_btype = THD_find_int_atr( dblk , ATRNAME_BRICK_TYPES ) ;
if( atr_btype == NULL ){
THD_init_datablock_brick( dblk , MRI_short , NULL ) ;
} else {
THD_init_datablock_brick( dblk , atr_btype->nin , atr_btype->in ) ;
}
if( !THD_datum_constant(dblk) ){ /* 15 Sep 2004 */
fprintf(stderr,
"\n** WARNING: File %s has mixed-type sub-bricks. ", MYHEAD ) ;
}
/* 25 April 1998: check if the byte order is stored inside */
atr_labs = THD_find_string_atr( dblk , ATRNAME_BYTEORDER ) ;
if( atr_labs != NULL && atr_labs->nch > 0 ){
if( strncmp(atr_labs->ch,LSB_FIRST_STRING,ORDER_LEN) == 0 )
dkptr->byte_order = LSB_FIRST ;
else if( strncmp(atr_labs->ch,MSB_FIRST_STRING,ORDER_LEN) == 0 )
dkptr->byte_order = MSB_FIRST ;
else
fprintf(stderr,"*** Unknown %s found in dataset %s\n",
ATRNAME_BYTEORDER , MYHEAD ) ;
} else if( !no_ordwarn &&
DBLK_BRICK_TYPE(dblk,0) != MRI_byte &&
dblk->diskptr->storage_mode == STORAGE_BY_BRICK ){ /* 20 Sep 1999 */
static int first=1 ;
if( first ){
fprintf(stderr,
"\n*** The situation below can be rectified with program '3drefit -byteorder':\n");
first = 0 ;
}
fprintf(stderr," ** Dataset %s: assuming byteorder %s\n",
MYHEAD , BYTE_ORDER_STRING(dkptr->byte_order) ) ;
}
/* if the data is not on disk, the flag remains at DATABLOCK_MEM_UNDEFINED,
otherwise the flag says how the memory for the bricks is to be created. */
if( dkptr->storage_mode == STORAGE_BY_BRICK ){
#if MMAP_THRESHOLD > 0
dblk->malloc_type = (dblk->total_bytes > MMAP_THRESHOLD)
? DATABLOCK_MEM_MMAP : DATABLOCK_MEM_MALLOC ;
DBLK_mmapfix(dblk) ; /* 18 Mar 2005 */
#else
dblk->malloc_type = DATABLOCK_MEM_MALLOC ;
#endif
/* must be malloc-ed if:
data is compressed,
data is not in native byte order, or
user explicity forbids use of mmap */
if( brick_ccode >= 0 || dkptr->byte_order != native_order || no_mmap )
dblk->malloc_type = DATABLOCK_MEM_MALLOC ;
}
/* 30 Nov 1997: create the labels for sub-bricks */
THD_init_datablock_labels( dblk ) ;
atr_labs = THD_find_string_atr( dblk , ATRNAME_BRICK_LABS ) ;
if( atr_labs != NULL && atr_labs->nch > 0 ){ /* create labels from attribute */
int ipos = -1 , ipold , ngood ;
for( ibr=0 ; ibr < nvals ; ibr++ ){ /* loop over bricks */
for( ipold = ipos++ ; /* skip to */
ipos < atr_labs->nch && atr_labs->ch[ipos] != '\0' ; /* next \0 */
ipos++ ) /* nada */ ; /* or end. */
ngood = ipos - ipold - 1 ; /* number of good chars */
if( ngood > 0 ){
XtFree(dblk->brick_lab[ibr]) ;
/* 27 Oct 2011 - increase to 64 */
if( ngood > THD_MAX_SBLABEL ) ngood = THD_MAX_SBLABEL;
dblk->brick_lab[ibr] = (char *) XtMalloc(sizeof(char)*(ngood+2)) ;
memcpy( dblk->brick_lab[ibr] , atr_labs->ch+(ipold+1) , ngood ) ;
dblk->brick_lab[ibr][ngood] = '\0' ;
}
if( ipos >= atr_labs->nch ) break ; /* nothing more to do */
} /* end of loop over sub-bricks */
}
/* create the keywords for sub-bricks */
THD_init_datablock_keywords( dblk ) ;
atr_labs = THD_find_string_atr( dblk , ATRNAME_BRICK_KEYWORDS ) ;
if( atr_labs != NULL && atr_labs->nch > 0 ){ /* create keywords from attribute */
int ipos = -1 , ipold , ngood ;
for( ibr=0 ; ibr < nvals ; ibr++ ){ /* loop over bricks */
for( ipold = ipos++ ; /* skip to */
ipos < atr_labs->nch && atr_labs->ch[ipos] != '\0' ; /* next \0 */
ipos++ ) /* nada */ ; /* or end. */
ngood = ipos - ipold - 1 ; /* number of good chars */
if( ngood > 0 ){
XtFree(dblk->brick_keywords[ibr]) ;
dblk->brick_keywords[ibr] = (char *) XtMalloc(sizeof(char)*(ngood+2)) ;
memcpy( dblk->brick_keywords[ibr] , atr_labs->ch+(ipold+1) , ngood ) ;
dblk->brick_keywords[ibr][ngood] = '\0' ;
}
if( ipos >= atr_labs->nch ) break ; /* nothing more to do */
} /* end of loop over sub-bricks */
}
/* create the auxiliary statistics stuff for each brick, if present */
atr_labs = THD_find_string_atr( dblk , "BRICK_STATSYM" ) ; /* 01 Jun 2005 */
if( atr_labs != NULL && atr_labs->nch > 0 ){
NI_str_array *sar ; int scode,np ; float parm[3] ;
sar = NI_decode_string_list( atr_labs->ch , ";" ) ;
if( sar != NULL && sar->num > 0 ){
for( ibr=0 ; ibr < nvals && ibr < sar->num ; ibr++ ){
NI_stat_decode( sar->str[ibr] , &scode , parm,parm+1,parm+2 ) ;
if( scode >= AFNI_FIRST_STATCODE && scode <= AFNI_LAST_STATCODE ){
np = NI_stat_numparam(scode) ;
THD_store_datablock_stataux( dblk , ibr,scode,np,parm ) ;
}
}
NI_delete_str_array(sar) ;
}
} else { /*--- the olde way to get ye brick stataux parameters ---*/
atr_flt = THD_find_float_atr( dblk , ATRNAME_BRICK_STATAUX ) ;
if( atr_flt != NULL && atr_flt->nfl >= 3 ){
int ipos=0 , iv,nv,jv ;
/* attribute stores all stataux stuff as follows:
sub-brick-index statcode no.-of-values value ... value
sub-brick-index statcode no.-of-values value ... value, etc. */
while( ipos <= atr_flt->nfl - 3 ){
iv = (int) ( atr_flt->fl[ipos++] ) ; /* which sub-brick */
jv = (int) ( atr_flt->fl[ipos++] ) ; /* statcode */
nv = (int) ( atr_flt->fl[ipos++] ) ; /* # of values that follow */
if( nv > atr_flt->nfl - ipos ) nv = atr_flt->nfl - ipos ;
THD_store_datablock_stataux( dblk , iv , jv , nv , atr_flt->fl + ipos ) ;
ipos += nv ;
}
}
}
#if 0
if( PRINT_TRACING ){
char str[256] ;
sprintf(str,"rank=%d nvals=%d dim[0]=%d dim[1]=%d dim[2]=%d",
dkptr->rank , dkptr->nvals ,
dkptr->dimsizes[0] , dkptr->dimsizes[1] , dkptr->dimsizes[2] ) ;
STATUS(str) ;
}
#endif
/*-- FDR curves [23 Jan 2008] --*/
for( ibr=0 ; ibr < dblk->nvals ; ibr++ ){
sprintf(name,"FDRCURVE_%06d",ibr) ;
