int main( int argc , char * argv[] )
{
THD_3dim_dataset * dset ;
THD_dataxes * daxes ;
FD_brick ** brarr , * baxi , * bsag , * bcor ;
int iarg , ii ;
Boolean ok ;
MRI_IMAGE * pim , * flim , * slim ;
float * flar ;
dset_range dr ;
float val , fimfac ;
int ival,ityp , kk ;
float xbot=BIGG,xtop=BIGG , ybot=BIGG,ytop=BIGG , zbot=BIGG,ztop=BIGG ;
int xgood=0 , ygood=0 , zgood=0 ,
proj_code=PROJ_SUM , mirror_code=MIRR_NO , nsize=0 ;
char root[THD_MAX_NAME] = "proj." ;
char fname[THD_MAX_NAME] ;
int ixbot=0,ixtop=0 , jybot=0,jytop=0 , kzbot=0,kztop=0 ;
THD_fvec3 fv ;
THD_ivec3 iv ;
/*--- read command line arguments ---*/
if( argc < 2 || strncmp(argv[1],"-help",6) == 0 ) Syntax() ;
INIT_EDOPT( &PRED_edopt ) ;
iarg = 1 ;
while( iarg < argc && argv[iarg][0] == '-' ){
DB("new arg:",argv[iarg]) ;
/**** check for editing option ****/
ii = EDIT_check_argv( argc , argv , iarg , &PRED_edopt ) ;
if( ii > 0 ){
iarg += ii ;
continue ;
}
/**** -sum or -max ****/
if( strncmp(argv[iarg],"-sum",6) == 0 ){
proj_code = PROJ_SUM ;
iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-max",6) == 0 ){
proj_code = PROJ_MMAX ;
iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-amax",6) == 0 ){
proj_code = PROJ_AMAX ;
iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-smax",6) == 0 ){
proj_code = PROJ_SMAX ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-first") == 0 ){ /* 02 Nov 2000 */
proj_code = PROJ_FIRST ;
first_thresh = strtod( argv[++iarg] , NULL ) ;
iarg++ ; continue ;
}
/**** -mirror ****/
if( strncmp(argv[iarg],"-mirror",6) == 0 ){
mirror_code = MIRR_YES ;
iarg++ ; continue ;
}
/**** -nsize ****/
if( strncmp(argv[iarg],"-nsize",6) == 0 ){
nsize = 1 ;
iarg++ ; continue ;
}
/**** -output root ****/
if( strncmp(argv[iarg],"-output",6) == 0 ||
strncmp(argv[iarg],"-root",6) == 0 ){
if( iarg+1 >= argc ){
fprintf(stderr,"\n*** no argument after option %s\n",argv[iarg]) ;
exit(-1) ;
}
MCW_strncpy( root , argv[++iarg] , THD_MAX_NAME-1 ) ;
ii = strlen(root) ;
if( ii == 0 ){
fprintf(stderr,"\n*** illegal rootname!\n") ; exit(-1) ;
}
if( root[ii-1] != '.' ){ root[ii] = '.' ; root[ii+1] = '\0' ; }
iarg++ ; continue ;
}
/**** -ALL ****/
if( strncmp(argv[iarg],"-ALL",6) == 0 ||
strncmp(argv[iarg],"-all",6) == 0 ){
xgood = ygood = zgood = 1 ;
xbot = ybot = zbot = -BIGG ;
xtop = ytop = ztop = BIGG ;
iarg++ ; continue ;
}
/**** -RL {all | x1 x2} ****/
if( strncmp(argv[iarg],"-RL",6) == 0 ||
strncmp(argv[iarg],"-LR",6) == 0 ||
strncmp(argv[iarg],"-rl",6) == 0 ||
strncmp(argv[iarg],"-lr",6) == 0 ||
strncmp(argv[iarg],"-sag",6)== 0 ){
char * cerr ; float tf ;
xgood = 1 ; /* mark for x projection */
if( iarg+1 >= argc ){
fprintf(stderr,"\n*** no argument after option %s\n",argv[iarg]) ;
exit(-1) ;
}
if( strncmp(argv[iarg+1],"all",6) == 0 ||
strncmp(argv[iarg+1],"ALL",6) == 0 ){
xbot = -BIGG;
xtop = BIGG ;
iarg += 2 ; continue ;
}
if( iarg+2 >= argc ){
fprintf(stderr,"\n*** no argument after option %s\n",argv[iarg]) ;
exit(-1) ;
}
xbot = strtod( argv[iarg+1] , &cerr ) ;
if( cerr == argv[iarg+1] ){
fprintf(stderr,"\n*** illegal argument after %s: %s\n",
