int main( int argc , char *argv[] )
{
THD_3dim_dataset *dset ;
MRI_IMAGE *im ;
int iarg=1 ;
if( strcmp(argv[1],"-nper") == 0 ){
nper = strtol( argv[2] , NULL , 10 ) ;
iarg = 3 ;
}
for( ; iarg < argc ; iarg++ ){
printf("======= dataset %s nper=%d ========\n",argv[iarg],nper) ;
dset = THD_open_dataset(argv[iarg]) ;
if( dset == NULL ) continue ;
DSET_load(dset) ;
im = DSET_BRICK(dset,0) ;
im->dx = DSET_DX(dset) ;
im->dy = DSET_DY(dset) ;
im->dz = DSET_DZ(dset) ;
(void) THD_orient_guess( im ) ;
printf( "Data Axes Orientation:\n"
" first (x) = %s\n"
" second (y) = %s\n"
" third (z) = %s\n" ,
ORIENT_typestr[dset->daxes->xxorient] ,
ORIENT_typestr[dset->daxes->yyorient] ,
ORIENT_typestr[dset->daxes->zzorient] ) ;
DSET_delete(dset) ;
}
exit(0) ;
}
int main( int argc , char *argv[] )
{
THD_3dim_dataset *inset=NULL , *outset=NULL ;
MCW_cluster *nbhd=NULL ;
byte *mask=NULL ; int mask_nx,mask_ny,mask_nz , automask=0 ;
char *prefix="./LocalCormat" ;
int iarg=1 , verb=1 , ntype=0 , kk,nx,ny,nz,nxy,nxyz,nt , xx,yy,zz, vstep ;
float na,nb,nc , dx,dy,dz ;
MRI_IMARR *imar=NULL ; MRI_IMAGE *pim=NULL ;
int mmlag=10 , ii,jj , do_arma=0 , nvout ;
MRI_IMAGE *concim=NULL ; float *concar=NULL ;
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf(
"Usage: 3dLocalCORMAT [options] inputdataset\n"
"\n"
"Compute the correlation matrix (in time) of the input dataset,\n"
"up to lag given by -maxlag. The matrix is averaged over the\n"
"neighborhood specified by the -nbhd option, and then the entries\n"
"are output at each voxel in a new dataset.\n"
"\n"
"Normally, the input to this program would be the -errts output\n"
"from 3dDeconvolve, or the equivalent residuals from some other\n"
"analysis. If you input a non-residual time series file, you at\n"
"least should use an appropriate -polort level for detrending!\n"
"\n"
"Options:\n"
" -input inputdataset\n"
" -prefix ppp\n"
" -mask mset {these 2 options are}\n"
" -automask {mutually exclusive.}\n"
" -nbhd nnn [e.g., 'SPHERE(9)' for 9 mm radius]\n"
" -polort ppp [default = 0, which is reasonable for -errts output]\n"
" -concat ccc [as in 3dDeconvolve]\n"
" -maxlag mmm [default = 10]\n"
" -ARMA [estimate ARMA(1,1) parameters into last 2 sub-bricks]\n"
"\n"
"A quick hack for my own benignant purposes -- RWCox -- June 2008\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
/*---- official startup ---*/
PRINT_VERSION("3dLocalCormat"); mainENTRY("3dLocalCormat main"); machdep();
AFNI_logger("3dLocalCormat",argc,argv); AUTHOR("Zhark the Toeplitzer");
/*---- loop over options ----*/
while( iarg < argc && argv[iarg][0] == '-' ){
#if 0
fprintf(stderr,"argv[%d] = %s\n",iarg,argv[iarg]) ;
#endif
if( strcmp(argv[iarg],"-ARMA") == 0 ){
do_arma = 1 ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-polort") == 0 ){
char *cpt ;
if( ++iarg >= argc )
ERROR_exit("Need argument after option %s",argv[iarg-1]) ;
pport = (int)strtod(argv[iarg],&cpt) ;
if( *cpt != '\0' )
WARNING_message("Illegal non-numeric value after -polort") ;
if( pport > 3 ){
pport = 3 ; WARNING_message("-polort set to 3 == max implemented") ;
} else if( pport < 0 ){
pport = 0 ; WARNING_message("-polort set to 0 == min implemented") ;
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-input") == 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]) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-mask") == 0 ){
THD_3dim_dataset *mset ; int mmm ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '-mask'") ;
if( 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_delete(mset) ;
if( mask == NULL ) ERROR_exit("Can't make mask from dataset '%s'",argv[iarg]) ;
mmm = THD_countmask( mask_nx*mask_ny*mask_nz , mask ) ;
INFO_message("Number of voxels in mask = %d",mmm) ;
if( mmm < 2 ) ERROR_exit("Mask is too small to process") ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-automask") == 0 ){
if( mask != NULL ) ERROR_exit("Can't have -automask and -mask") ;
automask = 1 ;
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 ) ;
if( na == 0.0f ) ERROR_exit("Can't have a SPHERE of radius 0") ;
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 {
ERROR_exit("Unknown -nbhd shape: '%s'",cpt) ;
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-maxlag") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after option %s",argv[iarg-1]) ;
mmlag = (int)strtod(argv[iarg],NULL) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-concat") == 0 ){
if( concim != NULL )
ERROR_exit("Can't have two %s options!",argv[iarg]) ;
if( ++iarg >= argc )
ERROR_exit("Need argument after option %s",argv[iarg-1]) ;
concim = mri_read_1D( argv[iarg] ) ;
if( concim == NULL )
ERROR_exit("Can't read -concat file '%s'",argv[iarg]) ;
if( concim->nx < 2 )
ERROR_exit("-concat file '%s' must have at least 2 entries!",
argv[iarg]) ;
concar = MRI_FLOAT_PTR(concim) ;
for( ii=1 ; ii < concim->nx ; ii++ )
if( (int)concar[ii-1] >= (int)concar[ii] )
ERROR_exit("-concat file '%s' is not ordered increasingly!",
argv[iarg]) ;
iarg++ ; continue ;
}
ERROR_exit("Unknown option '%s'",argv[iarg]) ;
} /*--- end of loop over options ---*/
if( do_arma && mmlag > 0 && mmlag < 5 )
ERROR_exit("Can't do -ARMA with -maxlag %d",mmlag) ;
/*---- deal with input dataset ----*/
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]) ;
}
ntime = DSET_NVALS(inset) ;
if( ntime < 9 )
ERROR_exit("Must have at least 9 values per voxel") ;
DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ;
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 ){
int mmm ;
mask = THD_automask( inset ) ;
if( mask == NULL )
ERROR_message("Can't create -automask from input dataset?") ;
mmm = THD_countmask( DSET_NVOX(inset) , mask ) ;
INFO_message("Number of voxels in automask = %d",mmm) ;
if( mmm < 2 ) ERROR_exit("Automask is too small to process") ;
}
/*-- set up blocks of continuous time data --*/
if( DSET_IS_TCAT(inset) ){
if( concim != NULL ){
WARNING_message("Ignoring -concat, since dataset is auto-catenated") ;
mri_free(concim) ;
}
concim = mri_new(inset->tcat_num,1,MRI_float) ;
concar = MRI_FLOAT_PTR(concim) ;
concar[0] = 0.0 ;
for( ii=0 ; ii < inset->tcat_num-1 ; ii++ )
concar[ii+1] = concar[ii] + inset->tcat_len[ii] ;
} else if( concim == NULL ){
concim = mri_new(1,1,MRI_float) ;
concar = MRI_FLOAT_PTR(concim) ; concar[0] = 0 ;
}
nbk = concim->nx ;
bk = (int *)malloc(sizeof(int)*(nbk+1)) ;
for( ii=0 ; ii < nbk ; ii++ ) bk[ii] = (int)concar[ii] ;
bk[nbk] = ntime ;
mri_free(concim) ;
mlag = DSET_NVALS(inset) ;
for( ii=0 ; ii < nbk ; ii++ ){
jj = bk[ii+1]-bk[ii] ; if( jj < mlag ) mlag = jj ;
if( bk[ii] < 0 || jj < 9 )
ERROR_exit("something is rotten in the dataset run lengths") ;
}
mlag-- ;
if( mmlag > 0 && mlag > mmlag ) mlag = mmlag ;
else INFO_message("Max lag set to %d",mlag) ;
if( do_arma && mlag < 5 )
ERROR_exit("Can't do -ARMA with maxlag=%d",mlag) ;
/*---- create neighborhood (as a cluster) -----*/
if( ntype <= 0 ){ /* default neighborhood */
ntype = NTYPE_SPHERE ; na = -1.01f ;
INFO_message("Using default neighborhood = self + 6 neighbors") ;
}
switch( ntype ){
default:
ERROR_exit("WTF? ntype=%d",ntype) ;
case NTYPE_SPHERE:{
if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; }
else { dx = fabsf(DSET_DX(inset)) ;
dy = fabsf(DSET_DY(inset)) ;
dz = fabsf(DSET_DZ(inset)) ; }
nbhd = MCW_spheremask( dx,dy,dz , na ) ;
}
break ;
case NTYPE_RECT:{
if( na < 0.0f ){ dx = 1.0f; na = -na; } else dx = fabsf(DSET_DX(inset));
if( nb < 0.0f ){ dy = 1.0f; nb = -nb; } else dy = fabsf(DSET_DY(inset));
if( nc < 0.0f ){ dz = 1.0f; nc = -nc; } else dz = fabsf(DSET_DZ(inset));
nbhd = MCW_rectmask( dx,dy,dz , na,nb,nc ) ;
}
break ;
case NTYPE_RHDD:{
if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; }
else { dx = fabsf(DSET_DX(inset)) ;
dy = fabsf(DSET_DY(inset)) ;
dz = fabsf(DSET_DZ(inset)) ; }
nbhd = MCW_rhddmask( dx,dy,dz , na ) ;
}
break ;
}
MCW_radsort_cluster( nbhd , dx,dy,dz ) ; /* 26 Feb 2008 */
INFO_message("Neighborhood comprises %d voxels",nbhd->num_pt) ;
/** create output dataset **/
outset = EDIT_empty_copy(inset) ;
nvout = mlag ; if( do_arma ) nvout += 2 ;
EDIT_dset_items( outset,
ADN_prefix , prefix,
ADN_brick_fac, NULL ,
ADN_nvals , nvout ,
ADN_ntt , nvout ,
ADN_none );
tross_Copy_History( inset , outset ) ;
tross_Make_History( "3dLocalCormat" , argc,argv , outset ) ;
for( kk=0 ; kk < nvout ; kk++ )
EDIT_substitute_brick( outset , kk , MRI_float , NULL ) ;
nx = DSET_NX(outset) ;
ny = DSET_NY(outset) ; nxy = nx*ny ;
nz = DSET_NZ(outset) ; nxyz = nxy*nz ;
vstep = (verb && nxyz > 999) ? nxyz/50 : 0 ;
if( vstep ) fprintf(stderr,"++ voxel loop: ") ;
/** actually do the long long slog through all voxels **/
for( kk=0 ; kk < nxyz ; kk++ ){
if( vstep && kk%vstep==vstep-1 ) vstep_print() ;
if( !INMASK(kk) ) continue ;
IJK_TO_THREE( kk , xx,yy,zz , nx,nxy ) ;
imar = THD_get_dset_nbhd_array( inset , mask , xx,yy,zz , nbhd ) ;
if( imar == NULL ) continue ;
pim = mri_cormat_vector(imar) ; DESTROY_IMARR(imar) ;
if( pim == NULL ) continue ;
THD_insert_series( kk, outset, pim->nx, MRI_float, MRI_FLOAT_PTR(pim), 0 ) ;
if( do_arma ){ /* estimate ARMA(1,1) params and store those, too */
float_pair ab ;
float *aa=DSET_ARRAY(outset,mlag), *bb=DSET_ARRAY(outset,mlag+1) ;
ab = estimate_arma11( pim->nx , MRI_FLOAT_PTR(pim) ) ;
aa[kk] = ab.a ; bb[kk] = ab.b ;
}
mri_free(pim) ;
}
if( vstep ) fprintf(stderr,"\n") ;
DSET_delete(inset) ;
DSET_write(outset) ;
WROTE_DSET(outset) ;
exit(0) ;
}
int main( int argc , char *argv[] )
{
THD_3dim_dataset *dset=NULL;
int iarg , verbose = -1 ;
char *outbuf, *stmp=NULL;
char *labelName = NULL;
char *sbdelim = {"|"};
char *NAflag = {"NA"};
char *atrdelim = {"\t"}, *form=NULL;
INFO_FIELDS sing[512];
int iis=0, N_sing = 0, isb=0, withhead = 0, itmp=0;
int ip=0, needpair = 0, namelen=0, monog_pairs = 0;
THD_3dim_dataset *tttdset=NULL, *dsetp=NULL;
char *tempstr = NULL;
int extinit = 0;
float RL_AP_IS[6];
mainENTRY("3dinfo main") ; machdep() ;
if( argc < 2) { Syntax(TXT,1) ; RETURN(0); }
iarg = 1 ;
while (iarg < argc && argv[iarg][0] == '-') {
CHECK_HELP(argv[iarg],Syntax);
if( strncmp(argv[iarg],"-verb" ,5) == 0 ){
verbose = 0; iarg++; continue; }
else if( strncmp(argv[iarg],"-VERB" ,5) == 0 ){
verbose = 1; iarg++; continue; }
else if( strncmp(argv[iarg],"-short",5) == 0 ){
verbose = -1; iarg++; continue; }
else if( strcasecmp(argv[iarg],"-header_line") == 0 ||
strcasecmp(argv[iarg],"-hdr") == 0 ){
withhead = 1; iarg++; continue; }
else if( strcasecmp(argv[iarg],"-monog_pairs") == 0 ){
monog_pairs = 1; iarg++; continue; }
else if ( strncmp(argv[iarg],"-label2",7) == 0 )
{
iarg++;
if (iarg >= argc)
ERROR_exit( "3dinfo needs an argument after -label2number\n");
labelName = malloc(sizeof(char) * 2048);
strcpy(labelName, argv[iarg]);
iarg++; continue;
}
else if( strcasecmp(argv[iarg],"-sb_delim") == 0) {
iarg++;
if (iarg >= argc)
ERROR_exit( "3dinfo needs a string after -sb_delim\n");
sbdelim = argv[iarg];
iarg++; continue;
}
else if( strcasecmp(argv[iarg],"-NA_flag") == 0) {
iarg++;
if (iarg >= argc)
ERROR_exit( "3dinfo needs a string after -NA_flag\n");
NAflag = argv[iarg];
iarg++; continue;
}
else if( strcasecmp(argv[iarg],"-atr_delim") == 0) {
iarg++;
if (iarg >= argc)
ERROR_exit( "3dinfo needs a string after -atr_delim\n");
atrdelim = argv[iarg];
iarg++; continue;
}
else if( strcasecmp(argv[iarg],"-space") == 0) {
sing[N_sing++] = DSET_SPACE; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-av_space") == 0) {
sing[N_sing++] = AV_DSET_SPACE; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-gen_space") == 0) {
sing[N_sing++] = DSET_GEN_SPACE; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-is_nifti") == 0) {
sing[N_sing++] = IS_NIFTI; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-is_atlas") == 0) {
sing[N_sing++] = IS_ATLAS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-exists") == 0) {
sing[N_sing++] = DSET_EXISTS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-is_oblique") == 0) {
sing[N_sing++] = IS_OBLIQUE; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-obliquity") == 0) {
sing[N_sing++] = OBLIQUITY; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-handedness") == 0) {
sing[N_sing++] = HANDEDNESS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-prefix") == 0) {
sing[N_sing++] = PREFIX; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-prefix_noext") == 0) {
sing[N_sing++] = PREFIX_NOEXT; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-ni") == 0) {
sing[N_sing++] = NI; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-nj") == 0) {
sing[N_sing++] = NJ; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-nk") == 0) {
sing[N_sing++] = NK; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-n4") == 0) {
sing[N_sing++] = NI;
sing[N_sing++] = NJ;
sing[N_sing++] = NK;
sing[N_sing++] = NV; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-Rextent") == 0) {
sing[N_sing++] = EXTENT_R; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-Lextent") == 0) {
sing[N_sing++] = EXTENT_L; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-Aextent") == 0) {
sing[N_sing++] = EXTENT_A; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-Pextent") == 0) {
sing[N_sing++] = EXTENT_P; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-Iextent") == 0) {
sing[N_sing++] = EXTENT_I; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-Sextent") == 0) {
sing[N_sing++] = EXTENT_S; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-extent") == 0) {
sing[N_sing++] = EXTENT_R;
sing[N_sing++] = EXTENT_L;
sing[N_sing++] = EXTENT_A;
sing[N_sing++] = EXTENT_P;
sing[N_sing++] = EXTENT_I;
sing[N_sing++] = EXTENT_S;
iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-di") == 0) {
sing[N_sing++] = DI; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-dj") == 0) {
sing[N_sing++] = DJ; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-dk") == 0) {
sing[N_sing++] = DK; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-d3") == 0) {
sing[N_sing++] = DI;
sing[N_sing++] = DJ;
sing[N_sing++] = DK; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-adi") == 0) {
sing[N_sing++] = ADI; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-adj") == 0) {
sing[N_sing++] = ADJ; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-adk") == 0) {
sing[N_sing++] = ADK; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-ad3") == 0) {
sing[N_sing++] = ADI;
sing[N_sing++] = ADJ;
sing[N_sing++] = ADK; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-voxvol") == 0) {
sing[N_sing++] = VOXVOL; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-iname") == 0) {
sing[N_sing++] = INAME; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-oi") == 0) {
sing[N_sing++] = OI; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-oj") == 0) {
sing[N_sing++] = OJ; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-ok") == 0) {
sing[N_sing++] = OK; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-o3") == 0) {
sing[N_sing++] = OI;
sing[N_sing++] = OJ;
sing[N_sing++] = OK; iarg++;
continue;
}else if( strcasecmp(argv[iarg],"-nt") == 0) {
sing[N_sing++] = NT; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-nti") == 0) {
sing[N_sing++] = NTI; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-nv") == 0) {
sing[N_sing++] = NV; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-nvi") == 0) {
sing[N_sing++] = NVI; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-ntimes") == 0) {
sing[N_sing++] = NTIMES; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-max_node") == 0) {
sing[N_sing++] = MAX_NODE; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-nijk") == 0) {
sing[N_sing++] = NIJK; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-labeltable") == 0) {
sing[N_sing++] = LTABLE; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-labeltable_as_atlas_points") == 0) {
sing[N_sing++] = LTABLE_AS_ATLAS_POINT_LIST; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-atlas_points") == 0) {
sing[N_sing++] = ATLAS_POINTS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-fac") == 0) {
sing[N_sing++] = FAC; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-datum") == 0) {
sing[N_sing++] = DATUM; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-label") == 0) {
sing[N_sing++] = LABEL; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-min") == 0) {
sing[N_sing++] = MIN; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-max") == 0) {
sing[N_sing++] = MAX; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-minus") == 0) {
sing[N_sing++] = MINUS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-maxus") == 0) {
sing[N_sing++] = MAXUS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-dmin") == 0) {
sing[N_sing++] = DMIN; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-dmax") == 0) {
sing[N_sing++] = DMAX; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-dminus") == 0) {
sing[N_sing++] = DMINUS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-dmaxus") == 0) {
sing[N_sing++] = DMAXUS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-TR") == 0) {
sing[N_sing++] = TR; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-header_name") == 0) {
sing[N_sing++] = HEADER_NAME; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-brick_name") == 0) {
