void EDIT_add_bricklist( THD_3dim_dataset *dset ,
int nbr, int *tbr, float *fbr , void *sbr[] )
{
int ibr , typ , nx,ny,nz , nvals,new_nvals ;
THD_datablock *dblk ;
MRI_IMAGE *qim ;
char str[32] ;
ENTRY("EDIT_add_bricklist") ;
/**-- Sanity Checks --**/
if( ! ISVALID_3DIM_DATASET(dset) || nbr <= 0 ) EXRETURN; /* error! */
if( dset->dblk->brick == NULL ) EXRETURN; /* error! */
if( dset->dblk->malloc_type != DATABLOCK_MEM_MALLOC )EXRETURN; /* error! */
dblk = dset->dblk ;
nvals = dblk->nvals ;
nx = dblk->diskptr->dimsizes[0] ;
ny = dblk->diskptr->dimsizes[1] ;
nz = dblk->diskptr->dimsizes[2] ;
/**-- reallocate the brick control information --**/
new_nvals = nvals + nbr ;
dblk->brick_bytes = (int64_t *) XtRealloc( (char *) dblk->brick_bytes ,
sizeof(int64_t) * new_nvals ) ;
dblk->brick_fac = (float *) XtRealloc( (char *) dblk->brick_fac ,
sizeof(float) * new_nvals ) ;
dblk->nvals = dblk->diskptr->nvals = new_nvals ;
/** allocate new sub-brick images **/
for( ibr=0 ; ibr < nbr ; ibr++ ){
typ = (tbr != NULL ) ? tbr[ibr] : MRI_short ;
qim = mri_new_vol_empty( nx,ny,nz , typ ) ; /* image with no data */
if( sbr != NULL && sbr[ibr] != NULL ) /* attach data to image */
mri_fix_data_pointer( sbr[ibr] , qim ) ;
ADDTO_IMARR( dblk->brick , qim ) ; /* attach image to dset */
dblk->brick_fac[nvals+ibr] = (fbr != NULL) ? fbr[ibr] : 0.0 ;
dblk->brick_bytes[nvals+ibr] = (int64_t)qim->pixel_size * (int64_t)qim->nvox ;
dblk->total_bytes += dblk->brick_bytes[ibr] ;
}
/** allocate new sub-brick auxiliary data: labels **/
if( dblk->brick_lab == NULL )
THD_init_datablock_labels( dblk ) ;
else
dblk->brick_lab = (char **) XtRealloc( (char *) dblk->brick_lab ,
sizeof(char *) * new_nvals ) ;
for( ibr=0 ; ibr < nbr ; ibr++ ){
sprintf( str , "#%d" , nvals+ibr ) ;
dblk->brick_lab[nvals+ibr] = NULL ;
THD_store_datablock_label( dblk , nvals+ibr , str ) ;
}
/** keywords **/
if( dblk->brick_keywords == NULL )
THD_init_datablock_keywords( dblk ) ;
else
dblk->brick_keywords = (char **) XtRealloc( (char *) dblk->brick_keywords ,
sizeof(char *) * new_nvals ) ;
for( ibr=0 ; ibr < nbr ; ibr++ ){
dblk->brick_keywords[nvals+ibr] = NULL ;
THD_store_datablock_keywords( dblk , nvals+ibr , NULL ) ;
}
/** stataux **/
if( dblk->brick_statcode != NULL ){
dblk->brick_statcode = (int *) XtRealloc( (char *) dblk->brick_statcode ,
sizeof(int) * new_nvals ) ;
dblk->brick_stataux = (float **) XtRealloc( (char *) dblk->brick_stataux ,
sizeof(float *) * new_nvals ) ;
for( ibr=0 ; ibr < nbr ; ibr++ ){
dblk->brick_statcode[nvals+ibr] = 0 ;
dblk->brick_stataux[nvals+ibr] = NULL ;
}
}
/** fdrcurve **/
if( dblk->brick_fdrcurve != NULL ){
dblk->brick_fdrcurve = (floatvec **) realloc( (void *)dblk->brick_fdrcurve ,
sizeof(floatvec *) * new_nvals ) ;
for( ibr=0 ; ibr < nbr ; ibr++ ) dblk->brick_fdrcurve[nvals+ibr] = NULL ;
}
if( dblk->brick_mdfcurve != NULL ){ /* 22 Oct 2008 */
dblk->brick_mdfcurve = (floatvec **) realloc( (void *)dblk->brick_mdfcurve ,
sizeof(floatvec *) * new_nvals ) ;
for( ibr=0 ; ibr < nbr ; ibr++ ) dblk->brick_mdfcurve[nvals+ibr] = NULL ;