atr_flt = THD_find_float_atr( dblk , name ) ;
if( atr_flt != NULL && atr_flt->nfl > 3 ){
int nv = atr_flt->nfl - 2 ; floatvec *fv ;
MAKE_floatvec(fv,nv) ;
fv->x0 = atr_flt->fl[0] ; fv->dx = atr_flt->fl[1] ;
memcpy( fv->ar , atr_flt->fl + 2 , sizeof(float)*nv ) ;
if( dblk->brick_fdrcurve == NULL )
dblk->brick_fdrcurve = (floatvec **)calloc(sizeof(floatvec *),dblk->nvals);
dblk->brick_fdrcurve[ibr] = fv ;
}
}
for( ibr=0 ; ibr < dblk->nvals ; ibr++ ){
sprintf(name,"MDFCURVE_%06d",ibr) ;
atr_flt = THD_find_float_atr( dblk , name ) ;
if( atr_flt != NULL && atr_flt->nfl > 3 ){
int nv = atr_flt->nfl - 2 ; floatvec *fv ;
MAKE_floatvec(fv,nv) ;
fv->x0 = atr_flt->fl[0] ; fv->dx = atr_flt->fl[1] ;
memcpy( fv->ar , atr_flt->fl + 2 , sizeof(float)*nv ) ;
if( dblk->brick_mdfcurve == NULL )
dblk->brick_mdfcurve = (floatvec **)calloc(sizeof(floatvec *),dblk->nvals);
dblk->brick_mdfcurve[ibr] = fv ;
}
}
RETURN(1) ;
}
SEG_OPTS *GenFeatureDist_ParseInput (SEG_OPTS *Opt, char *argv[], int argc)
{
static char FuncName[]={"GenFeatureDist_ParseInput"};
int kar, i, ind, exists;
char *outname, cview[10], *sbuf=NULL;
int brk = 0;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_ENTRY;
brk = 0;
kar = 1;
while (kar < argc) { /* loop accross command ine options */
/*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
Opt->helpfunc(0);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
#ifdef USE_TRACING
if( strncmp(argv[kar],"-trace",5) == 0 ){
DBG_trace = 1 ;
brk = 1 ;
}
if( strncmp(argv[kar],"-TRACE",5) == 0 ){
DBG_trace = 2 ;
brk = 1 ;
}
#endif
if (!brk && (strcmp(argv[kar], "-debug") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -debug \n");
exit (1);
}
Opt->debug = atoi(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-talk_afni") == 0)) {
Opt->ps->cs->talk_suma = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-openmp") == 0)) {
Opt->openmp = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-no_openmp") == 0)) {
Opt->openmp = 0;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-vox_debug") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need 1D vox index after -vox_debug \n");
exit (1);
}
if (kar+2<argc) { /* see if we have ijk */
int iii, jjj, kkk;
if (argv[kar][0]!='-' && argv[kar][1]!='-' && argv[kar][2]!='-' &&
(iii = atoi(argv[kar ])) >= 0 &&
(jjj = atoi(argv[kar+1])) >= 0 &&
(kkk = atoi(argv[kar+2])) >= 0 ) {
Opt->VoxDbg3[0]=iii;
Opt->VoxDbg3[1]=jjj;
Opt->VoxDbg3[2]=kkk;
++kar; ++kar;
}
}
if (Opt->VoxDbg3[0] < 0) {
Opt->VoxDbg = atoi(argv[kar]);
}
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-vox_debug_file") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need filename after -vox_debug_file \n");
exit (1);
}
if (!strcmp(argv[kar],"-")) {
Opt->VoxDbgOut = stdout;
} else if (!strcmp(argv[kar],"+")) {
Opt->VoxDbgOut = stderr;
} else {
Opt->VoxDbgOut = fopen(argv[kar],"w");
}
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-cmask") == 0)) {
kar ++;
if (kar >= argc) {
ERROR_exit("-cmask option requires a following argument!\n");
}
Opt->cmask = EDT_calcmask( argv[kar] , &(Opt->dimcmask), 0 ) ;
if( Opt->cmask == NULL ) ERROR_exit("Can't compute -cmask!\n");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-mask") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -mask \n");
exit (1);
}
Opt->mset_name = argv[kar];
brk = 1;
}
if( !brk && (strncmp(argv[kar],"-mrange",5) == 0) ){
if( kar+2 >= argc )
ERROR_exit("-mrange option requires 2 following arguments!\n");
Opt->mask_bot = strtod( argv[++kar] , NULL ) ;
Opt->mask_top = strtod( argv[++kar] , NULL ) ;
if( Opt->mask_top < Opt->mask_bot )
ERROR_exit("-mrange inputs are illegal!\n") ;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-anat") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -anat \n");
exit (1);
}
Opt->aset_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-sig") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -sig \n");
exit (1);
}
while (kar < argc && argv[kar][0] != '-') {
sbuf =
SUMA_append_replace_string(sbuf, argv[kar], " ", 1);
++kar;
}
if (kar < argc && argv[kar][0] == '-') --kar; /* unwind */
Opt->sig_names = SUMA_NI_str_array(Opt->sig_names, sbuf, "add");
SUMA_free(sbuf); sbuf = NULL;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-samp") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -samp \n");
exit (1);
}
while (kar < argc && argv[kar][0] != '-') {
sbuf =
SUMA_append_replace_string(sbuf, argv[kar], " ", 1);
++kar;
}
if (kar < argc && argv[kar][0] == '-') --kar; /* unwind */
Opt->samp_names = SUMA_NI_str_array(Opt->samp_names, sbuf, "add");
SUMA_free(sbuf); sbuf = NULL;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-hspec") == 0)) {
kar ++;
if (kar+3 >= argc) {
fprintf (stderr, "need 4 arguments after -hspec \n");
exit (1);
}
Opt->hspec = (SUMA_HIST **)
SUMA_realloc(Opt->hspec, (Opt->N_hspec+1)*sizeof(SUMA_HIST *));
Opt->hspec[Opt->N_hspec] = (SUMA_HIST*)SUMA_calloc(1,sizeof(SUMA_HIST));
Opt->hspec[Opt->N_hspec]->label = SUMA_copy_string(argv[kar++]);
Opt->hspec[Opt->N_hspec]->min = (float)strtod(argv[kar++],NULL);
Opt->hspec[Opt->N_hspec]->max = (float)strtod(argv[kar++],NULL);
Opt->hspec[Opt->N_hspec]->K = (float)strtod(argv[kar],NULL);
++Opt->N_hspec;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -prefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->proot = argv[kar];
