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) ; }
int main( int argc , char *argv[] ) { THD_3dim_dataset *inset=NULL , *outset ; THD_3dim_dataset **insar=NULL ; int nsar=0 ; int iarg=1 , ii,kk , ids ; MCW_cluster *nbhd=NULL ; char *prefix="./localhistog" ; int ntype=0 ; float na=0.0f,nb=0.0f,nc=0.0f ; int verb=1 , do_prob=0 ; int nx=0,ny=0,nz=0,nvox=0, rbot,rtop ; char *labfile=NULL ; NI_element *labnel=NULL ; int nlab=0 , *labval=NULL ; char **lablab=NULL ; char buf[THD_MAX_SBLABEL] ; UINT32 *ohist , *mhist=NULL ; char *ohist_name=NULL ; int ohzadd=0 ; int *rlist , numval ; float mincount=0.0f ; int mcc ; int *exlist=NULL, numex=0 ; int do_excNONLAB=0 ; /*---- for the clueless who wish to become clued-in ----*/ if( argc == 1 ){ usage_3dLocalHistog(1); exit(0); } /* Bob's help shortcut */ /*---- official startup ---*/ #if defined(USING_MCW_MALLOC) && !defined(USE_OMP) enable_mcw_malloc() ; #endif PRINT_VERSION("3dLocalHistog"); mainENTRY("3dLocalHistog main"); machdep(); AFNI_logger("3dLocalHistog",argc,argv); if( getpid()%2 ) AUTHOR("Bilbo Baggins"); else AUTHOR("Thorin Oakenshield"); AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */ /*---- loop over options ----*/ while( iarg < argc && argv[iarg][0] == '-' ){ if( strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0){ usage_3dLocalHistog(strlen(argv[iarg])>3 ? 2:1); exit(0); } if( strncmp(argv[iarg],"-qu",3) == 0 ){ verb = 0 ; iarg++ ; continue ; } if( strncmp(argv[iarg],"-verb",5) == 0 ){ verb++ ; iarg++ ; continue ; } #ifdef ALLOW_PROB if( strncmp(argv[iarg],"-prob",5) == 0 ){ do_prob = 1 ; iarg++ ; continue ; } #endif if( strcmp(argv[iarg],"-exclude") == 0 ){ int ebot=-6666666,etop=-6666666 , ee ; if( ++iarg >= argc ) ERROR_exit("Need argument after '-exclude'") ; sscanf(argv[iarg],"%d..%d",&ebot,&etop) ; if( ebot >= -TWO15 && ebot <= TWO15 ){ if( etop < -TWO15 || etop > TWO15 || etop < ebot ) etop = ebot ; exlist = (int *)realloc(exlist,sizeof(int)*(etop-ebot+1+numex+1)) ; for( ee=ebot ; ee <= etop ; ee++ ){ if( ee != 0 ) exlist[numex++] = ee ; } } iarg++ ; continue ; } if( strcmp(argv[iarg],"-excNONLAB") == 0 ){ do_excNONLAB = 1 ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-prefix") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '-prefix'") ; prefix = strdup(argv[iarg]) ; if( !THD_filename_ok(prefix) ) ERROR_exit("Bad -prefix!") ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-hsave") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '-hsave'") ; ohist_name = strdup(argv[iarg]) ; if( !THD_filename_ok(ohist_name) ) ERROR_exit("Bad -hsave!") ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-mincount") == 0 ){ char *cpt ; if( ++iarg >= argc ) ERROR_exit("Need argument after '-mincount'") ; mincount = (float)strtod(argv[iarg],&cpt) ; #if 0 if( mincount > 0.0f && mincount < 50.0f && *cpt == '%' ) /* percentage */ mincount = -0.01f*mincount ; #endif iarg++ ; continue ; } if( strcmp(argv[iarg],"-nbhd") == 0 ){ char *cpt ; if( ntype > 0 ) ERROR_exit("Can't have 2 '-nbhd' options") ; if( ++iarg >= argc ) ERROR_exit("Need argument after '-nbhd'") ; cpt = argv[iarg] ; if( strncasecmp(cpt,"SPHERE",6) == 0 ){ sscanf( cpt+7 , "%f" , &na ) ; ntype = NTYPE_SPHERE ; } else if( strncasecmp(cpt,"RECT",4) == 0 ){ sscanf( cpt+5 , "%f,%f,%f" , &na,&nb,&nc ) ; if( na == 0.0f && nb == 0.0f && nc == 0.0f ) ERROR_exit("'RECT(0,0,0)' is not a legal neighborhood") ; ntype = NTYPE_RECT ; } else if( strncasecmp(cpt,"RHDD",4) == 0 ){ sscanf( cpt+5 , "%f" , &na ) ; if( na == 0.0f ) ERROR_exit("Can't have