}
EXRETURN;
}
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) ;
}
void THD_datablock_apply_atr( THD_3dim_dataset *dset )
{
THD_datablock *blk ;
THD_diskptr *dkptr ;
THD_dataxes *daxes ;
ATR_int *atr_int = NULL ;
ATR_float *atr_flt = NULL;
ATR_string *atr_str = NULL ;
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_apply_atr") ;
if( !ISVALID_DSET(dset) ) EXRETURN ; /* bad input */
blk = dset->dblk ; if( blk == NULL ) EXRETURN ;
nvals = blk->nvals ; if( nvals <= 0 ) EXRETURN ;
daxes = dset->daxes ; if( daxes == NULL ) EXRETURN ;
dkptr = blk->diskptr ;
/*-- brick labels --*/
if( ATR_IS_STR(ATRNAME_BRICK_LABS) ){
int ipos = -1 , ipold , ngood ;
STATUS("brick labels") ;
if( blk->brick_lab == NULL ) THD_init_datablock_labels( blk ) ;
for( ibr=0 ; ibr < nvals ; ibr++ ){ /* loop over bricks */
for( ipold = ipos++ ; /* skip to */
ipos < atr_str->nch && atr_str->ch[ipos] != '\0' ; /* next \0 */
ipos++ ) /* nada */ ; /* or end. */
ngood = ipos - ipold - 1 ; /* number of good chars */
if( ngood > 0 ){
XtFree(blk->brick_lab[ibr]) ;
if( ngood > THD_MAX_SBLABEL ) ngood = THD_MAX_SBLABEL ;
blk->brick_lab[ibr] = (char *) XtMalloc(sizeof(char)*(ngood+2)) ;
memcpy( blk->brick_lab[ibr] , atr_str->ch+(ipold+1) , ngood ) ;
blk->brick_lab[ibr][ngood] = '\0' ;
}
if( ipos >= atr_str->nch ) break ; /* nothing more to do */
} /* end of loop over sub-bricks */
}
/*-- keywords for the dataset itself --*/
if( ATR_IS_STR(ATRNAME_KEYWORDS) ){
STATUS("dataset keywords") ;
dset->keywords = XtNewString( atr_str->ch ) ;
}
/*-- keywords for sub-bricks --*/
if( ATR_IS_STR(ATRNAME_BRICK_KEYWORDS) ){
int ipos = -1 , ipold , ngood ;
STATUS("brick keywords") ;
if( blk->brick_keywords == NULL ) THD_init_datablock_keywords( blk ) ;
for( ibr=0 ; ibr < nvals ; ibr++ ){ /* loop over bricks */
for( ipold = ipos++ ; /* skip to */
ipos < atr_str->nch && atr_str->ch[ipos] != '\0' ; /* next \0 */
ipos++ ) /* nada */ ; /* or end. */
ngood = ipos - ipold - 1 ; /* number of good chars */
if( ngood > 0 ){
XtFree(blk->brick_keywords[ibr]) ;
blk->brick_keywords[ibr] = (char *) XtMalloc(sizeof(char)*(ngood+2)) ;
memcpy( blk->brick_keywords[ibr] , atr_str->ch+(ipold+1) , ngood ) ;
blk->brick_keywords[ibr][ngood] = '\0' ;
}
if( ipos >= atr_str->nch ) break ; /* nothing more to do */
} /* end of loop over sub-bricks */
}
/*-- auxiliary statistics stuff for each brick --*/
if( ATR_IS_FLT(ATRNAME_BRICK_STATAUX) ){
int ipos=0 , iv,nv,jv ;
STATUS("brick stataux") ;
/* 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( blk , iv , jv , nv , atr_flt->fl + ipos ) ;
ipos += nv ;
}
}
/*-- FDR curves [23 Jan 2008] --*/
for( ibr=0 ; ibr < blk->nvals ; ibr++ ){
sprintf(name,"FDRCURVE_%06d",ibr) ;
atr_flt = THD_find_float_atr( blk , 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( blk->brick_fdrcurve == NULL )
blk->brick_fdrcurve = (floatvec **)calloc(sizeof(floatvec *),blk->nvals);
blk->brick_fdrcurve[ibr] = fv ;
}
}
for( ibr=0 ; ibr < blk->nvals ; ibr++ ){
sprintf(name,"MDFCURVE_%06d",ibr) ;