argv[iarg],argv[iarg+1] ) ; exit(-1) ;
}
if( *cerr == 'R' && xbot > 0.0 ) xbot = -xbot ;
xtop = strtod( argv[iarg+2] , &cerr ) ;
if( cerr == argv[iarg+2] ){
fprintf(stderr,"\n*** illegal argument after %s: %s\n",
argv[iarg],argv[iarg+2] ) ; exit(-1) ;
}
if( *cerr == 'R' && xtop > 0.0 ) xtop = -xtop ;
if( xbot > xtop ){ tf = xbot ; xbot = xtop ; xtop = tf ; }
iarg +=3 ; continue ;
}
/**** -AP {all | y1 y2} ****/
if( strncmp(argv[iarg],"-AP",6) == 0 ||
strncmp(argv[iarg],"-PA",6) == 0 ||
strncmp(argv[iarg],"-ap",6) == 0 ||
strncmp(argv[iarg],"-pa",6) == 0 ||
strncmp(argv[iarg],"-cor",6)== 0 ){
char * cerr ; float tf ;
ygood = 1 ; /* mark for y projection */
if( iarg+1 >= argc ){
fprintf(stderr,"\n*** no argument after option %s\n",argv[iarg]) ;
exit(-1) ;
}
if( strncmp(argv[iarg+1],"all",6) == 0 ||
strncmp(argv[iarg+1],"ALL",6) == 0 ){
ybot = -BIGG ;
ytop = BIGG ;
iarg += 2 ; continue ;
}
if( iarg+2 >= argc ){
fprintf(stderr,"\n*** no argument after option %s\n",argv[iarg]) ;
exit(-1) ;
}
ybot = strtod( argv[iarg+1] , &cerr ) ;
if( cerr == argv[iarg+1] ){
fprintf(stderr,"\n*** illegal argument after %s: %s\n",
argv[iarg],argv[iarg+1] ) ; exit(-1) ;
}
if( *cerr == 'A' && ybot > 0.0 ) ybot = -ybot ;
ytop = strtod( argv[iarg+2] , &cerr ) ;
if( cerr == argv[iarg+2] ){
fprintf(stderr,"\n*** illegal argument after %s: %s\n",
argv[iarg],argv[iarg+2] ) ; exit(-1) ;
}
if( *cerr == 'A' && ytop > 0.0 ) ytop = -ytop ;
if( ybot > ytop ){ tf = ybot ; ybot = ytop ; ytop = tf ; }
iarg +=3 ; continue ;
}
/**** -IS {all | z1 z2} ****/
if( strncmp(argv[iarg],"-IS",6) == 0 ||
strncmp(argv[iarg],"-SI",6) == 0 ||
strncmp(argv[iarg],"-is",6) == 0 ||
strncmp(argv[iarg],"-si",6) == 0 ||
strncmp(argv[iarg],"-axi",6)== 0 ){
char * cerr ; float tf ;
zgood = 1 ; /* mark for y projection */
if( iarg+1 >= argc ){
fprintf(stderr,"\n*** no argument after option %s\n",argv[iarg]) ;
exit(-1) ;
}
if( strncmp(argv[iarg+1],"all",6) == 0 ||
strncmp(argv[iarg+1],"ALL",6) == 0 ){
zbot = -BIGG ;
ztop = BIGG ;
iarg += 2 ; continue ;
}
if( iarg+2 >= argc ){
fprintf(stderr,"\n*** no argument after option %s\n",argv[iarg]) ;
exit(-1) ;
}
zbot = strtod( argv[iarg+1] , &cerr ) ;
if( cerr == argv[iarg+1] ){
fprintf(stderr,"\n*** illegal argument after %s: %s\n",
argv[iarg],argv[iarg+1] ) ; exit(-1) ;
}
if( *cerr == 'I' && zbot > 0.0 ) zbot = -zbot ;
ztop = strtod( argv[iarg+2] , &cerr ) ;
if( cerr == argv[iarg+2] ){
fprintf(stderr,"\n*** illegal argument after %s: %s\n",
argv[iarg],argv[iarg+2] ) ; exit(-1) ;
}
if( *cerr == 'I' && ztop > 0.0 ) ztop = -ztop ;
if( zbot > ztop ){ tf = zbot ; zbot = ztop ; ztop = tf ; }
iarg +=3 ; continue ;
}
/**** unknown option ****/
fprintf(stderr,"\n*** Unknown option: %s\n",argv[iarg]) ;
exit(-1) ;
} /* end of loop over input options */
if( ! xgood && ! ygood && ! zgood ){
fprintf(stderr,"\n*** No projections ordered!?\n") ; exit(-1) ;
}
/*--- open dataset and set up to extract data slices ---*/
dset = THD_open_dataset( argv[iarg] ) ;
if( dset == NULL ){
fprintf(stderr,"\n*** Can't open dataset file %s\n",argv[iarg]) ;
exit(-1) ;
}