sing[N_sing++] = BRICK_NAME; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-history") == 0) {
sing[N_sing++] = HISTORY; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-all_names") == 0) {
sing[N_sing++] = ALL_NAMES; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-orient") == 0) {
sing[N_sing++] = ORIENT; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-same_grid") == 0) {
sing[N_sing++] = SAME_GRID; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-same_dim") == 0) {
sing[N_sing++] = SAME_DIM; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-same_delta") == 0) {
sing[N_sing++] = SAME_DELTA; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-same_orient") == 0) {
sing[N_sing++] = SAME_ORIENT; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-same_center") == 0) {
sing[N_sing++] = SAME_CENTER; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-same_obl") == 0) {
sing[N_sing++] = SAME_OBL; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-slice_timing") == 0) {
sing[N_sing++] = SLICE_TIMING; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-sval_diff") == 0) {
sing[N_sing++] = SVAL_DIFF; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-val_diff") == 0) {
sing[N_sing++] = VAL_DIFF; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-same_all_grid") == 0) {
sing[N_sing++] = SAME_DIM;
sing[N_sing++] = SAME_DELTA;
sing[N_sing++] = SAME_ORIENT;
sing[N_sing++] = SAME_CENTER;
sing[N_sing++] = SAME_OBL; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-id") == 0) {
sing[N_sing++] = ID; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-smode") == 0) {
sing[N_sing++] = SMODE; iarg++; continue;
} else {
ERROR_message("Option %s unknown", argv[iarg]);
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
}
if (N_sing == 0) {
sing[N_sing++] = CLASSIC;
}
if (sing[iis] == CLASSIC) PRINT_VERSION("3dinfo") ;
THD_allow_empty_dataset(1) ; /* 21 Mar 2007 */
if (iarg == argc) {
ERROR_message("No dsets on command line? I have nothing to do.\n");
exit(1);
}
if (needpair && monog_pairs) needpair = 2; /* pair each couple separately */
if (needpair==2 && (argc-iarg) % 2) {
ERROR_message("Using options requiring dset pairs but have odd number\n"
"of dsets (%d) on command line.\n", (argc-iarg));
exit (1);
} else if (needpair==1 && (argc-iarg) < 2) {
ERROR_message("Using options requiring dset pairs but have less than\n"
"two dsets (%d) on command line.\n", (argc-iarg));
exit (1);
}
ip = 0;
for( ; iarg < argc ; iarg++ ){
if (ip == 0) {
int kkk, nml; char *etr;
namelen = 0;
for (kkk=iarg; kkk<argc; ++kkk) {
if ((etr = THD_trailname(argv[kkk],0))) {
nml=strlen(etr);
if (nml < 48 && nml > namelen) namelen = nml;
}
}
if (namelen < 6) namelen = 6;
if (withhead) {
int havenew=0;
for (iis = 0; iis < N_sing; ++iis) {
if (sing[iis] != CLASSIC) {
++havenew;
form = PrintForm(sing[iis], namelen, 1);
/*fprintf(stderr,"ZSS: %d %s >%s<\n",
sing[iis], Field_Names[sing[iis]], form);*/
fprintf(stdout, form, Field_Names[sing[iis]]);
}
if (havenew) {
if (N_sing > 1 && iis < N_sing-1)
fprintf(stdout,"%s",atrdelim);
else fprintf(stdout,"\n");
}
}
}
}
if( argv[iarg][0] == '\0' ) continue ; /* bad filename */
set_obliquity_report(0); /* silence obliquity */
if (!needpair) {
if (!(dset = load_3dinfo_dataset(argv[iarg]))) {
/* exit(1); */
}
} else {
if (needpair == 2) { /* Crazy idea of comparing each pair separately */
if (ip % 2 == 0) {
if (!(dset = load_3dinfo_dataset(argv[iarg] ))) {
/* exit(1); */
}
if (iarg+1==argc || argv[iarg+1][0] == '\0') {
ERROR_message("Bad dset pair for %s\n", argv[iarg]);
exit(1);
}
if (!(dsetp = load_3dinfo_dataset(argv[iarg+1] ))) {
/* exit(1); */
}
} else { /* swap the pair - this allows non pair requiring functions
to work as before.*/
tttdset = dsetp;
dsetp = dset;
dset = tttdset; tttdset=NULL;
}
} else { /* always compare to very first dset */
if (ip==0) {
if (!(dset = load_3dinfo_dataset(argv[iarg] ))) {
/*exit(1);*/
}
if (!(dsetp = load_3dinfo_dataset(argv[iarg+1] ))) {
/*exit(1);*/
}
} else if (ip==1) { /* switch order of first two */
tttdset = dsetp;
dsetp = dset; /* now dsetp is the very first dset */
dset = tttdset; tttdset=NULL;
} else { /* pair with very first, which is dsetp */
if (!(dset = load_3dinfo_dataset(argv[iarg] ))) {
/*exit(1);*/
}
}
}
}
++ip;
if (0 && !dset) { /* allow for DSET_EXISTS option */
ERROR_exit("Should not get here");
}
/* we should re-capture this per dataset 5 Feb 2019 [rickr] */
extinit = 0;
for (iis = 0; iis < N_sing; ++iis) {
if (!dset) {
if (sing[iis] == CLASSIC) {
if( dset == NULL ){ /* still not open? */
ERROR_exit("Can't open dataset %s\n", argv[iarg]) ;
}
} else if (sing[iis] != DSET_EXISTS && sing[iis] != INAME) {
fprintf(stdout, "NO-DSET");
SPIT_DELIM(iis, N_sing, atrdelim);
continue;
}
}
switch (sing[iis]) {
case CLASSIC:
if (labelName == NULL ) /*** get and output info ***/
{
outbuf = THD_dataset_info( dset , verbose ) ;
if( outbuf != NULL ){
printf("\n") ;
puts(outbuf) ;
free(outbuf) ; outbuf = NULL ;
} else {
ERROR_exit("Can't get info for dataset %s",argv[iarg]) ;
}
}
else /*** get and output label ***/
{
int nval_per = dset->dblk->nvals;
int foundLabel = 0;
int ival=0;
for (ival=0 ; ival < nval_per && !foundLabel; ival++ )
{
if (strcmp(DSET_BRICK_LAB(dset,ival), labelName) == 0)
{
printf("%d\n", ival); foundLabel = 1;
}
} /* end of for (ival=0 ; ival < nval_per ; ival++ ) */
if (!foundLabel) printf("\n");
}
THD_delete_3dim_dataset( dset , False ) ;
free(labelName);
break;
case DSET_EXISTS:
fprintf(stdout, "%d", dset ? 1:0);
break;
case DSET_SPACE:
tempstr = THD_get_space(dset);
if(tempstr==NULL)
fprintf(stdout, "-----");
else
fprintf(stdout, "%s", tempstr);
break;
case DSET_GEN_SPACE:
tempstr = THD_get_generic_space(dset);
if(tempstr==NULL)
fprintf(stdout, "-----");
else
fprintf(stdout, "%s", tempstr);
break;
case AV_DSET_SPACE:
/* don't allow anything but the three AFNI views */
tempstr = THD_get_view_space(dset);
if(tempstr==NULL)
fprintf(stdout, "+orig");
else if (!strncasecmp(tempstr,"ORIG",4))
fprintf(stdout, "+orig");
else if (!strncasecmp(tempstr,"ACPC",4))
fprintf(stdout, "+acpc");
else if (!strncasecmp(tempstr,"TLRC",4))
fprintf(stdout, "+tlrc");
else /* shouldn't get here */
fprintf(stdout, "+orig");
break;
case IS_NIFTI:
if ( dset->dblk->diskptr &&
dset->dblk->diskptr->storage_mode == STORAGE_BY_NIFTI ) {
fprintf(stdout,"1");
} else {
fprintf(stdout,"0");
}
break;
case IS_ATLAS:
if ( is_Dset_Atlasy(dset, NULL) ) {
fprintf(stdout,"1");
} else {
fprintf(stdout,"0");
}
break;
case IS_OBLIQUE:
if (dset_obliquity(dset,NULL) > 0) {
fprintf(stdout,"1");
} else {
fprintf(stdout,"0");
}
break;
case HANDEDNESS:
if (THD_handedness(dset) > 0) {
fprintf(stdout,"R");
} else {
fprintf(stdout,"L");
}
break;
case OBLIQUITY:
fprintf(stdout,"%.3f",
THD_compute_oblique_angle(dset->daxes->ijk_to_dicom_real, 0));
break;
case PREFIX:
form = PrintForm(sing[iis], namelen, 1);
fprintf(stdout,form, DSET_PREFIX(dset));
break;
case PREFIX_NOEXT:
{
form = PrintForm(sing[iis], namelen, 1);
stmp=DSET_prefix_noext(dset);
fprintf(stdout,form, stmp);
free(stmp); stmp=NULL;
}
break;
case HEADER_NAME:
fprintf(stdout,"%s", dset->dblk->diskptr->header_name);
break;
case BRICK_NAME:
fprintf(stdout,"%s", dset->dblk->diskptr->brick_name);
break;
case ALL_NAMES:
THD_show_dataset_names(dset, "FOR_3DINFO", stdout);
break;
case HISTORY:
stmp = tross_Get_History(dset);
fprintf(stdout,"%s", stmp ? stmp:NAflag);
if (stmp) free(stmp); stmp=NULL;
break;
case NI:
fprintf(stdout,"%d", DSET_NX(dset));
break;
case NJ:
fprintf(stdout,"%d", DSET_NY(dset));
break;
case NK:
fprintf(stdout,"%d", DSET_NZ(dset));
break;
case NIJK:
fprintf(stdout,"%d", DSET_NVOX(dset));
break;
case NTIMES:
fprintf(stdout,"%d", DSET_NUM_TIMES(dset));
break;
case MAX_NODE:
DSET_MAX_NODE(dset,itmp);
fprintf(stdout,"%d", itmp);
break;
case NT:
case NV:
fprintf(stdout,"%d", DSET_NVALS(dset));
break;
case NTI:
case NVI:
fprintf(stdout,"%d", DSET_NVALS(dset)-1);
break;
case DI:
fprintf(stdout,"%f", DSET_DX(dset));
break;
case DJ:
fprintf(stdout,"%f", DSET_DY(dset));
break;
case DK:
fprintf(stdout,"%f", DSET_DZ(dset));
break;
case OI:
fprintf(stdout,"%f", DSET_XORG(dset));
break;
case OJ:
fprintf(stdout,"%f", DSET_YORG(dset));
break;
case OK:
fprintf(stdout,"%f", DSET_ZORG(dset));
break;
case ADI:
fprintf(stdout,"%f", fabs(DSET_DX(dset)));
break;
case EXTENT_R:
case EXTENT_L:
case EXTENT_A:
case EXTENT_P:
case EXTENT_I:
case EXTENT_S:
{
if (!extinit) {
THD_dset_extent(dset, '-', RL_AP_IS);
extinit = 1;
}
fprintf(stdout,"%f", RL_AP_IS[sing[iis]-EXTENT_R]);
}
break;
case ADJ:
fprintf(stdout,"%f", fabs(DSET_DY(dset)));
break;
case ADK:
fprintf(stdout,"%f", fabs(DSET_DZ(dset)));
break;
case VOXVOL:
fprintf(stdout,"%f", fabs(DSET_DX(dset))*
fabs(DSET_DY(dset))*fabs(DSET_DZ(dset)));
break;
case INAME:
fprintf(stdout,"%s", argv[iarg]);
break;
case LTABLE:
{
char *str;
if ((str = Dtable_to_nimlstring(DSET_Label_Dtable(dset), "VALUE_LABEL_DTABLE"))) {
fprintf(stdout,"%s", str);
free(str);
} else {
fprintf(stdout,"NO_LABEL_TABLE");
}
}
break;
case LTABLE_AS_ATLAS_POINT_LIST:
{
ATLAS_POINT_LIST *apl=NULL;
if ((apl =
label_table_to_atlas_point_list(DSET_Label_Dtable(dset)))) {
atlas_list_to_niml(apl,NULL);
free_atlas_point_list(apl);
} else {
fprintf(stdout,"NO_LABEL_TABLE");
}
}
break;
case ATLAS_POINTS:
{
ATR_string *atr =
THD_find_string_atr( dset->dblk, "ATLAS_LABEL_TABLE");
if (atr) {
fprintf(stdout,"%s", atr->ch);
} else {
fprintf(stdout,"NO_APL");
}
}
break;
case FAC:
{
for (isb=0; isb<DSET_NVALS(dset); ++isb) {
fprintf(stdout,"%f%s",
DSET_BRICK_FACTOR(dset,isb),
(isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim);
}
break;
}
case DATUM:
{
for (isb=0; isb<DSET_NVALS(dset); ++isb) {
fprintf(stdout,"%s%s",
MRI_TYPE_name[DSET_BRICK_TYPE(dset,isb)],
(isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim);
}
break;
}
case LABEL:
{
for (isb=0; isb<DSET_NVALS(dset); ++isb) {
fprintf(stdout,"%s%s",
DSET_BRICK_LABEL(dset,isb) ? DSET_BRICK_LABEL(dset,isb):NAflag,
(isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim);
}
break;
}
case MIN:
case MINUS:
case MAX:
case MAXUS:
{
float vv=0.0, min, max;
for (isb=0; isb<DSET_NVALS(dset); ++isb) {
if (!THD_subbrick_minmax(dset, isb,
(sing[iis] == MINUS || sing[iis] == MAXUS) ? 0:1,
&min, &max)) {
fprintf(stdout,"%s%s",
NAflag,
(isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim);
} else {
if (sing[iis] == MINUS)
vv = min;
else if (sing[iis] == MAXUS)
vv = max;
else if (sing[iis] == MIN)
vv = min;
else if (sing[iis] == MAX)
vv = max;
fprintf(stdout,"%g%s",
vv,
(isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim);
}
}
break;
}
case DMIN:
case DMINUS:
case DMAX:
case DMAXUS:
{
float vv=0.0, min, max;
if (!THD_dset_minmax(dset,
(sing[iis] == DMINUS || sing[iis] == DMAXUS) ? 0:1,
&min, &max)) {
fprintf(stdout,"%s%s",
NAflag,
(isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim);
} else {
if (sing[iis] == DMINUS)
vv = min;
else if (sing[iis] == DMAXUS)
vv = max;
else if (sing[iis] == DMIN)
vv = min;
else if (sing[iis] == DMAX)
vv = max;
fprintf(stdout,"%g%s",
vv,
(isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim);
}
break;
}
case TR:
#if 0
fprintf(stdout,"%f", DSET_TR_SEC(dset));
#else
fprintf(stdout,"%f", DSET_TR(dset));
#endif
break;
case ORIENT:
{
/* fprintf(stdout,"%c%c%c",
* ORIENT_typestr[dset->daxes->xxorient][0], ... ); */
char ostr[4]; /* just to show 23 Jan 2013 [rickr] */
THD_fill_orient_str_3(dset->daxes, ostr);
fprintf(stdout,"%3s", ostr);
}
break;
case SAME_GRID:
fprintf(stdout,"%d",
!THD_dataset_mismatch( dset , dsetp ));
break;
case SAME_DIM:
fprintf(stdout,"%d",
!(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_DIMEN));
break;
case SAME_DELTA:
fprintf(stdout,"%d",
!(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_DELTA));
break;
case SAME_ORIENT:
fprintf(stdout,"%d",
!(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_ORIENT));
break;
case SAME_CENTER:
fprintf(stdout,"%d",
!(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_CENTER));
break;
case SAME_OBL:
fprintf(stdout,"%d",
!(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_OBLIQ));
break;
case SLICE_TIMING: /* 6 May 2013 [rickr] */
{
if( DSET_HAS_SLICE_TIMING(dset) ) {
DSET_UNMSEC(dset); /* make sure times are in seconds */
for (isb=0; isb<dset->taxis->nsl; ++isb) {
fprintf(stdout,"%s%f",
(isb > 0) ? sbdelim : "",
dset->taxis->toff_sl[isb]);
}
} else { /* all slices times are at t=0.0 */
for (isb=0; isb<DSET_NZ(dset); ++isb) {
fprintf(stdout,"%s%f", (isb > 0) ? sbdelim : "", 0.0);
}
}
}
break;
case SVAL_DIFF:
fprintf(stdout,"%f",THD_diff_vol_vals(dset, dsetp, 1));
break;
case VAL_DIFF:
fprintf(stdout,"%f",THD_diff_vol_vals(dset, dsetp, 0));
break;
case ID:
fprintf(stdout,"%s", DSET_IDCODE_STR(dset));
break;
case SMODE:
fprintf(stdout,"%s", DSET_STORAGE_MODE_STR(dset));
break;
default:
ERROR_message("Info field not set properly (%d)\n", sing[iis]);
exit(1);
}
if (sing[iis] != CLASSIC) {
SPIT_DELIM(iis, N_sing, atrdelim);
}
}
}
exit(0) ;
}
/*!
A function version of the program mc by Thomas Lewiner
see main.c in ./MarchingCubes
*/
SUMA_SurfaceObject *SUMA_MarchingCubesSurface(
SUMA_GENERIC_PROG_OPTIONS_STRUCT * Opt)
{
static char FuncName[]={"SUMA_MarchingCubesSurface"};
SUMA_SurfaceObject *SO=NULL;
int nxx, nyy, nzz, cnt, i, j, k, *FaceSetList=NULL;
float *NodeList=NULL;
SUMA_NEW_SO_OPT *nsoopt = NULL;
THD_fvec3 fv, iv;
MCB *mcp ;
SUMA_ENTRY;
if (Opt->obj_type < 0) {
nxx = DSET_NX(Opt->in_vol);
nyy = DSET_NY(Opt->in_vol);
nzz = DSET_NZ(Opt->in_vol);
if (Opt->debug) {
fprintf(SUMA_STDERR,
"%s:\nNxx=%d\tNyy=%d\tNzz=%d\n", FuncName, nxx, nyy, nzz);
}
mcp = MarchingCubes(-1, -1, -1);
set_resolution( mcp, nxx, nyy, nzz ) ;
init_all(mcp) ;
if (Opt->debug) fprintf(SUMA_STDERR,"%s:\nSetting data...\n", FuncName);
cnt = 0;
for( k = 0 ; k < mcp->size_z ; k++ ) {
for( j = 0 ; j < mcp->size_y ; j++ ) {
for( i = 0 ; i < mcp->size_x ; i++ ) {
SUMA_SET_MC_DATA ( mcp, Opt->mcdatav[cnt], i, j, k);
++cnt;
}
}
}
} else {
/* built in */
nxx = nyy = nzz = Opt->obj_type_res;
mcp = MarchingCubes(-1, -1, -1);
set_resolution( mcp, nxx, nyy, nzz) ;
init_all(mcp) ;
compute_data( *mcp , Opt->obj_type) ;
}
if (Opt->debug)
fprintf(SUMA_STDERR,"%s:\nrunning MarchingCubes...\n", FuncName);
run(mcp) ;
clean_temps(mcp) ;
if (Opt->debug > 1) {
fprintf(SUMA_STDERR,"%s:\nwriting out NodeList and FaceSetList...\n",
FuncName);
write1Dmcb(mcp);
}
if (Opt->debug) {
fprintf(SUMA_STDERR,"%s:\nNow creating SO...\n", FuncName);
}
NodeList = (float *)SUMA_malloc(sizeof(float)*3*mcp->nverts);
FaceSetList = (int *)SUMA_malloc(sizeof(int)*3*mcp->ntrigs);
if (!NodeList || !FaceSetList) {
SUMA_SL_Crit("Failed to allocate!");
SUMA_RETURN(SO);
}
nsoopt = SUMA_NewNewSOOpt();
if (Opt->obj_type < 0) {
nsoopt->LargestBoxSize = -1;
if (Opt->debug) {
fprintf(SUMA_STDERR,
"%s:\nCopying vertices, changing to DICOM \n"
"Orig:(%f %f %f) \nD:(%f %f %f)...\n",
FuncName,
DSET_XORG(Opt->in_vol),
DSET_YORG(Opt->in_vol), DSET_ZORG(Opt->in_vol),
DSET_DX(Opt->in_vol),
DSET_DY(Opt->in_vol), DSET_DZ(Opt->in_vol));
}
for ( i = 0; i < mcp->nverts; i++ ) {
j = 3*i; /* change from index coordinates to mm DICOM, next three lines are equivalent of SUMA_THD_3dfind_to_3dmm*/
fv.xyz[0] = DSET_XORG(Opt->in_vol) + mcp->vertices[i].x * DSET_DX(Opt->in_vol);
fv.xyz[1] = DSET_YORG(Opt->in_vol) + mcp->vertices[i].y * DSET_DY(Opt->in_vol);
fv.xyz[2] = DSET_ZORG(Opt->in_vol) + mcp->vertices[i].z * DSET_DZ(Opt->in_vol);
/* change mm to RAI coords */
iv = SUMA_THD_3dmm_to_dicomm( Opt->in_vol->daxes->xxorient, Opt->in_vol->daxes->yyorient, Opt->in_vol->daxes->zzorient, fv );
NodeList[j ] = iv.xyz[0];
NodeList[j+1] = iv.xyz[1];
NodeList[j+2] = iv.xyz[2];
}
for ( i = 0; i < mcp->ntrigs; i++ ) {
j = 3*i;
FaceSetList[j ] = mcp->triangles[i].v3;
FaceSetList[j+1] = mcp->triangles[i].v2;
FaceSetList[j+2] = mcp->triangles[i].v1;
}
} else {
nsoopt->LargestBoxSize = 100;
/* built in */
for ( i = 0; i < mcp->nverts; i++ ) {
j = 3*i;
NodeList[j ] = mcp->vertices[i].x;
NodeList[j+1] = mcp->vertices[i].y;
NodeList[j+2] = mcp->vertices[i].z;
}
for ( i = 0; i < mcp->ntrigs; i++ ) {
j = 3*i;
FaceSetList[j ] = mcp->triangles[i].v3;
FaceSetList[j+1] = mcp->triangles[i].v2;
FaceSetList[j+2] = mcp->triangles[i].v1;
}
}
SO = SUMA_NewSO(&NodeList, mcp->nverts, &FaceSetList, mcp->ntrigs, nsoopt);
if (Opt->obj_type < 0) {
/* not sure if anything needs to be done here ...*/
} else {
if (Opt->obj_type == 0) SO->normdir = 1;
else SO->normdir = -1;
}
if (Opt->debug) {
fprintf(SUMA_STDERR,"%s:\nCleaning mcp...\n", FuncName);
}
clean_all(mcp) ;
free(mcp);
nsoopt=SUMA_FreeNewSOOpt(nsoopt);
SUMA_RETURN(SO);
}
int AFNI_vedit( THD_3dim_dataset *dset , VEDIT_settings vednew , byte *mask )
{
THD_datablock *dblk ;
int ival ;
MRI_IMAGE *dim ;
ENTRY("AFNI_vedit") ;
if( !ISVALID_DSET(dset) ) RETURN(0) ;
dblk = dset->dblk ;
/*--- check if we are to clear any existing edits,
and also set future editing status to 'do nothing' ---*/
if( vednew.code <= 0 || vednew.code > VEDIT_LASTCODE ){
if( dblk->vedim != NULL ){ mri_free(dblk->vedim); dblk->vedim=NULL; }
dblk->vedset.code = 0; dblk->vedset.ival = -1; dblk->vedset.exinfo = NULL;
RETURN(0) ;
}
/* if we have existing editing results,
and they correspond to the same parameters as before, then are done.