atr_flt = THD_find_float_atr( blk , 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( blk->brick_mdfcurve == NULL )
blk->brick_mdfcurve = (floatvec **)calloc(sizeof(floatvec *),blk->nvals);
blk->brick_mdfcurve[ibr] = fv ;
}
}
/*-- ID codes --*/
if( ATR_IS_STR(ATRNAME_IDSTRING) )
MCW_strncpy( dset->idcode.str , atr_str->ch , MCW_IDSIZE ) ;
if( ATR_IS_STR(ATRNAME_IDDATE) )
MCW_strncpy( dset->idcode.date , atr_str->ch , MCW_IDDATE ) ;
if( ATR_IS_STR(ATRNAME_IDANATPAR) )
MCW_strncpy( dset->anat_parent_idcode.str , atr_str->ch , MCW_IDSIZE ) ;
if( ATR_IS_STR(ATRNAME_IDWARPPAR) )
MCW_strncpy( dset->warp_parent_idcode.str , atr_str->ch , MCW_IDSIZE ) ;
/*-- parent names --*/
if( ATR_IS_STR(ATRNAME_ANATOMY_PARENT) &&
ISZERO_IDCODE(dset->anat_parent_idcode) )
MCW_strncpy( dset->anat_parent_name , atr_str->ch , THD_MAX_NAME ) ;
if( ATR_IS_STR(ATRNAME_WARP_PARENT) &&
ISZERO_IDCODE(dset->warp_parent_idcode) )
MCW_strncpy( dset->warp_parent_name , atr_str->ch , THD_MAX_NAME ) ;
if( ATR_IS_STR(ATRNAME_DATANAME) )
MCW_strncpy( dset->self_name , atr_str->ch , THD_MAX_NAME ) ;
/*-- markers --*/
if( ATR_IS_FLT(ATRNAME_MARKSXYZ) && ATR_IS_STR(ATRNAME_MARKSLAB) ){
int im , llen ;
THD_ivec3 iv ;
float xxdown,xxup , yydown,yyup , zzdown,zzup ;
STATUS("markers") ;
if( dset->markers == NULL ){
dset->markers = myXtNew( THD_marker_set ) ; /* new set */
ADDTO_KILL(dset->kl , dset->markers) ;
}
COPY_INTO_STRUCT( *(dset->markers) , /* actual struct */
MARKS_FSTART , /* byte offset */
float , /* type being copied */
atr_flt->fl , /* start of source */
MARKS_FSIZE ) ; /* number of floats */
COPY_INTO_STRUCT( *(dset->markers) ,
MARKS_LSTART ,
char ,
atr_str->ch ,
MARKS_LSIZE ) ;
xxdown = daxes->xxmin ; xxup = daxes->xxmax ;
yydown = daxes->yymin ; yyup = daxes->yymax ;
zzdown = daxes->zzmin ; zzup = daxes->zzmax ;
dset->markers->numdef = dset->markers->numset = 0 ;
for( im=0 ; im < MARKS_MAXNUM ; im++ ){
llen = strlen( &(dset->markers->label[im][0]) ) ;
dset->markers->valid[im] =
(llen > 0) &&
( dset->markers->xyz[im][0] >= xxdown ) &&
( dset->markers->xyz[im][0] <= xxup ) &&
( dset->markers->xyz[im][1] >= yydown ) &&
( dset->markers->xyz[im][1] <= yyup ) &&
( dset->markers->xyz[im][2] >= zzdown ) &&
( dset->markers->xyz[im][2] <= zzup ) ;
if( dset->markers->valid[im] ) (dset->markers->numset)++ ;
if( llen > 0 ) (dset->markers->numdef)++ ;
dset->markers->ovcolor[im] = -1 ; /* default color */
}
if( ATR_IS_STR(ATRNAME_MARKSHELP) ){
COPY_INTO_STRUCT( *(dset->markers) ,
MARKS_HSTART ,
char ,
atr_str->ch ,
MARKS_HSIZE ) ;
} else {
for( im=0 ; im < MARKS_MAXNUM ; im++ ) /* no help */
THD_3dim_dataset * MAKER_4D_to_typed_fbuc( THD_3dim_dataset * old_dset ,
char * new_prefix , int new_datum ,
int ignore , int detrend ,
int nbrik , generic_func * user_func ,
void * user_data , byte *mmm,
int nscale)
{
THD_3dim_dataset * new_dset ; /* output dataset */
byte ** bptr = NULL ; /* one of these will be the array of */
short ** sptr = NULL ; /* pointers to input dataset sub-bricks */