Opt->prefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->crefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->pgrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->cgrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->frefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->xrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->prefix,"%s.p", argv[kar]);
sprintf(Opt->pgrefix,"%s.pg", argv[kar]);
sprintf(Opt->crefix,"%s.c", argv[kar]);
sprintf(Opt->cgrefix,"%s.cg", argv[kar]);
sprintf(Opt->frefix,"%s.f", argv[kar]);
sprintf(Opt->xrefix,"%s.x", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-classes") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -classes \n");
exit (1);
}
Opt->clss = NI_strict_decode_string_list(argv[kar] ,";, ");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-features") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -features \n");
exit (1);
}
Opt->feats = NI_strict_decode_string_list(argv[kar] ,";, ");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-keys") == 0)) {
NI_str_array *nstr=NULL; int ii;
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -keys \n");
exit (1);
}
if (!(nstr = NI_strict_decode_string_list(argv[kar] ,";, "))){
ERROR_exit("Bad option %s after -keys", argv[kar]);
}
Opt->keys = (int *)calloc(nstr->num, sizeof(int));
for (ii=0;ii<nstr->num; ++ii)
Opt->keys[ii] = strtol(nstr->str[ii],NULL,10);
NI_delete_str_array(nstr);nstr=NULL;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-labeltable") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -labeltable \n");
exit (1);
}
Opt->labeltable_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-uid") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -uid \n");
exit (1);
}
snprintf(Opt->uid,128,"%s",argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-ShowTheseHists") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -ShowTheseHists \n");
exit (1);
}
{
NI_str_array *hisnames=NULL;
SUMA_HIST *hh=NULL;
int ii=0;
hisnames = NI_strict_decode_string_list(argv[kar],";, ");
for (ii=0; ii<hisnames->num; ++ii) {
if ((hh = SUMA_read_hist(hisnames->str[ii]))) {
SUMA_Show_hist(hh, 1, NULL);
hh = SUMA_Free_hist(hh);
} else {
SUMA_S_Errv("Hist %s not found.\n", hisnames->str[ii]);
exit(1);
}
}
hisnames = SUMA_free_NI_str_array(hisnames);
}
exit(0);
brk = 1;
}
if (!brk) {
fprintf (stderr,"Option #%d %s not understood. \n"
"Try -help for usage\n", kar, argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = 0;
kar ++;
}
}
if (!Opt->prefix) Opt->prefix = strdup("./GenFeatureDistOut.p");
if (!Opt->frefix) Opt->frefix = strdup("./GenFeatureDistOut.f");
if (!Opt->xrefix) Opt->xrefix = strdup("./GenFeatureDistOut.x");
if (!Opt->crefix) Opt->crefix = strdup("./GenFeatureDistOut.c");
if (Opt->uid[0]=='\0') UNIQ_idcode_fill(Opt->uid);
if (Opt->VoxDbg > -1 && !Opt->VoxDbgOut) {
char stmp[256];
sprintf(stmp,"%d.GFD.dbg", Opt->VoxDbg);
Opt->VoxDbgOut = fopen(stmp,"w");
}
SUMA_RETURN(Opt);
}
int main( int argc , char * argv[] )
{
int nim , ii , jj , kk , nx, narg, oform ;
MRI_IMAGE **inim ;
float *far;
char *formatstr=NULL, *sel=NULL, *fname=NULL;
int nonconst=0 , ncol,ncold , cc , nonfixed=0 , stack=0;
intvec *ncv=NULL ;
char *hline=NULL ;
mainENTRY("1dcat:main");
/*-- help? --*/
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf(
"Usage: 1dcat [options] a.1D b.1D ...\n"
" where each file a.1D, b.1D, etc. is a 1D file.\n"
" In the simplest form, a 1D file is an ASCII file of numbers\n"
" arranged in rows and columns.\n"
"\n"
"1dcat takes as input one or more 1D files, and writes out a 1D file\n"
"containing the side-by-side concatenation of all or a subset of the\n"
"columns from the input files.\n"
"\n"
"* Output goes to stdout (the screen); redirect (e.g., '>') to save elsewhere.\n"
"* All files MUST have the same number of rows!\n"
"* Any header lines (i.e., lines that start with '#') will be lost.\n"
"* For generic 1D file usage help and information, see '1dplot -help'\n"
"\n"
"OPTIONS:\n"
"--------\n"
" -nonconst: Columns that are identically constant should be omitted\n"
" from the output.\n"
"\n"
" -nonfixed: Keep only columns that are marked as 'free' in the \n"
" 3dAllineate header from '-1Dparam_save'.\n"
" If there is no such header, all columns are kept.\n"
"\n"
" -form FORM: Format of the numbers to be output.\n"
" You can also substitute -form FORM with shortcuts such \n"
" as -i, -f, or -c.\n"
" For help on -form's usage, and its shortcut versions\n"
" see ccalc's help for the option of the same name. \n"
"\n"
" -stack: Stack the columns of the resultant matrix in the output.\n"
"\n"
" -sel SEL: Apply the same column/row selection string to all filenames\n"
" on the command line.\n"
" For example:\n"
" 1dcat -sel '[0,2]' f1.1D f2.1D\n"
" is the same as: 1dcat f1.1D'[1,2]' f2.1D'[1,2]'\n"
" The advantage of the option is that it allows wildcard use\n"
" in file specification so that you can run something like:\n"
" 1dcat -sel '[0,2]' f?.1D\n"
"\n"
"EXAMPLE:\n"
"--------\n"
" Input file 1:\n 1\n 2\n 3\n 4\n"
" Input file 2:\n 5\n 6\n 7\n 8\n"
"\n"
" 1dcat data1.1D data2.1D > catout.1D\n"
" Output file: \n 1 5\n 2 6\n 3 7\n 4 8\n"
"\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
machdep() ;
/* do we have any options? */
oform = CCALC_NOT_SET;
sel = NULL;
stack = 0;
narg = 1;
while (narg < argc && argv[narg][0] == '-') {
