int SUMA_ShortizeDset(THD_3dim_dataset **dsetp, float thisfac) {
static char FuncName[]={"SUMA_ShortizeDset"};
char sprefix[THD_MAX_PREFIX+10];
int i, j;
byte *bb=NULL;
short *sb=NULL;
float bbf=0.0;
THD_3dim_dataset *cpset=NULL, *dset=*dsetp;
SUMA_ENTRY;
if (!dset) {
SUMA_S_Err("NULL *dsetp at input!");
SUMA_RETURN(0);
}
sprintf(sprefix, "%s.s", dset->dblk->diskptr->prefix);
NEW_SHORTY(dset, DSET_NVALS(dset), "ss.cp", cpset);
for (i=0; i<DSET_NVALS(dset); ++i) {
if (DSET_BRICK_TYPE(dset,i) == MRI_byte) {
bb = (byte *)DSET_ARRAY(dset,i);
sb = (short *)DSET_ARRAY(cpset,i);
if (thisfac <= 0.0) {
for (j=0; j<DSET_NVOX(dset); ++j) {
sb[j] = (short)bb[j];
}
thisfac = DSET_BRICK_FACTOR(dset,i);
} else {
bbf = DSET_BRICK_FACTOR(dset,i); if (bbf == 0.0f) bbf = 1.0;
bbf = bbf/thisfac;
for (j=0; j<DSET_NVOX(dset); ++j) {
sb[j] = SHORTIZE((((float)bb[j])*bbf));
}
}
EDIT_BRICK_FACTOR( cpset,i,thisfac ) ;
} else {
EDIT_substscale_brick(cpset, i, DSET_BRICK_TYPE(dset,i),
DSET_ARRAY(dset,i), MRI_short, thisfac);
if (DSET_BRICK_TYPE(dset,i) != MRI_short) {
DSET_FREE_ARRAY(dset, i);
} else {
DSET_NULL_ARRAY(dset, i);
}
}
}
/* preserve tables, if any */
THD_copy_labeltable_atr( cpset->dblk, dset->dblk);
DSET_delete(dset); dset = NULL;
*dsetp=cpset;
SUMA_RETURN(1);
}
THD_3dim_dataset * THD_localhistog( int nsar , THD_3dim_dataset **insar ,
int numval , int *rlist , MCW_cluster *nbhd ,
int do_prob , int verb )
{
THD_3dim_dataset *outset=NULL , *inset ;
int nvox=DSET_NVOX(insar[0]) ;
int ids, iv, bb, nnpt=nbhd->num_pt ;
MRI_IMAGE *bbim ; int btyp ;
float **outar , **listar ;
ENTRY("THD_localhistog") ;
/*---- create output dataset ----*/
outset = EDIT_empty_copy(insar[0]) ;
EDIT_dset_items( outset ,
ADN_nvals , numval ,
ADN_datum_all , MRI_float ,
ADN_nsl , 0 ,
ADN_brick_fac , NULL ,
ADN_none ) ;
outar = (float **)malloc(sizeof(float *)*numval) ;
for( bb=0 ; bb < numval ; bb++ ){
EDIT_substitute_brick( outset , bb , MRI_float , NULL ) ;
outar[bb] = DSET_BRICK_ARRAY(outset,bb) ;
}
/*---- make mapping between values and arrays to get those values ----*/
listar = (float **)malloc(sizeof(float *)*TWO16) ;
for( bb=0 ; bb < TWO16 ; bb++ ) listar[bb] = outar[0] ;
for( bb=1 ; bb < numval ; bb++ ){
listar[ rlist[bb] + TWO15 ] = outar[bb] ;
}
/*----------- loop over datasets, add in counts for all voxels -----------*/
for( ids=0 ; ids < nsar ; ids++ ){ /* dataset loop */
inset = insar[ids] ; DSET_load(inset) ;
for( iv=0 ; iv < DSET_NVALS(inset) ; iv++ ){ /* sub-brick loop */
if( verb ) fprintf(stderr,".") ;
bbim = DSET_BRICK(inset,iv) ; btyp = bbim->kind ;
if( nnpt == 1 ){ /* only 1 voxel in nbhd */
int qq,ii,jj,kk,ib,nb ;
switch( bbim->kind ){
case MRI_short:{
short *sar = MRI_SHORT_PTR(bbim) ;
for( qq=0 ; qq < nvox ; qq++ ) listar[sar[qq]+TWO15][qq]++ ;
}
break ;
case MRI_byte:{
byte *bar = MRI_BYTE_PTR(bbim) ;
for( qq=0 ; qq < nvox ; qq++ ) listar[bar[qq]+TWO15][qq]++ ;
}
break ;
case MRI_float:{
float *far = MRI_FLOAT_PTR(bbim) ; short ss ;
for( qq=0 ; qq < nvox ; qq++ ){ ss = SHORTIZE(far[qq]); listar[ss+TWO15][qq]++; }
}
break ;
}
} else { /* multiple voxels in nbhd */
AFNI_OMP_START ;
#pragma omp parallel
{ int qq,ii,jj,kk,ib,nb ; void *nar ; short *sar,ss ; byte *bar ; float *far ;
nar = malloc(sizeof(float)*nnpt) ;