a RHDD of radius 0") ; ntype = NTYPE_RHDD ; } else if( strncasecmp(cpt,"TOHD",4) == 0 ){ sscanf( cpt+5 , "%f" , &na ) ; if( na == 0.0f ) ERROR_exit("Can't have a TOHD of radius 0") ; ntype = NTYPE_TOHD ; } else { ERROR_exit("Unknown -nbhd shape: '%s'",cpt) ; } iarg++ ; continue ; } if( strcmp(argv[iarg],"-lab_file") == 0 || strcmp(argv[iarg],"-labfile") == 0 ){ char **labnum ; int nbad=0 ; if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]) ; if( labfile != NULL ) ERROR_exit("Can't use '%s' twice!",argv[iarg-1]) ; labfile = strdup(argv[iarg]) ; labnel = THD_string_table_read(labfile,0) ; if( labnel == NULL || labnel->vec_num < 2 ) ERROR_exit("Can't read label file '%s'",labfile) ; nlab = labnel->vec_len ; labnum = (char **)labnel->vec[0] ; lablab = (char **)labnel->vec[1] ; labval = (int *)calloc(sizeof(int),nlab) ; for( ii=0 ; ii < nlab ; ii++ ){ if( labnum[ii] != NULL ){ labval[ii] = (int)strtod(labnum[ii],NULL) ; if( labval[ii] < -TWO15 || labval[ii] > TWO15 ){ labval[ii] = 0; nbad++; } } } if( nbad > 0 ) ERROR_message("%d label values are outside the range %d..%d :-(" , nbad , -TWO15 , TWO15 ) ; iarg++ ; continue ; } ERROR_message("** 3dLocalHistog: Illegal option: '%s'",argv[iarg]) ; suggest_best_prog_option(argv[0], argv[iarg]); exit(1) ; } /*--- end of loop over options ---*/ /*---- check for stupid user inputs ----*/ if( iarg >= argc ) ERROR_exit("No datasets on command line?") ; if( ohist_name == NULL && strcmp(prefix,"NULL") == 0 ) ERROR_exit("-prefix NULL is only meaningful if you also use -hsave :-(") ; /*------------ scan input datasets, built overall histogram ------------*/ nsar = argc - iarg ; insar = (THD_3dim_dataset **)malloc(sizeof(THD_3dim_dataset *)*nsar) ; if( verb ) fprintf(stderr,"Scanning %d datasets ",nsar) ; ohist = (UINT32 *)calloc(sizeof(UINT32),TWO16) ; for( ids=iarg ; ids < argc ; ids++ ){ /* dataset loop */ insar[ids-iarg] = inset = THD_open_dataset(argv[ids]) ; CHECK_OPEN_ERROR(inset,argv[ids]) ; if( ids == iarg ){ nx = DSET_NX(inset); ny = DSET_NY(inset); nz = DSET_NZ(inset); nvox = nx*ny*nz; } else if( nx != DSET_NX(inset) || ny != DSET_NY(inset) || nz != DSET_NZ(inset) ){ ERROR_exit("Dataset %s grid doesn't match!",argv[ids]) ; } if( !THD_datum_constant(inset->dblk) ) ERROR_exit("Dataset %s doesn't have a fixed data type! :-(",argv[ids]) ; if( THD_need_brick_factor(inset) ) ERROR_exit("Dataset %s has scale factors! :-(",argv[ids]) ; if( DSET_BRICK_TYPE(inset,0) != MRI_byte && DSET_BRICK_TYPE(inset,0) != MRI_short && DSET_BRICK_TYPE(inset,0) != MRI_float ) ERROR_exit("Dataset %s is not byte- or short-valued! :-(",argv[ids]) ; DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ; for( ii=0 ; ii < DSET_NVALS(inset) ; ii++ ){ /* add to overall histogram */ if( verb ) fprintf(stderr,".") ; switch( DSET_BRICK_TYPE(inset,ii) ){ case MRI_short:{ short *sar = (short *)DSET_BRICK_ARRAY(inset,ii) ; for( kk=0 ; kk < nvox ; kk++ ) ohist[ sar[kk]+TWO15 ]++ ; } break ; case MRI_byte:{ byte *bar = (byte *)DSET_BRICK_ARRAY(inset,ii) ; for( kk=0 ; kk < nvox ; kk++ ) ohist[ bar[kk]+TWO15 ]++ ; } break ; case MRI_float:{ float *far = (float *)DSET_BRICK_ARRAY(inset,ii) ; short ss ; for( kk=0 ; kk < nvox ; kk++ ){ ss = SHORTIZE(far[kk]); ohist[ss+TWO15]++; } } break ; } } /* end of sub-brick loop */ DSET_unload(inset) ; /* will re-load later, as needed */ } /* end of dataset loop */ if( verb ) fprintf(stderr,"\n") ; /*-------------- process overall histogram for fun and profit -------------*/ /* if we didn't actually find 0, put it in the histogram