MRI_IMAGE * mri_local_percmean( MRI_IMAGE *fim , float vrad , float p1, float p2 )
{
MRI_IMAGE *aim , *bim , *cim , *dim ;
float *aar , *bar , *car , *dar ;
byte *ams , *bms ;
MCW_cluster *nbhd ;
int ii , nx,ny,nz,nxy,nxyz ;
float vbot=0.0f ;
ENTRY("mri_local_percmean") ;
if( p1 > p2 ){ float val = p1; p1 = p2; p2 = val; }
if( fim == NULL || vrad < 4.0f || p1 < 0.0f || p2 > 100.0f ) RETURN(NULL) ;
/* just one percentile? */
if( p1 == p2 ) RETURN( mri_local_percentile(fim,vrad,p1) ) ;
if( verb ) fprintf(stderr,"A") ;
/* create automask of copy of input image */
aim = mri_to_float(fim) ; aar = MRI_FLOAT_PTR(aim) ;
ams = mri_automask_image(aim) ;
if( ams == NULL ){ mri_free(aim) ; RETURN(NULL) ; }
/* apply automask to copy of input image */
for( ii=0 ; ii < aim->nvox ; ii++ ) if( ams[ii] == 0 ) aar[ii] = 0.0f ;
free(ams) ;
/* shrink image by 2 for speed */
if( verb ) fprintf(stderr,"D") ;
bim = mri_double_down(aim) ; bar = MRI_FLOAT_PTR(bim) ; mri_free(aim) ;
bms = (byte *)malloc(sizeof(byte)*bim->nvox) ;
for( ii=0 ; ii < bim->nvox ; ii++ ) bms[ii] = (bar[ii] != 0.0f) ;
if( !USE_ALL_VALS ){
vbot = 0.00666f * mri_max(bim) ;
}
/* create neighborhood mask (1/2 radius in the shrunken copy) */
nbhd = MCW_spheremask( 1.0f,1.0f,1.0f , 0.5f*vrad+0.001f ) ;
cim = mri_new_conforming(bim,MRI_float) ; car = MRI_FLOAT_PTR(cim) ;
SetSearchAboutMaskedVoxel(1) ;
nx = bim->nx ; ny = bim->ny ; nz = bim->nz ; nxy = nx*ny ; nxyz = nxy*nz ;
/* for each output voxel,
extract neighborhood array, sort it, average desired range.
Since this is the slowest part of the code, it is now OpenMP-ized. */
#ifndef USE_OMP /* old serial code */
{ int vvv,vstep , ii,jj,kk , nbar_num ; float val , *nbar ;
nbar = (float *)malloc(sizeof(float)*nbhd->num_pt) ;
vstep = (verb) ? nxyz/50 : 0 ;
if( vstep ) fprintf(stderr,"\n + Voxel loop: ") ;
for( vvv=kk=0 ; kk < nz ; kk++ ){
for( jj=0 ; jj < ny ; jj++ ){
for( ii=0 ; ii < nx ; ii++,vvv++ ){
if( vstep && vvv%vstep == vstep-1 ) vstep_print() ;
nbar_num = mri_get_nbhd_array( bim,bms , ii,jj,kk , nbhd,nbar ) ;
if( nbar_num < 1 ){ /* no data */
val = 0.0f ;
} else {
qsort_float(nbar_num,nbar) ; /* sort */
if( nbar_num == 1 ){ /* stoopid case */
val = nbar[0] ;
} else { /* average values from p1 to p2 percentiles */
int q1,q2,qq , qb;
if( !USE_ALL_VALS ){ /* Ignore tiny values [17 May 2016] */
for( qb=0 ; qb < nbar_num && nbar[qb] <= vbot ; qb++ ) ; /*nada*/
if( qb == nbar_num ){
val = 0.0f ;
} else if( qb == nbar_num-1 ){
val = nbar[qb] ;
} else {
q1 = (int)( 0.01f*p1*(nbar_num-1-qb)) + qb; if( q1 > nbar_num-1 ) q1 = nbar_num-1;
q2 = (int)( 0.01f*p2*(nbar_num-1-qb)) + qb; if( q2 > nbar_num-1 ) q2 = nbar_num-1;
for( qq=q1,val=0.0f ; qq <= q2 ; qq++ ) val += nbar[qq] ;
val /= (q2-q1+1.0f) ;
}
} else { /* Use all values [the olden way] */
q1 = (int)( 0.01f*p1*(nbar_num-1) ) ; /* p1 location */
q2 = (int)( 0.01f*p2*(nbar_num-1) ) ; /* p2 location */
for( qq=q1,val=0.0f ; qq <= q2 ; qq++ ) val += nbar[qq] ;
val /= (q2-q1+1.0f) ;
}
}
}
FSUB(car,ii,jj,kk,nx,nxy) = val ;
}}}
free(nbar) ;
if( vstep ) fprintf(stderr,"!") ;
}
#else /* new parallel code [06 Mar 2013 = Snowquestration Day!] */
AFNI_OMP_START ;
if( verb ) fprintf(stderr,"V") ;
#pragma omp parallel
{ int vvv , ii,jj,kk,qq , nbar_num ; float val , *nbar ;
nbar = (float *)malloc(sizeof(float)*nbhd->num_pt) ;
#pragma omp for
for( vvv=0 ; vvv < nxyz ; vvv++ ){
ii = vvv % nx ; kk = vvv / nxy ; jj = (vvv-kk*nxy) / nx ;