otherwise, we clear out the existing results so they can be replaced. */
if( dblk->vedim != NULL && (vednew.flags&1) == 0 ){
if( memcmp(&(dblk->vedset),&vednew,sizeof(VEDIT_settings)) == 0 )
RETURN(0) ; /* exactly the same as before */
mri_free(dblk->vedim); dblk->vedim=NULL; /* clear old results */
}
/*--- at this point, must edit dataset brick ---*/
dblk->vedset = vednew ; /* save settings for next time in */
dblk->vedset.flags = 0 ;
/*--- create edited volume ---*/
if( vednew.code == VEDIT_CLUST ){ /*----- Clusterize -----*/
MRI_IMAGE *tim=NULL ;
float thr,rmm,vmul,thb,tht ;
int thrsign,posfunc,ithr ;
ival = vednew.ival ;
if( ival < 0 || ival > DSET_NVALS(dset) ) RETURN(0) ;
dim = DBLK_BRICK(dblk,ival) ;
if( dim == NULL || mri_data_pointer(dim) == NULL ){
DSET_load(dset) ;
dim = DBLK_BRICK(dblk,ival) ;
if( dim == NULL || mri_data_pointer(dim) == NULL ) RETURN(0) ;
}
dim->dx = fabs(DSET_DX(dset));
dim->dy = fabs(DSET_DY(dset));
dim->dz = fabs(DSET_DZ(dset));
ithr = (int)vednew.param[0] ;
thrsign = (int)vednew.param[4] ;
posfunc = (int)vednew.param[5] ;
if( ithr >= 0 && ithr < DSET_NVALS(dset) )
tim = DBLK_BRICK(dblk,ithr) ;
thr = vednew.param[1] ;
if( DSET_BRICK_FACTOR(dset,ithr) > 0.0f )
thr /= DSET_BRICK_FACTOR(dset,ithr) ;
thb = THBOT(thr) ; tht = THTOP(thr) ;
rmm = vednew.param[2] ; vmul = vednew.param[3] ;
dblk->vedim = mri_clusterize( rmm,vmul,dim,thb,tht,tim,posfunc , mask );
}
/*--- done ---*/
RETURN(1) ;
}
int main( int argc , char * argv[] )
{
float mrad=0.0f , fwhm=0.0f ;
int nrep=1 ;
char *prefix = "Polyfit" ;
char *resid = NULL ;
char *cfnam = NULL ;
int iarg , verb=0 , do_automask=0 , nord=3 , meth=2 , do_mclip=0 ;
THD_3dim_dataset *inset ;
MRI_IMAGE *imout , *imin ;
byte *mask=NULL ; int nvmask=0 , nmask=0 , do_mone=0 , do_byslice=0 ;
MRI_IMARR *exar=NULL ;
floatvec *fvit=NULL ; /* 26 Feb 2019 */
if( argc < 2 || strcasecmp(argv[1],"-help") == 0 ){
printf("\n"
"Usage: 3dPolyfit [options] dataset ~1~\n"
"\n"
"* Fits a polynomial in space to the input dataset and outputs that fitted dataset.\n"
"\n"
"* You can also add your own basis datasets to the fitting mix, using the\n"
" '-base' option.\n"
"\n"
"* You can get the fit coefficients using the '-1Dcoef' option.\n"
"\n"
"--------\n"
"Options: ~1~\n"
"--------\n"
"\n"
" -nord n = Maximum polynomial order (0..9) [default order=3]\n"
" [n=0 is the constant 1]\n"
" [n=-1 means only use volumes from '-base']\n"
"\n"
" -blur f = Gaussian blur input dataset (inside mask) with FWHM='f' (mm)\n"
"\n"
" -mrad r = Radius (voxels) of preliminary median filter of input\n"
" [default is no blurring of either type; you can]\n"
" [do both types (Gaussian and median), but why??]\n"
" [N.B.: median blur is slower than Gaussian]\n"
"\n"
" -prefix pp = Use 'pp' for prefix of output dataset (the fit).\n"
" [default prefix is 'Polyfit'; use NULL to skip this output]\n"
"\n"
" -resid rr = Use 'rr' for the prefix of the residual dataset.\n"
" [default is not to output residuals]\n"
"\n"
" -1Dcoef cc = Save coefficients of fit into text file cc.1D.\n"
" [default is not to save these coefficients]\n"
"\n"
" -automask = Create a mask (a la 3dAutomask)\n"
" -mask mset = Create a mask from nonzero voxels in 'mset'.\n"
" [default is not to use a mask, which is probably a bad idea]\n"
"\n"
" -mone = Scale the mean value of the fit (inside the mask) to 1.\n"
" [probably this option is not useful for anything]\n"
"\n"
" -mclip = Clip fit values outside the rectilinear box containing the\n"
" mask to the edge of that box, to avoid weird artifacts.\n"
"\n"
" -meth mm = Set 'mm' to 2 for least squares fit;\n"
" set it to 1 for L1 fit [default method=2]\n"
" [Note that L1 fitting is slower than L2 fitting!]\n"
"\n"
" -base bb = In addition to the polynomial fit, also use\n"
" the volumes in dataset 'bb' as extra basis functions.\n"
" [If you use a base dataset, then you can set nord]\n"
" [to -1, to skip using any spatial polynomial fit.]\n"
"\n"
" -verb = Print fun and useful progress reports :-)\n"
"\n"
"------\n"
"Notes: ~1~\n"
"------\n"
"* Output dataset is always stored in float format.\n"
"\n"
"* If the input dataset has more than 1 sub-brick, only sub-brick #0\n"
" is processed. To fit more than one volume, you'll have to use a script\n"
" to loop over the input sub-bricks, and then glue (3dTcat) the results\n"
" together to get a final result. A simple example:\n"
" #!/bin/tcsh\n"
" set base = model.nii\n"
" set dset = errts.nii\n"
" set nval = `3dnvals $dset`\n"
" @ vtop = $nval - 1\n"
" foreach vv ( `count 0 $vtop` )\n"
" 3dPolyfit -base \"$base\" -nord 0 -mask \"$base\" -1Dcoef QQ.$vv -prefix QQ.$vv.nii $dset\"[$vv]\"\n"
" end\n"
" 3dTcat -prefix QQall.nii QQ.0*.nii\n"
" 1dcat QQ.0*.1D > QQall.1D\n"
" \rm QQ.0*\n"
" exit 0\n"
"\n"
"* If the '-base' dataset has multiple sub-bricks, all of them are used.\n"
"\n"
"* You can use the '-base' option more than once, if desired or needed.\n"
"\n"
"* The original motivation for this program was to fit a spatial model\n"
" to a field map MRI, but that didn't turn out to be useful. Nevertheless,\n"
" I make this program available to someone who might find it beguiling.\n"
"\n"
"* If you really want, I could allow you to put sign constraints on the\n"
" fit coefficients (e.g., say that the coefficient for a given base volume\n"
" should be non-negative). But you'll have to beg for this.\n"
"\n"
"-- Emitted by RWCox\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
/*-- startup paperwork --*/
mainENTRY("3dPolyfit main"); machdep(); AFNI_logger("3dPolyfit",argc,argv);
PRINT_VERSION("3dPolyfit") ;
/*-- scan command line --*/
iarg = 1 ;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcasecmp(argv[iarg],"-base") == 0 ){
THD_3dim_dataset *bset ; int kk ; MRI_IMAGE *bim ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '-base'") ;
bset = THD_open_dataset(argv[iarg]) ;
CHECK_OPEN_ERROR(bset,argv[iarg]) ;
DSET_load(bset) ; CHECK_LOAD_ERROR(bset) ;
if( exar == NULL ) INIT_IMARR(exar) ;
for( kk=0 ; kk < DSET_NVALS(bset) ; kk++ ){
bim = THD_extract_float_brick(kk,bset) ;
if( bim != NULL ) ADDTO_IMARR(exar,bim) ;
DSET_unload_one(bset,kk) ;
}
DSET_delete(bset) ;
iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-verb") == 0 ){
verb++ ; iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-hermite") == 0 ){ /* 25 Mar 2013 [New Year's Day] */
mri_polyfit_set_basis("hermite") ; /* HIDDEN */
iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-byslice") == 0 ){ /* 25 Mar 2013 [New Year's Day] */
do_byslice++ ; iarg++ ; continue ; /* HIDDEN */
}
if( strcasecmp(argv[iarg],"-mask") == 0 ){
THD_3dim_dataset *mset ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '-mask'") ;
if( mask != NULL || do_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) ;
nvmask = DSET_NVOX(mset) ;
mask = THD_makemask( mset , 0 , 0.5f, 0.0f ) ; DSET_delete(mset) ;
if( mask == NULL ) ERROR_exit("Can't make mask from dataset '%s'",argv[iarg]) ;
nmask = THD_countmask( nvmask , mask ) ;
if( nmask < 99 ) ERROR_exit("Too few voxels in mask (%d)",nmask) ;
if( verb ) INFO_message("Number of voxels in mask = %d",nmask) ;
iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-nord") == 0 ){
nord = (int)strtol( argv[++iarg], NULL , 10 ) ;
if( nord < -1 || nord > 9 )
ERROR_exit("Illegal value after -nord :(") ;
iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-meth") == 0 ){
meth = (int)strtol( argv[++iarg], NULL , 10 ) ;
if( meth < 1 || meth > 2 )
ERROR_exit("Illegal value after -meth :(") ;
iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-automask",5) == 0 ){
if( mask != NULL ) ERROR_exit("Can't use -mask and -automask together!") ;
do_automask++ ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-mclip",5) == 0 ){
do_mclip++ ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-mone",5) == 0 ){
do_mone++ ; iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-mrad") == 0 ){
mrad = strtod( argv[++iarg] , NULL ) ; iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-blur") == 0 ){
fwhm = strtod( argv[++iarg] , NULL ) ; iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-prefix") == 0 ){
prefix = argv[++iarg] ;
if( !THD_filename_ok(prefix) )
ERROR_exit("Illegal value after -prefix :(");
if( strcasecmp(prefix,"NULL") == 0 ) prefix = NULL ;
iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-resid") == 0 ){
resid = argv[++iarg] ;
if( !THD_filename_ok(resid) )
ERROR_exit("Illegal value after -resid :(");
if( strcasecmp(resid,"NULL") == 0 ) resid = NULL ;
iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-1Dcoef") == 0 ){ /* 26 Feb 2019 */
cfnam = argv[++iarg] ;
if( !THD_filename_ok(cfnam) )
ERROR_exit("Illegal value after -1Dcoef :(");
if( strcasecmp(cfnam,"NULL") == 0 ) cfnam = NULL ;
iarg++ ; continue ;
}
ERROR_exit("Unknown option: %s\n",argv[iarg]);
}
/*--- check for blatant errors ---*/
if( iarg >= argc )
ERROR_exit("No input dataset name on command line?");
if( prefix == NULL && resid == NULL && cfnam == NULL )
ERROR_exit("-prefix and -resid and -1Dcoef are all NULL?!") ;
if( do_byslice && cfnam != NULL ){
WARNING_message("-byslice does not work with -1Dcoef option :(") ;
cfnam = NULL ;
}
if( nord < 0 && exar == NULL )
ERROR_exit("no polynomial fit AND no -base option ==> nothing to compute :(") ;
/*-- read input --*/
if( verb ) INFO_message("Load input dataset") ;
inset = THD_open_dataset( argv[iarg] ) ;
CHECK_OPEN_ERROR(inset,argv[iarg]) ;
DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ;
if( DSET_NVALS(inset) > 1 )
WARNING_message( "Only processing sub-brick #0 (out of %d)" , DSET_NVALS(inset) );
/* check input mask or create automask */
if( mask != NULL ){
if( nvmask != DSET_NVOX(inset) )
ERROR_exit("-mask and input datasets don't match in voxel counts :-(") ;
} else if( do_automask ){
THD_automask_verbose( (verb > 1) ) ;
THD_automask_extclip( 1 ) ;
mask = THD_automask( inset ) ; nvmask = DSET_NVOX(inset) ;
nmask = THD_countmask( nvmask , mask ) ;
if( nmask < 99 ) ERROR_exit("Too few voxels in automask (%d)",nmask) ;
if( verb ) ININFO_message("Number of voxels in automask = %d",nmask) ;
} else {
WARNING_message("3dPolyfit is running without a mask") ;
}
#undef GOOD
#define GOOD(i) (mask == NULL || mask[i])
/* check -base input datasets */
if( exar != NULL ){
int ii,kk , nvbad=0 , nvox=DSET_NVOX(inset),nm ; float *ex , exb ;
for( kk=0 ; kk < IMARR_COUNT(exar) ; kk++ ){
if( nvox != IMARR_SUBIM(exar,kk)->nvox ){
if( IMARR_SUBIM(exar,kk)->nvox != nvbad ){
ERROR_message("-base volume (%d voxels) doesn't match input dataset grid size (%d voxels)",
IMARR_SUBIM(exar,kk)->nvox , nvox ) ;
nvbad = IMARR_SUBIM(exar,kk)->nvox ;
}
}
}
if( nvbad != 0 ) ERROR_exit("Cannot continue :-(") ;
/* subtract mean from each base input, if is a constant polynomial in the fit */
if( nord >= 0 ){
if( verb ) INFO_message("subtracting spatial mean from '-base'") ;
for( kk=0 ; kk < IMARR_COUNT(exar) ; kk++ ){
exb = 0.0f ; ex = MRI_FLOAT_PTR(IMARR_SUBIM(exar,kk)) ;
for( nm=ii=0 ; ii < nvox ; ii++ ){ if( GOOD(ii) ){ exb += ex[ii]; nm++; } }
exb /= nm ;
for( ii=0 ; ii < nvox ; ii++ ) ex[ii] -= exb ;
}
}
}
/* if blurring, edit mask a little */
if( mask != NULL && (fwhm > 0.0f || mrad > 0.0f) ){
int ii ;
ii = THD_mask_remove_isolas( DSET_NX(inset),DSET_NY(inset),DSET_NZ(inset),mask ) ;
if( ii > 0 ){
nmask = THD_countmask( nvmask , mask ) ;
if( verb )
ININFO_message("Removed %d isola%s from mask, leaving %d voxels" ,
ii,(ii==1)?"\0":"s" , nmask ) ;
if( nmask < 99 )
ERROR_exit("Too few voxels left in mask after isola removal :-(") ;
}
}
/* convert input to float, which is simpler to deal with */
imin = THD_extract_float_brick(0,inset) ;
if( imin == NULL ) ERROR_exit("Can't extract input dataset brick?! :-(") ;
DSET_unload(inset) ;
if( verb ) INFO_message("Start fitting process") ;
/* do the Gaussian blurring */
if( fwhm > 0.0f ){
if( verb ) ININFO_message("Gaussian blur: FWHM=%g mm",fwhm) ;
imin->dx = fabsf(DSET_DX(inset)) ;
imin->dy = fabsf(DSET_DY(inset)) ;
imin->dz = fabsf(DSET_DZ(inset)) ;
mri_blur3D_addfwhm( imin , mask , fwhm ) ;
}
/* do the fitting */
mri_polyfit_verb(verb) ;
if( do_byslice )
imout = mri_polyfit_byslice( imin , nord , exar , mask , mrad , meth ) ;
else
imout = mri_polyfit ( imin , nord , exar , mask , mrad , meth ) ;
/* WTF? */
if( imout == NULL )
ERROR_exit("Can't compute polynomial fit :-( !?") ;
if( resid == NULL ) mri_free(imin) ;
if( ! do_byslice )
fvit = mri_polyfit_get_fitvec() ; /* get coefficients of fit [26 Feb 2019] */
/* scale the fit dataset? */
if( do_mone ){
float sum=0.0f ; int nsum=0 , ii,nvox ; float *par=MRI_FLOAT_PTR(imout) ;
nvox = imout->nvox ;
for( ii=0 ; ii < nvox ; ii++ ){
if( mask != NULL && mask[ii] == 0 ) continue ;
sum += par[ii] ; nsum++ ;
}
if( nsum > 0 && sum != 0.0f ){
sum = nsum / sum ;
if( verb ) ININFO_message("-mone: scaling fit by %g",sum) ;
for( ii=0 ; ii < nvox ; ii++ ) par[ii] *= sum ;
}
}
/* if there's a mask, clip values outside of its box */
#undef PF
#define PF(i,j,k) par[(i)+(j)*nx+(k)*nxy]
if( mask != NULL && do_mclip ){
int xm,xp,ym,yp,zm,zp , ii,jj,kk , nx,ny,nz,nxy ; float *par ;
MRI_IMAGE *bim = mri_empty_conforming( imout , MRI_byte ) ;
mri_fix_data_pointer(mask,bim) ;
if( verb ) ININFO_message("-mclip: polynomial fit to autobox of mask") ;
MRI_autobbox( bim , &xm,&xp , &ym,&yp , &zm,&zp ) ;
mri_clear_data_pointer(bim) ; mri_free(bim) ;
nx = imout->nx ; ny = imout->ny ; nz = imout->nz ; nxy = nx*ny ;
par = MRI_FLOAT_PTR(imout) ;
for( ii=0 ; ii < xm ; ii++ )
for( kk=0 ; kk < nz ; kk++ )
for( jj=0 ; jj < ny ; jj++ ) PF(ii,jj,kk) = PF(xm,jj,kk) ;
for( ii=xp+1 ; ii < nx ; ii++ )
for( kk=0 ; kk < nz ; kk++ )
for( jj=0 ; jj < ny ; jj++ ) PF(ii,jj,kk) = PF(xp,jj,kk) ;
for( jj=0 ; jj < ym ; jj++ )
for( kk=0 ; kk < nz ; kk++ )
for( ii=0 ; ii < nx ; ii++ ) PF(ii,jj,kk) = PF(ii,ym,kk) ;
for( jj=yp+1 ; jj < ny ; jj++ )
for( kk=0 ; kk < nz ; kk++ )
for( ii=0 ; ii < nx ; ii++ ) PF(ii,jj,kk) = PF(ii,yp,kk) ;
for( kk=0 ; kk < zm ; kk++ )
for( jj=0 ; jj < ny ; jj++ )
for( ii=0 ; ii < nx ; ii++ ) PF(ii,jj,kk) = PF(ii,jj,zm) ;
for( kk=zp+1 ; kk < nz ; kk++ )
for( jj=0 ; jj < ny ; jj++ )
for( ii=0 ; ii < nx ; ii++ ) PF(ii,jj,kk) = PF(ii,jj,zp) ;
}
if( mask != NULL ) free(mask) ;
/* write outputs */
if( prefix != NULL ){
THD_3dim_dataset *outset = EDIT_empty_copy( inset ) ;
EDIT_dset_items( outset ,
ADN_prefix , prefix ,
ADN_nvals , 1 ,
ADN_ntt , 0 ,
ADN_none ) ;
EDIT_substitute_brick( outset , 0 , MRI_float , MRI_FLOAT_PTR(imout) ) ;
tross_Copy_History( inset , outset ) ;
tross_Make_History( "3dPolyfit" , argc,argv , outset ) ;
DSET_write(outset) ;
WROTE_DSET(outset) ;
}
if( resid != NULL ){
THD_3dim_dataset *outset = EDIT_empty_copy( inset ) ;
float *inar=MRI_FLOAT_PTR(imin) , *outar=MRI_FLOAT_PTR(imout) ;
int nx,ny,nz , nxyz , kk ;
nx = imout->nx ; ny = imout->ny ; nz = imout->nz ; nxyz = nx*ny*nz ;
for( kk=0 ; kk < nxyz ; kk++ ) outar[kk] = inar[kk] - outar[kk] ;
mri_free(imin) ;
EDIT_dset_items( outset ,
ADN_prefix , resid ,
ADN_nvals , 1 ,