sar = (short *)nar ; bar = (byte *)nar ; far = (float *)nar ;
#pragma omp for
for( qq=0 ; qq < nvox ; qq++ ){ /* qq=voxel index */
ii = DSET_index_to_ix(inset,qq) ;
jj = DSET_index_to_jy(inset,qq) ;
kk = DSET_index_to_kz(inset,qq) ;
nb = mri_get_nbhd_array( bbim , NULL , ii,jj,kk , nbhd , nar ) ;
if( nb == 0 ) continue ;
switch( btyp ){
case MRI_short:
for( ib=0 ; ib < nb ; ib++ ) listar[sar[ib]+TWO15][qq]++ ;
break ;
case MRI_byte:
for( ib=0 ; ib < nb ; ib++ ) listar[bar[ib]+TWO15][qq]++ ;
break ;
case MRI_float:
for( ib=0 ; ib < nb ; ib++ ){ ss = SHORTIZE(far[ib]); listar[ss+TWO15][qq]++; }
break ;
}
} /* end of voxel loop */
free(nar) ;
} /* end of OpenMP */
AFNI_OMP_END ;
}
} /* end of sub-brick loop */
DSET_unload(inset) ;
} /* end of dataset loop */
if( verb ) fprintf(stderr,"\n") ;
free(listar) ;
/*---- post-process output ---*/
if( do_prob ){
byte **bbar ; int pp ;
if( verb ) INFO_message("Conversion to probabilities") ;
AFNI_OMP_START ;
#pragma omp parallel
{ int qq , ib ; float pfac , val ; byte **bbar ;
#pragma omp for
for( qq=0 ; qq < nvox ; qq++ ){
pfac = 0.0001f ;
for( ib=0 ; ib < numval ; ib++ ) pfac += outar[ib][qq] ;
pfac = 250.0f / pfac ;
for( ib=0 ; ib < numval ; ib++ ){
val = outar[ib][qq]*pfac ; outar[ib][qq] = BYTEIZE(val) ;
}
}
} /* end OpenMP */
AFNI_OMP_END ;
bbar = (byte **)malloc(sizeof(byte *)*numval) ;
for( bb=0 ; bb < numval ; bb++ ){
bbar[bb] = (byte *)malloc(sizeof(byte)*nvox) ;
for( pp=0 ; pp < nvox ; pp++ ) bbar[bb][pp] = (byte)outar[bb][pp] ;
EDIT_substitute_brick(outset,bb,MRI_byte,bbar[bb]) ;
EDIT_BRICK_FACTOR(outset,bb,0.004f) ;
}
free(bbar) ;
} /* end of do_prob */
free(outar) ;
RETURN(outset) ;
}
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) ;
}
char * MASKAVE_main( PLUGIN_interface * plint )
{
MCW_idcode * idc ;
THD_3dim_dataset * input_dset , * mask_dset ;
int iv , mcount , nvox , ii , sigmait , nvals=0 , doall , ivbot,ivtop ;
float mask_bot=666.0 , mask_top=-666.0 ;
double sum=0.0 , sigma=0.0 ;
float * sumar=NULL , * sigmar=NULL ;
char * tag , * str , buf[64] , abuf[32],sbuf[32] ;
byte * mmm ;
char * cname=NULL ; /* 06 Aug 1998 */
int cdisk=0 ; /* 22 Aug 2000 */
int miv=0 ;
/*--------------------------------------------------------------------*/
/*----- Check inputs from AFNI to see if they are reasonable-ish -----*/
if( plint == NULL )
return "*************************\n"
"MASKAVE_main: NULL input\n"
"*************************" ;
/*-- read 1st line --*/
PLUTO_next_option(plint) ;
idc = PLUTO_get_idcode(plint) ;
input_dset = PLUTO_find_dset(idc) ;
if( input_dset == NULL )
return "********************************\n"
"MASKAVE_main: bad input dataset\n"
"********************************" ;
iv = (int) PLUTO_get_number(plint) ;
if( iv >= DSET_NVALS(input_dset) )
return "**********************************\n"
"MASKAVE_main: bad input sub-brick\n"
"**********************************" ;
doall = (iv < 0) ;
if( doall ){
nvals = DSET_NVALS(input_dset) ;
ivbot = 0 ; ivtop = nvals-1 ;
} else {
ivbot = ivtop = iv ;
}
DSET_load(input_dset) ;
if( DSET_ARRAY(input_dset,ivbot) == NULL )
return "*********************************\n"
"MASKAVE_main: can't load dataset\n"
"*********************************" ;
nvox = DSET_NVOX(input_dset) ;
/*-- read 2nd line --*/
PLUTO_next_option(plint) ;
idc = PLUTO_get_idcode(plint) ;