if( strncmp(argv[narg],"-nonconst",7) == 0 ){ /* 04 Dec 2010 */
nonconst++ ; narg++ ; continue ;
}
if( strncmp(argv[narg],"-nonfixed",7) == 0 ){ /* 06 Dec 2010 */
nonfixed++ ; narg++ ; continue ;
}
if( strncmp(argv[narg],"-stack",6) == 0 ){ /* 05 Sep 2013 */
stack = 1 ; narg++ ; continue ;
}
if (strcmp(argv[narg],"-form") == 0) {
++narg;
if (narg >= argc) {
fprintf (stderr, "need argument after -form ");
exit (1);
}
if (strcmp(argv[narg],"double") == 0 ) oform = CCALC_DOUBLE;
else if (strcmp(argv[narg],"nice") == 0 ) oform = CCALC_NICE;
else if (strcmp(argv[narg],"int") == 0 ) oform = CCALC_INT;
else if (strcmp(argv[narg],"rint") == 0 ) oform = CCALC_INT;
else if (strcmp(argv[narg],"fint") == 0 ) oform = CCALC_FINT;
else if (strcmp(argv[narg],"cint") == 0 ) oform = CCALC_CINT;
else if (strlen(argv[narg])<=256) {
oform = CCALC_CUSTOM;
formatstr = argv[narg];
}
else {
fprintf (stderr, "Format type '%s' not supported.\n"
"See -help for details.\n", argv[narg]);
exit (1);
}
++narg;
} else if (strcmp(argv[narg],"-sel") == 0) {
++narg;
if (narg >= argc) {
fprintf (stderr, "need argument after -sel ");
exit (1);
}
sel = argv[narg]; ++narg;
} else if (strncmp(argv[narg],"-d",2) == 0) {
oform = CCALC_DOUBLE; ++narg;
} else if (strncmp(argv[narg],"-n",2) == 0) {
oform = CCALC_NICE; ++narg;
} else if (strncmp(argv[narg],"-i",2) == 0) {
oform = CCALC_INT; ++narg;
} else if (strncmp(argv[narg],"-r",2) == 0) {
oform = CCALC_INT; ++narg;
} else if (strncmp(argv[narg],"-f",2) == 0) {
oform = CCALC_FINT; ++narg;
} else if (strncmp(argv[narg],"-c",2) == 0) {
oform = CCALC_CINT; ++narg;
} else { /* break if option is not recognized */
++narg;
break;
}
}
/* read input files */
nim = argc-narg ;
inim = (MRI_IMAGE **) malloc( sizeof(MRI_IMAGE *) * nim ) ;
ncol = 0 ;
if( nonconst || nonfixed ) MAKE_intvec(ncv,1) ;
for( jj=0 ; jj < nim ; jj++ ){
#if 0 /** for testing only **/
if( AFNI_yesenv("ragged") ){
MRI_IMAGE *qim ;
qim = mri_read_ascii_ragged( argv[jj+narg] , 3.e+33 ) ;
fprintf(stderr,"qim: nx=%d ny=%d\n",qim->nx,qim->ny) ;
inim[jj] = mri_transpose(qim) ; mri_free(qim) ;
} else
#endif
if (sel) {
fname = (char *)
calloc((strlen(argv[jj+narg])+strlen(sel)+1), sizeof(char));
strcat(fname, argv[jj+narg]); strcat(fname, sel);
} else {
fname = argv[jj+narg];
}
inim[jj] = mri_read_1D( fname ) ;
if( inim[jj] == NULL )
ERROR_exit("Can't read input file '%s'",fname) ;
if( jj > 0 && inim[jj]->nx != inim[0]->nx )
ERROR_exit("Input file %s doesn't match first file %s in length!",
fname,argv[1]) ;
ncold = ncol ; ncol += inim[jj]->ny ;
if( ncv != NULL ){ /* check for constant columns [04 Dec 2010] */
RESIZE_intvec(ncv,ncol) ;
for( kk=0 ; kk < inim[jj]->ny ; kk++ ) ncv->ar[ncold+kk] = 1 ;
far = MRI_FLOAT_PTR(inim[jj]) ; nx = inim[jj]->nx ;
if( nonconst ){
for( kk=0 ; kk < inim[jj]->ny ; kk++ ){ /* loop over columns */
for( ii=1 ; ii < nx ; ii++ ){ /* loop down column */
if( far[ii+kk*nx] != far[kk*nx] ) break ;
}
if( ii == nx ) ncv->ar[ncold+kk] = 0 ; /* constant */
}
}
if( nonfixed ){
char *hl = mri_read_1D_headerlines( fname ) ;
if( hl != NULL && *hl == '#' ){
char *spt = strchr(hl,'\n') ;
if( spt != NULL ) spt = strchr(spt,'#') ; /* start of line 2 */
if( spt != NULL ){
NI_str_array *sar = NI_decode_string_list( spt+1 , "~" ) ;
if( sar != NULL && sar->num >= inim[jj]->ny ){
for( kk=0 ; kk < inim[jj]->ny ; kk++ ){
spt = strchr(sar->str[kk],'$') ;
if( spt != NULL && spt[1] == '\0' ) ncv->ar[ncold+kk] = 0 ;
else {
if( hline == NULL ) hline = strdup("#") ;
hline = THD_zzprintf( hline , " %s" , sar->str[kk] ) ;
}
}
}
NI_delete_str_array(sar) ;
}
}
}
} /* end of computing ncv = array marking non-constant vectors */
if (sel) {
free(fname); fname = NULL;
}
} /* end of input loop */
/* now do the output */
if( hline != NULL ) printf("%s\n",hline) ;
nx = inim[0]->nx ;
if (stack) {
if (oform == CCALC_NOT_SET) {
for( cc=jj=0 ; jj < nim ; jj++ ){
far = MRI_FLOAT_PTR(inim[jj]) ;
for( kk=0 ; kk < inim[jj]->ny ; kk++,cc++ ){
for( ii=0 ; ii < nx ; ii++ ){
if( ncv == NULL || ncv->ar[cc] )
printf(" %g\n", far[ii+kk*nx] ) ;
}
}
}
} else {
for( cc=jj=0 ; jj < nim ; jj++ ){
far = MRI_FLOAT_PTR(inim[jj]) ;
for( kk=0 ; kk < inim[jj]->ny ; kk++,cc++ ){
for( ii=0 ; ii < nx ; ii++ ){
if( ncv == NULL || ncv->ar[cc] )
printf(" %s\n",
format_value_4print(far[ii+kk*nx], oform, formatstr ));
}
}
}
}
} else {
if (oform == CCALC_NOT_SET) {
for( ii=0 ; ii < nx ; ii++ ){
for( cc=jj=0 ; jj < nim ; jj++ ){
far = MRI_FLOAT_PTR(inim[jj]) ;
for( kk=0 ; kk < inim[jj]->ny ; kk++,cc++ ){
if( ncv == NULL || ncv->ar[cc] )
printf(" %g", far[ii+kk*nx] ) ;
/* printf(" %+.2f", far[ii+kk*nx] ) ;*/
}
}
printf("\n") ;
}
} else {
for( ii=0 ; ii < nx ; ii++ ){
for( cc=jj=0 ; jj < nim ; jj++ ){
far = MRI_FLOAT_PTR(inim[jj]) ;
for( kk=0 ; kk < inim[jj]->ny ; kk++,cc++ ){
if( ncv == NULL || ncv->ar[cc] )
printf(" %s",
format_value_4print(far[ii+kk*nx], oform, formatstr ));
}
}
printf("\n") ;
}
}
}
exit(0) ;
}
floatvecvec * SYM_expand_ranges( int nlast, int nrang, SYM_irange *rang, char *str )
{
floatvec *fv ;
floatvecvec *fvv=NULL ;
int rr , ii , ss , gg, *qlist , nvec=0 , iv ;
NI_str_array *sar ;
char qname[64] , *qstr , *qpt , *qls ;
float fac ;
ENTRY("SYM_expand_ranges") ;
if( nlast < 0 ) RETURN(NULL) ; /* bad input */
/* check if have anything to scan for */
if( nrang < 1 || rang == NULL || str == NULL || *str == '\0' ) RETURN(NULL) ;