ADN_ntt , 0 ,
ADN_none ) ;
EDIT_substitute_brick( outset , 0 , MRI_float , MRI_FLOAT_PTR(imout) ) ;
tross_Copy_History( inset , outset ) ;
tross_Make_History( "3dPolyfit" , argc,argv , outset ) ;
DSET_write(outset) ;
WROTE_DSET(outset) ;
}
if( cfnam != NULL && fvit != NULL ){ /* won't work with '-byslice' */
char *qn ;
qn = STRING_HAS_SUFFIX(cfnam,".1D") ? cfnam : modify_afni_prefix(cfnam,NULL,".1D") ;
mri_write_floatvec( qn , fvit ) ;
}
exit(0) ;
}
int main( int argc , char *argv[] )
{
char *aname ;
THD_3dim_dataset *dset ;
int ii , scl ;
MRI_IMAGE *im , *qim ;
char *fname ;
float fac ;
int do_4D=0 , iarg=1 ; /* 30 Sep 2002 */
FILE *ifp=NULL ;
int xxor=-1,yyor=0,zzor=0 , xdir=0,ydir=0,zdir=0; /* 19 Mar 2003 */
float xdel=0.0 ,ydel=0.0,zdel=0.0;
char orient_code[4] ;
/*-- help me if you can --*/
WARNING_message("This program (3dAFNItoANALYZE) is old, not maintained, and probably useless!") ;
if( argc < 3 || strcmp(argv[1],"-help") == 0 ){
printf("Usage: 3dAFNItoANALYZE [-4D] [-orient code] aname dset\n"
"Writes AFNI dataset 'dset' to 1 or more ANALYZE 7.5 format\n"
".hdr/.img file pairs (one pair for each sub-brick in the\n"
"AFNI dataset). The ANALYZE files will be named\n"
" aname_0000.hdr aname_0000.img for sub-brick #0\n"
" aname_0001.hdr aname_0001.img for sub-brick #1\n"
"and so forth. Each file pair will contain a single 3D array.\n"
"\n"
"* If the AFNI dataset does not include sub-brick scale\n"
" factors, then the ANALYZE files will be written in the\n"
" datum type of the AFNI dataset.\n"
"* If the AFNI dataset does have sub-brick scale factors,\n"
" then each sub-brick will be scaled to floating format\n"
" and the ANALYZE files will be written as floats.\n"
"* The .hdr and .img files are written in the native byte\n"
" order of the computer on which this program is executed.\n"
"\n"
"Options\n"
"-------\n"
"-4D [30 Sep 2002]:\n"
" If you use this option, then all the data will be written to\n"
" one big ANALYZE file pair named aname.hdr/aname.img, rather\n"
" than a series of 3D files. Even if you only have 1 sub-brick,\n"
" you may prefer this option, since the filenames won't have\n"
" the '_0000' appended to 'aname'.\n"
"\n"
"-orient code [19 Mar 2003]:\n"
" This option lets you flip the dataset to a different orientation\n"
" when it is written to the ANALYZE files. The orientation code is\n"
" formed as follows:\n"
" The code must be 3 letters, one each from the\n"
" pairs {R,L} {A,P} {I,S}. The first letter gives\n"
" the orientation of the x-axis, the second the\n"
" orientation of the y-axis, the third the z-axis:\n"
" R = Right-to-Left L = Left-to-Right\n"
" A = Anterior-to-Posterior P = Posterior-to-Anterior\n"
" I = Inferior-to-Superior S = Superior-to-Inferior\n"
" For example, 'LPI' means\n"
" -x = Left +x = Right\n"
" -y = Posterior +y = Anterior\n"
" -z = Inferior +z = Superior\n"
" * For display in SPM, 'LPI' or 'RPI' seem to work OK.\n"
" Be careful with this: you don't want to confuse L and R\n"
" in the SPM display!\n"
" * If you DON'T use this option, the dataset will be written\n"
" out in the orientation in which it is stored in AFNI\n"
" (e.g., the output of '3dinfo dset' will tell you this.)\n"
" * The dataset orientation is NOT stored in the .hdr file.\n"
" * AFNI and ANALYZE data are stored in files with the x-axis\n"
" varying most rapidly and the z-axis most slowly.\n"
" * Note that if you read an ANALYZE dataset into AFNI for\n"
" display, AFNI assumes the LPI orientation, unless you\n"
" set environment variable AFNI_ANALYZE_ORIENT.\n"
) ;
PRINT_COMPILE_DATE; exit(0) ;
}
mainENTRY("3dAFNItoANALYZE main"); machdep(); PRINT_VERSION("3dAFNItoANALYZE");
/*-- read inputs --*/
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-4D") == 0 ){ /* 30 Sep 2002 */
do_4D = 1 ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-orient") == 0 ){ /* 19 Mar 2003 */
char acod ;
if( iarg+1 >= argc ){
fprintf(stderr,"** Need something after -orient!\n"); exit(1);
}
MCW_strncpy(orient_code,argv[++iarg],4) ;
if( strlen(orient_code) != 3 ){
fprintf(stderr,"** Illegal code '%s' after -orient!\n",argv[iarg]); exit(1);
}
acod = toupper(orient_code[0]) ; xxor = ORCODE(acod) ;
acod = toupper(orient_code[1]) ; yyor = ORCODE(acod) ;
acod = toupper(orient_code[2]) ; zzor = ORCODE(acod) ;
if( xxor<0 || yyor<0 || zzor<0 || !OR3OK(xxor,yyor,zzor) ){
fprintf(stderr,"** Unusable code after -orient!\n"); exit(1);
}
iarg++ ; continue ;
}
fprintf(stderr,"** Illegal option: %s\n",argv[iarg]); exit(1);
}
if( iarg >= argc-1 ){
fprintf(stderr,"** Not enough arguments on command line!\n"); exit(1);
}
aname = argv[iarg++] ;
if( !THD_filename_ok(aname) ){
fprintf(stderr,"** Illegal aname string %s\n",aname) ;
exit(1) ;
}
fname = malloc( strlen(aname)+16 ) ;
dset = THD_open_dataset( argv[iarg++] ); CHECK_OPEN_ERROR(dset,argv[iarg-1]);
if( xxor >= 0 ){ /* 19 Mar 2003: figure how to flip */
xdir = THD_get_axis_direction( dset->daxes , xxor ) ;
ydir = THD_get_axis_direction( dset->daxes , yyor ) ;
zdir = THD_get_axis_direction( dset->daxes , zzor ) ;
if( ydir == 0 || zdir == 0 ) xdir = 0 ;
if( xdir == 1 && ydir == 2 && zdir == 3 ) xdir = 0 ;
}
if( xdir != 0 ){
float dx=fabs(DSET_DX(dset)) ,
dy=fabs(DSET_DY(dset)) ,
dz=fabs(DSET_DZ(dset)) ;
DSET_mallocize(dset) ;
switch( xdir ){
case 1: case -1: xdel = dx ; break ;
case 2: case -2: xdel = dy ; break ;
case 3: case -3: xdel = dz ; break ;
}
switch( ydir ){
case 1: case -1: ydel = dx ; break ;
case 2: case -2: ydel = dy ; break ;
case 3: case -3: ydel = dz ; break ;
}
switch( zdir ){
case 1: case -1: zdel = dx ; break ;
case 2: case -2: zdel = dy ; break ;
case 3: case -3: zdel = dz ; break ;
}
} else {
xdel = fabs(DSET_DX(dset)) ;
ydel = fabs(DSET_DY(dset)) ;
zdel = fabs(DSET_DZ(dset)) ;
}
DSET_load(dset) ; CHECK_LOAD_ERROR(dset) ;
/* determine if we scale to floats */
scl = THD_need_brick_factor( dset ) ;
/* 30 Sep 2002: if doing a 4D file, write single .hdr now */
if( do_4D ){
im = mri_empty_conforming( DSET_BRICK(dset,0) ,
(scl) ? MRI_float
: DSET_BRICK_TYPE(dset,0) ) ;
if( xdir != 0 ){
qim = mri_flip3D( xdir,ydir,zdir , im ) ;
if( qim == NULL){
fprintf(stderr,"mri_flip3D fails?!\n"); exit(1);
}
mri_free(im); im = qim;
}
im->dx = xdel ; /* load voxel sizes */
im->dy = ydel ;
im->dz = zdel ;
im->dw = 1.0 ;
if( AFNI_yesenv("AFNI_ANALYZE_ORIGINATOR") ){
im->xo = dset->daxes->xxorg ; /* load voxel origin */
im->yo = dset->daxes->yyorg ; /* 03/11/04 KRH added this bit for SPM */
im->zo = dset->daxes->zzorg ;
if( ORIENT_sign[dset->daxes->xxorient] == '-' ){
im->dx = -im->dx ;
/* im->xo = -im->xo ; */
}
if( ORIENT_sign[dset->daxes->yyorient] == '-' ){
im->dy = -im->dy ;
/* im->yo = -im->yo ; */
}
if( ORIENT_sign[dset->daxes->zzorient] == '-' ){
im->dz = -im->dz ;
/* im->zo = -im->zo ; */
}
}
im->nt = DSET_NVALS(dset) ; /* add a time axis */
im->dt = DSET_TR(dset) ;
if( im->dt <= 0.0 ) im->dt = 1.0 ;
if( DSET_TIMEUNITS(dset) == UNITS_MSEC_TYPE ) im->dt *= 0.001 ; /* 05 Jul 2005 */
mri_write_analyze( aname , im ) ; /* output 4D .hdr file */
mri_free(im) ;
sprintf(fname,"%s.img",aname) ; /* open output .img file */
ifp = fopen( fname , "wb" ) ;
if( ifp == NULL ){
fprintf(stderr,"** Can't open file %s for output!\n",fname) ;
exit(1) ;
}
}
/* loop over sub-bricks */
for( ii=0 ; ii < DSET_NVALS(dset) ; ii++ ){
im = DSET_BRICK(dset,ii) ; /* get the sub-brick */
if( scl ){ /* scale it to floats */
fac = DSET_BRICK_FACTOR(dset,ii) ;
if( fac == 0.0 ) fac = 1.0 ;
qim = mri_scale_to_float( fac , im ) ;
} else {
qim = im ;
}
if( xdir != 0 ){ /* 19 Mar 2003: flip it */
MRI_IMAGE *fim ;
fim = mri_flip3D( xdir,ydir,zdir , qim ) ;
if( fim == NULL ){
fprintf(stderr,"mri_flip3D fails at ii=%d ?!\n",ii); exit(1);
}
if( qim != im ) mri_free(qim) ;
qim = fim ;
}
if( do_4D ){ /* 30 Sep 2002: write into 4D .img file */
fwrite( mri_data_pointer(qim) , qim->nvox , qim->pixel_size , ifp ) ;
} else { /* write separate 3D .hdr/.img files */
qim->dx = xdel ; /* load voxel sizes */
qim->dy = ydel ;
qim->dz = zdel ;
qim->dw = 1.0 ;
if( AFNI_yesenv("AFNI_ANALYZE_ORIGINATOR") ){
qim->xo = dset->daxes->xxorg ; /* load voxel origin */
qim->yo = dset->daxes->yyorg ; /* 03/11/04 KRH added this bit for SPM */
qim->zo = dset->daxes->zzorg ;
if( ORIENT_sign[dset->daxes->xxorient] == '-' ){
qim->dx = -qim->dx ;
/* qim->xo = -qim->xo ; */
}
if( ORIENT_sign[dset->daxes->yyorient] == '-' ){
qim->dy = -qim->dy ;
/* qim->yo = -qim->yo ; */
}
if( ORIENT_sign[dset->daxes->zzorient] == '-' ){
qim->dz = -qim->dz ;
/* qim->zo = -qim->zo ; */
}
}
sprintf(fname,"%s_%04d",aname,ii) ; /* make up a filename */
mri_write_analyze( fname , qim ) ; /* do the real work */
}
if( qim != im ) mri_free(qim) ;
DSET_unload_one(dset,ii) ; /* clean up the trash */
}
if( ifp != NULL ) fclose(ifp) ; /* 30 Sep 2002 */
free(fname) ; exit(0) ;
}
int main( int argc , char * argv[] )
{
THD_dfvec3 *xx , *yy , dv ;
int nvec=0 , ii,jj, iarg ;
THD_dvecmat rt , rtinv ;
THD_dmat33 pp,ppt , rr ;
THD_dfvec3 tt ;
THD_3dim_dataset *mset=NULL , *dset=NULL ;
double *ww=NULL ;
int nww=0 ;
int keeptags=1 , wtval=0 , verb=0 , dummy=0 ;
char * prefix = "tagalign" , *mfile=NULL ;
float *fvol , cbot,ctop , dsum ;
int nval , nvox , clipit , ival, RMETH=MRI_CUBIC;
float matar[12] ;
int use_3dWarp=1 , matrix_type=ROTATION ;
mainENTRY("3dTagalign main");
/*--- help? ---*/
/*- scan args -*/
iarg = 1 ; RMETH=MRI_CUBIC;
while( iarg < argc && argv[iarg][0] == '-' ){
/*-----*/
if( strcmp(argv[iarg],"-h") == 0 ||
strcmp(argv[iarg],"-help") == 0){ /* 22 Apr 2003 */
usage_3dTagalign(strlen(argv[iarg]) > 3 ? 2:1);
exit(0);
}
/*-----*/
if( strcmp(argv[iarg],"-NN") == 0 ){
RMETH = MRI_NN ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-linear") == 0 ){
RMETH = MRI_LINEAR ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-cubic") == 0 ){
RMETH = MRI_CUBIC ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-quintic") == 0 ){
RMETH = MRI_QUINTIC ; iarg++ ; continue ;
}
/*-----*/
if( strcmp(argv[iarg],"-rotate") == 0 ){ /* 22 Apr 2003 */
matrix_type = ROTATION ; use_3dWarp = 1 ;
iarg++ ; continue ;
}
/*-----*/
if( strcmp(argv[iarg],"-affine") == 0 ){ /* 21 Apr 2003 */
matrix_type = AFFINE ; use_3dWarp = 1 ;
iarg++ ; continue ;
}
/*-----*/
if( strcmp(argv[iarg],"-rotscl") == 0 ){ /* 22 Apr 2003 */
matrix_type = ROTSCL ; use_3dWarp = 1 ;
iarg++ ; continue ;
}
#if 0
/*-----*/
if( strcmp(argv[iarg],"-3dWarp") == 0 ){ /* 21 Apr 2003 */
use_3dWarp = 1 ;
iarg++ ; continue ;
}
#endif
/*-----*/
if( strcmp(argv[iarg],"-master") == 0 ){
if( mset != NULL ) ERREX("Can only have one -master option") ;
if( ++iarg >= argc ) ERREX("Need an argument after -master") ;
mset = THD_open_dataset( argv[iarg] ) ;
if( mset == NULL ) ERREX("Can't open -master dataset") ;
if( mset->tagset == NULL ) ERREX("No tags in -master dataset") ;
if( TAGLIST_COUNT(mset->tagset) < 3 ) ERREX("Not enough tags in -master dataset") ;
for( nvec=ii=0 ; ii < TAGLIST_COUNT(mset->tagset) ; ii++ )
if( TAG_SET(TAGLIST_SUBTAG(mset->tagset,ii)) ) nvec++ ;
if( nvec < 3 ) ERREX("Not enough tags set in -master dataset") ;
if( nvec < TAGLIST_COUNT(mset->tagset) )
fprintf(stderr,"++ WARNING: not all tags are set in -master dataset\n") ;
if( verb ) fprintf(stderr,"++ Found %d tags in -master dataset\n",nvec) ;
iarg++ ; continue ;
}
#if 0
/*-----*/
if( strcmp(argv[iarg],"-wtval") == 0 ){
if( ww != NULL ) ERREX("Can't have -wtval after -wt1D") ;
wtval++ ;
iarg++ ; continue ;
}
/*-----*/
if( strcmp(argv[iarg],"-wt1D") == 0 ){
MRI_IMAGE * wtim ; float * wtar ;
if( wtval ) ERREX("Can't have -wt1D after -wtval") ;
if( ww != NULL ) ERREX("Can't have two -wt1D options!") ;
if( ++iarg >= argc ) ERREX("Need an argument after -wt1D") ;
wtim = mri_read_1D( argv[iarg] ) ;
if( wtim == NULL ) ERREX("Can't read -wtim file") ;
if( wtim->ny > 1 ) ERREX("-wtim file has more than one columm") ;
wtar = MRI_FLOAT_PTR(wtim) ;
ww = (double *) malloc(sizeof(double)*wtim->nx) ; nww = wtim->nx ;
for( ii=0 ; ii < nww ; ii++ ){
ww[ii] = (double) wtar[ii] ;
if( ww[ii] < 0.0 ) ERREX("Negative value found in -wt1D file") ;
}
mri_free(wtim) ;
iarg++ ; continue ;
}
#endif
/*-----*/
if( strcmp(argv[iarg],"-nokeeptags") == 0 ){
keeptags = 0 ;
iarg++ ; continue ;
}
/*-----*/
if( strncmp(argv[iarg],"-verb",5) == 0 ){
verb++ ;
iarg++ ; continue ;
}
/*-----*/
if( strcmp(argv[iarg],"-dummy") == 0 ){
dummy++ ;
iarg++ ; continue ;
}
/*-----*/
if( strcmp(argv[iarg],"-prefix") == 0 ){
if( ++iarg >= argc ) ERREX("Need an argument after -prefix") ;
prefix = argv[iarg] ;
if( !THD_filename_ok(prefix) ) ERREX("-prefix string is illegal") ;
iarg++ ; continue ;
}
/*-----*/
if( strcmp(argv[iarg],"-matvec") == 0 ){
if( ++iarg >= argc ) ERREX("Need an argument after -matvec") ;
mfile = argv[iarg] ;
if( !THD_filename_ok(mfile) ) ERREX("-matvec string is illegal") ;
iarg++ ; continue ;
}
/*-----*/
fprintf(stderr,"** Unknown option: %s\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1) ;
} /* end of scanning command line for options */
if( argc < 2 ){
ERROR_message("Too few options");
usage_3dTagalign(0);
exit(1) ;
}
if( mset == NULL ) ERREX("No -master option found on command line") ;
#if 0
if( ww != NULL && nww < nvec ) ERREX("Not enough weights found in -wt1D file") ;
/*-- if -wtval, setup weights from master tag values --*/
if( wtval ){
ww = (double *) malloc(sizeof(double)*nvec) ; nww = nvec ;
for( ii=jj=0 ; ii < TAGLIST_COUNT(mset->tagset) ; ii++ ){
if( TAG_SET(TAGLIST_SUBTAG(mset->tagset,ii)) ){
ww[jj] = (double) TAG_VAL(TAGLIST_SUBTAG(mset->tagset,ii)) ;
if( ww[jj] < 0.0 ) ERREX("Negative value found in -master tag values") ;
jj++ ;
}
}
}
#endif
/*-- read input dataset (to match to master dataset) --*/
if( iarg >= argc ) ERREX("No input dataset?") ;
dset = THD_open_dataset( argv[iarg] ) ;
if( dset == NULL ) ERREX("Can't open input dataset") ;
if( dset->tagset == NULL ) ERREX("No tags in input dataset") ;
if( TAGLIST_COUNT(dset->tagset) !=
TAGLIST_COUNT(mset->tagset) ) ERREX("Tag counts don't match in -master and input") ;
/* check if set tags match exactly */
for( ii=0 ; ii < TAGLIST_COUNT(mset->tagset) ; ii++ ){
if( TAG_SET(TAGLIST_SUBTAG(mset->tagset,ii)) !=
TAG_SET(TAGLIST_SUBTAG(dset->tagset,ii)) )
ERREX("Set tags don't match in -master and input") ;
}
/*-- load vector lists: xx=master, yy=input --*/
xx = (THD_dfvec3 *) malloc( sizeof(THD_dfvec3) * nvec ) ;
yy = (THD_dfvec3 *) malloc( sizeof(THD_dfvec3) * nvec ) ;
dsum = 0.0 ;
for( ii=jj=0 ; ii < nvec ; ii++ ){
if( TAG_SET(TAGLIST_SUBTAG(mset->tagset,ii)) ){
LOAD_DFVEC3( xx[jj] , /* N.B.: */
TAG_X( TAGLIST_SUBTAG(mset->tagset,ii) ) , /* these are */
TAG_Y( TAGLIST_SUBTAG(mset->tagset,ii) ) , /* in Dicom */
TAG_Z( TAGLIST_SUBTAG(mset->tagset,ii) ) ) ; /* order now */
LOAD_DFVEC3( yy[jj] ,
TAG_X( TAGLIST_SUBTAG(dset->tagset,ii) ) ,
TAG_Y( TAGLIST_SUBTAG(dset->tagset,ii) ) ,
TAG_Z( TAGLIST_SUBTAG(dset->tagset,ii) ) ) ;
dv = SUB_DFVEC3( xx[jj] , yy[jj] ) ;
dsum += dv.xyz[0]*dv.xyz[0] + dv.xyz[1]*dv.xyz[1] + dv.xyz[2]*dv.xyz[2] ;
jj++ ;
}
}
dsum = sqrt(dsum/nvec) ;