mask_dset = PLUTO_find_dset(idc) ;
if( mask_dset == NULL )
return "*******************************\n"
"MASKAVE_main: bad mask dataset\n"
"*******************************" ;
if( DSET_NVOX(mask_dset) != nvox )
return "*************************************************************\n"
"MASKAVE_main: mask input dataset doesn't match source dataset\n"
"*************************************************************" ;
miv = (int) PLUTO_get_number(plint) ; /* 06 Aug 1998 */
if( miv >= DSET_NVALS(mask_dset) )
return "*****************************************************\n"
"MASKAVE_main: mask dataset sub-brick index is too big\n"
"*****************************************************" ;
DSET_load(mask_dset) ;
if( DSET_ARRAY(mask_dset,0) == NULL )
return "**************************************\n"
"MASKAVE_main: can't load mask dataset\n"
"**************************************" ;
/*-- read optional lines --*/
while( (tag=PLUTO_get_optiontag(plint)) != NULL ){
if( strcmp(tag,"Range") == 0 ){
mask_bot = PLUTO_get_number(plint) ;
mask_top = PLUTO_get_number(plint) ;
continue ;
}
if( strcmp(tag,"1D Save") == 0 ){
char * yn ;
cname = PLUTO_get_string(plint) ;
yn = PLUTO_get_string(plint) ;
cdisk = (strcmp(yn,yesno_list[0]) == 0) ;
continue ;
}
}
/*------------------------------------------------------*/
/*---------- At this point, the inputs are OK ----------*/
/*-- build a byte mask array --*/
mmm = (byte *) malloc( sizeof(byte) * nvox ) ;
if( mmm == NULL )
return "*** Can't malloc workspace! ***" ;
/* separate code for each input data type */
switch( DSET_BRICK_TYPE(mask_dset,miv) ){
default:
free(mmm) ;
return "*** Can't use mask dataset -- illegal data type! ***" ;
case MRI_short:{
short mbot , mtop ;
short * mar = (short *) DSET_ARRAY(mask_dset,miv) ;
float mfac = DSET_BRICK_FACTOR(mask_dset,miv) ;
if( mfac == 0.0 ) mfac = 1.0 ;
if( mask_bot <= mask_top ){
mbot = SHORTIZE(mask_bot/mfac) ;
mtop = SHORTIZE(mask_top/mfac) ;
} else {
mbot = (short) -MRI_TYPE_maxval[MRI_short] ;
mtop = (short) MRI_TYPE_maxval[MRI_short] ;
}
for( mcount=0,ii=0 ; ii < nvox ; ii++ )
if( mar[ii] >= mbot && mar[ii] <= mtop && mar[ii] != 0 ){ mmm[ii] = 1 ; mcount++ ; }
else { mmm[ii] = 0 ; }
}
break ;
case MRI_byte:{
byte mbot , mtop ;
byte * mar = (byte *) DSET_ARRAY(mask_dset,miv) ;
float mfac = DSET_BRICK_FACTOR(mask_dset,miv) ;
if( mfac == 0.0 ) mfac = 1.0 ;
if( mask_bot <= mask_top ){
mbot = BYTEIZE(mask_bot/mfac) ;
mtop = BYTEIZE(mask_top/mfac) ;
if( mtop == 0 ){
free(mmm) ;
return "*** Illegal mask range for mask dataset of bytes. ***" ;
}
} else {
mbot = 0 ;
mtop = (byte) MRI_TYPE_maxval[MRI_short] ;
}
for( mcount=0,ii=0 ; ii < nvox ; ii++ )
if( mar[ii] >= mbot && mar[ii] <= mtop && mar[ii] != 0 ){ mmm[ii] = 1 ; mcount++ ; }
else { mmm[ii] = 0 ; }
}
break ;
case MRI_float:{
float mbot , mtop ;
float * mar = (float *) DSET_ARRAY(mask_dset,miv) ;
float mfac = DSET_BRICK_FACTOR(mask_dset,miv) ;
if( mfac == 0.0 ) mfac = 1.0 ;
if( mask_bot <= mask_top ){
mbot = (float) (mask_bot/mfac) ;
mtop = (float) (mask_top/mfac) ;
} else {
mbot = -WAY_BIG ;
mtop = WAY_BIG ;
}
for( mcount=0,ii=0 ; ii < nvox ; ii++ )
if( mar[ii] >= mbot && mar[ii] <= mtop && mar[ii] != 0 ){ mmm[ii] = 1 ; mcount++ ; }
else { mmm[ii] = 0 ; }
}
break ;
}
if( mcount == 0 ){
free(mmm) ;