if( DSET_NUM_TIMES(dset) > 1 ){
fprintf(stderr,"\n*** Can't project time-dependent dataset!\n") ;
exit(1) ;
}
EDIT_one_dataset( dset, &PRED_edopt ) ;
daxes = dset->daxes ;
brarr = THD_setup_bricks( dset ) ;
baxi = brarr[0] ; bsag = brarr[1] ; bcor = brarr[2] ;
/*--- determine index range for each direction ---*/
dr = PR_get_range( dset ) ;
if( xgood ){
if( xbot < dr.xbot ) xbot = dr.xbot ;
if( xtop > dr.xtop ) xtop = dr.xtop ;
fv = THD_dicomm_to_3dmm( dset , TEMP_FVEC3(xbot,0,0) ) ;
iv = THD_3dmm_to_3dind ( dset , fv ) ;
iv = THD_3dind_to_fdind( bsag , iv ) ; ixbot = iv.ijk[2] ;
fv = THD_dicomm_to_3dmm( dset , TEMP_FVEC3(xtop,0,0) ) ;
iv = THD_3dmm_to_3dind ( dset , fv ) ;
iv = THD_3dind_to_fdind( bsag , iv ) ; ixtop = iv.ijk[2] ;
if( ixbot > ixtop ) { ii = ixbot ; ixbot = ixtop ; ixtop = ii ; }
if( ixbot < 0 ) ixbot = 0 ;
if( ixtop >= bsag->n3 ) ixtop = bsag->n3 - 1 ;
}
if( ygood ){
if( ybot < dr.ybot ) ybot = dr.ybot ;
if( ytop > dr.ytop ) ytop = dr.ytop ;
fv = THD_dicomm_to_3dmm( dset , TEMP_FVEC3(0,ybot,0) ) ;
iv = THD_3dmm_to_3dind ( dset , fv ) ;
iv = THD_3dind_to_fdind( bcor , iv ) ; jybot = iv.ijk[2] ;
fv = THD_dicomm_to_3dmm( dset , TEMP_FVEC3(0,ytop,0) ) ;
iv = THD_3dmm_to_3dind ( dset , fv ) ;
iv = THD_3dind_to_fdind( bcor , iv ) ; jytop = iv.ijk[2] ;
if( jybot > jytop ) { ii = jybot ; jybot = jytop ; jytop = ii ; }
if( jybot < 0 ) jybot = 0 ;
if( jytop >= bcor->n3 ) jytop = bcor->n3 - 1 ;
}
if( zgood ){
if( zbot < dr.zbot ) zbot = dr.zbot ;
if( ztop > dr.ztop ) ztop = dr.ztop ;
fv = THD_dicomm_to_3dmm( dset , TEMP_FVEC3(0,0,zbot) ) ;
iv = THD_3dmm_to_3dind ( dset , fv ) ;
iv = THD_3dind_to_fdind( baxi , iv ) ; kzbot = iv.ijk[2] ;
fv = THD_dicomm_to_3dmm( dset , TEMP_FVEC3(0,0,ztop) ) ;
iv = THD_3dmm_to_3dind ( dset , fv ) ;
iv = THD_3dind_to_fdind( baxi , iv ) ; kztop = iv.ijk[2] ;
if( kzbot > kztop ) { ii = kzbot ; kzbot = kztop ; kztop = ii ; }
if( kzbot < 0 ) kzbot = 0 ;
if( kztop >= baxi->n3 ) kztop = baxi->n3 - 1 ;
}
ival = DSET_PRINCIPAL_VALUE(dset) ; /* index to project */
ityp = DSET_BRICK_TYPE(dset,ival) ; /* type of this data */
fimfac = DSET_BRICK_FACTOR(dset,ival) ; /* scale factor of this data */
/*--- project the x direction, if desired ---*/
if( xgood ){
int n1 = bsag->n1 , n2 = bsag->n2 ;
int ss , npix ;
float fmax , fmin , scl ;
/*-- set up --*/
npix = n1*n2 ;
flim = mri_new( n1 , n2 , MRI_float ) ;
flar = mri_data_pointer( flim ) ;
for( ii=0 ; ii < npix ; ii++ ) flar[ii] = 0.0 ;
/*-- actually project --*/
for( ss=ixbot ; ss <= ixtop ; ss++ ){
slim = FD_brick_to_mri( ss , ival , bsag ) ;
if( slim->kind != MRI_float ){
pim = mri_to_float( slim ) ;
mri_free( slim ) ; slim = pim ;
}
PR_one_slice( proj_code , slim , flim ) ;
mri_free( slim ) ;
}
/*-- form output --*/
if( fimfac != 0.0 && fimfac != 1.0 ){
slim = mri_scale_to_float( 1.0/fimfac , flim ) ;
mri_free(flim) ; flim = slim ;
}
scl = PR_type_scale( ityp , flim ) ;
pim = mri_to_mri_scl( ityp , scl , flim ) ; mri_free( flim ) ;
if( nsize ){
slim = mri_nsize( pim ) ;
if( slim != NULL && slim != pim ) { mri_free(pim) ; pim = slim ; }
}
if( scl != 1.0 )