/* check if input line is a comment */
for( ii=0 ; str[ii] != '\0' && isspace(str[ii]) ; ii++ ) ; /*nada*/
if( str[ii] == '\0' || /* all blank */
str[ii] == '#' || /* starts with "#" */
(str[ii] == '/' && str[ii+1] == '/') /* starts with "//" */
) RETURN(NULL) ;
fv = (floatvec *)malloc(sizeof(floatvec)) ; /* create empty output */
fv->nar = nlast+1 ;
fv->ar = (float *)calloc(sizeof(float),nlast+1) ;
/* break input string into separate chunks */
sar = NI_decode_string_list( str , "~" ) ;
if( sar == NULL ){
fvv = (floatvecvec *)malloc(sizeof(floatvecvec)) ;
fvv->nvec = 1 ;
fvv->fvar = fv ;
ERROR_message("empty line in -gltsym?") ; nerr++ ;
RETURN(fvv) ;
}
/* scan each chunk */
for( ss=0 ; ss < sar->num ; ss++ ){
qstr = sar->str[ss] ;
if( qstr == NULL || *qstr == '\0' ) continue ; /* bad entry? */
if( *qstr == '#' || /* comment ends line */
(*qstr == '/' && *(qstr+1) == '/') ) break ;
qstr = strdup(sar->str[ss]) ; /* duplicate for surgery */
qls = strchr(qstr,'[') ; /* find and decode "[...]" subscripts */
qlist = NULL ; /* if they are present, that is */
if( qls != NULL ){
*qls = '\0' ; /* cut string off at '[' subscripts */
qls++ ; /* will scan for intlist starting here */
}
qpt = strchr(qstr,'*') ; /* find and decode factor in front */
if( qpt != NULL ){ /* if it is present, that is */
char *ept ;
fac = (float)strtod(qstr,&ept) ;
if( fac == 0.0f && ept == qstr ){ /* bad factor interpretation? */
fac = 1.0f ; /* ==> replace with 1, and bitch about it */
WARNING_message(
"-gltsym: Can't interpret '*' scale factor in '%s' -- replaced by 1",
qstr) ;
}
if( ept != qpt ) /* 27 May 2008 */
WARNING_message(
"-gltsym: '*' scale factor in '%s' not at start of string?",qstr ) ;
qpt++ ;
} else if( *qstr == '+' ){ /* "+" is same as "+1.0*" */
qpt = qstr+1 ; fac = 1.0 ;
} else if( *qstr == '-' ){ /* "-" is same as "-1.0*" */
qpt = qstr+1 ; fac = -1.0 ;
} else { /* default is "+" */
qpt = qstr ; fac = 1.0 ;
}
for( rr=0 ; rr < nrang ; rr++ ) /* match name in list */
if( strcmp(qpt,rang[rr].name) == 0 ) break ;
if( rr == nrang ){ /* no match!? */
ERROR_message("-gltsym: can't match symbolic name '%s'\n",qpt) ;
nerr++ ; free((void *)qstr) ; continue ;
}
/* now scan for intlist, if present */
if( qls != NULL ){
MCW_intlist_allow_negative( (rang[rr].nbot < 0) ) ;
qlist = MCW_get_intlist( rang[rr].ntop+1 , qls ) ;
if( qlist != NULL && *qls == '[' ){ /** [[...]] type of subscript **/
if( nvec == 0 ){
nvec = qlist[0] ;
fvv = (floatvecvec *)malloc(sizeof(floatvecvec)) ;
fvv->nvec = nvec ;
fvv->fvar = (floatvec *)calloc(sizeof(floatvec),nvec) ;
for( iv=0 ; iv < nvec ; iv++ ){
fvv->fvar[iv].nar = nlast+1 ;
fvv->fvar[iv].ar = (float *)calloc(sizeof(float),nlast+1) ;
}
} else if( qlist[0] != nvec ){
ERROR_message("mismatch in use of -gltsym [[...]]: '%s'\n",
sar->str[ss] ) ;
nerr++ ;free((void *)qlist) ; free((void *)qstr) ;
continue ;
}
for( iv=0 ; iv < nvec ; iv++ ){
gg = qlist[iv+1] - rang[rr].nbot + rang[rr].gbot ;
if( gg >= 0 && gg <= nlast ) fvv->fvar[iv].ar[gg] = fac ;
}
free((void *)qlist) ; free((void *)qstr) ;
continue ; /** skip to next one, since this was special **/
}
}
/* make up a fake list, if needed */
if( qlist == NULL ){
qlist = (int *)malloc(sizeof(int)*(rang[rr].ntop-rang[rr].nbot+2)) ;
qlist[0] = rang[rr].ntop-rang[rr].nbot+1 ;
for( ii=0 ; ii < qlist[0] ; ii++ ) qlist[ii+1] = rang[rr].nbot+ii ;
}
/* insert values into output list */
for( ii=0 ; ii < qlist[0] ; ii++ ){
if( qlist[ii+1] < rang[rr].nbot || qlist[ii+1] > rang[rr].ntop ){
ERROR_message("-gltsym subscript %s[%d] out of range %d..%d\n",
rang[rr].name , qlist[ii+1] , rang[rr].nbot,rang[rr].ntop ) ;
nerr++ ; continue ;
}
gg = qlist[ii+1] - rang[rr].nbot + rang[rr].gbot ;
if( gg >= 0 && gg <= nlast ) fv->ar[gg] = fac ;
}
free((void *)qlist) ; free((void *)qstr) ;
}
MCW_intlist_allow_negative(0) ;
NI_delete_str_array(sar);
/* if had no [[...]] subscripts, only have 1 vector for output */
if( nvec == 0 ){
fvv = (floatvecvec *)malloc(sizeof(floatvecvec)) ;
fvv->nvec = 1 ;
fvv->fvar = fv ;
} else { /* have multiple outputs */
for( iv=0 ; iv < nvec ; iv++ ){
for( gg=0 ; gg <= nlast ; gg++ ){
if( fvv->fvar[iv].ar[gg] == 0.0f ) fvv->fvar[iv].ar[gg] = fv->ar[gg] ;
}
}
KILL_floatvec(fv) ;
}
RETURN(fvv) ;
}
SEG_OPTS *Seg_ParseInput (SEG_OPTS *Opt, char *argv[], int argc)
{
static char FuncName[]={"Seg_ParseInput"};
int kar, i, ind, exists;
char *outname, cview[10];
int brk = 0;
ENTRY("Seg_ParseInput");
brk = 0;
kar = 1;
while (kar < argc) { /* loop accross command ine options */
/*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
Opt->helpfunc(0);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
#ifdef USE_TRACING
if( strncmp(argv[kar],"-trace",5) == 0 ){
DBG_trace = 1 ;
brk = 1 ;
}
if( strncmp(argv[kar],"-TRACE",5) == 0 ){
DBG_trace = 2 ;
brk = 1 ;
}
#endif
if (!brk && (strcmp(argv[kar], "-debug") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -debug \n");
exit (1);
}
Opt->debug = atoi(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-talk_afni") == 0)) {
Opt->ps->cs->talk_suma = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-do") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -do \n");
exit (1);
}
if (strchr(argv[kar], 'c')) Opt->DO_c = 1;
if (strchr(argv[kar], 'f')) Opt->DO_f = 1;
if (strchr(argv[kar], 'x')) Opt->DO_x = 1;
if (strchr(argv[kar], 'p')) Opt->DO_p = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-L2") == 0)) {