return "*** No voxels survive the masking operations! ***" ;
}
sigmait = (mcount > 1) ;
/*-- compute statistics --*/
if( doall ){
sumar = (float *) malloc( sizeof(float) * nvals ) ;
sigmar = (float *) malloc( sizeof(float) * nvals ) ;
}
for( iv=ivbot ; iv <= ivtop ; iv++ ){
sum = sigma = 0.0 ; /* 13 Dec 1999 */
switch( DSET_BRICK_TYPE(input_dset,iv) ){
default:
free(mmm) ; if( doall ){ free(sumar) ; free(sigmar) ; }
return "*** Can't use source dataset -- illegal data type! ***" ;
case MRI_short:{
short * bar = (short *) DSET_ARRAY(input_dset,iv) ;
float mfac = DSET_BRICK_FACTOR(input_dset,iv) ;
if( mfac == 0.0 ) mfac = 1.0 ;
for( ii=0 ; ii < nvox ; ii++ ) if( mmm[ii] ) sum += bar[ii] ;
sum = sum / mcount ;
if( sigmait ){
for( ii=0 ; ii < nvox ; ii++ )
if( mmm[ii] ) sigma += SQR(bar[ii]-sum) ;
sigma = mfac * sqrt( sigma/(mcount-1) ) ;
}
sum = mfac * sum ;
}
break ;
case MRI_byte:{
byte * bar = (byte *) DSET_ARRAY(input_dset,iv) ;
float mfac = DSET_BRICK_FACTOR(input_dset,iv) ;
if( mfac == 0.0 ) mfac = 1.0 ;
for( ii=0 ; ii < nvox ; ii++ ) if( mmm[ii] ) sum += bar[ii] ;
sum = sum / mcount ;
if( sigmait ){
for( ii=0 ; ii < nvox ; ii++ )
if( mmm[ii] ) sigma += SQR(bar[ii]-sum) ;
sigma = mfac * sqrt( sigma/(mcount-1) ) ;
}
sum = mfac * sum ;
}
break ;
case MRI_float:{
float * bar = (float *) DSET_ARRAY(input_dset,iv) ;
float mfac = DSET_BRICK_FACTOR(input_dset,iv) ;
if( mfac == 0.0 ) mfac = 1.0 ;
for( ii=0 ; ii < nvox ; ii++ ) if( mmm[ii] ) sum += bar[ii] ;
sum = sum / mcount ;
if( sigmait ){
for( ii=0 ; ii < nvox ; ii++ )
if( mmm[ii] ) sigma += SQR(bar[ii]-sum) ;
sigma = mfac * sqrt( sigma/(mcount-1) ) ;
}
sum = mfac * sum ;
}
break ;
}
if( doall ){ sumar[iv] = sum ; sigmar[iv] = sigma ; }
}
free(mmm) ;
/*-- send report --*/
if( doall ){
str = (char *) malloc( 1024 + 64*nvals ) ;
sprintf(str," ****** ROI statistics ****** \n"
" Source = %s [all sub-bricks] \n"
" Mask = %s [%s]" ,
DSET_FILECODE(input_dset) ,
DSET_FILECODE(mask_dset) , DSET_BRICK_LABEL(mask_dset,miv) ) ;
if( mask_bot <= mask_top ){
sprintf(buf," [range %g .. %g]" , mask_bot , mask_top ) ;
strcat(str,buf) ;
}
strcat(str," \n") ;
sprintf(buf," Count = %d voxels\n",mcount) ; strcat(str,buf) ;
for( iv=0 ; iv < nvals ; iv++ ){
AV_fval_to_char( sumar[iv] , abuf ) ;
AV_fval_to_char( sigmar[iv] , sbuf ) ;
sprintf(buf," Average = %9.9s Sigma = %9.9s [%s] \n",
abuf,sbuf , DSET_BRICK_LABEL(input_dset,iv) ) ;
strcat(str,buf) ;
}
PLUTO_popup_textwin( plint , str ) ;
/* 06 Aug 1998 */
if( cname != NULL && cname[0] != '\0' ){
MRI_IMAGE * qim = mri_new_vol_empty( nvals,1,1 , MRI_float ) ;
mri_fix_data_pointer( sumar , qim ) ;
PLUTO_register_timeseries( cname , qim ) ;
if( cdisk ){ /* 22 Aug 2000 */
if( PLUTO_prefix_ok(cname) ){
char * cn ;
if( strstr(cname,".1D") == NULL ){
cn = malloc(strlen(cname)+8) ;
strcpy(cn,cname) ; strcat(cn,".1D") ;
} else {
cn = cname ;
}
mri_write_1D( cn , qim ) ;
if( cn != cname ) free(cn) ;
} else {
PLUTO_popup_transient(plint," \n"
"** Illegal filename **\n"
"** in 'To Disk?' !! **\n" ) ;
}
}
mri_fix_data_pointer( NULL , qim ) ; mri_free(qim) ;
}
free(str) ; free(sumar) ; free(sigmar) ;
} else if( mask_bot <= mask_top ){
str = (char *) malloc( 1024 ) ;
sprintf( str , " *** ROI Statistics *** \n"
" Source = %s [%s] \n"
" Mask = %s [%s] [range %g .. %g] \n"