float ** fptr = NULL ; /* (depending on input datum type) */
complex ** cptr = NULL ;
float * fxar = NULL ; /* array loaded from input dataset */
float * fac = NULL ; /* array of input brick scaling factors */
float ** fout = NULL ; /* will be arrays of output floats */
float * dtr = NULL ; /* will be array of detrending coeff */
float * val = NULL ; /* will be array of output values */
float d0fac , d1fac , x0,x1;
double tzero=0 , tdelta , ts_mean , ts_slope ;
int ii , old_datum , nuse , use_fac , iz,izold, nxy,nvox , iv ;
register int kk ;
int nbad=0 ; /* 08 Aug 2000 */
void (*ufunc)(double,double,int,float *,double,double,void *,int,float *)
= (void (*)(double,double,int,float *,double,double,void *,int,float *)) user_func;
/*----------------------------------------------------------*/
/*----- Check inputs to see if they are reasonable-ish -----*/
if( ! ISVALID_3DIM_DATASET(old_dset) ) return NULL ;
if( new_datum >= 0 &&
new_datum != MRI_byte &&
new_datum != MRI_short &&
new_datum != MRI_float ) return NULL ;
if( user_func == NULL ) return NULL ;
if( nbrik <= 0 ) return NULL ;
if( ignore < 0 ) ignore = 0 ;
/*--------- set up pointers to each sub-brick in the input dataset ---------*/
old_datum = DSET_BRICK_TYPE( old_dset , 0 ) ; /* get old dataset datum */
nuse = DSET_NUM_TIMES(old_dset) - ignore ; /* # of points on time axis */
/* maybe allow nuse == 1 2 Nov 2010 [rickr] */
if( nuse < 1 ) return NULL ;
if( nuse == 1 && ! g_thd_maker_allow_1brick ) return NULL ;
g_thd_maker_allow_1brick = 0; /* and beware repeat calls from plugins */
if( new_datum < 0 ) new_datum = old_datum ; /* output datum = input */
if( new_datum == MRI_complex ) return NULL ; /* but complex = bad news */
DSET_load( old_dset ) ; /* must be in memory before we get pointers to it */
kk = THD_count_databricks( old_dset->dblk ) ; /* check if it was */
if( kk < DSET_NVALS(old_dset) ){ /* loaded correctly */
DSET_unload( old_dset ) ;
return NULL ;
}
switch( old_datum ){ /* pointer type depends on input datum type */
default: /** don't know what to do **/
DSET_unload( old_dset ) ;
return NULL ;
/** create array of pointers into old dataset sub-bricks **/
/*--------- input is bytes ----------*/
/* voxel #i at time #k is bptr[k][i] */
/* for i=0..nvox-1 and k=0..nuse-1. */
case MRI_byte:
bptr = (byte **) malloc( sizeof(byte *) * nuse ) ;
if( bptr == NULL ) return NULL ;
for( kk=0 ; kk < nuse ; kk++ )
bptr[kk] = (byte *) DSET_ARRAY(old_dset,kk+ignore) ;
break ;
/*--------- input is shorts ---------*/
/* voxel #i at time #k is sptr[k][i] */
/* for i=0..nvox-1 and k=0..nuse-1. */
case MRI_short:
sptr = (short **) malloc( sizeof(short *) * nuse ) ;
if( sptr == NULL ) return NULL ;
for( kk=0 ; kk < nuse ; kk++ )
sptr[kk] = (short *) DSET_ARRAY(old_dset,kk+ignore) ;
break ;
/*--------- input is floats ---------*/
/* voxel #i at time #k is fptr[k][i] */
/* for i=0..nvox-1 and k=0..nuse-1. */
case MRI_float:
fptr = (float **) malloc( sizeof(float *) * nuse ) ;
if( fptr == NULL ) return NULL ;
for( kk=0 ; kk < nuse ; kk++ )