printf("Sagittal projection pixels scaled by %g to avoid overflow!\n",
scl ) ;
fmax = mri_max(pim) ; fmin = mri_min(pim) ;
printf("Sagittal projection min = %g max = %g\n",fmin,fmax) ;
strcpy(fname,root) ; strcat(fname,"sag") ;
mri_write( fname, pim ) ;
mri_free(pim) ;
}
/*--- project the y direction, if desired ---*/
if( ygood ){
int n1 = bcor->n1 , n2 = bcor->n2 ;
int ss , npix ;
float fmax , fmin , scl ;
/*-- set up --*/
npix = n1*n2 ;
flim = mri_new( n1 , n2 , MRI_float ) ;
flar = mri_data_pointer( flim ) ;
for( ii=0 ; ii < npix ; ii++ ) flar[ii] = 0.0 ;
/*-- actually project --*/
for( ss=jybot ; ss <= jytop ; ss++ ){
slim = FD_brick_to_mri( ss , ival , bcor ) ;
if( slim->kind != MRI_float ){
pim = mri_to_float( slim ) ;
mri_free( slim ) ; slim = pim ;
}
PR_one_slice( proj_code , slim , flim ) ;
mri_free( slim ) ;
}
/*-- form output --*/
if( fimfac != 0.0 && fimfac != 1.0 ){
slim = mri_scale_to_float( 1.0/fimfac , flim ) ;
mri_free(flim) ; flim = slim ;
}
scl = PR_type_scale( ityp , flim ) ;
pim = mri_to_mri_scl( ityp , scl , flim ) ; mri_free( flim ) ;
if( nsize ){
slim = mri_nsize( pim ) ;
if( slim != NULL && slim != pim ) { mri_free(pim) ; pim = slim ; }
}
if( scl != 1.0 )
printf("Coronal projection pixels scaled by %g to avoid overflow!\n",
scl ) ;
fmax = mri_max(pim) ; fmin = mri_min(pim) ;
printf("Coronal projection min = %g max = %g\n",fmin,fmax) ;
if( mirror_code == MIRR_YES ){
slim = mri_flippo( MRI_ROT_0 , TRUE , pim ) ;
mri_free(pim) ; pim = slim ;
}
strcpy(fname,root) ; strcat(fname,"cor") ;
mri_write( fname, pim ) ;
mri_free(pim) ;
}
/*--- project the z direction, if desired ---*/
if( zgood ){
int n1 = baxi->n1 , n2 = baxi->n2 ;
int ss , npix ;
float fmax , fmin , scl ;
/*-- set up --*/
npix = n1*n2 ;
flim = mri_new( n1 , n2 , MRI_float ) ;
flar = mri_data_pointer( flim ) ;
for( ii=0 ; ii < npix ; ii++ ) flar[ii] = 0.0 ;
/*-- actually project --*/
for( ss=kzbot ; ss <= kztop ; ss++ ){
slim = FD_brick_to_mri( ss , ival , baxi ) ;
if( slim->kind != MRI_float ){
pim = mri_to_float( slim ) ;
mri_free( slim ) ; slim = pim ;
}
PR_one_slice( proj_code , slim , flim ) ;
mri_free( slim ) ;
}
/*-- form output --*/
if( fimfac != 0.0 && fimfac != 1.0 ){
slim = mri_scale_to_float( 1.0/fimfac , flim ) ;
mri_free(flim) ; flim = slim ;
}
scl = PR_type_scale( ityp , flim ) ;
pim = mri_to_mri_scl( ityp , scl , flim ) ; mri_free( flim ) ;
if( nsize ){
slim = mri_nsize( pim ) ;
if( slim != NULL && slim != pim ) { mri_free(pim) ; pim = slim ; }
}
if( scl != 1.0 )
printf("Axial projection pixels scaled by %g to avoid overflow!\n",
scl ) ;
fmax = mri_max(pim) ; fmin = mri_min(pim) ;
printf("Axial projection min = %g max = %g\n",fmin,fmax) ;
if( mirror_code == MIRR_YES ){
slim = mri_flippo( MRI_ROT_0 , TRUE , pim ) ;
mri_free(pim) ; pim = slim ;
}
strcpy(fname,root) ; strcat(fname,"axi") ;
mri_write( fname, pim ) ;
mri_free(pim) ;
}
exit(0) ;
}
byte * THD_boxballmask( THD_3dim_dataset *dset ,
int boxball_num , float *boxball_dat )
{
int nx,ny,nz , nxy,nxyz , ii,jj,kk ;
byte *bmask ;
int bb, ibot,itop, jbot,jtop, kbot,ktop , btyp ;