Opt->fitmeth = SEG_LSQFIT;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-L1") == 0)) {
Opt->fitmeth = SEG_L1FIT;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-openmp") == 0)) {
Opt->openmp = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-no_openmp") == 0)) {
Opt->openmp = 0;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-pweight") == 0)) {
Opt->pweight = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-no_pweight") == 0)) {
Opt->pweight = 0;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-no_edge") == 0)) {
Opt->edge = 0;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-edge") == 0)) {
Opt->edge = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-edge1") == 0)) {
Opt->edge = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-edge2") == 0)) {
Opt->edge = 2;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-vox_debug") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need 1D vox index after -vox_debug \n");
exit (1);
}
if (kar+2<argc) { /* see if we have ijk */
int iii, jjj, kkk;
if ( argv[kar ][0]!='-' &&
argv[kar+1][0]!='-' &&
argv[kar+2][0]!='-' &&
(iii = atoi(argv[kar ])) >= 0 &&
(jjj = atoi(argv[kar+1])) >= 0 &&
(kkk = atoi(argv[kar+2])) >= 0 ) {
Opt->VoxDbg3[0]=iii;
Opt->VoxDbg3[1]=jjj;
Opt->VoxDbg3[2]=kkk;
++kar; ++kar;
}
}
if (Opt->VoxDbg3[0] < 0) {
Opt->VoxDbg = atoi(argv[kar]);
}
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-vox_debug_file") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need filename after -vox_debug_file \n");
exit (1);
}
if (!strcmp(argv[kar],"-")) {
Opt->VoxDbgOut = stdout;
} else if (!strcmp(argv[kar],"+")) {
Opt->VoxDbgOut = stderr;
} else {
Opt->VoxDbgOut = fopen(argv[kar],"w");
}
brk = 1;
}
if (strcmp(argv[kar],"-logp") == 0 ) {
Opt->logp = 1;
brk = 1;
}
if (strcmp(argv[kar],"-p") == 0 ) {
Opt->logp = 0;
brk = 1;
}
if( strcmp(argv[kar],"-use_tmp") == 0 ){
Opt->UseTmp = 1 ;
brk = 1;
}
if( strcmp(argv[kar],"-no_tmp") == 0 ){
Opt->UseTmp = 0 ;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-vox_debug") == 0)) {
kar ++;
if (kar+2 >= argc) {
fprintf (stderr, "need 3 arguments after -vox_debug \n");
exit (1);
}
Opt->idbg = atoi(argv[kar]); ++kar;
Opt->jdbg = atoi(argv[kar]); ++kar;
Opt->kdbg = atoi(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-cmask") == 0)) {
kar ++;
if (kar >= argc) {
ERROR_exit("-cmask option requires a following argument!\n");
}
Opt->cmask = EDT_calcmask( argv[kar] , &(Opt->dimcmask), 0 ) ;
if( Opt->cmask == NULL ) ERROR_exit("Can't compute -cmask!\n");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-mask") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -mask \n");
exit (1);
}
Opt->mset_name = argv[kar];
brk = 1;
}
if( !brk && (strncmp(argv[kar],"-mrange",5) == 0) ){
if( kar+2 >= argc )
ERROR_exit("-mrange option requires 2 following arguments!\n");
Opt->mask_bot = strtod( argv[++kar] , NULL ) ;
Opt->mask_top = strtod( argv[++kar] , NULL ) ;
if( Opt->mask_top < Opt->mask_bot )
ERROR_exit("-mrange inputs are illegal!\n") ;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-anat") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -anat \n");
exit (1);
}
Opt->aset_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-sig") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -sig \n");
exit (1);
}
Opt->sig_name = SUMA_copy_string(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-pset") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -pset \n");
exit (1);
}
Opt->this_pset_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-gold") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -gold \n");
exit (1);
}
Opt->gold_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-gold_bias") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -gold_bias \n");
exit (1);
}
Opt->gold_bias_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-pstCgALL") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -pstCgALL \n");
exit (1);
}
Opt->pstCgALLname = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-priCgL") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -priCgL \n");
exit (1);
}
Opt->priCgLname = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-priCgALL") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -priCgALL \n");
exit (1);
}
Opt->priCgALLname = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-wL") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -wL \n");
exit (1);
}
Opt->wL = atof(argv[kar]);
if (Opt->wL < 0.0 || Opt->wL > 1.0) {
SUMA_S_Errv("-wL must be between 0 and 1.0, have %s", argv[kar]);
exit(1);
}
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-priCgA") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -priCgA \n");
exit (1);
}
Opt->priCgAname = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-wA") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -wA \n");
exit (1);
}
Opt->wA = atof(argv[kar]);
if (Opt->wA < 0.0 || Opt->wA > 1.0) {
SUMA_S_Errv("-wA must be between 0 and 1.0, have %s", argv[kar]);
exit(1);
}
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-cset") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -cset \n");
exit (1);
}
Opt->this_cset_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-fset") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -fset \n");
exit (1);
}