nbar_num = mri_get_nbhd_array( bim,bms , ii,jj,kk , nbhd,nbar ) ;
if( nbar_num < 1 ){ /* no data */
val = 0.0f ;
} else {
qsort_float(nbar_num,nbar) ; /* sort */
if( nbar_num == 1 ){ /* stoopid case */
val = nbar[0] ;
} else { /* average values from p1 to p2 percentiles */
int q1,q2,qq , qb;
if( !USE_ALL_VALS ){ /* Ignore tiny values [17 May 2016] */
for( qb=0 ; qb < nbar_num && nbar[qb] <= vbot ; qb++ ) ; /*nada*/
if( qb == nbar_num ){
val = 0.0f ;
} else if( qb == nbar_num-1 ){
val = nbar[qb] ;
} else {
q1 = (int)( 0.01f*p1*(nbar_num-1-qb)) + qb; if( q1 > nbar_num-1 ) q1 = nbar_num-1;
q2 = (int)( 0.01f*p2*(nbar_num-1-qb)) + qb; if( q2 > nbar_num-1 ) q2 = nbar_num-1;
for( qq=q1,val=0.0f ; qq <= q2 ; qq++ ) val += nbar[qq] ;
val /= (q2-q1+1.0f) ;
}
} else { /* Use all values [the olden way] */
q1 = (int)( 0.01f*p1*(nbar_num-1) ) ; /* p1 location */
q2 = (int)( 0.01f*p2*(nbar_num-1) ) ; /* p2 location */
for( qq=q1,val=0.0f ; qq <= q2 ; qq++ ) val += nbar[qq] ;
val /= (q2-q1+1.0f) ;
}
if( verb && vvv%66666==0 ) fprintf(stderr,".") ;
}
}
car[vvv] = val ;
}
free(nbar) ;
} /* end parallel code */
AFNI_OMP_END ;
#endif
mri_free(bim) ; free(bms) ; KILL_CLUSTER(nbhd) ;
/* expand output image back to original size */
dim = mri_double_up( cim , fim->nx%2 , fim->ny%2 , fim->nz%2 ) ;
if( verb ) fprintf(stderr,"U") ;
mri_free(cim) ;
RETURN(dim) ;
}
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) ;
}
MRI_IMAGE * mri_local_percentile( MRI_IMAGE *fim , float vrad , float perc )
{
MRI_IMAGE *aim , *bim , *cim , *dim ;
float *aar , *bar , *car , *dar , *nbar ;
byte *ams , *bms ;
MCW_cluster *nbhd ;
int ii,jj,kk , nbar_num , nx,ny,nz,nxy ;
float fq,val ; int qq,qp,qm ;
ENTRY("mri_local_percentile") ;
if( fim == NULL || vrad < 4.0f || perc < 0.0f || perc > 100.0f ) RETURN(NULL) ;
/* compute automask */
aim = mri_to_float(fim) ; aar = MRI_FLOAT_PTR(aim) ;
ams = mri_automask_image(aim) ;
if( ams == NULL ){ mri_free(aim) ; RETURN(NULL) ; }
/* apply automask to image copy */
for( ii=0 ; ii < aim->nvox ; ii++ ) if( ams[ii] == 0 ) aar[ii] = 0.0f ;
free(ams) ;
/* shrink image by 2 for speedup */
bim = mri_double_down(aim) ; bar = MRI_FLOAT_PTR(bim) ; mri_free(aim) ;
bms = (byte *)malloc(sizeof(byte)*bim->nvox) ;
for( ii=0 ; ii < bim->nvox ; ii++ ) bms[ii] = (bar[ii] != 0.0f) ;
/* neighborhood has 1/2 radius in the shrunken volume */
nbhd = MCW_spheremask( 1.0f,1.0f,1.0f , 0.5f*vrad+0.001f ) ;
nbar = (float *)malloc(sizeof(float)*nbhd->num_pt) ;
cim = mri_new_conforming(bim,MRI_float) ; car = MRI_FLOAT_PTR(cim) ;
SetSearchAboutMaskedVoxel(1) ;
nx = bim->nx ; ny = bim->ny ; nz = bim->nz ; nxy = nx*ny ;
/* for each voxel:
extract neighborhood array, sort it, get result */
for( kk=0 ; kk < nz ; kk++ ){
for( jj=0 ; jj < ny ; jj++ ){
for( ii=0 ; ii < nx ; ii++ ){
nbar_num = mri_get_nbhd_array( bim,bms , ii,jj,kk , nbhd,nbar ) ;
if( nbar_num < 1 ){
val = 0.0f ;
} else {
qsort_float(nbar_num,nbar) ;
if( nbar_num == 1 || perc <= 0.000001f ){
val = nbar[0] ;
} else if( perc >= 99.9999f ){
val = nbar[nbar_num-1] ;
} else {
fq = (0.01f*perc)*nbar_num ;
qq = (int)fq ; qp = qq+1 ; if( qp == nbar_num ) qp = qq ;
qm = qq-1 ; if( qm < 0 ) qm = 0 ;
val = 0.3333333f * ( nbar[qm] + nbar[qq] + nbar[qp] ) ;
}
}
FSUB(car,ii,jj,kk,nx,nxy) = val ;
}}}
mri_free(bim) ; free(bms) ; free(nbar) ; KILL_CLUSTER(nbhd) ;
dim = mri_double_up( cim , fim->nx%2 , fim->ny%2 , fim->nz%2 ) ;
mri_free(cim) ;
RETURN(dim) ;
}