fprintf(stderr,"++ RMS distance between tags before = %.2f mm\n" , dsum ) ;
/*-- compute best transformation from mset to dset coords --*/
switch( matrix_type ){
default:
case ROTATION:
rt = DLSQ_rot_trans( nvec , yy , xx , ww ) ; /* in thd_rot3d.c */
break ;
case AFFINE:
rt = DLSQ_affine ( nvec , yy , xx ) ; /* 21 Apr 2003 */
break ;
case ROTSCL:
rt = DLSQ_rotscl ( nvec , yy , xx , (DSET_NZ(dset)==1) ? 2 : 3 ) ;
break ;
}
rtinv = INV_DVECMAT(rt) ;
/*-- check for floating point legality --*/
nval = 0 ;
for( ii=0 ; ii < 3 ; ii++ ){
dsum = rt.vv.xyz[ii] ; nval += thd_floatscan(1,&dsum) ;
for( jj=0 ; jj < 3 ; jj++ ){
dsum = rt.mm.mat[ii][jj] ; nval += thd_floatscan(1,&dsum) ;
}
}
if( nval > 0 ){
fprintf(stderr,"** Floating point errors during calculation\n"
"** of transform matrix and translation vector\n" ) ;
exit(1) ;
}
/*-- check for rotation matrix legality --*/
dsum = DMAT_DET(rt.mm) ;
if( dsum == 0.0 || (matrix_type == ROTATION && fabs(dsum-1.0) > 0.01) ){
fprintf(stderr,"** Invalid transform matrix computed: tags dependent?\n"
"** computed [matrix] and [vector] follow:\n" ) ;
for( ii=0 ; ii < 3 ; ii++ )
fprintf(stderr," [ %10.5f %10.5f %10.5f ] [ %10.5f ] \n",
rt.mm.mat[ii][0],rt.mm.mat[ii][1],rt.mm.mat[ii][2],rt.vv.xyz[ii] );
exit(1) ;
}
/*-- print summary --*/
if( verb ){
fprintf(stderr,"++ Matrix & Vector [Dicom: x=R-L; y=A-P; z=I-S]\n") ;
for( ii=0 ; ii < 3 ; ii++ )
fprintf(stderr," %10.5f %10.5f %10.5f %10.5f\n",
rt.mm.mat[ii][0],rt.mm.mat[ii][1],rt.mm.mat[ii][2],rt.vv.xyz[ii] );
}
if( matrix_type == ROTATION || matrix_type == ROTSCL ){
double theta, costheta , dist , fac=1.0 ;
if( matrix_type == ROTSCL ){
fac = DMAT_DET(rt.mm); fac = fabs(fac);
if( DSET_NZ(dset) == 1 ) fac = sqrt(fac) ;
else fac = cbrt(fac) ;
}
costheta = 0.5 * sqrt(1.0 + DMAT_TRACE(rt.mm)/fac ) ;
theta = 2.0 * acos(costheta) * 180/3.14159265 ;
dist = SIZE_DFVEC3(rt.vv) ;
fprintf(stderr,"++ Total rotation=%.2f degrees; translation=%.2f mm; scaling=%.2f\n",
theta,dist,fac) ;
}
if( mfile ){
FILE * mp ;
if( THD_is_file(mfile) )
fprintf(stderr,"++ Warning: -matvec will overwrite file %s\n",mfile) ;
mp = fopen(mfile,"w") ;
if( mp == NULL ){
fprintf(stderr,"** Can't write to -matvec %s\n",mfile) ;
} else {
for( ii=0 ; ii < 3 ; ii++ )
fprintf(mp," %10.5f %10.5f %10.5f %10.5f\n",
rt.mm.mat[ii][0],rt.mm.mat[ii][1],rt.mm.mat[ii][2],rt.vv.xyz[ii] );
fclose(mp) ;
if( verb ) fprintf(stderr,"++ Wrote matrix+vector to %s\n",mfile) ;
}
}
if( dummy ){
fprintf(stderr,"++ This was a -dummy run: no output dataset\n") ; exit(0) ;
}
/*-- 21 Apr 2003: transformation can be done the old way (a la 3drotate),
or the new way (a la 3dWarp). --*/
#if 0
if( !use_3dWarp ){ /**** the old way ****/
/*-- now must scramble the rotation matrix and translation
vector from Dicom coordinate order to dataset brick order --*/
pp = DBLE_mat_to_dicomm( dset ) ;
ppt = TRANSPOSE_DMAT(pp) ;
rr = DMAT_MUL(ppt,rt.mm) ; rr = DMAT_MUL(rr,pp) ; tt = DMATVEC(ppt,rt.vv) ;
/*-- now create the output dataset by screwing with the input dataset
(this code is adapted from 3drotate.c) --*/
DSET_mallocize(dset) ;
DSET_load( dset ) ; CHECK_LOAD_ERROR(dset) ;
dset->idcode = MCW_new_idcode() ;
dset->dblk->diskptr->storage_mode = STORAGE_BY_BRICK ; /* 14 Jan 2004 */
EDIT_dset_items( dset ,
ADN_prefix , prefix ,
ADN_label1 , prefix ,
ADN_none ) ;
if( !THD_ok_overwrite() &&
(THD_deathcon() && THD_is_file(dset->dblk->diskptr->header_name) )){
fprintf(stderr,
"** Output file %s already exists -- cannot continue!\n",
dset->dblk->diskptr->header_name ) ;
exit(1) ;
}
tross_Make_History( "3dTagalign" , argc,argv , dset ) ;
/*-- if desired, keep old tagset --*/
if( keeptags ){
THD_dfvec3 rv ;
dsum = 0.0 ;
for( jj=ii=0 ; ii < TAGLIST_COUNT(dset->tagset) ; ii++ ){
if( TAG_SET(TAGLIST_SUBTAG(dset->tagset,ii)) ){
rv = DMATVEC( rt.mm , yy[jj] ) ; /* operating on */
rv = ADD_DFVEC3( rt.vv , rv ) ; /* Dicom order */
dv = SUB_DFVEC3( xx[jj] , rv ) ;
dsum += dv.xyz[0]*dv.xyz[0] + dv.xyz[1]*dv.xyz[1]
+ dv.xyz[2]*dv.xyz[2] ;
UNLOAD_DFVEC3( rv , TAG_X( TAGLIST_SUBTAG(dset->tagset,ii) ) ,
TAG_Y( TAGLIST_SUBTAG(dset->tagset,ii) ) ,
TAG_Z( TAGLIST_SUBTAG(dset->tagset,ii) ) ) ;
jj++ ;
}
}
dsum = sqrt(dsum/nvec) ;
fprintf(stderr,"++ RMS distance between tags after = %.2f mm\n" , dsum ) ;
} else {
myXtFree(dset->tagset) ; /* send it to the dustbin */
}
/*-- rotate sub-bricks --*/
if( verb ) fprintf(stderr,"++ computing output BRIK") ;
nvox = DSET_NVOX(dset) ;
nval = DSET_NVALS(dset) ;
fvol = (float *) malloc( sizeof(float) * nvox ) ;
THD_rota_method( MRI_HEPTIC ) ;
clipit = 1 ;
for( ival=0 ; ival < nval ; ival++ ){
/*- get sub-brick out of dataset -*/
EDIT_coerce_type( nvox ,
DSET_BRICK_TYPE(dset,ival),DSET_ARRAY(dset,ival) ,
MRI_float,fvol ) ;
if( clipit ){
register int ii ; register float bb,tt ;
bb = tt = fvol[0] ;
for( ii=1 ; ii < nvox ; ii++ ){
if( fvol[ii] < bb ) bb = fvol[ii] ;
else if( fvol[ii] > tt ) tt = fvol[ii] ;
}
cbot = bb ; ctop = tt ;
}
if( verb && nval < 5 ) fprintf(stderr,".") ;
/*- rotate it -*/
THD_rota_vol_matvec( DSET_NX(dset) , DSET_NY(dset) , DSET_NZ(dset) ,
fabs(DSET_DX(dset)) , fabs(DSET_DY(dset)) ,
fabs(DSET_DZ(dset)) ,
fvol , rr , tt ) ;
if( verb ) fprintf(stderr,".") ;
if( clipit ){
register int ii ; register float bb,tt ;
bb = cbot ; tt = ctop ;
for( ii=0 ; ii < nvox ; ii++ ){
if( fvol[ii] < bb ) fvol[ii] = bb ;
else if( fvol[ii] > tt ) fvol[ii] = tt ;
}
}
if( verb && nval < 5 ) fprintf(stderr,".") ;
/*- put it back into dataset -*/
EDIT_coerce_type( nvox, MRI_float,fvol ,
DSET_BRICK_TYPE(dset,ival),DSET_ARRAY(dset,ival) );
} /* end of loop over sub-brick index */
if( verb ) fprintf(stderr,":") ;
/* save matrix+vector into dataset, too */
UNLOAD_DMAT(rt.mm,matar[0],matar[1],matar[2],
matar[4],matar[5],matar[6],
matar[8],matar[9],matar[10] ) ;
UNLOAD_DFVEC3(rt.vv,matar[3],matar[7],matar[11]) ;
THD_set_atr( dset->dblk, "TAGALIGN_MATVEC", ATR_FLOAT_TYPE, 12, matar ) ;
/* write dataset to disk */
dset->dblk->master_nvals = 0 ; /* in case this was a mastered dataset */
DSET_write(dset) ;
if( verb ) fprintf(stderr,"\n") ;
} else
#endif
{ /**** the new way: use 3dWarp type transformation ****/
THD_3dim_dataset *oset ;
THD_vecmat tran ;
#if 0
DFVEC3_TO_FVEC3( rt.vv , tran.vv ) ;
DMAT_TO_MAT ( rt.mm , tran.mm ) ;
#else
DFVEC3_TO_FVEC3( rtinv.vv , tran.vv ) ;
DMAT_TO_MAT ( rtinv.mm , tran.mm ) ;
#endif
mri_warp3D_method( RMETH ) ;
oset = THD_warp3D_affine( dset, tran, mset, prefix, 0, WARP3D_NEWDSET ) ;
if( oset == NULL ){
fprintf(stderr,"** ERROR: THD_warp3D() fails!\n"); exit(1);
}
tross_Copy_History( dset , oset ) ;
tross_Make_History( "3dTagalign" , argc,argv , oset ) ;
UNLOAD_DMAT(rt.mm,matar[0],matar[1],matar[2],
matar[4],matar[5],matar[6],
matar[8],matar[9],matar[10] ) ;
UNLOAD_DFVEC3(rt.vv,matar[3],matar[7],matar[11]) ;
THD_set_atr( oset->dblk, "TAGALIGN_MATVEC", ATR_FLOAT_TYPE, 12, matar ) ;
/*-- if desired, keep old tagset --*/
if( keeptags ){
THD_dfvec3 rv ;
oset->tagset = myXtNew(THD_usertaglist) ;
*(oset->tagset) = *(dset->tagset) ;
dsum = 0.0 ;
for( jj=ii=0 ; ii < TAGLIST_COUNT(oset->tagset) ; ii++ ){
if( TAG_SET(TAGLIST_SUBTAG(oset->tagset,ii)) ){
rv = DMATVEC( rt.mm , yy[jj] ) ;
rv = ADD_DFVEC3( rt.vv , rv ) ;
dv = SUB_DFVEC3( xx[jj] , rv ) ;
dsum += dv.xyz[0]*dv.xyz[0] + dv.xyz[1]*dv.xyz[1]
+ dv.xyz[2]*dv.xyz[2] ;
UNLOAD_DFVEC3( rv , TAG_X( TAGLIST_SUBTAG(oset->tagset,ii) ) ,
TAG_Y( TAGLIST_SUBTAG(oset->tagset,ii) ) ,
TAG_Z( TAGLIST_SUBTAG(oset->tagset,ii) ) ) ;
jj++ ;
}
}
dsum = sqrt(dsum/nvec) ;
fprintf(stderr,"++ RMS distance between tags after = %.2f mm\n" , dsum ) ;
}
DSET_write(oset) ;
} /* end of 3dWarp-like work */
exit(0) ;
}
MRI_vectim * THD_2dset_to_vectim( THD_3dim_dataset *dset1, byte *mask1 ,
THD_3dim_dataset *dset2, byte *mask2 ,
int ignore )
{
byte *mmmv[2]={NULL, NULL}, *mmmt=NULL;
THD_3dim_dataset *dsetv[2]={NULL, NULL};
MRI_vectim *mrv=NULL ;
int kk2, kk,iv,id, nvals , nvoxv[2]={0,0} , nmaskv[2]={0,0} ;
int *ivvectmp=NULL;
ENTRY("THD_2dset_to_vectim") ;
mmmv[0] = mask1;
mmmv[1] = mask2;
dsetv[0] = dset1;
dsetv[1] = dset2;
for (id=0; id<2;++id) {
if( !ISVALID_DSET(dsetv[id]) ) RETURN(NULL) ;
DSET_load(dsetv[id]) ; if( !DSET_LOADED(dsetv[id]) ) RETURN(NULL) ;
nvoxv[id] = DSET_NVOX(dsetv[id]) ;
}
if (DSET_NVALS(dsetv[0]) != DSET_NVALS(dsetv[1])) {
RETURN(NULL) ;
}
if( ignore < 0 ) ignore = 0 ;
nvals = DSET_NVALS(dsetv[0]) - ignore ; if( nvals <= 0 ) RETURN(NULL) ;
for (id=0; id<2; ++id) {
if( mmmv[id] != NULL ){
nmaskv[id] = THD_countmask( nvoxv[id] , mmmv[id] ) ;/* number to keep */
if( nmaskv[id] <= 0 ) RETURN(NULL) ;
} else {
nmaskv[id] = nvoxv[id] ; /* keep them all */
#pragma omp critical (MALLOC)
mmmv[id] = (byte *)malloc(sizeof(byte)*nmaskv[id]) ;
if( mmmv[id] == NULL ){
ERROR_message("THD_2dset_to_vectim: out of memory") ;
RETURN(NULL) ;
}
memset( mmmv[id] , 1 , sizeof(byte)*nmaskv[id] ) ;
}
}
#pragma omp critical (MALLOC)
mrv = (MRI_vectim *)malloc(sizeof(MRI_vectim)) ;
mrv->nvec = nmaskv[0]+nmaskv[1] ;
mrv->nvals = nvals ;
mrv->ignore = ignore ;
#pragma omp critical (MALLOC)
mrv->ivec = (int *)malloc(sizeof(int)*(nmaskv[0]+nmaskv[1])) ;
#pragma omp critical (MALLOC)
ivvectmp = (int *)malloc(sizeof(int)*(nmaskv[1])) ;
if( mrv->ivec == NULL || ivvectmp == NULL){
ERROR_message("THD_2dset_to_vectim: out of memory") ;
if (mrv->ivec) free(mrv->ivec) ;
if (ivvectmp) free(ivvectmp) ;
free(mrv) ;
if( mmmv[0] != mask1 ) free(mmmv[0]) ;
if( mmmv[1] != mask2 ) free(mmmv[1]) ;
RETURN(NULL) ;
}
#pragma omp critical (MALLOC)
mrv->fvec = (float *)malloc(sizeof(float)*(nmaskv[0]+nmaskv[1])*(size_t)nvals) ;
if( mrv->fvec == NULL ){
ERROR_message("THD_2dset_to_vectim: out of memory") ;
if (ivvectmp) free(ivvectmp) ;
free(mrv->ivec) ; free(mrv) ;
if( mmmv[0] != mask1 ) free(mmmv[0]) ;
if( mmmv[1] != mask2 ) free(mmmv[1]) ;
RETURN(NULL) ;
}
/* store desired voxel time series */
mmmt = mmmv[0];
for( kk=iv=0 ; iv < nvoxv[0] ; iv++ ){
if( mmmt[iv] ) mrv->ivec[kk++] = iv ; /* build index list to 1st dset */
}
mmmt = mmmv[1]; kk2 = 0;
for( iv=0 ; iv < nvoxv[1] ; iv++ ){
if( mmmt[iv] ) {
mrv->ivec[kk++] = iv + nvoxv[0] ;
/* build index list to 2nd dset*/
ivvectmp[kk2++] = iv;
}
}
if( ignore > 0 ){ /* extract 1 at a time, save what we want */
#pragma omp critical (MALLOC)
float *var = (float *)malloc(sizeof(float)*(nvals+ignore)) ;
mmmt = mmmv[0];
for( kk=iv=0 ; iv < nvoxv[0] ; iv++ ){
if( mmmt[iv] == 0 ) continue ;
(void)THD_extract_array( iv , dsetv[0] , 0 , var ) ;
AAmemcpy( VECTIM_PTR(mrv,kk) , var+ignore , sizeof(float)*nvals ) ;
kk++ ;
}
mmmt = mmmv[1];
for( iv=0 ; iv < nvoxv[1] ; iv++ ){
if( mmmt[iv] == 0 ) continue ;
(void)THD_extract_array( iv , dsetv[1] , 0 , var ) ;
AAmemcpy( VECTIM_PTR(mrv,kk) , var+ignore , sizeof(float)*nvals ) ;
kk++ ;
}
free(var) ;
} else { /* do all at once: this way is a lot faster */
THD_extract_many_arrays( nmaskv[0] , mrv->ivec ,
dsetv[0] , mrv->fvec ) ;
THD_extract_many_arrays( nmaskv[1] , ivvectmp,
dsetv[1] , (mrv->fvec+(size_t)nmaskv[0]*(size_t)mrv->nvals) ) ;
}
mrv->nx = DSET_NX(dsetv[0]) + DSET_NX(dsetv[1]);
mrv->dx = fabs(DSET_DX(dsetv[0])) ;
mrv->ny = DSET_NY(dsetv[0]) ; mrv->dy = fabs(DSET_DY(dsetv[0])) ;
mrv->nz = DSET_NZ(dsetv[0]) ; mrv->dz = fabs(DSET_DZ(dsetv[0])) ;
DSET_UNMSEC(dsetv[0]) ; mrv->dt = DSET_TR(dsetv[0]) ;
if( mrv->dt <= 0.0f ) mrv->dt = 1.0f ;
if( mmmv[0] != mask1 ) free(mmmv[0]) ;
if( mmmv[1] != mask2 ) free(mmmv[1]) ;
if (ivvectmp) free(ivvectmp) ;
if (0) {
int ShowThisTs=38001;
float *fff=NULL;
fprintf(stderr,"++ ZSS mrv->nvec = %d, mrv->nvals = %d\n",
mrv->nvec, mrv->nvals);
for( kk=0 ; kk < mrv->nvals; ++kk) {
fff=mrv->fvec+((size_t)mrv->nvals*(size_t)ShowThisTs);
fprintf(stderr," %f \t", *(fff+kk));
}
}
VECTIM_scan(mrv) ; /* 09 Nov 2010 */
RETURN(mrv) ;
}
MRI_vectim * THD_dset_to_vectim_stend( THD_3dim_dataset *dset, byte *mask , int start, int end )
{
byte *mmm=mask ;
MRI_vectim *mrv=NULL ;
int kk,iv , nvals , nvox , nmask ;
ENTRY("THD_dset_to_vectim_stend") ;
if( !ISVALID_DSET(dset) ) RETURN(NULL) ;
DSET_load(dset) ; if( !DSET_LOADED(dset) ) RETURN(NULL) ;
if( start < 0 ) start = 0 ;
if( end < start ) end = DSET_NVALS(dset)-1 ;
nvals = end - start + 1 ; if( nvals <= 0 ) RETURN(NULL) ;
nvox = DSET_NVOX(dset) ;
if( mmm != NULL ){
nmask = THD_countmask( nvox , mmm ) ; /* number to keep */
if( nmask <= 0 ) RETURN(NULL) ;
} else {
nmask = nvox ; /* keep them all */
#pragma omp critical (MALLOC)
mmm = (byte *)malloc(sizeof(byte)*nmask) ;
if( mmm == NULL ){
ERROR_message("THD_dset_to_vectim: out of memory") ;
RETURN(NULL) ;
}
memset( mmm , 1 , sizeof(byte)*nmask ) ;
}
#pragma omp critical (MALLOC)
mrv = (MRI_vectim *)malloc(sizeof(MRI_vectim)) ;
mrv->nvec = nmask ;
mrv->nvals = nvals ;
mrv->ignore = start ;
#pragma omp critical (MALLOC)
mrv->ivec = (int *)malloc(sizeof(int)*nmask) ;
if( mrv->ivec == NULL ){
ERROR_message("THD_dset_to_vectim: out of memory") ;
free(mrv) ; if( mmm != mask ) free(mmm) ;
RETURN(NULL) ;
}
#pragma omp critical (MALLOC)
mrv->fvec = (float *)malloc(sizeof(float)*(size_t)nmask*(size_t)nvals) ;
if( mrv->fvec == NULL ){
ERROR_message("THD_dset_to_vectim: out of memory") ;
free(mrv->ivec) ; free(mrv) ; if( mmm != mask ) free(mmm) ;
RETURN(NULL) ;
}
/* store desired voxel time series */
for( kk=iv=0 ; iv < nvox ; iv++ ){
if( mmm[iv] ) mrv->ivec[kk++] = iv ; /* build index list */
}
if( nvals < DSET_NVALS(dset) ){ /* extract 1 at a time, save what we want */
#pragma omp critical (MALLOC)
float *var = (float *)malloc(sizeof(float)*(DSET_NVALS(dset))) ;
for( kk=iv=0 ; iv < nvox ; iv++ ){
if( mmm[iv] == 0 ) continue ;
(void)THD_extract_array( iv , dset , 0 , var ) ;
AAmemcpy( VECTIM_PTR(mrv,kk) , var+start , sizeof(float)*nvals ) ;
kk++ ;
}
free(var) ;
} else { /* do all at once: this way is a lot faster */
THD_extract_many_arrays( nmask , mrv->ivec , dset , mrv->fvec ) ;
}
mrv->nx = DSET_NX(dset) ; mrv->dx = fabs(DSET_DX(dset)) ;
mrv->ny = DSET_NY(dset) ; mrv->dy = fabs(DSET_DY(dset)) ;
mrv->nz = DSET_NZ(dset) ; mrv->dz = fabs(DSET_DZ(dset)) ;
DSET_UNMSEC(dset) ; mrv->dt = DSET_TR(dset) ;
if( mrv->dt <= 0.0f ) mrv->dt = 1.0f ;
if( mmm != mask ) free(mmm) ;
VECTIM_scan(mrv) ; /* 09 Nov 2010 */
RETURN(mrv) ;
}
MRI_vectim * THD_dset_to_vectim( THD_3dim_dataset *dset, byte *mask , int ignore )
{
byte *mmm=mask ;
MRI_vectim *mrv=NULL ;
int kk,iv , nvals , nvox , nmask ;
size_t ntot ;
ENTRY("THD_dset_to_vectim") ;
if( !ISVALID_DSET(dset) ) RETURN(NULL) ;
DSET_load(dset) ; if( !DSET_LOADED(dset) ) RETURN(NULL) ;
if( ignore < 0 ) ignore = 0 ;
nvals = DSET_NVALS(dset) - ignore ; if( nvals <= 0 ) RETURN(NULL) ;
nvox = DSET_NVOX(dset) ;
if( mmm != NULL ){
nmask = THD_countmask( nvox , mmm ) ; /* number to keep */
if( nmask <= 0 ) RETURN(NULL) ;
} else {
nmask = nvox ; /* keep them all */
#pragma omp critical (MALLOC)
mmm = (byte *)malloc(sizeof(byte)*nmask) ;
if( mmm == NULL ){
ERROR_message("THD_dset_to_vectim: out of memory") ;
RETURN(NULL) ;
}
memset( mmm , 1 , sizeof(byte)*nmask ) ;
}
#pragma omp critical (MALLOC)
mrv = (MRI_vectim *)malloc(sizeof(MRI_vectim)) ;