fptr[kk] = (float *) DSET_ARRAY(old_dset,kk+ignore) ;
break ;
/*--------- input is complex ---------*/
/* voxel #i at time #k is cptr[k][i] */
/* for i=0..nvox-1 and k=0..nuse-1. */
case MRI_complex:
cptr = (complex **) malloc( sizeof(complex *) * nuse ) ;
if( cptr == NULL ) return NULL ;
for( kk=0 ; kk < nuse ; kk++ )
cptr[kk] = (complex *) DSET_ARRAY(old_dset,kk+ignore) ;
break ;
} /* end of switch on input type */
/*---- allocate space for 1 voxel timeseries ----*/
fxar = (float *) malloc( sizeof(float) * nuse ) ; /* voxel timeseries */
if( fxar == NULL ){ FREE_WORKSPACE ; return NULL ; }
/*--- get scaling factors for input sub-bricks ---*/
fac = (float *) malloc( sizeof(float) * nuse ) ; /* factors */
if( fac == NULL ){ FREE_WORKSPACE ; return NULL ; }
use_fac = 0 ;
for( kk=0 ; kk < nuse ; kk++ ){
fac[kk] = DSET_BRICK_FACTOR(old_dset,kk+ignore) ;
if( fac[kk] != 0.0 ) use_fac++ ;
else fac[kk] = 1.0 ;
}
if( !use_fac ) FREEUP(fac) ;
/*--- setup for detrending ---*/
dtr = (float *) malloc( sizeof(float) * nuse ) ;
if( dtr == NULL ){ FREE_WORKSPACE ; return NULL ; }
d0fac = 1.0 / nuse ;
d1fac = 12.0 / nuse / (nuse*nuse - 1.0) ;
for( kk=0 ; kk < nuse ; kk++ )
dtr[kk] = kk - 0.5 * (nuse-1) ; /* linear trend, orthogonal to 1 */
/*---------------------- make a new dataset ----------------------*/
new_dset = EDIT_empty_copy( old_dset ) ; /* start with copy of old one */
/*-- edit some of its internal parameters --*/
ii = EDIT_dset_items(
new_dset ,
ADN_prefix , new_prefix , /* filename prefix */
ADN_malloc_type , DATABLOCK_MEM_MALLOC , /* store in memory */
ADN_datum_all , new_datum , /* atomic datum */
ADN_nvals , nbrik , /* # sub-bricks */
ADN_ntt , 0 , /* # time points */
ADN_type , ISHEAD(old_dset) /* dataset type */
? HEAD_FUNC_TYPE
: GEN_FUNC_TYPE ,
ADN_func_type , FUNC_BUCK_TYPE , /* function type */
ADN_none ) ;
if( ii != 0 ){
ERROR_message("Error creating dataset '%s'",new_prefix) ;
THD_delete_3dim_dataset( new_dset , False ) ; /* some error above */
FREE_WORKSPACE ; return NULL ;
}
THD_init_datablock_labels( new_dset->dblk ) ;
THD_init_datablock_keywords( new_dset->dblk ) ;
THD_init_datablock_stataux( new_dset->dblk ) ;
/*------ make floating point output bricks
(only at the end will scale to byte or shorts) ------*/
nvox = old_dset->daxes->nxx * old_dset->daxes->nyy * old_dset->daxes->nzz ;
fout = (float **) malloc( sizeof(float *) * nbrik ) ;
if( fout == NULL ){
THD_delete_3dim_dataset( new_dset , False ) ;
FREE_WORKSPACE ; return NULL ;
}
for( iv=0 ; iv < nbrik ; iv++ ) fout[iv] = NULL ;
for( iv=0 ; iv < nbrik ; iv++ ){
fout[iv] = (float *) malloc( sizeof(float) * nvox ) ;
if( fout[iv] == NULL ){
THD_delete_3dim_dataset( new_dset , False ) ;
FREE_WORKSPACE ; return NULL ;
}
}
/*-- floating point storage for output from 1 voxel --*/
val = (float *) malloc( sizeof(float) * nbrik ) ;
if( val == NULL ){
THD_delete_3dim_dataset( new_dset , False ) ;
FREE_WORKSPACE ; return NULL ;
}
/*----- set up to find time at each voxel -----*/
tdelta = old_dset->taxis->ttdel ;