now */ if( ohist[0+TWO15] == 0 ){ ohist[0+TWO15] = 1 ; ohzadd = 1 ; } /* excNONLAB? */ if( nlab > 0 && do_excNONLAB ){ byte *klist = (byte *)calloc(sizeof(byte),TWO16) ; int nee ; for( ii=0 ; ii < nlab ; ii++ ){ if( labval[ii] != 0 ) klist[labval[ii]+TWO15] = 1 ; } for( nee=ii=0 ; ii < TWO16 ; ii++ ){ if( !klist[ii] ) nee++ ; } exlist = (int *)realloc(exlist,sizeof(int)*(numex+nee+1)) ; for( ii=0 ; ii < TWO16 ; ii++ ){ if( ii != TWO15 && !klist[ii] ) exlist[numex++] = ii-TWO15 ; } free(klist) ; } /* make a copy of ohist and edit it for mincount, etc */ mhist = (UINT32 *)malloc(sizeof(UINT32)*TWO16) ; memcpy(mhist,ohist,sizeof(UINT32)*TWO16) ; mcc = (mincount < 0.0f) ? (int)(-mincount*nvox) : (int)mincount ; if( mcc > 1 ){ for( ids=ii=0 ; ii < TWO16 ; ii++ ){ if( ii != TWO15 && mhist[ii] > 0 && mhist[ii] < mcc ){ mhist[ii] = 0; ids++; } } if( ids > 0 && verb ) INFO_message("Edited out %d values with overall histogram counts less than %d",ids,mcc) ; } if( numex > 0 ){ int ee ; for( ids=0,ii=0 ; ii < numex ; ii++ ){ ee = exlist[ii] ; if( mhist[ee+TWO15] > 0 ){ mhist[ee+TWO15] = 0; ids++; } } free(exlist) ; if( ids > 0 && verb ) INFO_message("Edited out %d values from the exclude list",ids) ; } /* count number of values with nonzero (edited) counts */ numval = 0 ; for( ii=0 ; ii < TWO16 ; ii++ ) if( mhist[ii] != 0 ) numval++ ; if( numval == 0 ) ERROR_exit("Nothing found! WTF?") ; /* should not happen */ /* make list of all values with nonzero (edited) count */ rlist = (int *)malloc(sizeof(int)*numval) ; if( verb > 1 ) fprintf(stderr,"++ Include list:") ; for( ii=kk=0 ; ii < TWO16 ; ii++ ){ if( mhist[ii] != 0 ){ rlist[kk++] = ii-TWO15 ; if( verb > 1 ) fprintf(stderr," %d[%u]",ii-TWO15,mhist[ii]) ; } } if( verb > 1 ) fprintf(stderr,"\n") ; rbot = rlist[0] ; rtop = rlist[numval-1] ; /* smallest and largest values found */ if( rbot == rtop ) ERROR_exit("Only one value (%d) found in all inputs!",rbot) ; /* if 0 isn't first in rlist, then put it in first place and move negative values up by one spot */ if( rbot < 0 ){ for( kk=0 ; kk < numval && rlist[kk] != 0 ; kk++ ) ; /*nada*/ if( kk < numval ){ /* should always be true */ for( ii=kk-1 ; ii >= 0 ; ii-- ) rlist[ii+1] = rlist[ii] ; rlist[0] = 0 ; } } if( verb ) INFO_message("Value range = %d..%d (%d distinct values)",rbot,rtop,numval ); /* save overall histogram? */ if( ohist_name != NULL ){ FILE *fp = fopen(ohist_name,"w") ; int nl=0 ; if( fp == NULL ) ERROR_exit("Can't open -hsave '%s' for output!",ohist_name) ; if( ohzadd ) ohist[0+TWO15] = 0 ; for( ii=0 ; ii < TWO16 ; ii++ ){ if( ohist[ii] != 0 ){ fprintf(fp,"%6d %u\n",ii-TWO15,ohist[ii]); nl++; } } fclose(fp) ; if( verb ) INFO_message("Wrote %d lines to -hsave file %s",nl,ohist_name) ; } free(ohist) ; free(mhist) ; mhist = ohist = NULL ; /* done with this */ if( strcmp(prefix,"NULL") == 0 ) exit(0) ; /* special case */ /*----------- build the neighborhood mask -----------*/ if( ntype <= 0 ){ /* default neighborhood */ ntype = NTYPE_SPHERE ; na = 0.0f ; if( verb ) INFO_message("Using default neighborhood = self") ; } switch( ntype ){ default: ERROR_exit("WTF? ntype=%d",ntype) ; /* should not happen */ case NTYPE_SPHERE:{ float dx , dy , dz ; if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; } else { dx = fabsf(DSET_DX(insar[0])) ; dy = fabsf(DSET_DY(insar[0])) ; dz = fabsf(DSET_DZ(insar[0])) ; } nbhd = MCW_spheremask( dx,dy,dz , na ) ; } break ; case NTYPE_RECT:{ float dx , dy , dz ; if( na < 0.0f ){ dx = 1.0f; na = -na; } else dx = fabsf(DSET_DX(insar[0])); if( nb < 0.0f ){ dy = 1.0f; nb = -nb; } else dy = fabsf(DSET_DY(insar[0])); if( nc < 0.0f ){ dz = 1.0f; nc = -nc; } else dz = fabsf(DSET_DZ(insar[0])); nbhd = MCW_rectmask( dx,dy,dz , na,nb,nc ) ; } break ; case NTYPE_RHDD:{ float dx , dy , dz ; if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; } else { dx = fabsf(DSET_DX(insar[0])) ; dy = fabsf(DSET_DY(insar[0])) ; dz = fabsf(DSET_DZ(insar[0])) ; } nbhd = MCW_rhddmask( dx,dy,dz , na ) ; } break ; case NTYPE_TOHD:{ float dx , dy , dz ; if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; } else { dx = fabsf(DSET_DX(insar[0])) ; dy = fabsf(DSET_DY(insar[0])) ; dz = fabsf(DSET_DZ(insar[0])) ; } nbhd = MCW_tohdmask( dx,dy,dz , na ) ; } break ; } if( verb ) INFO_message("Neighborhood comprises %d voxels",nbhd->num_pt) ; /*------- actually do some work for a change (is it lunchtime yet?) -------*/ if( verb ) fprintf(stderr,"Voxel-wise histograms ") ; outset = THD_localhistog( nsar,insar , numval,rlist , nbhd , do_prob,verb ) ; if( outset == NULL ) ERROR_exit("Function THD_localhistog() fails?!") ; /*---- save resulting dataset ----*/ EDIT_dset_items( outset , ADN_prefix,prefix , ADN_none ) ; tross_Copy_History( insar[0] , outset ) ; tross_Make_History( "3dLocalHistog" , argc,argv , outset ) ; /* but first attach labels to sub-bricks */ EDIT_BRICK_LABEL(outset,0,"0:Other") ; for( kk=1 ; kk < numval ; kk++ ){ sprintf(buf,"%d:",rlist[kk]) ; for( ii=0 ; ii < nlab ; ii++ ){ if( labval[ii] == rlist[kk] && lablab[ii] != NULL ){ ids = strlen(buf) ; MCW_strncpy(buf+ids,lablab[ii],THD_MAX_SBLABEL-ids) ; break ; } } EDIT_BRICK_LABEL(outset,kk,buf) ; } DSET_write( outset ) ; if( verb ) WROTE_DSET( outset ) ; exit(0) ; }
int main( int argc , char *argv[] ) { int iarg=1 , ii,nvox , nvals ; THD_3dim_dataset *inset=NULL, *outset=NULL , *mset=NULL ; char *prefix="./blurinmask" ; float fwhm_goal=0.0f ; int fwhm_2D=0 ; byte *mask=NULL ; int mask_nx=0,mask_ny=0,mask_nz=0 , automask=0 , nmask=0 ; float dx,dy,dz=0.0f , *bar , val ; int floatize=0 ; /* 18 May 2009 */ MRI_IMAGE *immask=NULL ; /* 07 Oct 2009 */ short *mmask=NULL ; short *unval_mmask=NULL ; int nuniq_mmask=0 ; int do_preserve=0 , use_qsar ; /* 19 Oct 2009 */ THD_3dim_dataset *fwhmset=NULL ; MRI_IMAGE *fxim=NULL, *fyim=NULL, *fzim=NULL ; /* 13 Jun 2016 */ int niter_fxyz=0 ; float dmax=0.0f , dmin=0.0f ; /*------- help the pitifully ignorant luser? -------*/ AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */ if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ printf( "Usage: ~1~\n" "3dBlurInMask [options]\n" "Blurs a dataset spatially inside a mask. That's all. Experimental.\n" "\n" "OPTIONS ~1~\n" "-------\n" " -input ddd = This required 'option' specifies the dataset\n" " that will be smoothed and output.\n" " -FWHM f = Add 'f' amount of smoothness to the dataset (in mm).\n" " **N.B.: This is also a required 'option'.\n" " -FWHMdset d = Read in dataset 'd' and add the amount of smoothness\n" " given at each voxel -- spatially variable blurring.\n" " ** EXPERIMENTAL EXPERIMENTAL EXPERIMENTAL **\n" " -mask mmm = Mask dataset, if desired. Blurring will\n" " occur only within the mask. Voxels NOT in\n" " the mask will be set to zero in the output.\n" " -Mmask mmm = Multi-mask dataset -- each distinct nonzero\n" " value in dataset 'mmm' will be treated as\n" " a separate mask for blurring purposes.\n" " **N.B.: 'mmm' must be byte- or short-valued!\n" " -automask = Create an automask from the input dataset.\n" " **N.B.: only 1 masking option can be used!