mrv->nvec = nmask ;
mrv->nvals = nvals ;
mrv->ignore = ignore ;
#pragma omp critical (MALLOC)
mrv->ivec = (int *)malloc(sizeof(int)*nmask) ;
if( mrv->ivec == NULL ){
ERROR_message("THD_dset_to_vectim: out of memory") ;
free(mrv) ; if( mmm != mask ) free(mmm) ;
RETURN(NULL) ;
}
ntot = sizeof(float)*(size_t)nmask*(size_t)nvals ;
#pragma omp critical (MALLOC)
mrv->fvec = (float *)malloc(ntot) ;
if( mrv->fvec == NULL ){
ERROR_message("THD_dset_to_vectim: out of memory -- tried to get %lld bytes",(long long)ntot) ;
free(mrv->ivec) ; free(mrv) ; if( mmm != mask ) free(mmm) ;
RETURN(NULL) ;
} else if( ntot > 1000000000 ){
INFO_message("THD_dset_to_vectim: allocated %lld bytes",(long long)ntot) ;
}
/* store desired voxel time series */
STATUS("create index list") ;
for( kk=iv=0 ; iv < nvox ; iv++ ){
if( mmm[iv] ) mrv->ivec[kk++] = iv ; /* build index list */
}
if( ignore > 0 ){ /* extract 1 at a time, save what we want */
#pragma omp critical (MALLOC)
float *var = (float *)malloc(sizeof(float)*(nvals+ignore)) ;
STATUS("ignore > 0 --> extracting one at a time") ;
for( kk=iv=0 ; iv < nvox ; iv++ ){
if( mmm[iv] == 0 ) continue ;
(void)THD_extract_array( iv , dset , 0 , var ) ;
AAmemcpy( VECTIM_PTR(mrv,kk) , var+ignore , sizeof(float)*nvals ) ;
kk++ ;
}
free(var) ;
} else { /* do all at once: this way is a lot faster */
STATUS("ignore==0 --> extracting all at once") ;
THD_extract_many_arrays( nmask , mrv->ivec , dset , mrv->fvec ) ;
}
STATUS("setting parameters in vectim header") ;
mrv->nx = DSET_NX(dset) ; mrv->dx = fabs(DSET_DX(dset)) ;
mrv->ny = DSET_NY(dset) ; mrv->dy = fabs(DSET_DY(dset)) ;
mrv->nz = DSET_NZ(dset) ; mrv->dz = fabs(DSET_DZ(dset)) ;
DSET_UNMSEC(dset) ; mrv->dt = DSET_TR(dset) ;
if( mrv->dt <= 0.0f ) mrv->dt = 1.0f ;
if( mmm != mask ){
STATUS("free(mmm)") ;
free(mmm) ;
}
STATUS("VECTIM_scan()") ;
VECTIM_scan(mrv) ; /* 09 Nov 2010 */
RETURN(mrv) ;
}
MRI_vectim * THD_dset_censored_to_vectim( THD_3dim_dataset *dset,
byte *mask , int nkeep , int *keep )
{
byte *mmm=mask ;
MRI_vectim *mrv=NULL ;
int kk,iv,jj , nvals , nvox , nmask ;
ENTRY("THD_dset_censored_to_vectim") ;
if( !ISVALID_DSET(dset) ) RETURN(NULL) ;
if( nkeep <= 0 || keep == NULL ){
mrv = THD_dset_to_vectim( dset , mask , 0 ) ;
RETURN(mrv) ;
}
if( ! THD_subset_loaded(dset,nkeep,keep) ){
DSET_load(dset) ; if( !DSET_LOADED(dset) ) RETURN(NULL) ;
}
nvals = nkeep ;
nvox = DSET_NVOX(dset) ;
if( mmm != NULL ){
nmask = THD_countmask( nvox , mmm ) ; /* number to keep */
if( nmask <= 0 ) RETURN(NULL) ;
} else {
nmask = nvox ; /* keep them all */
#pragma omp critical (MALLOC)
mmm = (byte *)malloc(sizeof(byte)*nmask) ;
if( mmm == NULL ){
ERROR_message("THD_dset_to_vectim: out of memory") ;
RETURN(NULL) ;
}
memset( mmm , 1 , sizeof(byte)*nmask ) ;
}
#pragma omp critical (MALLOC)
mrv = (MRI_vectim *)malloc(sizeof(MRI_vectim)) ;
mrv->nvec = nmask ;
mrv->nvals = nvals ;
mrv->ignore = 0 ;
#pragma omp critical (MALLOC)
mrv->ivec = (int *)malloc(sizeof(int)*nmask) ;
if( mrv->ivec == NULL ){
ERROR_message("THD_dset_to_vectim: out of memory") ;
free(mrv) ; if( mmm != mask ) free(mmm) ;
RETURN(NULL) ;
}
#pragma omp critical (MALLOC)
mrv->fvec = (float *)malloc(sizeof(float)*(size_t)nmask*(size_t)nvals) ;
if( mrv->fvec == NULL ){
ERROR_message("THD_dset_to_vectim: out of memory") ;
free(mrv->ivec) ; free(mrv) ; if( mmm != mask ) free(mmm) ;
RETURN(NULL) ;
}
/* store desired voxel time series */
for( kk=iv=0 ; iv < nvox ; iv++ ){
if( mmm[iv] ) mrv->ivec[kk++] = iv ; /* build index list */
}
#pragma omp critical (MALLOC)
{ float *var = (float *)malloc(sizeof(float)*DSET_NVALS(dset)) ;
float *vpt ;
for( kk=iv=0 ; iv < nvox ; iv++ ){
if( mmm[iv] == 0 ) continue ;
vpt = VECTIM_PTR(mrv,kk) ; kk++ ;
if( nkeep > 1 ){
(void)THD_extract_array( iv , dset , 0 , var ) ;
for( jj=0 ; jj < nkeep ; jj++ ) vpt[jj] = var[keep[jj]] ;
} else {
vpt[0] = THD_get_float_value(iv,keep[0],dset) ;
}
}
free(var) ;
}
mrv->nx = DSET_NX(dset) ; mrv->dx = fabs(DSET_DX(dset)) ;
mrv->ny = DSET_NY(dset) ; mrv->dy = fabs(DSET_DY(dset)) ;
mrv->nz = DSET_NZ(dset) ; mrv->dz = fabs(DSET_DZ(dset)) ;
DSET_UNMSEC(dset) ; mrv->dt = DSET_TR(dset) ;
if( mrv->dt <= 0.0f ) mrv->dt = 1.0f ;
if( mmm != mask ) free(mmm) ;
VECTIM_scan(mrv) ; /* 09 Nov 2010 */
RETURN(mrv) ;
}
int main( int argc , char *argv[] )
{
THD_3dim_dataset *inset=NULL , *jnset=NULL , *outset , *wset=NULL;
int ncode=0 , code[MAX_NCODE] , iarg=1 , ii ;
MCW_cluster *nbhd=NULL ;
byte *mask=NULL ; int mask_nx=0,mask_ny=0,mask_nz=0 , automask=0 ;
char *prefix="./localstat" ;
int ntype=0 ; float na=0.0f,nb=0.0f,nc=0.0f ;
double hist_pow=0.3333333 ; int hist_nbin=0 ;
float hbot1=1.0f , htop1=-1.0f ; int hbot1_perc=0, htop1_perc=0 ;
float hbot2=1.0f , htop2=-1.0f ; int hbot2_perc=0, htop2_perc=0 ;
/*---- for the clueless who wish to become clued-in ----*/
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf(
"Usage: 3dLocalBistat [options] dataset1 dataset2\n"
"\n"
"This program computes statistics between 2 datasets,\n"
"at each voxel, based on a local neighborhood of that voxel.\n"
" - The neighborhood is defined by the '-nbhd' option.\n"
" - Statistics to be calculated are defined by the '-stat' option(s).\n"
" - The 2 input datasets should have the same number of sub-bricks.\n"
" - OR dataset1 should have 1 sub-brick and dataset2 can have more than 1:\n"
" - In which case, the statistics of dataset2 against dataset1 are\n"
" calculated for the #0 sub-brick of dataset1 against each sub-brick\n"
" of dataset2.\n"
"\n"
"OPTIONS\n"
"-------\n"
" -nbhd 'nnn' = The string 'nnn' defines the region around each\n"
" voxel that will be extracted for the statistics\n"
" calculation. The format of the 'nnn' string are:\n"
" * 'SPHERE(r)' where 'r' is the radius in mm;\n"
" the neighborhood is all voxels whose center-to-\n"
" center distance is less than or equal to 'r'.\n"
" ** A negative value for 'r' means that the region\n"
" is calculated using voxel indexes rather than\n"
" voxel dimensions; that is, the neighborhood\n"
" region is a \"sphere\" in voxel indexes of\n"
" \"radius\" abs(r).\n"
" * 'RECT(a,b,c)' is a rectangular block which\n"
" proceeds plus-or-minus 'a' mm in the x-direction,\n"
" 'b' mm in the y-direction, and 'c' mm in the\n"
" z-direction. The correspondence between the\n"
" dataset xyz axes and the actual spatial orientation\n"
" can be determined by using program 3dinfo.\n"
" ** A negative value for 'a' means that the region\n"
" extends plus-and-minus abs(a) voxels in the\n"
" x-direction, rather than plus-and-minus a mm.\n"
" Mutatis mutandum for negative 'b' and/or 'c'.\n"
" * 'RHDD(r)' is a rhombic dodecahedron of 'radius' r.\n"
" * 'TOHD(r)' is a truncated octahedron of 'radius' r.\n"
"\n"
" -stat sss = Compute the statistic named 'sss' on the values\n"
" extracted from the region around each voxel:\n"
" * pearson = Pearson correlation coefficient\n"
" * spearman = Spearman correlation coefficient\n"
" * quadrant = Quadrant correlation coefficient\n"
" * mutinfo = Mutual Information\n"
" * normuti = Normalized Mutual Information\n"
" * jointent = Joint entropy\n"
" * hellinger= Hellinger metric\n"
" * crU = Correlation ratio (Unsymmetric)\n"
" * crM = Correlation ratio (symmetrized by Multiplication)\n"
" * crA = Correlation ratio (symmetrized by Addition)\n"
" * L2slope = slope of least-squares (L2) linear regression of\n"
" the data from dataset1 vs. the dataset2\n"
" (i.e., d2 = a + b*d1 ==> this is 'b')\n"
" * L1slope = slope of least-absolute-sum (L1) linear regression\n"
" of the data from dataset1 vs. the dataset2\n"
" * num = number of the values in the region:\n"
" with the use of -mask or -automask,\n"
" the size of the region around any given\n"
" voxel will vary; this option lets you\n"
" map that size.\n"
#if 0
" * ncd = Normalized Compression Distance (zlib; very slow)\n"
#endif
#if 0 /* activate after testing */
" * euclidian = Euclidian distance.\n"
" * cityblock = City Block distance.\n"
#endif
" * ALL = all of the above, in that order\n"
" More than one '-stat' option can be used.\n"
"\n"
" -mask mset = Read in dataset 'mset' and use the nonzero voxels\n"
" therein as a mask. Voxels NOT in the mask will\n"
" not be used in the neighborhood of any voxel. Also,\n"
" a voxel NOT in the mask will have its statistic(s)\n"
" computed as zero (0).\n"
" -automask = Compute the mask as in program 3dAutomask.\n"
" -mask and -automask are mutually exclusive: that is,\n"
" you can only specify one mask.\n"
" -weight ws = Use dataset 'ws' as a weight. Only applies to 'pearson'.\n"
"\n"
" -prefix ppp = Use string 'ppp' as the prefix for the output dataset.\n"
" The output dataset is always stored as floats.\n"
"\n"
"ADVANCED OPTIONS\n"
"----------------\n"
" -histpow pp = By default, the number of bins in the histogram used\n"
" for calculating the Hellinger, Mutual Information,\n"
" and Correlation Ratio statistics is n^(1/3), where n\n"
" is the number of data points in the -nbhd mask. You\n"
" can change that exponent to 'pp' with this option.\n"
" -histbin nn = Or you can just set the number of bins directly to 'nn'.\n"
" -hclip1 a b = Clip dataset1 to lie between values 'a' and 'b'. If 'a'\n"
" and 'b' end in '%%', then these values are percentage\n"
" points on the cumulative histogram.\n"
" -hclip2 a b = Similar to '-hclip1' for dataset2.\n"
"\n"
"-----------------------------\n"
"Author: RWCox - October 2006.\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
/*---- official startup ---*/
PRINT_VERSION("3dLocalBistat"); mainENTRY("3dLocalBistat main"); machdep();
AFNI_logger("3dLocalBistat",argc,argv) ;
/*---- loop over options ----*/
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-hclip1") == 0 ){
char *cpt1, *cpt2 ;
if( ++iarg >= argc-1 ) ERROR_exit("need 2 arguments after -hclip1") ;
hbot1 = (float)strtod(argv[iarg],&cpt1) ; iarg++ ;
htop1 = (float)strtod(argv[iarg],&cpt2) ;
if( hbot1 >= htop1 ) ERROR_exit("illegal values after -hclip1") ;
if( *cpt1 == '%' ){
hbot1_perc = 1 ; hbot1 = (int)rint((double)hbot1) ;
if( hbot1 < 0 || hbot1 > 99 ) ERROR_exit("illegal bot percentage after -hclip1") ;
}
if( *cpt2 == '%' ){
htop1_perc = 1 ; htop1 = (int)rint((double)htop1) ;
if( htop1 < 1 || htop1 > 100 ) ERROR_exit("illegal top percentage after -hclip1") ;
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-hclip2") == 0 ){
char *cpt1, *cpt2 ;
if( ++iarg >= argc-1 ) ERROR_exit("need 2 arguments after -hclip2") ;
hbot2 = (float)strtod(argv[iarg],&cpt1) ; iarg++ ;
htop2 = (float)strtod(argv[iarg],&cpt2) ;
if( hbot2 >= htop2 ) ERROR_exit("illegal values after -hclip2") ;
if( *cpt1 == '%' ){
hbot2_perc = 1 ; hbot2 = (int)rint((double)hbot2) ;
if( hbot2 < 0 || hbot2 > 99 ) ERROR_exit("illegal bot percentage after -hclip2") ;
}
if( *cpt2 == '%' ){
htop2_perc = 1 ; htop2 = (int)rint((double)htop2) ;
if( htop2 < 1 || htop2 > 100 ) ERROR_exit("illegal top percentage after -hclip2") ;
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-histpow") == 0 ){
if( ++iarg >= argc ) ERROR_exit("no argument after '%s'!",argv[iarg-1]) ;
hist_pow = strtod(argv[iarg],NULL) ;
if( hist_pow <= 0.0 || hist_pow > 0.5 ){
WARNING_message("Illegal value after -histpow"); hist_pow = 0.33333;
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-histbin") == 0 ){
if( ++iarg >= argc ) ERROR_exit("no argument after '%s'!",argv[iarg-1]) ;
hist_nbin = (int)strtod(argv[iarg],NULL) ;
if( hist_nbin <= 1 ) WARNING_message("Illegal value after -histbin");
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( strcmp(argv[iarg],"-mask") == 0 ){
THD_3dim_dataset *mset ; int mmm ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '-mask'") ;
if( 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_delete(mset) ;
if( mask == NULL ) ERROR_exit("Can't make mask from dataset '%s'",argv[iarg]) ;
mmm = THD_countmask( mask_nx*mask_ny*mask_nz , mask ) ;
INFO_message("Number of voxels in mask = %d",mmm) ;
if( mmm < 2 ) ERROR_exit("Mask is too small to process") ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-weight") == 0 ){ /* 14 Aug 2007 */
if( ++iarg >= argc ) ERROR_exit("Need argument after '-weight'") ;
if( wset != NULL ) ERROR_exit("Can't have two weight inputs") ;
wset = THD_open_dataset( argv[iarg] ) ;
CHECK_OPEN_ERROR(wset,argv[iarg]) ;
DSET_load(wset) ; CHECK_LOAD_ERROR(wset) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-automask") == 0 ){
if( mask != NULL ) ERROR_exit("Can't have -automask and -mask") ;
automask = 1 ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-stat") == 0 ){
char *cpt ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '-stat'") ;
cpt = argv[iarg] ; if( *cpt == '-' ) cpt++ ;
if( strcasecmp(cpt,"pearson") == 0 ) code[ncode++] = NBISTAT_PEARSON_CORR ;
else if( strcasecmp(cpt,"spearman") == 0 ) code[ncode++] = NBISTAT_SPEARMAN_CORR;
else if( strcasecmp(cpt,"quadrant") == 0 ) code[ncode++] = NBISTAT_QUADRANT_CORR;
else if( strcasecmp(cpt,"mutinfo") == 0 ) code[ncode++] = NBISTAT_MUTUAL_INFO ;
else if( strcasecmp(cpt,"normuti") == 0 ) code[ncode++] = NBISTAT_NORMUT_INFO ;
else if( strcasecmp(cpt,"jointent") == 0 ) code[ncode++] = NBISTAT_JOINT_ENTROPY;
else if( strcasecmp(cpt,"hellinger")== 0 ) code[ncode++] = NBISTAT_HELLINGER ;
else if( strcasecmp(cpt,"crU") == 0 ) code[ncode++] = NBISTAT_CORR_RATIO_U ;
else if( strcasecmp(cpt,"crM") == 0 ) code[ncode++] = NBISTAT_CORR_RATIO_M ;
else if( strcasecmp(cpt,"crA") == 0 ) code[ncode++] = NBISTAT_CORR_RATIO_A ;
else if( strcasecmp(cpt,"L2slope") == 0 ) code[ncode++] = NBISTAT_L2SLOPE ;
else if( strcasecmp(cpt,"L1slope") == 0 ) code[ncode++] = NBISTAT_L1SLOPE ;
else if( strcasecmp(cpt,"num") == 0 ) code[ncode++] = NBISTAT_NUM ;
#if 0
else if( strcasecmp(cpt,"ncd") == 0 ) code[ncode++] = NBISTAT_NCD ;
#endif
#if 0 /* activate after testing */
else if( strcasecmp(cpt,"euclidian") == 0 )
code[ncode++] = NBISTAT_EUCLIDIAN_DIST ;
else if( strcasecmp(cpt,"cityblock") == 0 )
code[ncode++] = NBISTAT_CITYBLOCK_DIST ;
#endif
else if( strcasecmp(cpt,"ALL") == 0 ){
code[ncode++] = NBISTAT_PEARSON_CORR ; code[ncode++] = NBISTAT_SPEARMAN_CORR;
code[ncode++] = NBISTAT_QUADRANT_CORR; code[ncode++] = NBISTAT_MUTUAL_INFO ;
code[ncode++] = NBISTAT_NORMUT_INFO ; code[ncode++] = NBISTAT_JOINT_ENTROPY;
code[ncode++] = NBISTAT_HELLINGER ; code[ncode++] = NBISTAT_CORR_RATIO_U ;
code[ncode++] = NBISTAT_CORR_RATIO_M ; code[ncode++] = NBISTAT_CORR_RATIO_A ;
code[ncode++] = NBISTAT_L2SLOPE ; code[ncode++] = NBISTAT_L1SLOPE ;
code[ncode++] = NBISTAT_NUM ;
#if 0
code[ncode++] = NBISTAT_NCD ;
#endif
#if 0 /* activate after testing */
code[ncode++] = NBISTAT_EUCLIDIAN_DIST;
code[ncode++] = NBISTAT_CITYBLOCK_DIST;
#endif
}
else
ERROR_exit("-stat '%s' is an unknown statistic type",argv[iarg]) ;
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 ) ;
if( na == 0.0f ) ERROR_exit("Can't have a SPHERE of radius 0") ;
ntype = NTYPE_SPHERE ;
} 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 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 {