if( DSET_TIMEUNITS(old_dset) == UNITS_MSEC_TYPE ) tdelta *= 0.001 ;
if( tdelta == 0.0 ) tdelta = 1.0 ;
izold = -666 ;
nxy = old_dset->daxes->nxx * old_dset->daxes->nyy ;
/*----------------------------------------------------*/
/*----- Setup has ended. Now do some real work. -----*/
/* start notification */
#if 0
user_func( 0.0 , 0.0 , nvox , NULL,0.0,0.0 , user_data , nbrik , NULL ) ;
#else
ufunc( 0.0 , 0.0 , nvox , NULL,0.0,0.0 , user_data , nbrik , NULL ) ;
#endif
/***** loop over voxels *****/
for( ii=0 ; ii < nvox ; ii++ ){ /* 1 time series at a time */
/*** load data from input dataset, depending on type ***/
switch( old_datum ){
/*** input = bytes ***/
case MRI_byte:
for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = bptr[kk][ii] ;
break ;
/*** input = shorts ***/
case MRI_short:
for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = sptr[kk][ii] ;
break ;
/*** input = floats ***/
case MRI_float:
for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = fptr[kk][ii] ;
break ;
/*** input = complex (note we use absolute value) ***/
case MRI_complex:
for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = CABS(cptr[kk][ii]) ;
break ;
} /* end of switch over input type */
/*** scale? ***/
if( use_fac )
for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] *= fac[kk] ;
/** compute mean and slope **/
x0 = x1 = 0.0 ;
for( kk=0 ; kk < nuse ; kk++ ){
x0 += fxar[kk] ; x1 += fxar[kk] * dtr[kk] ;
}
x0 *= d0fac ; x1 *= d1fac ; /* factors to remove mean and trend */
ts_mean = x0 ;
ts_slope = x1 / tdelta ;
/** detrend? **/
if( detrend )
for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] -= (x0 + x1 * dtr[kk]) ;
/** compute start time of this timeseries **/
iz = ii / nxy ; /* which slice am I in? */
if( iz != izold ){ /* in a new slice? */
tzero = THD_timeof( ignore ,
old_dset->daxes->zzorg
+ iz*old_dset->daxes->zzdel , old_dset->taxis ) ;
izold = iz ;
if( DSET_TIMEUNITS(old_dset) == UNITS_MSEC_TYPE ) tzero *= 0.001 ;
}
/*** compute output ***/
for( iv=0 ; iv < nbrik ; iv++ ) val[iv] = 0.0 ;
if (!mmm || mmm[ii]) { /* not the most efficient place to
mask, but it is the least obtrusive */
#if 0
user_func( tzero,tdelta, nuse,fxar,ts_mean,ts_slope, user_data, nbrik,val );
#else
ufunc( tzero,tdelta, nuse,fxar,ts_mean,ts_slope, user_data, nbrik,val );
#endif
}
for( iv=0 ; iv < nbrik ; iv++ ) fout[iv][ii] = val[iv] ;
} /* end of outer loop over 1 voxels at a time */
DSET_unload( old_dset ) ; /* don't need this no more */
/* end notification */
#if 0
user_func( 0.0 , 0.0 , 0 , NULL,0.0,0.0 , user_data , nbrik , NULL ) ;
#else
ufunc( 0.0 , 0.0 , 0 , NULL,0.0,0.0 , user_data , nbrik , NULL ) ;
#endif
/*---- Count and correct float errors ----*/
for( iv=0 ; iv < nbrik ; iv++ )
nbad += thd_floatscan( nvox, fout[iv] ) ;
if( nbad > 0 )
fprintf(stderr,
"++ Warning: %d bad floats computed in MAKER_4D_to_typed_fbuc\n\a",
nbad ) ;
/*------------------------------------------------------------------------*/
/*------- The output is now in fout[iv][ii], iv=0..nbrik-1, ii=0..nvox-1.