\n" " -preserve = Normally, voxels not in the mask will be\n" " set to zero in the output. If you want the\n" " original values in the dataset to be preserved\n" " in the output, use this option.\n" " -prefix ppp = Prefix for output dataset will be 'ppp'.\n" " **N.B.: Output dataset is always in float format.\n" " -quiet = Don't be verbose with the progress reports.\n" " -float = Save dataset as floats, no matter what the\n" " input data type is.\n" " **N.B.: If the input dataset is unscaled shorts, then\n" " the default is to save the output in short\n" " format as well. In EVERY other case, the\n" " program saves the output as floats. Thus,\n" " the ONLY purpose of the '-float' option is to\n" " force an all-shorts input dataset to be saved\n" " as all-floats after blurring.\n" "\n" "NOTES ~1~\n" "-----\n" " * If you don't provide a mask, then all voxels will be included\n" " in the blurring. (But then why are you using this program?)\n" " * Note that voxels inside the mask that are not contiguous with\n" " any other voxels inside the mask will not be modified at all!\n" " * Works iteratively, similarly to 3dBlurToFWHM, but without\n" " the extensive overhead of monitoring the smoothness.\n" " * But this program will be faster than 3dBlurToFWHM, and probably\n" " slower than 3dmerge.\n" " * Since the blurring is done iteratively, rather than all-at-once as\n" " in 3dmerge, the results will be slightly different than 3dmerge's,\n" " even if no mask is used here (3dmerge, of course, doesn't take a mask).\n" " * If the original FWHM of the dataset was 'S' and you input a value\n" " 'F' with the '-FWHM' option, then the output dataset's smoothness\n" " will be about sqrt(S*S+F*F). The number of iterations will be\n" " about (F*F/d*d) where d=grid spacing; this means that a large value\n" " of F might take a lot of CPU time!\n" " * The spatial smoothness of a 3D+time dataset can be estimated with a\n" " command similar to the following:\n" " 3dFWHMx -detrend -mask mmm+orig -input ddd+orig\n" ) ; printf( " * The minimum number of voxels in the mask is %d\n",MASK_MIN) ; printf( " * Isolated voxels will be removed from the mask!\n") ; PRINT_AFNI_OMP_USAGE("3dBlurInMask",NULL) ; PRINT_COMPILE_DATE ; exit(0) ; } /*---- official startup ---*/ PRINT_VERSION("3dBlurInMask"); mainENTRY("3dBlurInMask main"); machdep(); AFNI_logger("3dBlurInMask",argc,argv); AUTHOR("RW Cox") ; /*---- loop over options ----*/ while( iarg < argc && argv[iarg][0] == '-' ){ if( strncmp(argv[iarg],"-preserve",5) == 0 ){ /* 19 Oct 2009 */ do_preserve = 1 ; iarg++ ; continue ; } if( strncmp(argv[iarg],"-qui",4) == 0 ){ verb = 0 ; iarg++ ; continue ; } if( strncmp(argv[iarg],"-ver",4) == 0 ){ verb++ ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-input") == 0 || strcmp(argv[iarg],"-dset") == 0 ){ if( inset != NULL ) ERROR_exit("Can't have two -input options") ; if( ++iarg >= argc ) ERROR_exit("Need argument after '-input'") ; inset = THD_open_dataset( argv[iarg] ); CHECK_OPEN_ERROR(inset,argv[iarg]) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-prefix") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '-prefix'") ; prefix = strdup(argv[iarg]) ; if( !THD_filename_ok(prefix) ) ERROR_exit("Bad name after '-prefix'") ; iarg++ ; continue ; } if( strcasecmp(argv[iarg],"-Mmask") == 0 ){ /* 07 Oct 2009 */ if( ++iarg >= argc ) ERROR_exit("Need argument after '-Mmask'") ; if( mmask != NULL || mask != NULL || automask ) ERROR_exit("Can't have two mask inputs") ; mset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(mset,argv[iarg]) ; DSET_load(mset) ; CHECK_LOAD_ERROR(mset) ; mask_nx = DSET_NX(mset); mask_ny = DSET_NY(mset); mask_nz = DSET_NZ(mset); #if 0 if( !MRI_IS_INT_TYPE(DSET_BRICK_TYPE(mset,0)) ) ERROR_exit("-Mmask dataset is not integer type!") ; #endif immask = mri_to_short( 1.0 , DSET_BRICK(mset,0) ) ; mmask = MRI_SHORT_PTR(immask) ; unval_mmask = UniqueShort( mmask, mask_nx*mask_ny*mask_nz, &nuniq_mmask, 0 ) ; if( unval_mmask == NULL || nuniq_mmask == 0 ) ERROR_exit("-Mmask dataset cannot be processed!?") ; if( nuniq_mmask == 1 && unval_mmask[0] == 0 ) ERROR_exit("-Mmask dataset is all zeros!?") ; if( verb ){ int qq , ww ; for( ii=qq=0 ; ii < nuniq_mmask ; ii++ ) if( unval_mmask[ii] != 0 ) qq++ ; for( ii=ww=0 ; ii < immask->nvox ; ii++ ) if( mmask[ii] != 0 ) ww++ ; INFO_message("%d unique nonzero values in -Mmask; %d nonzero voxels",qq,ww) ; } iarg++ ; continue ; } if( strcmp(argv[iarg],"-mask") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '-mask'") ; if( mmask != NULL || mask != NULL || automask ) ERROR_exit("Can't have two mask inputs") ; mset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(mset,argv[iarg]) ; DSET_load(mset) ; CHECK_LOAD_ERROR(mset) ; mask_nx = DSET_NX(mset); mask_ny = DSET_NY(mset); mask_nz = DSET_NZ(mset); mask = THD_makemask( mset , 0 , 0.5f, 0.0f ) ; DSET_unload(mset) ; if( mask == NULL ) ERROR_exit("Can't make mask from dataset '%s'",argv[iarg]) ; ii = THD_mask_remove_isolas( mask_nx,mask_ny,mask_nz , mask ) ; if( verb && ii > 0 ) INFO_message("Removed %d isola%s from mask dataset",ii,(ii==1)?"\0":"s") ; nmask = THD_countmask( mask_nx*mask_ny*mask_nz , mask ) ; if( verb ) INFO_message("Number of voxels in mask = %d",nmask) ; if( nmask < MASK_MIN ) ERROR_exit("Mask is too small to process") ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-automask") == 0 ){ if( mmask != NULL || mask != NULL ) ERROR_exit("Can't have 2 mask inputs") ; automask = 1 ; iarg++ ; continue ; } if( strcasecmp(argv[iarg],"-FWHM") == 0 || strcasecmp(argv[iarg],"-FHWM") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]); val = (float)strtod(argv[iarg],NULL) ; if( val <= 0.0f ) ERROR_exit("Illegal value after '%s': '%s'", argv[iarg-1],argv[iarg]) ; fwhm_goal = val ; fwhm_2D = 0 ; iarg++ ; continue ; } if( strcasecmp(argv[iarg],"-FWHMdset") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]); if( fwhmset != NULL ) ERROR_exit("You can't use option '-FWHMdset' twice :(") ; fwhmset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(fwhmset,argv[iarg]) ; do_preserve = 1 ; iarg++ ; continue ; } if( strncmp(argv[iarg],"-float",6) == 0 ){ /* 18 May 2009 */ floatize = 1 ; iarg++ ; continue ; } #if 0 if( strcmp(argv[iarg],"-FWHMxy") == 0 || strcmp(argv[iarg],"-FHWMxy") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]); val = (float)strtod(argv[iarg],NULL) ; if( val <= 0.0f ) ERROR_exit("Illegal value after '%s': '%s'", argv[iarg-1],argv[iarg]) ; fwhm_goal = val ; fwhm_2D = 1 ; iarg++ ; continue ; } #endif ERROR_exit("Uknown option '%s'",argv[iarg]) ; } /*--- end of loop over options ---*/ /*----- check for stupid inputs, load datasets, et cetera -----*/ if( fwhmset == NULL && fwhm_goal == 0.0f ) ERROR_exit("No -FWHM option given! What do you want?") ; if( fwhmset != NULL && fwhm_goal > 0.0f ){ WARNING_message("-FWHMdset option replaces -FWHM value") ; fwhm_goal = 0.0f ; } if( fwhmset != NULL && mmask != NULL ) ERROR_exit("Sorry: -FWHMdset and -Mmask don't work together (yet)") ; if( inset == NULL ){ if( iarg >= argc ) ERROR_exit("No input dataset on command