Opt->this_fset_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-xset") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -xset \n");
exit (1);
}
Opt->this_xset_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-tdist") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -tdist \n");
exit (1);
}
Opt->ndist_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-labeltable") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -labeltable \n");
exit (1);
}
Opt->labeltable_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-sphere_hood") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -sphere_hood \n");
exit (1);
}
Opt->na = atof(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-blur_meth") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -blur_meth \n");
exit (1);
}
if (!strcmp(argv[kar],"BIM")) Opt->blur_meth = SEG_BIM;
else if (!strncmp(argv[kar],"LS",2)) Opt->blur_meth = SEG_LSB;
else if (!strcmp(argv[kar],"BNN")) Opt->blur_meth = SEG_BNN;
else if (!strcmp(argv[kar],"BFT")) Opt->blur_meth = SEG_BFT;
else {
SUMA_S_Errv("-blur_meth %s not valid\n", argv[kar]);
exit(1);
}
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -prefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->proot = argv[kar];
Opt->prefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->crefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->pgrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->cgrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->frefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->xrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->prefix,"%s.p", argv[kar]);
sprintf(Opt->pgrefix,"%s.pg", argv[kar]);
sprintf(Opt->crefix,"%s.c", argv[kar]);
sprintf(Opt->cgrefix,"%s.cg", argv[kar]);
sprintf(Opt->frefix,"%s.f", argv[kar]);
sprintf(Opt->xrefix,"%s.x", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-pprefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -pprefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->prefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->prefix,"%s", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-fprefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -fprefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->frefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->frefix,"%s", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-cprefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -cprefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->crefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->crefix,"%s", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-cgprefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -cgprefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->cgrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->cgrefix,"%s", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-pgprefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -pgprefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->pgrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->pgrefix,"%s", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-xprefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -xprefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->xrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->xrefix,"%s", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-bias_classes") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -bias_classes \n");
exit (1);
}
Opt->bias_classes = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-group_classes") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -group_classes \n");
exit (1);
}
Opt->group_classes = NI_strict_decode_string_list(argv[kar] ,";");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-group_keys") == 0)) {
NI_str_array *nstr=NULL; int ii;
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -group_keys \n");
exit (1);
}
if (!(nstr = NI_strict_decode_string_list(argv[kar] ,";, "))){
ERROR_exit("Bad option %s after -group_keys", argv[kar]);
}
Opt->group_keys = (int *)calloc(nstr->num, sizeof(int));
for (ii=0;ii<nstr->num; ++ii)
Opt->group_keys[ii] = strtol(nstr->str[ii],NULL,10);
NI_delete_str_array(nstr);nstr=NULL;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-classes") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -classes \n");
exit (1);
}
Opt->clss = NI_strict_decode_string_list(argv[kar] ,";, ");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-split_classes") == 0)) {
NI_str_array *nstr=NULL; int ii;
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -split_classes \n");
exit (1);
}
nstr = NI_strict_decode_string_list(argv[kar] ,";, ");
Opt->Split = (int *)calloc(nstr->num+1, sizeof(int));
for (ii=0;ii<nstr->num; ++ii) {
Opt->Split[ii] = strtol(nstr->str[ii],NULL,10);
if (Opt->Split[ii]<1 || Opt->Split[ii]>9) {
SUMA_S_Errv("Bad split value of %d in %s\n",
Opt->Split[ii], argv[kar]);
exit(1);
}
}
Opt->Split[nstr->num]=-1; /* plug */
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-other") == 0)) {
Opt->Other = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-no_other") == 0)) {
Opt->Other = 0;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-keys") == 0)) {
NI_str_array *nstr=NULL; int ii;
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -keys \n");
exit (1);
}
if (!(nstr = NI_strict_decode_string_list(argv[kar] ,";, "))){
ERROR_exit("Bad option %s after -keys", argv[kar]);