ERROR_exit("Unknown -nbhd shape: '%s'",cpt) ;
}
iarg++ ; continue ;
}
ERROR_exit("Unknown option '%s'",argv[iarg]) ;
} /*--- end of loop over options ---*/
/*---- check for stupid user inputs ----*/
if( ncode <= 0 ) ERROR_exit("No '-stat' options given?") ;
if( ntype <= 0 ) ERROR_exit("No '-nbhd' option given?!") ;
/*---- deal with input datasets ----*/
if( iarg > argc-1 ) ERROR_exit("No first input dataset on command line?") ;
inset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(inset,argv[iarg]) ;
iarg++ ;
if( iarg > argc-1 ) ERROR_exit("No second input dataset on command line?") ;
jnset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(jnset,argv[iarg]) ;
if( jnset == NULL ) ERROR_exit("Can't open dataset '%s'",argv[iarg]) ;
if( DSET_NVOX(jnset) != DSET_NVOX(inset) )
ERROR_exit("Input datasets have different numbers of voxels!?");
if( DSET_NVALS(jnset) != DSET_NVALS(inset) ){
if( DSET_NVALS(inset) > 1 ){
ERROR_exit("Input datasets have different numbers of sub-bricks!?");
} else {
INFO_message("first input dataset has 1 sub-brick, second has %d",DSET_NVALS(jnset)) ;
}
}
DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ;
DSET_load(jnset) ; CHECK_LOAD_ERROR(jnset) ;
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 ){
int mmm , nvox ; byte *jask ;
mask = THD_automask( inset ) ;
if( mask == NULL )
ERROR_message("Can't create -automask from input dataset #1?") ;
jask = THD_automask( jnset ) ;
if( jask == NULL )
ERROR_message("Can't create -automask from input dataset #2?") ;
nvox = DSET_NVOX(inset) ;
for( ii=0 ; ii < nvox ; ii++ ) mask[ii] = (mask[ii] || jask[ii]) ;
free(jask) ;
mmm = THD_countmask( nvox , mask ) ;
INFO_message("Number of voxels in dual automask = %d",mmm) ;
if( mmm < 11 ) ERROR_exit("Automask is too small to process") ;
}
if( wset != NULL ){ /* 14 Aug 2007 */
MRI_IMAGE *wim ; float *war ;
if( DSET_NVOX(wset) != DSET_NVOX(inset) )
ERROR_exit("-weight dataset mismatch with input datasets!") ;
wim = mri_scale_to_float( DSET_BRICK_FACTOR(wset,0), DSET_BRICK(wset,0) );
war = MRI_FLOAT_PTR(wim) ;
DSET_delete(wset) ;
if( mask != NULL ){
int nvox = DSET_NVOX(inset) ;
for( ii=0 ; ii < nvox ; ii++ ) if( !mask[ii] ) war[ii] = 0.0f ;
}
mri_bistat_setweight( wim ) ; mri_free(wim) ;
}
/*---- create neighborhood -----*/
switch( ntype ){
default:
ERROR_exit("WTF? ntype=%d",ntype) ;
case NTYPE_SPHERE:{
float dx , dy , dz ;
if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; }
else { dx = fabsf(DSET_DX(inset)) ;
dy = fabsf(DSET_DY(inset)) ;
dz = fabsf(DSET_DZ(inset)) ; }
nbhd = MCW_spheremask( dx,dy,dz , na ) ;
}
break ;
case NTYPE_RHDD:{
float dx , dy , dz ;
if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; }
else { dx = fabsf(DSET_DX(inset)) ;
dy = fabsf(DSET_DY(inset)) ;
dz = fabsf(DSET_DZ(inset)) ; }
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(inset)) ;
dy = fabsf(DSET_DY(inset)) ;
dz = fabsf(DSET_DZ(inset)) ; }
nbhd = MCW_tohdmask( 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(inset));
if( nb < 0.0f ){ dy = 1.0f; nb = -nb; } else dy = fabsf(DSET_DY(inset));
if( nc < 0.0f ){ dz = 1.0f; nc = -nc; } else dz = fabsf(DSET_DZ(inset));
nbhd = MCW_rectmask( dx,dy,dz , na,nb,nc ) ;
}
break ;
}
INFO_message("Neighborhood comprises %d voxels",nbhd->num_pt) ;
if( hist_nbin <= 1 ) hist_nbin = (int)pow((double)nbhd->num_pt,hist_pow) ;
if( hist_nbin <= 1 ) hist_nbin = 2 ;
INFO_message("2D histogram size = %d",hist_nbin) ;
set_2Dhist_hbin( hist_nbin ) ;
if( hbot1_perc || htop1_perc ){
MRI_IMAGE *fim ; float perc[101] ;
fim = THD_median_brick(inset) ;
mri_percents(fim,100,perc) ; mri_free(fim) ;
if( hbot1_perc ) hbot1 = perc[(int)hbot1] ;
if( htop1_perc ) htop1 = perc[(int)htop1] ;
INFO_message("Clipping dataset '%s' between %g and %g" ,
DSET_BRIKNAME(inset),hbot1,htop1 ) ;
}
if( hbot2_perc || htop2_perc ){
MRI_IMAGE *fim ; float perc[101] ;
fim = THD_median_brick(jnset) ;
mri_percents(fim,100,perc) ; mri_free(fim) ;
if( hbot2_perc ) hbot2 = perc[(int)hbot2] ;
if( htop2_perc ) htop2 = perc[(int)htop2] ;
INFO_message("Clipping dataset '%s' between %g and %g" ,
DSET_BRIKNAME(jnset),hbot2,htop2 ) ;
}
mri_nbistat_setclip( hbot1,htop1 , hbot2,htop2 ) ;
/*---- actually do some work for a change ----*/
THD_localbistat_verb(1) ;
outset = THD_localbistat( inset,jnset , mask , nbhd , ncode , code ) ;
DSET_unload(inset) ; DSET_unload(jnset) ;
if( outset == NULL ) ERROR_exit("Function THD_localbistat() fails?!") ;
EDIT_dset_items( outset , ADN_prefix,prefix , ADN_none ) ;
tross_Copy_History( inset , outset ) ;
tross_Make_History( "3dLocalBistat" , argc,argv , outset ) ;
#if 1
{ char *lcode[66] , lll[66] ;
lcode[0] = "Rank cor" ;
lcode[1] = "Quad cor" ;
lcode[2] = "Pear cor" ;
lcode[3] = "MI" ;
lcode[4] = "NMI" ;
lcode[5] = "Jnt Entropy" ;
lcode[6] = "Hlngr metric" ;
lcode[7] = "CorRat Sym*" ;
lcode[8] = "CorRat Sym+" ;
lcode[9] = "CorRatUnsym" ;
lcode[10]= "Number" ;
lcode[11]= "NCD" ;
lcode[12]= "Euclidian Dist";
lcode[13]= "CityBlock Dist";
if( DSET_NVALS(inset) == 1 ){
for( ii=0 ; ii < DSET_NVALS(outset) ; ii++ )
EDIT_dset_items( outset ,
ADN_brick_label_one+ii, lcode[code[ii%ncode]-NBISTAT_BASE],
ADN_none ) ;
} else {
for( ii=0 ; ii < DSET_NVALS(outset) ; ii++ ){
sprintf(lll,"%s[%d]",lcode[code[ii%ncode]-NBISTAT_BASE],(ii/ncode)) ;
EDIT_dset_items( outset , ADN_brick_label_one+ii,lll, ADN_none ) ;
}
}
}
#endif
DSET_write( outset ) ;
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) ;
}
int main(int argc, char *argv[]) {
int i,j,k,m,n,aa,ii,jj,kk,mm,rr;
int iarg;
int nmask1=0;
int nmask2=0;
THD_3dim_dataset *insetFA = NULL, *insetV1 = NULL,
*insetMD = NULL, *insetL1 = NULL;
THD_3dim_dataset *insetEXTRA=NULL;
THD_3dim_dataset *mset2=NULL;
THD_3dim_dataset *mset1=NULL;
THD_3dim_dataset *outsetMAP=NULL, *outsetMASK=NULL;
char *prefix="tracky";
int LOG_TYPE=0;
char in_FA[300];
char in_V1[300];
char in_MD[300];
char in_L1[300];
int EXTRAFILE=0; // switch for whether other file is input as WM map
char OUT_bin[300];
char OUT_tracstat[300];
char prefix_mask[300];
char prefix_map[300];
// FACT algopts
FILE *fout0;
float MinFA=0.2,MaxAngDeg=45,MinL=20.0;
float MaxAng;
int SeedPerV[3]={2,2,2};
int ArrMax=0;
float tempvmagn;
int Nvox=-1; // tot number vox
int Dim[3]={0,0,0}; // dim in each dir
int Nseed=0,M=30,bval=1000;
int DimSeed[3]; // number of seeds there will be
float Ledge[3]; // voxel edge lengths
int *ROI1, *ROI2;
short int *temp_arr;
char *temp_byte;
int **Tforw, **Tback;
int **Ttot;
float **flTforw, **flTback;
float ****coorded;
int ****INDEX;
int len_forw, len_back; // int count of num of squares through
float phys_forw[1], phys_back[1];
int idx;
float ave_tract_len, ave_tract_len_phys;
int inroi1, inroi2, KEEPIT; // switches for detecting
int in[3]; // to pass to trackit
float physin[3]; // also for trackit, physical loc,
int totlen;
float totlen_phys;
int Numtract;
int READS_in;
float READS_fl;
int end[2][3];
int test_ind[2][3];
int roi3_ct=0, id=0;
float roi3_mu_MD = 0.,roi3_mu_RD = 0.,roi3_mu_L1 = 0.,roi3_mu_FA = 0.;
float roi3_sd_MD = 0.,roi3_sd_RD = 0.,roi3_sd_L1 = 0.,roi3_sd_FA = 0.;
float tempMD,tempFA,tempRD,tempL1;
char dset_or[4] = "RAI";
THD_3dim_dataset *dsetn;
int TV_switch[3] = {0,0,0};
TAYLOR_BUNDLE *tb=NULL;
TAYLOR_TRACT *tt=NULL;
char *mode = "NI_fast_binary";
NI_element *nel=NULL;
int dump_opts=0;
tv_io_header header1 = {.id_string = "TRACK\0",
.origin = {0,0,0},
.n_scalars = 3,
.scal_n[0] = "FA",
.scal_n[1] = "MD",
.scal_n[2] = "L1",
.n_properties = 0,
.vox_to_ras = {{0.,0.,0.,0.},{0.,0.,0.,0.},
{0.,0.,0.,0.},{0.,0.,0.,0.}},
// reset this later based on actual data set
.voxel_order = "RAI\0",
.invert_x = 0,
.invert_y = 0,
.invert_z = 0,
.swap_xy = 0,
.swap_yz = 0,
.swap_zx = 0,
.n_count = 0,
.version = 2,
.hdr_size = 1000};
// for testing names...
char *postfix[4]={"+orig.HEAD\0",".nii.gz\0",".nii\0","+tlrc.HEAD\0"};
int FOUND =-1;
int RECORD_ORIG = 0;
float Orig[3] = {0.0,0.0,0.0};
mainENTRY("3dTrackID"); machdep();
// ****************************************************************
// ****************************************************************
// load AFNI stuff
// ****************************************************************
// ****************************************************************
INFO_message("version: MU");
/** scan args **/
if (argc == 1) { usage_TrackID(1); exit(0); }
iarg = 1;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 ||
strcmp(argv[iarg],"-h") == 0 ) {
usage_TrackID(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
if( strcmp(argv[iarg],"-verb") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need argument after '-verb'") ;
set_tract_verb(atoi(argv[iarg]));
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-write_opts") == 0) {
dump_opts=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-rec_orig") == 0) {
RECORD_ORIG=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-tract_out_mode") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need argument after '-tract_out_mode'") ;
if (strcmp(argv[iarg], "NI_fast_binary") &&
strcmp(argv[iarg], "NI_fast_text") &&
strcmp(argv[iarg], "NI_slow_binary") &&
strcmp(argv[iarg], "NI_slow_text") ) {
ERROR_message("Bad value (%s) for -tract_out_mode",argv[iarg]);
exit(1);
}
mode = argv[iarg];
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-mask1") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-mask1'") ;
mset1 = THD_open_dataset( argv[iarg] ) ;
if( mset1 == NULL )
ERROR_exit("Can't open mask1 dataset '%s'", argv[iarg]) ;
DSET_load(mset1) ; CHECK_LOAD_ERROR(mset1) ;
nmask1 = DSET_NVOX(mset1) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-mask2") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-mask2'") ;
mset2 = THD_open_dataset( argv[iarg] ) ;
if( mset2 == NULL )
ERROR_exit("Can't open mask2 dataset '%s'",
argv[iarg]) ;
DSET_load(mset2) ; CHECK_LOAD_ERROR(mset2) ;
nmask2 = DSET_NVOX(mset2) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-prefix") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-prefix'");
prefix = strdup(argv[iarg]) ;
if( !THD_filename_ok(prefix) )
ERROR_exit("Illegal name after '-prefix'");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-input") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-input'");
for( i=0 ; i<4 ; i++) {
sprintf(in_FA,"%s_FA%s", argv[iarg],postfix[i]);
if(THD_is_ondisk(in_FA)) {
FOUND = i;
break;
}
}
insetFA = THD_open_dataset(in_FA) ;
if( (insetFA == NULL ) || (FOUND==-1))
ERROR_exit("Can't open dataset '%s': for FA.",in_FA);
DSET_load(insetFA) ; CHECK_LOAD_ERROR(insetFA) ;
Nvox = DSET_NVOX(insetFA) ;
Dim[0] = DSET_NX(insetFA); Dim[1] = DSET_NY(insetFA);
Dim[2] = DSET_NZ(insetFA);
Ledge[0] = fabs(DSET_DX(insetFA)); Ledge[1] = fabs(DSET_DY(insetFA));
Ledge[2] = fabs(DSET_DZ(insetFA));
Orig[0] = DSET_XORG(insetFA); Orig[1] = DSET_YORG(insetFA);
Orig[2] = DSET_ZORG(insetFA);
// check tot num vox match (as proxy for dims...)
if( (Nvox != nmask1) || (Nvox != nmask2) )
ERROR_exit("Input dataset does not match both mask volumes!");
// this stores the original data file orientation for later use,
// as well since we convert everything to RAI temporarily, as
// described below
header1.voxel_order[0]=ORIENT_typestr[insetFA->daxes->xxorient][0];
header1.voxel_order[1]=ORIENT_typestr[insetFA->daxes->yyorient][0];
header1.voxel_order[2]=ORIENT_typestr[insetFA->daxes->zzorient][0];
for( i=0 ; i<3 ; i++) {
header1.dim[i] = Dim[i];
header1.voxel_size[i] = Ledge[i];
// will want this when outputting file later for TrackVis.
TV_switch[i] = !(dset_or[i]==header1.voxel_order[i]);
}
dset_or[3]='\0';
FOUND = -1;
for( i=0 ; i<4 ; i++) {
sprintf(in_V1,"%s_V1%s", argv[iarg],postfix[i]);
if(THD_is_ondisk(in_V1)) {
FOUND = i;
break;
}
}
insetV1 = THD_open_dataset(in_V1);
if( insetV1 == NULL )
ERROR_exit("Can't open dataset '%s':V1",in_V1);
DSET_load(insetV1) ; CHECK_LOAD_ERROR(insetV1) ;
FOUND = -1;
for( i=0 ; i<4 ; i++) {
sprintf(in_L1,"%s_L1%s", argv[iarg],postfix[i]);
if(THD_is_ondisk(in_L1)) {
FOUND = i;
break;
}
}
insetL1 = THD_open_dataset(in_L1);
if( insetL1 == NULL )
ERROR_exit("Can't open dataset '%s':L1",in_L1);
DSET_load(insetL1) ; CHECK_LOAD_ERROR(insetL1) ;
FOUND = -1;
for( i=0 ; i<4 ; i++) {
sprintf(in_MD,"%s_MD%s", argv[iarg],postfix[i]);
if(THD_is_ondisk(in_MD)) {
FOUND = i;
break;
}
}
insetMD = THD_open_dataset(in_MD);
if( insetMD == NULL )
ERROR_exit("Can't open dataset '%s':MD",in_MD);
DSET_load(insetMD) ; CHECK_LOAD_ERROR(insetMD) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-algopt") == 0 ){
iarg++ ;
if( iarg >= argc )
ERROR_exit("Need argument after '-algopt'");
if (!(nel = ReadTractAlgOpts(argv[iarg]))) {
ERROR_message("Failed to read options in %s\n", argv[iarg]);
exit(19);
}
if (NI_getTractAlgOpts(nel, &MinFA, &MaxAngDeg, &MinL,
SeedPerV, &M, &bval)) {
ERROR_message("Failed to get options");
exit(1);
}
NI_free_element(nel); nel=NULL;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-logic") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-logic'");
INFO_message("ROI logic type is: %s",argv[iarg]);
if( strcmp(argv[iarg],"AND") == 0 )
LOG_TYPE = 1;
else if( strcmp(argv[iarg],"OR") == 0 )
LOG_TYPE = 0;
else if( strcmp(argv[iarg],"ALL") == 0 )
LOG_TYPE = -1;
else
ERROR_exit("Illegal after '-logic': need 'OR' or 'AND'");
iarg++ ; continue ;
}
//@@
if( strcmp(argv[iarg],"-extra_set") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need argument after '-extra_set'");
EXTRAFILE = 1; // switch on
insetEXTRA = THD_open_dataset(argv[iarg]);
if( (insetEXTRA == NULL ) )
ERROR_exit("Can't open dataset '%s': for extra set.",argv[iarg]);
DSET_load(insetEXTRA) ; CHECK_LOAD_ERROR(insetEXTRA) ;
if( !((Dim[0] == DSET_NX(insetEXTRA)) && (Dim[1] == DSET_NY(insetEXTRA)) && (Dim[2] == DSET_NZ(insetEXTRA))))
ERROR_exit("Dimensions of extra set '%s' don't match those of the DTI prop ones ('%s', etc.).",argv[iarg], in_FA);
iarg++ ; continue ;
}
ERROR_message("Bad option '%s'\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
if (iarg < 4) {
ERROR_message("Too few options. Try -help for details.\n");
exit(1);
}
if (dump_opts) {
nel = NI_setTractAlgOpts(NULL, &MinFA, &MaxAngDeg, &MinL,
SeedPerV, &M, &bval);
WriteTractAlgOpts(prefix, nel);
NI_free_element(nel); nel=NULL;
}
// Process the options a little
for( i=0 ; i<3 ; i++)
DimSeed[i] = Dim[i]*SeedPerV[i];
Nseed = Nvox*SeedPerV[0]*SeedPerV[1]*SeedPerV[2];
// convert to cos of rad value for comparisons, instead of using acos()
MaxAng = cos(CONV*MaxAngDeg);
// switch to add header-- option for now, added Sept. 2012
// for use with map_TrackID to map tracks to different space
if(RECORD_ORIG) {
for( i=0 ; i<3 ; i++)
header1.origin[i] = Orig[i];
}
// at some point, we will have to convert indices into
// pseudo-locations; being forced into this choice means that
// different data set orientations would be represented differently
// and incorrectly in some instances... so, for now, we'll resample
// everything to RAI, and then resample back later. guess this will
// just slow things down slightly.