line?") ; inset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(inset,argv[iarg]) ; } nvox = DSET_NVOX(inset) ; dx = fabs(DSET_DX(inset)) ; if( dx == 0.0f ) dx = 1.0f ; dy = fabs(DSET_DY(inset)) ; if( dy == 0.0f ) dy = 1.0f ; dz = fabs(DSET_DZ(inset)) ; if( dz == 0.0f ) dz = 1.0f ; dmax = MAX(dx,dy) ; if( dmax < dz ) dmax = dz ; /* 13 Jun 2016 */ dmin = MIN(dx,dy) ; if( dmin > dz ) dmin = dz ; if( !floatize ){ /* 18 May 2009 */ if( !THD_datum_constant(inset->dblk) || THD_need_brick_factor(inset) || DSET_BRICK_TYPE(inset,0) != MRI_short ){ if( verb ) INFO_message("forcing output to be stored in float format") ; floatize = 1 ; } else { if( verb ) INFO_message("output dataset will be stored as shorts") ; } } else { if( verb ) INFO_message("output dataset will be stored as floats") ; } #if 0 if( DSET_NZ(inset) == 1 && !fwhm_2D ){ WARNING_message("Dataset is 2D ==> switching from -FWHM to -FWHMxy") ; fwhm_2D = 1 ; } #endif /*--- deal with mask or automask ---*/ if( mask != NULL ){ if( mask_nx != DSET_NX(inset) || mask_ny != DSET_NY(inset) || mask_nz != DSET_NZ(inset) ) ERROR_exit("-mask dataset grid doesn't match input dataset") ; } else if( automask ){ mask = THD_automask( inset ) ; if( mask == NULL ) ERROR_message("Can't create -automask from input dataset?") ; nmask = THD_countmask( DSET_NVOX(inset) , mask ) ; if( verb ) INFO_message("Number of voxels in automask = %d",nmask); if( nmask < MASK_MIN ) ERROR_exit("Automask is too small to process") ; } else if( mmask != NULL ){ if( mask_nx != DSET_NX(inset) || mask_ny != DSET_NY(inset) || mask_nz != DSET_NZ(inset) ) ERROR_exit("-Mmask dataset grid doesn't match input dataset") ; } else { mask = (byte *)malloc(sizeof(byte)*nvox) ; nmask = nvox ; memset(mask,1,sizeof(byte)*nvox) ; if( verb ) INFO_message("No mask ==> processing all %d voxels",nvox); } /*--- process FWHMdset [13 Jun 2016] ---*/ if( fwhmset != NULL ){ float *fxar,*fyar,*fzar , *fwar ; MRI_IMAGE *fwim ; float fwmax=0.0f , fsx,fsy,fsz ; int ii, nfpos=0 ; if( DSET_NX(inset) != DSET_NX(fwhmset) || DSET_NY(inset) != DSET_NY(fwhmset) || DSET_NZ(inset) != DSET_NZ(fwhmset) ) ERROR_exit("grid dimensions for FWHMdset and input dataset do not match :(") ; STATUS("get fwim") ; DSET_load(fwhmset) ; fwim = mri_scale_to_float(DSET_BRICK_FACTOR(fwhmset,0),DSET_BRICK(fwhmset,0)); fwar = MRI_FLOAT_PTR(fwim); DSET_unload(fwhmset) ; STATUS("process fwar") ; for( ii=0 ; ii < nvox ; ii++ ){ if( mask[ii] && fwar[ii] > 0.0f ){ nfpos++ ; if( fwar[ii] > fwmax ) fwmax = fwar[ii] ; } else { fwar[ii] = 0.0f ; mask[ii] = 0 ; } } if( nfpos < 100 ) ERROR_exit("Cannot proceed: too few (%d) voxels are positive in -FWHMdset!",nfpos) ; niter_fxyz = (int)rintf(2.0f*fwmax*fwmax*FFAC/(0.05f*dmin*dmin)) + 1 ; if( verb ) INFO_message("-FWHMdset: niter=%d npos=%d",niter_fxyz,nfpos) ; STATUS("create fxim etc.") ; fxim = mri_new_conforming(fwim,MRI_float); fxar = MRI_FLOAT_PTR(fxim); fyim = mri_new_conforming(fwim,MRI_float); fyar = MRI_FLOAT_PTR(fyim); fzim = mri_new_conforming(fwim,MRI_float); fzar = MRI_FLOAT_PTR(fzim); fsx = FFAC/(dx*dx*niter_fxyz) ; fsy = FFAC/(dy*dy*niter_fxyz) ; fsz = FFAC/(dz*dz*niter_fxyz) ; /** INFO_message("fsx=%g fsy=%g fsz=%g",fsx,fsy,fsz) ; **/ for( ii=0 ; ii < nvox ; ii++ ){ if( fwar[ii] > 0.0f ){ fxar[ii] = fwar[ii]*fwar[ii] * fsx ; fyar[ii] = fwar[ii]*fwar[ii] * fsy ; fzar[ii] = fwar[ii]*fwar[ii] * fsz ; } else { fxar[ii] = fyar[ii] = fzar[ii] = 0.0f ; } } STATUS("free(fwim)") ; mri_free(fwim) ; } /*--- process input dataset ---*/ STATUS("load input") ; DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ; outset = EDIT_empty_copy( inset ) ; /* moved here 04 Jun 2007 */ EDIT_dset_items( outset , ADN_prefix , prefix , ADN_none ) ; EDIT_dset_items( outset , ADN_brick_fac , NULL , ADN_none ) ; /* 11 Sep 2007 */ tross_Copy_History( inset , outset ) ; tross_Make_History( "3dBlurInMask" , argc,argv , outset ) ; nvals = DSET_NVALS(inset) ; use_qsar = (do_preserve || mmask != NULL) ; /* 19 Oct 20090 */ AFNI_OMP_START ; #pragma omp parallel if( nvals > 1 ) { MRI_IMAGE *dsim ; int ids,qit ; byte *qmask=NULL ; register int vv ; MRI_IMAGE *qim=NULL, *qsim=NULL; float *qar=NULL, *dsar, *qsar=NULL; #pragma omp critical (MALLOC) { if( use_qsar ){ qsim = mri_new_conforming(DSET_BRICK(inset,0),MRI_float); qsar = MRI_FLOAT_PTR(qsim); } if( mmask != NULL ){ qmask = (byte *)malloc(sizeof(byte)*nvox) ; qim = mri_new_conforming(immask,MRI_float); qar = MRI_FLOAT_PTR(qim); qim->dx = dx ; qim->dy = dy ; qim->dz = dz ; } } #pragma omp for for( ids=0 ; ids < nvals ; ids++ ){ #pragma omp critical (MALLOC) { dsim = mri_scale_to_float(DSET_BRICK_FACTOR(inset,ids),DSET_BRICK(inset,ids)); DSET_unload_one(inset,ids) ; } dsim->dx = dx ; dsim->dy = dy ; dsim->dz = dz ; dsar = MRI_FLOAT_PTR(dsim) ; /* if needed, initialize qsar with data to be preserved in output */ if( do_preserve ){ for( vv=0 ; vv < nvox ; vv++ ) qsar[vv] = dsar[vv] ; } else if( mmask != NULL ){ for( vv=0 ; vv < nvox ; vv++ ) qsar[vv] = 0.0f ; } if( fwhmset != NULL ){ /* 13 Jun 2016: spatially variable blurring */ for( qit=0 ; qit < niter_fxyz ; qit++ ){ mri_blur3D_variable( dsim , mask , fxim,fyim,fzim ) ; } if( do_preserve ){ for( vv=0 ; vv < nvox ; vv++ ) if( mask[vv] ) qsar[vv] = dsar[vv] ; } } else if( mmask != NULL ){ /* 07 Oct 2009: multiple masks */ int qq ; register short uval ; for( qq=0 ; qq < nuniq_mmask ; qq++ ){ uval = unval_mmask[qq] ; if( uval == 0 ) continue ; for( vv=0 ; vv < nvox ; vv++ ) qmask[vv] = (mmask[vv]==uval) ; /* make mask */ (void)THD_mask_remove_isolas( mask_nx,mask_ny,mask_nz , qmask ) ; nmask = THD_countmask( nvox , qmask ) ; if( verb && ids==0 ) ININFO_message("voxels in Mmask[%d] = %d",uval,nmask) ; if( nmask >= MASK_MIN ){ /* copy data from dataset to qar */ for( vv=0 ; vv < nvox ; vv++ ) if( qmask[vv] ) qar[vv] = dsar[vv] ; /* blur qar (output will be zero where qmask==0) */ mri_blur3D_addfwhm( qim , qmask , fwhm_goal ) ; /** the real work **/ /* copy results back to qsar */ for( vv=0 ; vv < nvox ; vv++ ) if( qmask[vv] ) qsar[vv] = qar[vv] ; } } } else { /* the olden way: 1 mask */ mri_blur3D_addfwhm( dsim , mask , fwhm_goal ) ; /** all the work **/ /* dsim will be zero where mask==0; if we want to preserve the input values, copy dsar into qsar now at all mask!=0 voxels, since qsar contains the original data values */ if( do_preserve ){ for( vv=0 ; vv < nvox ; vv++ ) if( mask[vv] ) qsar[vv] = dsar[vv] ; } } /* if necessary, copy combined results in qsar to dsar for output */ if( use_qsar ){ for( vv=0 ; vv < nvox ; vv++ ) dsar[vv] = qsar[vv] ; } if( floatize ){ EDIT_substitute_brick( outset , ids , MRI_float , dsar ) ; } else { #pragma omp critical (MALLOC) { EDIT_substscale_brick( outset , ids , MRI_float , dsar , MRI_short , 1.0f ) ; mri_free(dsim) ; } } } /* end of loop over sub-bricks */ #pragma omp critical (MALLOC) { if( qsim != NULL ) mri_free(qsim); if( immask != NULL ){ free(qmask); mri_free(qim); } } } /* end OpenMP */ AFNI_OMP_END ; if( mask != NULL ) free( mask) ; if( immask != NULL ) mri_free(immask) ; DSET_unload(inset) ; DSET_write(outset) ; WROTE_DSET(outset) ; exit(0) ; }