" Count = %d voxels \n"
" Average = %g \n"
" Sigma = %g " ,
DSET_FILECODE(input_dset) , DSET_BRICK_LABEL(input_dset,ivbot) ,
DSET_FILECODE(mask_dset) , DSET_BRICK_LABEL(mask_dset,miv) ,
mask_bot , mask_top , mcount , sum , sigma ) ;
PLUTO_popup_message(plint,str) ;
free(str) ;
} else {
str = (char *) malloc( 1024 ) ;
sprintf( str , " *** ROI Statistics *** \n"
" Source = %s [%s] \n"
" Mask = %s [%s] \n"
" Count = %d voxels \n"
" Average = %g \n"
" Sigma = %g " ,
DSET_FILECODE(input_dset) , DSET_BRICK_LABEL(input_dset,ivbot) ,
DSET_FILECODE(mask_dset) , DSET_BRICK_LABEL(mask_dset,miv) ,
mcount , sum , sigma ) ;
PLUTO_popup_message(plint,str) ;
free(str) ;
}
return NULL ;
}
MRI_IMAGE *mri_to_short_sclip( double scl , double lev ,
int bot , int top , MRI_IMAGE *oldim )
{
MRI_IMAGE *newim ;
register int ii , npix ;
double imin,imax ;
register double dscale , dbbot ;
register float scale , flbot , val ;
register short * ar ;
ENTRY("mri_to_short_sclip") ;
if( oldim == NULL ) RETURN( NULL ); /* 09 Feb 1999 */
newim = mri_new_conforming( oldim , MRI_short ) ;
npix = oldim->nvox ;
if( scl == 0 ){ /* compute scaling to make [min..max] -> [0..lev] */
imin = (oldim->kind==MRI_complex || oldim->kind==MRI_rgb) ? (0) : mri_min(oldim) ;
imax = mri_max( oldim ) ;
imax = (imax <= imin) ? imin+1 : imax ;
scale = dscale = (lev+0.99) / (imax-imin) ;
flbot = dbbot = imin ;
} else { /* user controlled scaling, with lev -> 0 */
scale = dscale = scl ;
flbot = dbbot = lev ;
}
ar = mri_data_pointer( newim ) ; /* fast access to data */
switch( oldim->kind ){
case MRI_rgb:{
register byte * rgb = mri_data_pointer(oldim) ;
float rfac=0.299*scale , gfac=0.587*scale , bfac=0.114*scale ;
for( ii=0 ; ii < npix ; ii++ )
ar[ii] = (short) ( rfac * rgb[3*ii]
+ gfac * rgb[3*ii+1]
+ bfac * rgb[3*ii+2] ) ;
}
break ;
case MRI_byte:{
register byte * oar = mri_data_pointer(oldim) ;
for( ii=0 ; ii < npix ; ii++ ){
val = scale * (oar[ii]-flbot) ;
ar[ii] = BYTEIZE(val) ;
}
break ;
}
case MRI_short:{
register short * oar = mri_data_pointer(oldim) ;
for( ii=0 ; ii < npix ; ii++ ){
val = scale * (oar[ii]-flbot) ;
ar[ii] = SHORTIZE(val) ;
}
break ;
}
case MRI_int:{
register int * oar = mri_data_pointer(oldim) ;
for( ii=0 ; ii < npix ; ii++ )
ar[ii] = scale * (oar[ii]-flbot) ;
break ;
}
case MRI_float:{
register float * oar = mri_data_pointer(oldim) ;
for( ii=0 ; ii < npix ; ii++ )
ar[ii] = scale * (oar[ii]-flbot) ;
break ;
}
case MRI_double:{
register double * oar = mri_data_pointer(oldim) ;
for( ii=0 ; ii < npix ; ii++ )
ar[ii] = dscale * (oar[ii]-dbbot) ;
break ;
}
case MRI_complex:{
register complex * oar = mri_data_pointer(oldim) ;
for( ii=0 ; ii < npix ; ii++ )
ar[ii] = scale * CABS(oar[ii]) ;
break ;
}
default:
fprintf( stderr , "mri_to_short_scl: unrecognized image kind\n" ) ;
MRI_FATAL_ERROR ;
}
/* clip, if desired */
if( bot < top ){
register short bb = bot , tt = top ;
for( ii=0 ; ii < npix ; ii++ ){
if( ar[ii] < bb ) ar[ii] = bb ;
else if( ar[ii] > tt ) ar[ii] = tt ;
}
}
MRI_COPY_AUX(newim,oldim) ;
RETURN( newim );
}
MRI_IMAGE *mri_to_short( double scl , MRI_IMAGE *oldim )
{
MRI_IMAGE *newim ;
register int ii , npix ;
register double scale , val ;
register short *sar ;
ENTRY("mri_to_short") ;
if( oldim == NULL ) RETURN( NULL ); /* 09 Feb 1999 */