float xbot,xtop, ybot,ytop, zbot,ztop ;
float xcen,ycen,zcen , icen,jcen,kcen ;
float xmin,xmax , ymin,ymax , zmin,zmax , rad,dist , xx,yy,zz ;
THD_fvec3 dv,xv ;
ENTRY("THD_boxballmask") ;
if( !ISVALID_DSET(dset) || boxball_num <= 0 || boxball_dat == NULL ) RETURN(NULL) ;
xmin=dset->daxes->xxmin ; xmax=dset->daxes->xxmax ;
ymin=dset->daxes->yymin ; ymax=dset->daxes->yymax ;
zmin=dset->daxes->zzmin ; zmax=dset->daxes->zzmax ;
nx = DSET_NX(dset) ;
ny = DSET_NY(dset) ; nxy = nx*ny ;
nz = DSET_NZ(dset) ; nxyz = nxy*nz ;
bmask = (byte *)calloc(sizeof(byte),nxyz) ;
for( bb=0 ; bb < boxball_num ; bb++ ){
btyp = boxball_dat[0+BOXLEN*bb] ;
if( btyp < BALL_XYZ ){ /*---- box ----*/
xbot = boxball_dat[1+BOXLEN*bb]; xtop = boxball_dat[2+BOXLEN*bb];
ybot = boxball_dat[3+BOXLEN*bb]; ytop = boxball_dat[4+BOXLEN*bb];
zbot = boxball_dat[5+BOXLEN*bb]; ztop = boxball_dat[6+BOXLEN*bb];
if( btyp != BOX_IJK ){ /* convert coords to indexes */
if( btyp == BOX_NEU ){ /* coords from Neuroscience to DICOM */
xbot = -xbot; xtop = -xtop; ybot = -ybot; ytop = -ytop; btyp = BOX_DIC;
}
if( btyp == BOX_DIC ){ /* coords from DICOM to dataset */
LOAD_FVEC3(dv,xbot,ybot,zbot) ;
xv = THD_dicomm_to_3dmm( dset , dv ) ;
UNLOAD_FVEC3(xv,xbot,ybot,zbot) ;
LOAD_FVEC3(dv,xtop,ytop,ztop) ;
xv = THD_dicomm_to_3dmm( dset , dv ) ;
UNLOAD_FVEC3(xv,xtop,ytop,ztop) ;
}
if( xbot < xmin && xtop < xmin ) continue ; /* skip box if outside dataset */
if( xbot > xmax && xtop > xmax ) continue ;
if( ybot < ymin && ytop < ymin ) continue ;
if( ybot > ymax && ytop > ymax ) continue ;
if( zbot < zmin && ztop < zmin ) continue ;
if( zbot > zmax && ztop > zmax ) continue ;
LOAD_FVEC3(dv,xbot,ybot,zbot) ;
xv = THD_3dmm_to_3dfind( dset , dv ) ; /* coords from dataset to index */
UNLOAD_FVEC3(xv,xbot,ybot,zbot) ;
LOAD_FVEC3(dv,xtop,ytop,ztop) ;
xv = THD_3dmm_to_3dfind( dset , dv ) ;
UNLOAD_FVEC3(xv,xtop,ytop,ztop) ;
}
ibot = rint(xbot) ; jbot = rint(ybot) ; kbot = rint(zbot) ; /* round */
itop = rint(xtop) ; jtop = rint(ytop) ; ktop = rint(ztop) ;
if( ibot > itop ){ btyp = ibot; ibot = itop; itop = btyp; } /* flip? */
if( jbot > jtop ){ btyp = jbot; jbot = jtop; jtop = btyp; }
if( kbot > ktop ){ btyp = kbot; kbot = ktop; ktop = btyp; }
/* skip box if outside dataset */
if ( itop < 0 || ibot >= nx ) continue;
if ( jtop < 0 || jbot >= ny ) continue;
if ( ktop < 0 || kbot >= nz ) continue;
/* constrain values to dataset dimensions */
if ( ibot < 0 ) ibot = 0; if ( itop >= nx ) itop = nx-1;
if ( jbot < 0 ) jbot = 0; if ( jtop >= ny ) jtop = ny-1;
if ( kbot < 0 ) kbot = 0; if ( ktop >= nz ) ktop = nz-1;
for( kk=kbot ; kk <= ktop ; kk++ )
for( jj=jbot ; jj <= jtop ; jj++ )
for( ii=ibot ; ii <= itop ; ii++ ) bmask[ii+jj*nx+kk*nxy] = 1 ;
} else { /*---- ball ----*/
xcen = boxball_dat[1+BOXLEN*bb] ; ycen = boxball_dat[2+BOXLEN*bb] ;
zcen = boxball_dat[3+BOXLEN*bb] ; rad = boxball_dat[4+BOXLEN*bb] ;
/* convert center coords to dataset indexes */
if( btyp == BALL_NEU ){ /* coords from Neuroscience to DICOM */
xcen = -xcen; ycen = -ycen; btyp = BALL_DIC;
}
if( btyp == BALL_DIC ){ /* coords from DICOM to dataset */