We must now put this into the output dataset. ------------------*/
switch( new_datum ){
/*** output is floats is the simplest:
we just have to attach the fout brick to the dataset ***/
case MRI_float:
for( iv=0 ; iv < nbrik ; iv++ ){
EDIT_substitute_brick( new_dset , iv , MRI_float , fout[iv] ) ;
fout[iv] = NULL ; /* so it won't be freed later */
}
break ;
/*** output is shorts:
we have to create scaled sub-bricks from fout ***/
case MRI_short:{
short * bout ;
float sfac ;
for( iv=0 ; iv < nbrik ; iv++ ){
bout = (short *) malloc( sizeof(short) * nvox ) ;
if( bout == NULL ){
fprintf(stderr,
"\nFinal malloc error in MAKER_4D_to_fbuc - is memory exhausted?\n\a");
EXIT(1) ;
}
if (nscale) {
sfac = 0.0;
EDIT_coerce_type( nvox, MRI_float, fout[iv] ,
MRI_short, bout ) ;
} else {
sfac = MCW_vol_amax( nvox,1,1 , MRI_float , fout[iv] ) ;
if( sfac > 0.0 ){
sfac = 32767.0 / sfac ;
EDIT_coerce_scale_type( nvox,sfac ,
MRI_float,fout[iv] , MRI_short,bout ) ;
sfac = 1.0 / sfac ;
}
}
val[iv] = sfac ;
EDIT_substitute_brick( new_dset , iv , MRI_short , bout ) ;
}
EDIT_dset_items( new_dset , ADN_brick_fac , val , ADN_none ) ;
}
break ;
/*** output is bytes (byte = unsigned char)
we have to create a scaled sub-brick from fout ***/
case MRI_byte:{
byte * bout ;
float sfac ;
for( iv=0 ; iv < nbrik ; iv++ ){
bout = (byte *) malloc( sizeof(byte) * nvox ) ;
if( bout == NULL ){
fprintf(stderr,
"\nFinal malloc error in MAKER_4D_to_fbuc - is memory exhausted?\n\a");
EXIT(1) ;
}
if (nscale) {
sfac = 0.0;
EDIT_coerce_type( nvox, MRI_float, fout[iv] ,
MRI_byte, bout ) ;
} else {
sfac = MCW_vol_amax( nvox,1,1 , MRI_float , fout[iv] ) ;
if( sfac > 0.0 ){
sfac = 255.0 / sfac ;
EDIT_coerce_scale_type( nvox,sfac ,
MRI_float,fout[iv] , MRI_byte,bout ) ;
sfac = 1.0 / sfac ;
}
}
val[iv] = sfac ;
EDIT_substitute_brick( new_dset , iv , MRI_byte , bout ) ;
}
EDIT_dset_items( new_dset , ADN_brick_fac , val , ADN_none ) ;
}
break ;
} /* end of switch on output data type */
/*-------------- Cleanup and go home ----------------*/
FREE_WORKSPACE ;
return new_dset ;
}