}
Opt->keys = (int *)calloc(nstr->num, sizeof(int));
for (ii=0;ii<nstr->num; ++ii)
Opt->keys[ii] = strtol(nstr->str[ii],NULL,10);
NI_delete_str_array(nstr);nstr=NULL;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-bias_order") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need integer after -bias_order \n");
exit (1);
}
Opt->bias_param = atof(argv[kar]);
Opt->bias_meth = "Poly";
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-bias_fwhm") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need integer after -bias_fwhm \n");
exit (1);
}
Opt->bias_param = atof(argv[kar]);
Opt->bias_meth = "Wells";
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-enhance_cset_init") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need integer after -enhance_cset_init \n");
exit (1);
}
Opt->N_enhance_cset_init = atoi(argv[kar]);
SUMA_S_Err("Option not in use at the moment");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-main_N") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need integer after -main_N \n");
exit (1);
}
Opt->N_main = atoi(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-mixfloor") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need value between 0 and 1/(number of classes)"
" after -mixfloor \n");
exit (1);
}
Opt->mix_frac_floor = atof(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-clust_cset_init") == 0)) {
Opt->clust_cset_init = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-no_clust_cset_init") == 0)) {
Opt->clust_cset_init = 0;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-uid") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -uid \n");
exit (1);
}
snprintf(Opt->uid,128,"%s",argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-mixfrac") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -mixfrac \n");
exit (1);
}
Opt->mixopt = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-Bmrf") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need value after -Bmrf \n");
exit (1);
}
Opt->B = atof(argv[kar]);
brk = 1;
}
if (!brk) {
fprintf (stderr,"Option %s not understood. \n"
"Try -help for usage\n", argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = 0;
kar ++;
}
}
if (!Opt->prefix) Opt->prefix = strdup("./GenPriorsOut.p");
if (!Opt->frefix) Opt->frefix = strdup("./GenPriorsOut.f");
if (!Opt->xrefix) Opt->xrefix = strdup("./GenPriorsOut.x");
if (!Opt->crefix) Opt->crefix = strdup("./GenPriorsOut.c");
if (Opt->uid[0]=='\0') UNIQ_idcode_fill(Opt->uid);
if (Opt->VoxDbg > -1 && !Opt->VoxDbgOut) {
char stmp[256];
sprintf(stmp,"%d.dbg", Opt->VoxDbg);
Opt->VoxDbgOut = fopen(stmp,"w");
}
RETURN(Opt);
}
SEG_OPTS *free_SegOpts(SEG_OPTS *Opt) {
static char FuncName[]={"free_SegOpts"};
SUMA_ENTRY;
if (!Opt) SUMA_RETURN(NULL);
if (Opt->gold) DSET_delete(Opt->gold); Opt->gold = NULL;
if (Opt->gold_bias) DSET_delete(Opt->gold_bias); Opt->gold_bias = NULL;
if (Opt->aset) DSET_delete(Opt->aset); Opt->aset = NULL;
if (Opt->mset) DSET_delete(Opt->mset); Opt->mset = NULL;
if (Opt->pset) DSET_delete(Opt->pset); Opt->pset = NULL;
if (Opt->cset) DSET_delete(Opt->cset); Opt->cset = NULL;
if (Opt->fset) DSET_delete(Opt->fset); Opt->fset = NULL;
if (Opt->xset) DSET_delete(Opt->xset); Opt->xset = NULL;
if (Opt->gset) DSET_delete(Opt->gset); Opt->gset = NULL;
if (Opt->outl) DSET_delete(Opt->outl); Opt->outl = NULL;
if (Opt->sig) DSET_delete(Opt->sig); Opt->sig = NULL;
if (Opt->priCgA) DSET_delete(Opt->priCgA); Opt->priCgA = NULL;
if (Opt->priCgL) DSET_delete(Opt->priCgL); Opt->priCgL = NULL;
if (Opt->priCgALL) DSET_delete(Opt->priCgALL); Opt->priCgALL = NULL;
if (Opt->feats) NI_delete_str_array(Opt->feats);Opt->feats = NULL;
if (Opt->featsfam) NI_delete_str_array(Opt->featsfam);Opt->featsfam = NULL;
if (Opt->feat_exp) {
if (!Opt->clss) {
SUMA_S_Err("This should not happen!");
} else {
SUMA_free2D((char**)Opt->feat_exp, Opt->clss->num);
}
Opt->feat_exp = NULL;
}
if (Opt->clss) NI_delete_str_array(Opt->clss );Opt->clss = NULL;
if (Opt->keys) free(Opt->keys); Opt->keys = NULL;
if (Opt->mixfrac) free(Opt->mixfrac);Opt->mixfrac = NULL;
if (Opt->VoxDbgOut && Opt->VoxDbgOut != stdout) fclose(Opt->VoxDbgOut);
Opt->VoxDbgOut = NULL;
if (Opt->prefix) free(Opt->prefix);Opt->prefix = NULL;
if (Opt->frefix) free(Opt->frefix);Opt->frefix = NULL;
if (Opt->crefix) free(Opt->crefix);Opt->crefix = NULL;
if (Opt->xrefix) free(Opt->xrefix);Opt->xrefix = NULL;
if (Opt->cgrefix) free(Opt->cgrefix); Opt->cgrefix = NULL;
if (Opt->pgrefix) free(Opt->pgrefix); Opt->pgrefix = NULL;
if (Opt->group_classes) NI_delete_str_array(Opt->group_classes) ;
Opt->group_classes = NULL;
if (Opt->group_keys) free(Opt->group_keys); Opt->group_keys = NULL;
if (Opt->cs) Opt->cs = SUMA_Free_Class_Stat(Opt->cs);
if (Opt->Gcs) Opt->cs = SUMA_Free_Class_Stat(Opt->Gcs);
if (Opt->hist) free(Opt->hist); Opt->hist=NULL;
if (Opt->Split) free(Opt->Split); Opt->Split=NULL;
if (Opt->samp_names)
Opt->samp_names = SUMA_free_NI_str_array(Opt->samp_names);
if (Opt->sig_names)
Opt->sig_names = SUMA_free_NI_str_array(Opt->sig_names);
if (Opt->sig_name) SUMA_free(Opt->sig_name);
if (Opt->N_hspec && Opt->hspec) {
int ii;
for (ii=0; ii<Opt->N_hspec; ++ii) {
SUMA_Free_hist(Opt->hspec[ii]);
}
}
if (Opt->hspec) SUMA_free(Opt->hspec); Opt->hspec = NULL;
Opt->N_hspec = 0;
Opt->FDV = SUMA_free_dists(Opt->FDV);
free(Opt); Opt = NULL;
SUMA_RETURN(NULL);
}