LOAD_FVEC3(dv,xcen,ycen,zcen) ;
xv = THD_dicomm_to_3dmm( dset , dv ) ;
UNLOAD_FVEC3(xv,xcen,ycen,zcen) ;
}
if( xcen < xmin || xcen > xmax ) continue ; /* skip ball if outside */
if( ycen < ymin || ycen > ymax ) continue ;
if( zcen < zmin || zcen > zmax ) continue ;
LOAD_FVEC3(dv,xcen,ycen,zcen) ;
xv = THD_3dmm_to_3dfind( dset , dv ) ; /* coords from dataset to index */
UNLOAD_FVEC3(xv,icen,jcen,kcen) ;
ibot = rint(icen-rad) ; itop = rint(icen+rad) ; /* box around ball */
jbot = rint(jcen-rad) ; jtop = rint(jcen+rad) ;
kbot = rint(kcen-rad) ; ktop = rint(kcen+rad) ;
rad = rad*rad ;
for( kk=kbot ; kk <= ktop ; kk++ ){
for( jj=jbot ; jj <= jtop ; jj++ ){
for( ii=ibot ; ii <= itop ; ii++ ){
LOAD_FVEC3( dv , ii,jj,kk ) ; /* convert to xyz coords */
xv = THD_3dfind_to_3dmm( dset , dv ) ; /* then test distance^2 */
UNLOAD_FVEC3( xv , xx,yy,zz ) ; /* xyz of ball center. */
dist = SQR(xx-xcen) + SQR(yy-ycen) + SQR(zz-zcen) ;
if( dist <= rad ) bmask[ii+jj*nx+kk*nxy] = 1 ;
}}}
}
} /*----- end of loop over box/ball list -----*/
RETURN(bmask) ;
}
void AFNI_lock_carryout( Three_D_View *im3d )
{
Three_D_View *qq3d ;
int ii,jj,kk , cc , glock ;
THD_fvec3 old_fv , fv ;
THD_ivec3 iv ;
THD_dataxes *qaxes , *daxes ;
static int busy = 0 ; /* !=0 if this routine is "busy" */
ENTRY("AFNI_lock_carryout") ;
/* first, determine if there is anything to do */
glock = GLOBAL_library.controller_lock ;
if( busy ) EXRETURN ; /* routine already busy */
if( glock == 0 ) EXRETURN ; /* nothing to do */
if( !IM3D_OPEN(im3d) ) EXRETURN ; /* bad input */
if( GLOBAL_library.ignore_lock ) EXRETURN ; /* ordered not to do anything */
ii = AFNI_controller_index(im3d) ; /* which one am I? */
if( ii < 0 ) EXRETURN ; /* nobody? bad input! */
if( ((1<<ii) & glock) == 0 ) EXRETURN ; /* input not locked */
/* something to do? */
busy = 1 ; /* don't let this routine be called recursively */
/* load Dicom location of current point of view in this controller */
LOAD_FVEC3( old_fv , im3d->vinfo->xi, im3d->vinfo->yj, im3d->vinfo->zk ) ;
LOAD_ANAT_VIEW(im3d) ; /* prepare coordinates */
daxes = CURRENT_DAXES(im3d->anat_now) ;
/* loop through other controllers:
for those that ARE open, ARE NOT the current one,
and ARE locked, transform the above vector to the
controller's dataset, and then jump to that point */
for( cc=0 ; cc < MAX_CONTROLLERS ; cc++ ){
qq3d = GLOBAL_library.controllers[cc] ; /* controller */
if( IM3D_OPEN(qq3d) && qq3d != im3d && ((1<<cc) & glock) != 0 ){
LOAD_ANAT_VIEW(qq3d) ; /* prepare coordinates */
qaxes = CURRENT_DAXES(qq3d->anat_now) ;
if( !GLOBAL_library.ijk_lock ){ /* xyz coord lock */
fv = AFNI_transform_vector( im3d->anat_now, old_fv, qq3d->anat_now ) ;
fv = THD_dicomm_to_3dmm( qq3d->anat_now , fv ) ;
iv = THD_3dmm_to_3dind ( qq3d->anat_now , fv ) ;
ii = iv.ijk[0] ; jj = iv.ijk[1] ; kk = iv.ijk[2] ;
} else { /* 11 Sep 2000: ijk index lock */
ii = im3d->vinfo->i1 * qaxes->nxx / daxes->nxx ;
jj = im3d->vinfo->j2 * qaxes->nyy / daxes->nyy ;
kk = im3d->vinfo->k3 * qaxes->nzz / daxes->nzz ;
}
/* if have good new ijk coords, jump to them */
if( ii >= 0 && ii < qaxes->nxx &&