newim = mri_new_conforming( oldim , MRI_short ) ;
sar = MRI_SHORT_PTR(newim) ;
npix = oldim->nvox ;
if( scl == 0.0 ){
switch( oldim->kind ){
case MRI_int:
case MRI_float:
case MRI_double:
case MRI_complex:
scale = mri_maxabs( oldim ) ;
if( scale != 0.0 ) scale = 10000.0 / scale ;
#ifdef MRI_DEBUG
fprintf( stderr , "mri_to_short: scale factor = %e\n" , scale ) ;
#endif
break ;
default:
scale = 1.0 ;
break ;
}
} else {
scale = scl ;
}
switch( oldim->kind ){
case MRI_rgb:{
byte *rgb = MRI_RGB_PTR(oldim) ;
float rfac=0.299*scale , gfac=0.587*scale , bfac=0.114*scale ;
for( ii=0 ; ii < npix ; ii++ )
sar[ii] = (short)( rfac * rgb[3*ii]
+ gfac * rgb[3*ii+1]
+ bfac * rgb[3*ii+2] ) ;
}
break ;
case MRI_byte:{
byte *qar = MRI_BYTE_PTR(oldim) ;
if( scale != 1.0 )
for( ii=0 ; ii < npix ; ii++ ){
val = scale * qar[ii] ;
sar[ii] = SHORTIZE(val) ;
}
else
for( ii=0 ; ii < npix ; ii++ )
sar[ii] = (short) qar[ii] ;
break ;
}
case MRI_short:{
short *qar = MRI_SHORT_PTR(oldim) ;
if( scale != 1.0 )
for( ii=0 ; ii < npix ; ii++ ){
val = scale * qar[ii] ;
sar[ii] = SHORTIZE(val) ;
}
else
(void) memcpy( sar , qar , sizeof(short)*npix ) ;
break ;
}
case MRI_int:{
int *qar = MRI_INT_PTR(oldim) ;
if( scale != 1.0 )
for( ii=0 ; ii < npix ; ii++ ){
val = scale * qar[ii] ;
sar[ii] = SHORTIZE(val) ;
}
else
for( ii=0 ; ii < npix ; ii++ )
sar[ii] = SHORTIZE(qar[ii]) ;
break ;
}
case MRI_float:{
float *qar = MRI_FLOAT_PTR(oldim) ;
if( scale != 1.0 )
for( ii=0 ; ii < npix ; ii++ ){
val = scale * qar[ii] ;
sar[ii] = SHORTIZE(val) ;
}
else
for( ii=0 ; ii < npix ; ii++ )
sar[ii] = SHORTIZE(qar[ii]) ;
break ;
}
case MRI_double:{
double *qar = MRI_DOUBLE_PTR(oldim) ;
for( ii=0 ; ii < npix ; ii++ )
sar[ii] = scale * qar[ii] ;
break ;
}
case MRI_complex:{
complex *qar = MRI_COMPLEX_PTR(oldim) ;
for( ii=0 ; ii < npix ; ii++ )
sar[ii] = scale * CABS(qar[ii]) ;
break ;
}
default:
fprintf( stderr , "mri_to_short: unrecognized image kind\n" ) ;
MRI_FATAL_ERROR ;
}
MRI_COPY_AUX(newim,oldim) ;
RETURN( newim );
}
int thd_mask_from_brick(THD_3dim_dataset * dset, int volume, float thresh,
byte ** mask, int absolute)
{
float factor;
byte * tmask;
int nvox, type, c, size = 0;
ENTRY("thd_mask_from_brick");
if ( mask ) *mask = NULL; /* to be sure */
if ( !ISVALID_DSET(dset) || ! mask || volume < 0 )
RETURN(-1);
if ( volume >= DSET_NVALS(dset) )
{
fprintf(stderr,"** tmfb: sub-brick %d out-of-range\n", volume);
RETURN(-1);
}
if( !DSET_LOADED(dset) ) DSET_load(dset);
nvox = DSET_NVOX(dset);
type = DSET_BRICK_TYPE(dset, volume);
if ( type != MRI_byte && type != MRI_short &&
type != MRI_int && type != MRI_float )
{
fprintf(stderr,"** tmfb: invalid dataset type %s, sorry...\n",
MRI_type_name[type]);
RETURN(-1);
}
tmask = (byte *)calloc(nvox, sizeof(byte));
if ( ! tmask )
{
fprintf(stderr,"** tmfb: failed to allocate mask of %d bytes\n", nvox);
RETURN(-1);
}
factor = DSET_BRICK_FACTOR(dset, volume);
/* cheat: adjust threshold, not data */
if ( factor != 0.0 ) thresh /= factor;
switch( DSET_BRICK_TYPE(dset, volume) )
{
case MRI_byte:
{
if (thresh <= (float)MRI_maxbyte) { /* ZSS: Oct 2011
Without this test, a high threshold value might end up
equal to MRI_maxbyte when BYTEIZED below, resulting in
the highest voxel making it to the mask no matter how
much higher the threshold is set. */
byte * dp = DSET_ARRAY(dset, volume);