jj >= 0 && jj < qaxes->nyy && kk >= 0 && kk < qaxes->nzz ){
SAVE_VPT(qq3d) ;
AFNI_set_viewpoint( qq3d , ii,jj,kk , REDISPLAY_ALL ) ; /* jump */
}
}
}
busy = 0 ; /* OK, let this routine be activated again */
EXRETURN ;
}
int main( int argc , char * argv[] )
{
int narg=1, do_automask=0 , iv , nxyz , do_set=0 ,
*rois=NULL, N_rois=0, all_rois = 0;
THD_3dim_dataset *xset ;
byte *mmm=NULL ; int nmask=0 , nvox_mask=0 ;
THD_fvec3 cmv , setv ;
/*-- read command line arguments --*/
if( argc < 2 || strncmp(argv[1],"-help",5) == 0 ){
printf("Usage: 3dCM [options] dset\n"
"Output = center of mass of dataset, to stdout.\n"
" -mask mset Means to use the dataset 'mset' as a mask:\n"
" Only voxels with nonzero values in 'mset'\n"
" will be averaged from 'dataset'. Note\n"
" that the mask dataset and the input dataset\n"
" must have the same number of voxels.\n"
" -automask Generate the mask automatically.\n"
" -set x y z After computing the CM of the dataset, set the\n"
" origin fields in the header so that the CM\n"
" will be at (x,y,z) in DICOM coords.\n"
" -roi_vals v0 v1 v2 ... : Compute center of mass for each blob\n"
" with voxel value of v0, v1, v2, etc.\n"
" This option is handy for getting ROI \n"
" centers of mass.\n"
" -all_rois Don't bother listing the values of ROIs you want\n"
" the program will find all of them and produce a \n"
" full list.\n"
" NOTE: Masking options are ignored with -roi_vals and -all_rois\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
LOAD_FVEC3(setv,0,0,0) ; /* ZSS: To quiet init. warnings */
narg = 1 ;
while( narg < argc && argv[narg][0] == '-' ){
if( strcmp(argv[narg],"-set") == 0 ){
float xset,yset,zset ;
if( narg+3 >= argc ){
fprintf(stderr,"*** -set need 3 args following!\n") ; exit(1) ;
}
xset = strtod( argv[++narg] , NULL ) ;
yset = strtod( argv[++narg] , NULL ) ;
zset = strtod( argv[++narg] , NULL ) ;
LOAD_FVEC3(setv,xset,yset,zset) ; do_set = 1 ;
THD_set_write_compression(COMPRESS_NONE); /* do not alter compression*/
narg++ ; continue ;
}
if( strncmp(argv[narg],"-mask",5) == 0 ){
THD_3dim_dataset *mask_dset ;
if( mmm != NULL ){
fprintf(stderr,"*** Cannot have two -mask options!\n") ; exit(1) ;
}
if( do_automask ){
fprintf(stderr,"*** Can't have -mask and -automask!\n") ; exit(1) ;
}
if( narg+1 >= argc ){
fprintf(stderr,"*** -mask option requires a following argument!\n");
exit(1) ;
}
mask_dset = THD_open_dataset( argv[++narg] ) ;
CHECK_OPEN_ERROR(mask_dset,argv[narg]) ;
if( DSET_BRICK_TYPE(mask_dset,0) == MRI_complex ){
fprintf(stderr,"*** Cannot deal with complex-valued mask dataset!\n");
exit(1) ;
}
mmm = THD_makemask( mask_dset , 0 , 1.0,0.0 ) ;
nvox_mask = DSET_NVOX(mask_dset) ;
nmask = THD_countmask( nvox_mask , mmm ) ;
if( mmm == NULL || nmask <= 0 ){
fprintf(stderr,"*** Can't make mask from dataset %s\n",argv[narg-1]);
exit(1) ;
}
DSET_delete( mask_dset ) ;
narg++ ; continue ;
}
if( strncmp(argv[narg],"-roi_vals",5) == 0 ){
if( narg+1 >= argc ){
fprintf(stderr,"*** -mask option requires a following argument(s)!\n");
exit(1) ;
}
rois = (int *)calloc(argc, sizeof(int));
N_rois = 0;
++narg;
while (narg < argc-1 && argv[narg][0] != '-') {
rois[N_rois++] = atoi(argv[narg]);
++narg;
}
continue ;
}
if( strncmp(argv[narg],"-all_rois",5) == 0 ){
all_rois = 1;
narg++ ; continue ;
}
if( strcmp(argv[narg],"-automask") == 0 ){
if( mmm != NULL ){
fprintf(stderr,"*** Can't have -mask and -automask!\n") ; exit(1) ;
}
do_automask = 1 ; narg++ ; continue ;
}
fprintf(stderr,"*** Unknown option: %s\n",argv[narg]) ; exit(1) ;
}
/* should have at least 1 more argument */
if( argc <= narg ){
fprintf(stderr,"*** No input dataset!?\n") ; exit(1) ;
}
for( ; narg < argc ; narg++ ){
xset = THD_open_dataset( argv[narg] ) ;
if( xset == NULL ){
fprintf(stderr,"+++ Can't open dataset %s -- skipping\n",argv[narg]);
continue ;
}
DSET_load(xset) ;
if( !DSET_LOADED(xset) ){
fprintf(stderr,"+++ Can't load dataset %s -- skipping\n",argv[narg]);
DSET_delete(xset) ; continue ;
}
if( do_automask ){
if( mmm != NULL ){ free(mmm); mmm = NULL; }
mmm = THD_automask(xset) ;
nvox_mask = DSET_NVOX(xset) ;
nmask = THD_countmask( nvox_mask , mmm ) ;
if( mmm == NULL || nmask <= 0 ){
fprintf( stderr,
"+++ Can't make automask from dataset %s "
"-- skipping\n",argv[narg]) ;
DSET_delete(xset) ; continue ;
}
}
nxyz = DSET_NVOX(xset) ;
if( mmm != NULL && nxyz != nvox_mask ){
fprintf(stderr,"+++ Mask/Dataset grid size mismatch at %s\n -- skipping\n",argv[narg]) ;
DSET_delete(xset) ; continue ;
}
if (all_rois) {
if (!(rois = THD_unique_vals(xset, 0, &N_rois, NULL)) || N_rois == 0) {
ERROR_message("No rois or error in THD_unique_vals"); continue;
}
fprintf(stderr,"#%d distinct ROIs", N_rois);
}
if (!N_rois) {
cmv = THD_cmass( xset , 0 , mmm ) ;
printf("%g %g %g\n",cmv.xyz[0],cmv.xyz[1],cmv.xyz[2]) ;
DSET_unload(xset) ;
if( do_set ){
THD_fvec3 dv , ov ;
if( DSET_IS_MASTERED(xset) ){
fprintf(stderr,"+++ Can't modify CM of dataset %s\n",argv[narg]) ;
} else {
/* lose obliquity */
/* recompute Tc(Cardinal transformation matrix for new grid output */
THD_make_cardinal(xset);
LOAD_FVEC3(ov,DSET_XORG(xset),DSET_YORG(xset),DSET_ZORG(xset)) ;
ov = THD_3dmm_to_dicomm( xset , ov ) ;
dv = SUB_FVEC3(setv,cmv) ;
ov = ADD_FVEC3(dv,ov) ;
ov = THD_dicomm_to_3dmm( xset , ov ) ;
xset->daxes->xxorg = ov.xyz[0] ;
xset->daxes->yyorg = ov.xyz[1] ;
xset->daxes->zzorg = ov.xyz[2] ;
/* allow overwriting header for all types of output data */
putenv("AFNI_DECONFLICT=OVERWRITE") ;
tross_Make_History( "3dCM" , argc,argv , xset );/* ZSS Dec. 09 08 */
if(DSET_IS_BRIK(xset)) {
INFO_message("Rewriting header %s",DSET_HEADNAME(xset)) ;
DSET_overwrite_header( xset ) ;
}
else { /* for other dataset types like NIFTI, rewrite whole dset */
DSET_load( xset ) ;
DSET_overwrite(xset) ;
INFO_message("Wrote new dataset: %s",DSET_BRIKNAME(xset)) ;
}
}
}
} else {
float *xyz;
if ((xyz = THD_roi_cmass(xset , 0 , rois, N_rois))) {
printf("#Dset %s\n",DSET_BRIKNAME(xset));
for (iv=0; iv<N_rois; ++iv) {
printf("#ROI %d\n", rois[iv]);
printf("%g %g %g\n",xyz[3*iv],xyz[3*iv+1],xyz[3*iv+2]) ;
}
free(xyz); free(rois);
} else {
ERROR_message("Failed in THD_roi_cmass"); continue;
}
}
DSET_delete(xset) ;
}
exit(0);
}