byte thr = BYTEIZE(thresh + 0.99999); /* ceiling */
for ( c = 0; c < nvox; c++ )
if ( dp[c] != 0 && ( dp[c] >= thr ) )
{
size++;
tmask[c] = 1;
}
}
}
break;
case MRI_short:
{
if (thresh <= (float)MRI_maxshort) { /* ZSS: Oct 2011 */
short * dp = DSET_ARRAY(dset, volume);
short thr = SHORTIZE(thresh + 0.99999); /* ceiling */
for ( c = 0; c < nvox; c++, dp++ )
if ( *dp != 0 && ( *dp >= thr || (absolute && *dp <= -thr) ) )
{
size++;
tmask[c] = 1;
}
}
}
break;
case MRI_int:
{
int * dp = DSET_ARRAY(dset, volume);
int thr = (int)(thresh + 0.99999); /* ceiling */
for ( c = 0; c < nvox; c++, dp++ )
if ( *dp != 0 && ( *dp >= thr || (absolute && *dp <= -thr) ) )
{
size++;
tmask[c] = 1;
}
}
break;
case MRI_float:
{
float * dp = DSET_ARRAY(dset, volume);
for ( c = 0; c < nvox; c++, dp++ )
if (*dp != 0 && (*dp >= thresh || (absolute && *dp <= -thresh)))
{
size++;
tmask[c] = 1;
}
}
break;
default: /* let's be sure */
{
fprintf(stderr,"** tmfb: invalid dataset type, sorry...\n");
free(tmask);
}
break;
}
*mask = tmask;
RETURN(size);
}
byte * THD_makemask( THD_3dim_dataset *mask_dset ,
int miv , float mask_bot , float mask_top )
{
float maxval ; /* for computing limits for an empty mask */
byte *mmm = NULL ;
int nvox , ii ;
int empty = 0 ; /* do we return an empty mask */
if( !ISVALID_DSET(mask_dset) ||
miv < 0 ||
miv >= DSET_NVALS(mask_dset) ) return NULL ;
nvox = DSET_NVOX(mask_dset) ;
DSET_load(mask_dset) ; if( !DSET_LOADED(mask_dset) ) return NULL ;
mmm = (byte *) calloc( sizeof(byte) * nvox , 1 ) ;
switch( DSET_BRICK_TYPE(mask_dset,miv) ){
default:
free(mmm) ; DSET_unload(mask_dset) ; return NULL ;
case MRI_short:{
short mbot , mtop ;
short *mar = (short *) DSET_ARRAY(mask_dset,miv) ;
float mfac = DSET_BRICK_FACTOR(mask_dset,miv) ;
if( mfac == 0.0 ) mfac = 1.0 ;
if( mask_bot <= mask_top ){
/* maybe this mask is empty, allow for rounding */
maxval = MRI_TYPE_maxval[MRI_short] + 0.5 ;
if( mask_bot/mfac >= maxval || mask_top/mfac <= -maxval ) empty=1;
mbot = SHORTIZE(mask_bot/mfac) ;
mtop = SHORTIZE(mask_top/mfac) ;
} else {
mbot = (short) -MRI_TYPE_maxval[MRI_short] ;
mtop = (short) MRI_TYPE_maxval[MRI_short] ;
}
if( !empty ) /* 6 Jun 2007 */
for( ii=0 ; ii < nvox ; ii++ )
if( mar[ii] >= mbot && mar[ii] <= mtop && mar[ii] != 0 )
mmm[ii]=1;
}
break ;
case MRI_byte:{
byte mbot , mtop ;
byte *mar = (byte *) DSET_ARRAY(mask_dset,miv) ;
float mfac = DSET_BRICK_FACTOR(mask_dset,miv) ;
if( mfac == 0.0 ) mfac = 1.0 ;
if( mask_bot <= mask_top && mask_top > 0.0 ){
/* maybe this mask is empty, allow for rounding */
/* (top <= 0 is flag for full mask) */
maxval = MRI_TYPE_maxval[MRI_byte] + 0.5 ;
if( mask_bot/mfac >= maxval ) empty = 1;
mbot = BYTEIZE(mask_bot/mfac) ;
mtop = BYTEIZE(mask_top/mfac) ;
} else {
mbot = 0 ;
mtop = (byte) MRI_TYPE_maxval[MRI_short] ;
}
if( !empty ) /* 6 Jun 2007 */
for( ii=0 ; ii < nvox ; ii++ )
if( mar[ii] >= mbot && mar[ii] <= mtop && mar[ii] != 0 )
mmm[ii]=1;
}
break ;
case MRI_float:{
float mbot , mtop ;
float *mar = (float *) DSET_ARRAY(mask_dset,miv) ;
float mfac = DSET_BRICK_FACTOR(mask_dset,miv) ;
if( mfac == 0.0 ) mfac = 1.0 ;
if( mask_bot <= mask_top ){
mbot = (float) (mask_bot/mfac) ;
mtop = (float) (mask_top/mfac) ;
} else {
mbot = -WAY_BIG ;
mtop = WAY_BIG ;
}
for( ii=0 ; ii < nvox ; ii++ )
if( mar[ii] >= mbot && mar[ii] <= mtop && mar[ii] != 0 ) mmm[ii]=1;
}
break ;
}
return mmm ;
}
int THD_makedsetmask( THD_3dim_dataset *mask_dset ,
int miv , float mask_bot , float mask_top,
byte *cmask )
{
float maxval ; /* for computing limits for an empty mask */
int nvox , ii, nonzero=-1 , empty = 0 ;
if( !ISVALID_DSET(mask_dset) ||
miv < 0 ||
miv >= DSET_NVALS(mask_dset) ) return (-1) ;
nvox = DSET_NVOX(mask_dset) ;
DSET_mallocize(mask_dset); /* do this or else it could be a read only dset! */
DSET_load(mask_dset) ; if( !DSET_LOADED(mask_dset) ) return (-1) ;
nonzero = 0;
switch( DSET_BRICK_TYPE(mask_dset,miv) ){
default:
DSET_unload(mask_dset) ; return (-1) ;
case MRI_short:{
short mbot , mtop ;
short *mar = (short *) DSET_ARRAY(mask_dset,miv) ;
float mfac = DSET_BRICK_FACTOR(mask_dset,miv) ;
if( mfac == 0.0 ) mfac = 1.0 ;
if( mask_bot <= mask_top ){
/* maybe this mask is empty, allow for rounding */
maxval = MRI_TYPE_maxval[MRI_short] + 0.5 ;
if( mask_bot/mfac >= maxval || mask_top/mfac <= -maxval ) empty=1;
mbot = SHORTIZE(mask_bot/mfac) ;
mtop = SHORTIZE(mask_top/mfac) ;
} else {
mbot = (short) -MRI_TYPE_maxval[MRI_short] ;
mtop = (short) MRI_TYPE_maxval[MRI_short] ;
}
if (empty) { /* if empty, clear result 6 Jun 2007 */
for( ii=0 ; ii < nvox ; ii++ ) mar[ii] = 0;
} else if (cmask) {
for( ii=0 ; ii < nvox ; ii++ )
if( mar[ii] >= mbot && mar[ii] <= mtop && mar[ii] != 0 && cmask[ii]) { mar[ii]=1; ++nonzero; }
else { mar[ii] = 0; }
} else {
for( ii=0 ; ii < nvox ; ii++ )
if( mar[ii] >= mbot && mar[ii] <= mtop && mar[ii] != 0 ) { mar[ii]=1; ++nonzero; }
else { mar[ii] = 0; }
}
}
break ;
case MRI_byte:{
byte mbot , mtop ;
byte *mar = (byte *) DSET_ARRAY(mask_dset,miv) ;
float mfac = DSET_BRICK_FACTOR(mask_dset,miv) ;
if( mfac == 0.0 ) mfac = 1.0 ;
if( mask_bot <= mask_top && mask_top > 0.0 ){
/* maybe this mask is empty, allow for rounding */
/* (top <= 0 is flag for full mask) */
maxval = MRI_TYPE_maxval[MRI_byte] + 0.5 ;
if( mask_bot/mfac >= maxval ) empty = 1;
mbot = BYTEIZE(mask_bot/mfac) ;
mtop = BYTEIZE(mask_top/mfac) ;
} else {
mbot = 0 ;
mtop = (byte) MRI_TYPE_maxval[MRI_short] ;
}
if (empty) { /* if empty, clear result 6 Jun 2007 */
for( ii=0 ; ii < nvox ; ii++ ) mar[ii] = 0;
} else if (cmask) {
for( ii=0 ; ii < nvox ; ii++ )
if( mar[ii] >= mbot && mar[ii] <= mtop && mar[ii] != 0 && cmask[ii]){ mar[ii]=1; ++nonzero; }
else { mar[ii] = 0; }
} else {
for( ii=0 ; ii < nvox ; ii++ )
if( mar[ii] >= mbot && mar[ii] <= mtop && mar[ii] != 0 ){ mar[ii]=1; ++nonzero; }
else { mar[ii] = 0; }
}
}
break ;
case MRI_float:{
float mbot , mtop ;
float *mar = (float *) DSET_ARRAY(mask_dset,miv) ;
float mfac = DSET_BRICK_FACTOR(mask_dset,miv) ;
if( mfac == 0.0 ) mfac = 1.0 ;
if( mask_bot <= mask_top ){
mbot = (float) (mask_bot/mfac) ;
mtop = (float) (mask_top/mfac) ;
} else {
mbot = -WAY_BIG ;
mtop = WAY_BIG ;
}
if (cmask) {
for( ii=0 ; ii < nvox ; ii++ )
if( mar[ii] >= mbot && mar[ii] <= mtop && mar[ii] != 0 && cmask[ii]) { mar[ii]=1; ++nonzero; }
else { mar[ii] = 0; }
} else {
for( ii=0 ; ii < nvox ; ii++ )
if( mar[ii] >= mbot && mar[ii] <= mtop && mar[ii] != 0 ) { mar[ii]=1; ++nonzero; }
else { mar[ii] = 0; }
}
}
break ;
}
/* remove any scaling factor ZSS April 24 06*/
EDIT_BRICK_FACTOR(mask_dset,miv , 0.0);
return (nonzero) ;
}