// have all be RAI for processing here
if(TV_switch[0] || TV_switch[1] || TV_switch[2]) {
dsetn = r_new_resam_dset(insetFA, NULL, 0.0, 0.0, 0.0,
dset_or, RESAM_NN_TYPE, NULL, 1, 0);
DSET_delete(insetFA);
insetFA=dsetn;
dsetn=NULL;
dsetn = r_new_resam_dset(insetMD, NULL, 0.0, 0.0, 0.0,
dset_or, RESAM_NN_TYPE, NULL, 1, 0);
DSET_delete(insetMD);
insetMD=dsetn;
dsetn=NULL;
dsetn = r_new_resam_dset(insetV1, NULL, 0.0, 0.0, 0.0,
dset_or, RESAM_NN_TYPE, NULL, 1, 0);
DSET_delete(insetV1);
insetV1=dsetn;
dsetn=NULL;
dsetn = r_new_resam_dset(insetL1, NULL, 0.0, 0.0, 0.0,
dset_or, RESAM_NN_TYPE, NULL, 1, 0);
DSET_delete(insetL1);
insetL1=dsetn;
dsetn=NULL;
dsetn = r_new_resam_dset(mset1, NULL, 0.0, 0.0, 0.0,
dset_or, RESAM_NN_TYPE, NULL, 1, 0);
DSET_delete(mset1);
mset1=dsetn;
dsetn=NULL;
dsetn = r_new_resam_dset(mset2, NULL, 0.0, 0.0, 0.0,
dset_or, RESAM_NN_TYPE, NULL, 1, 0);
DSET_delete(mset2);
mset2=dsetn;
dsetn=NULL;
if(EXTRAFILE) {
dsetn = r_new_resam_dset(insetEXTRA, NULL, 0.0, 0.0, 0.0,
dset_or, RESAM_NN_TYPE, NULL, 1, 0);
DSET_delete(insetEXTRA);
insetEXTRA=dsetn;
dsetn=NULL;
}
}
// ****************************************************************
// ****************************************************************
// make arrays for tracking
// ****************************************************************
// ****************************************************************
// for temp storage array, just a multiple of longest dimension!
if(Dim[0] > Dim[1])
ArrMax = Dim[0] * 4;
else
ArrMax = Dim[1] * 4;
if(4*Dim[2] > ArrMax)
ArrMax = Dim[2] * 4;
ROI1 = (int *)calloc(Nvox, sizeof(int));
ROI2 = (int *)calloc(Nvox, sizeof(int));
temp_arr = (short int *)calloc(Nvox, sizeof(short int));
temp_byte = (char *)calloc(Nvox, sizeof(char));
// temp storage whilst tracking
Tforw = calloc(ArrMax, sizeof(Tforw));
for(i=0 ; i<ArrMax ; i++)
Tforw[i] = calloc(3, sizeof(int));
Ttot = calloc(2*ArrMax , sizeof(Ttot));
for(i=0 ; i<2*ArrMax ; i++)
Ttot[i] = calloc(3, sizeof(int));
Tback = calloc(ArrMax, sizeof(Tback));
for(i=0 ; i<ArrMax ; i++)
Tback[i] = calloc(3, sizeof(int));
// temp storage whilst tracking, physical loc
flTforw = calloc(ArrMax, sizeof(flTforw));
for(i=0 ; i<ArrMax ; i++)
flTforw[i] = calloc(3, sizeof(int));
flTback = calloc(ArrMax,sizeof(flTback));
for(i=0 ; i<ArrMax ; i++)
flTback[i] = calloc(3, sizeof(int));
if( (ROI1 == NULL) || (ROI2 == NULL) || (temp_arr == NULL)
|| (Tforw == NULL) || (Tback == NULL) || (flTforw == NULL)
|| (flTback == NULL) || (Ttot == NULL)) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(12);
}
coorded = (float ****) calloc( Dim[0], sizeof(float ***) );
for ( i = 0 ; i < Dim[0] ; i++ )
coorded[i] = (float ***) calloc( Dim[1], sizeof(float **) );
for ( i = 0 ; i < Dim[0] ; i++ )
for ( j = 0 ; j < Dim[1] ; j++ )
coorded[i][j] = (float **) calloc( Dim[2], sizeof(float *) );
for ( i=0 ; i<Dim[0] ; i++ )
for ( j=0 ; j<Dim[1] ; j++ )
for ( k= 0 ; k<Dim[2] ; k++ ) //3 comp of V1 and FA
coorded[i][j][k] = (float *) calloc( 4, sizeof(float) );
INDEX = (int ****) calloc( Dim[0], sizeof(int ***) );
for ( i = 0 ; i < Dim[0] ; i++ )
INDEX[i] = (int ***) calloc( Dim[1], sizeof(int **) );
for ( i = 0 ; i < Dim[0] ; i++ )
for ( j = 0 ; j < Dim[1] ; j++ )
INDEX[i][j] = (int **) calloc( Dim[2], sizeof(int *) );
for ( i=0 ; i<Dim[0] ; i++ )
for ( j=0 ; j<Dim[1] ; j++ )
for ( k= 0 ; k<Dim[2] ; k++ )
INDEX[i][j][k] = (int *) calloc( 4, sizeof(int) );
// this statement will never be executed if allocation fails above
if( (INDEX == NULL) || (coorded == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(122);
}
for(i=0 ; i<Nvox ; i++) {
if(THD_get_voxel( mset1, i, 0) >0.5){
ROI1[i] = 1;
}
if(THD_get_voxel( mset2, i, 0) >0.5)
ROI2[i] = 1;
}
// set up eigvecs in 3D coord sys,
// mark off where ROIs are and keep index handy
idx=0;
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ ) {
for( m=0 ; m<3 ; m++ )
coorded[i][j][k][m] = THD_get_voxel(insetV1, idx, m);
if(EXTRAFILE)
coorded[i][j][k][3] = THD_get_voxel(insetEXTRA, idx, 0);
else
coorded[i][j][k][3] = THD_get_voxel(insetFA, idx, 0);
// make sure that |V1| == 1 for all eigenvects, otherwise it's
/// a problem in the tractography; currently, some from
// 3dDWItoDT do not have this property...
tempvmagn = sqrt(coorded[i][j][k][0]*coorded[i][j][k][0]+
coorded[i][j][k][1]*coorded[i][j][k][1]+
coorded[i][j][k][2]*coorded[i][j][k][2]);
if( tempvmagn<0.99 )
for( m=0 ; m<3 ; m++ )
coorded[i][j][k][m]/= tempvmagn;
INDEX[i][j][k][0] =idx; // first value is the index itself
if( ROI1[idx]==1 )
INDEX[i][j][k][1]=1; // second value identifies ROI1 mask
else
INDEX[i][j][k][1]=0;
if( ROI2[idx]==1 )
INDEX[i][j][k][2]=1; // third value identifies ROI2 mask
else
INDEX[i][j][k][2]=0;
// fourth value will be counter for number of kept tracks
// passing through
INDEX[i][j][k][3] = 0;
idx+= 1;
}
// *************************************************************
// *************************************************************
// Beginning of main loop
// *************************************************************
// *************************************************************
Numtract = 0;
ave_tract_len = 0.;
ave_tract_len_phys = 0.;
sprintf(OUT_bin,"%s.trk",prefix);
if( (fout0 = fopen(OUT_bin, "w")) == NULL) {
fprintf(stderr, "Error opening file %s.",OUT_bin);
exit(16);
}
fwrite(&header1,sizeof(tv_io_header),1,fout0);
if (get_tract_verb()) {
INFO_message("Begin tracking...");
}
tb = AppCreateBundle(NULL, 0, NULL, insetFA); // start bundle
id = 0;
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ )
if(coorded[i][j][k][3] >= MinFA) {
for( ii=0 ; ii<SeedPerV[0] ; ii++ )
for( jj=0 ; jj<SeedPerV[1] ; jj++ )
for( kk=0 ; kk<SeedPerV[2] ; kk++ ) {
in[0] = i;
in[1] = j;
in[2] = k;
physin[0] = ((float) in[0] +
(0.5 + (float) ii)/SeedPerV[0])*Ledge[0];
physin[1] = ((float) in[1] +
(0.5 + (float) jj)/SeedPerV[1])*Ledge[1];
physin[2] = ((float) in[2] +
(0.5 + (float) kk)/SeedPerV[2])*Ledge[2];
len_forw = TrackIt(coorded, in, physin, Ledge, Dim,
MinFA, MaxAng, ArrMax, Tforw,
flTforw, 1, phys_forw);
// reset, because it's changed in TrackIt func
in[0] = i;
in[1] = j;
in[2] = k;
physin[0] = ((float) in[0] +
(0.5 + (float) ii)/SeedPerV[0])*Ledge[0];
physin[1] = ((float) in[1] +
(0.5 + (float) jj)/SeedPerV[1])*Ledge[1];
physin[2] = ((float) in[2] +
(0.5 + (float) kk)/SeedPerV[2])*Ledge[2];
len_back = TrackIt(coorded, in, physin, Ledge, Dim,
MinFA, MaxAng, ArrMax, Tback,
flTback, -1, phys_back);
KEEPIT = 0; // a simple switch
totlen = len_forw+len_back-1; // NB: overlap of starts
totlen_phys = phys_forw[0] + phys_back[0];
if( totlen_phys >= MinL ) {
// glue together for simpler notation later
for( n=0 ; n<len_back ; n++) { // all of this
rr = len_back-n-1; // read in backward
for(m=0;m<3;m++)
Ttot[rr][m] = Tback[n][m];
}
for( n=1 ; n<len_forw ; n++){// skip first->overlap
rr = n+len_back-1; // put after
for(m=0;m<3;m++)
Ttot[rr][m] = Tforw[n][m];
}
// <<So close and orthogonal condition>>:
// test projecting ends, to see if they abut ROI.
for(m=0;m<3;m++) {
//actual projected ends
end[1][m] = 2*Ttot[totlen-1][m]-Ttot[totlen-2][m];
end[0][m] = 2*Ttot[0][m]-Ttot[1][m];
// default choice, just retest known ends
// as default
test_ind[1][m] = test_ind[0][m] = Ttot[0][m];
}
tt = Create_Tract(len_back, flTback, len_forw,
flTforw, id, insetFA); ++id;
if (LOG_TYPE == -1) {
KEEPIT = 1;
} else {
inroi1 = 0;
// check forw
for( n=0 ; n<len_forw ; n++) {
if(INDEX[Tforw[n][0]][Tforw[n][1]][Tforw[n][2]][1]==1){
inroi1 = 1;
break;
} else
continue;
}
if( inroi1==0 ){// after 1st half, check 2nd half
for( m=0 ; m<len_back ; m++) {
if(INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][1]==1){
inroi1 = 1;
break;
} else
continue;
}
}
// after 1st&2nd halves, check bound/neigh
if( inroi1==0 ) {
if(INDEX[test_ind[1][0]][test_ind[1][1]][test_ind[1][2]][1]==1)
inroi1 = 1;
if(INDEX[test_ind[0][0]][test_ind[0][1]][test_ind[0][2]][1]==1)
inroi1 = 1;
}
if( ((LOG_TYPE ==0) && (inroi1 ==0)) ||
((LOG_TYPE ==1) && (inroi1 ==1))) {
// have to check in ROI2
inroi2 = 0;
// check forw
for( n=0 ; n<len_forw ; n++) {
if(INDEX[Tforw[n][0]][Tforw[n][1]][Tforw[n][2]][2]==1){
inroi2 = 1;
break;
} else
continue;
}
//after 1st half, check 2nd half
if( inroi2==0 ) {
for( m=0 ; m<len_back ; m++) {
if(INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][2]==1){
inroi2 = 1;
break;
} else
continue;
}
}
// after 1st&2nd halves, check bound/neigh
if( inroi2==0 ) {
if(INDEX[test_ind[1][0]][test_ind[1][1]][test_ind[1][2]][2]==1)
inroi2 = 1;
if(INDEX[test_ind[0][0]][test_ind[0][1]][test_ind[0][2]][2]==1)
inroi2 = 1;
}
// for both cases, need to see it here to keep
if( inroi2 ==1 )
KEEPIT = 1; // otherwise, it's gone
} else if((LOG_TYPE ==0) && (inroi1 ==1))
KEEPIT = 1;
}
}
// by now, we *know* if we're keeping this or not.
if( KEEPIT == 1 ) {
tb = AppCreateBundle(tb, 1, tt, NULL);
tt = Free_Tracts(tt, 1);
READS_in = totlen;
fwrite(&READS_in,sizeof(READS_in),1,fout0);
for( n=0 ; n<len_back ; n++) {
//put this one in backwords, to make it connect
m = len_back - 1 - n;
for(aa=0 ; aa<3 ; aa++) {
// recenter phys loc for trackvis, if nec...
// just works this way (where they define
// origin)
READS_fl = flTback[m][aa];
if(!TV_switch[aa])
READS_fl = Ledge[aa]*Dim[aa]-READS_fl;
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
}
mm = INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][0];
READS_fl =THD_get_voxel(insetFA, mm, 0); // FA
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
READS_fl =THD_get_voxel(insetMD, mm, 0); // MD
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
READS_fl =THD_get_voxel(insetL1, mm, 0); // L1
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
// count this voxel for having a tract
INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][3]+= 1;
}
for( m=1 ; m<len_forw ; m++) {
for(aa=0 ; aa<3 ; aa++) {
// recenter phys loc for trackvis, if nec...
READS_fl = flTforw[m][aa];
if(!TV_switch[aa])
READS_fl = Ledge[aa]*Dim[aa]-READS_fl;
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
}
mm = INDEX[Tforw[m][0]][Tforw[m][1]][Tforw[m][2]][0];
READS_fl =THD_get_voxel(insetFA, mm, 0); // FA
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
READS_fl =THD_get_voxel(insetMD, mm, 0); // MD
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
READS_fl =THD_get_voxel(insetL1, mm, 0); // L1
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
// count this voxel for having a tract
INDEX[Tforw[m][0]][Tforw[m][1]][Tforw[m][2]][3]+= 1;
}
ave_tract_len+= totlen;
ave_tract_len_phys+= totlen_phys;
Numtract+=1;
}
}
}
fclose(fout0);
if (get_tract_verb()) {
INFO_message("Done tracking, have %d tracks.", tb->N_tracts);
Show_Taylor_Bundle(tb, NULL, 3);
}
if (!Write_Bundle(tb,prefix,mode)) {
ERROR_message("Failed to write the bundle");
}
// **************************************************************
// **************************************************************
// Some simple stats on ROIs and outputs
// **************************************************************
// **************************************************************
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ ) {
if( INDEX[i][j][k][3]>=1 ) {
tempMD = THD_get_voxel(insetMD,INDEX[i][j][k][0],0);
tempFA = THD_get_voxel(insetFA,INDEX[i][j][k][0],0);
tempL1 = THD_get_voxel(insetL1,INDEX[i][j][k][0],0);
tempRD = 0.5*(3*tempMD-tempL1);
roi3_mu_MD+= tempMD;
roi3_mu_FA+= tempFA;
roi3_mu_L1+= tempL1;
roi3_mu_RD+= tempRD;
roi3_sd_MD+= tempMD*tempMD;
roi3_sd_FA+= tempFA*tempFA;
roi3_sd_L1+= tempL1*tempL1;
roi3_sd_RD+= tempRD*tempRD;
roi3_ct+= 1;
}
}
if(roi3_ct > 0 ) { // !!!! make into afni file
roi3_mu_MD/= (float) roi3_ct;
roi3_mu_FA/= (float) roi3_ct;
roi3_mu_L1/= (float) roi3_ct;
roi3_mu_RD/= (float) roi3_ct;
roi3_sd_MD-= roi3_ct*roi3_mu_MD*roi3_mu_MD;
roi3_sd_FA-= roi3_ct*roi3_mu_FA*roi3_mu_FA;
roi3_sd_L1-= roi3_ct*roi3_mu_L1*roi3_mu_L1;
roi3_sd_RD-= roi3_ct*roi3_mu_RD*roi3_mu_RD;
roi3_sd_MD/= (float) roi3_ct-1;
roi3_sd_FA/= (float) roi3_ct-1;
roi3_sd_L1/= (float) roi3_ct-1;
roi3_sd_RD/= (float) roi3_ct-1;
roi3_sd_MD = sqrt(roi3_sd_MD);
roi3_sd_FA = sqrt(roi3_sd_FA);
roi3_sd_L1 = sqrt(roi3_sd_L1);
roi3_sd_RD = sqrt(roi3_sd_RD);
sprintf(OUT_tracstat,"%s.stats",prefix);
if( (fout0 = fopen(OUT_tracstat, "w")) == NULL) {
fprintf(stderr, "Error opening file %s.",OUT_tracstat);
exit(19);
}
fprintf(fout0,"%d\t%d\n",Numtract,roi3_ct);
fprintf(fout0,"%.3f\t%.3f\n",ave_tract_len/Numtract,
ave_tract_len_phys/Numtract);
// as usual, these next values would have to be divided by the
// bval to get their actual value in standard phys units
fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_FA,roi3_sd_FA);
fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_MD,roi3_sd_MD);
fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_RD,roi3_sd_RD);
fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_L1,roi3_sd_L1);
fclose(fout0);
sprintf(prefix_map,"%s_MAP",prefix);
sprintf(prefix_mask,"%s_MASK",prefix);
outsetMAP = EDIT_empty_copy( mset1 ) ;
EDIT_dset_items( outsetMAP ,
ADN_datum_all , MRI_short ,
ADN_prefix , prefix_map ,
ADN_none ) ;
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMAP)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outsetMAP));
outsetMASK = EDIT_empty_copy( mset1 ) ;
EDIT_dset_items( outsetMASK ,
ADN_datum_all , MRI_byte ,
ADN_prefix , prefix_mask ,
ADN_none ) ;
if(!THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMASK)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outsetMASK));
m=0;
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ ) {
temp_arr[m]=INDEX[i][j][k][3];
if(temp_arr[m]>0.5)
temp_byte[m]=1;
else
temp_byte[m]=0;
m++;
}
// re-orient the data as original inputs
// (this function copies the pointer)
EDIT_substitute_brick(outsetMAP, 0, MRI_short, temp_arr);
temp_arr=NULL;
if(TV_switch[0] || TV_switch[1] || TV_switch[2]) {
dsetn = r_new_resam_dset(outsetMAP, NULL, 0.0, 0.0, 0.0,
header1.voxel_order, RESAM_NN_TYPE,
NULL, 1, 0);
DSET_delete(outsetMAP);
outsetMAP=dsetn;
dsetn=NULL;
}
EDIT_dset_items( outsetMAP ,
ADN_prefix , prefix_map ,
ADN_none ) ;
THD_load_statistics(outsetMAP );
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMAP)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outsetMAP));
tross_Make_History( "3dTrackID" , argc , argv , outsetMAP) ;
THD_write_3dim_dataset(NULL, NULL, outsetMAP, True);
// re-orient the data as original inputs
EDIT_substitute_brick(outsetMASK, 0, MRI_byte, temp_byte);
temp_byte=NULL;
if(TV_switch[0] || TV_switch[1] || TV_switch[2]) {
dsetn = r_new_resam_dset(outsetMASK, NULL, 0.0, 0.0, 0.0,
header1.voxel_order, RESAM_NN_TYPE,
NULL, 1, 0);
DSET_delete(outsetMASK);
outsetMASK=dsetn;
dsetn=NULL;
}
EDIT_dset_items( outsetMASK ,
ADN_prefix , prefix_mask ,
ADN_none ) ;
THD_load_statistics(outsetMASK);
if(!THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMASK)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outsetMASK));
tross_Make_History( "3dTrackID" , argc , argv , outsetMASK) ;
THD_write_3dim_dataset(NULL, NULL, outsetMASK, True);
INFO_message("Number of tracts found = %d",Numtract) ;
}
else
INFO_message("\n No Tracts Found!!!\n");
// ************************************************************
// ************************************************************
// Freeing
// ************************************************************
// ************************************************************
// !!! need to free afni-sets?
DSET_delete(insetFA);
DSET_delete(insetMD);
DSET_delete(insetL1);
DSET_delete(insetV1);
DSET_delete(insetEXTRA);
//DSET_delete(outsetMAP);
//DSET_delete(outsetMASK);
DSET_delete(mset2);
DSET_delete(mset1);
free(prefix);
free(insetV1);
free(insetFA);
free(mset1);
free(mset2);
free(insetEXTRA);
free(ROI1);
free(ROI2);
free(temp_byte);
for( i=0 ; i<ArrMax ; i++) {
free(Tforw[i]);
free(Tback[i]);
free(flTforw[i]);
free(flTback[i]);
}
free(Tforw);
free(Tback);
free(flTforw);
free(flTback);
for( i=0 ; i<Dim[0] ; i++)
for( j=0 ; j<Dim[1] ; j++)
for( k=0 ; k<Dim[2] ; k++)
free(coorded[i][j][k]);
for( i=0 ; i<Dim[0] ; i++)
for( j=0 ; j<Dim[1] ; j++)
free(coorded[i][j]);
for( i=0 ; i<Dim[0] ; i++)
free(coorded[i]);
free(coorded);
for( i=0 ; i<Dim[0] ; i++)
for( j=0 ; j<Dim[1] ; j++)
for( k=0 ; k<Dim[2] ; k++)
free(INDEX[i][j][k]);
for( i=0 ; i<Dim[0] ; i++)
for( j=0 ; j<Dim[1] ; j++)
free(INDEX[i][j]);
for( i=0 ; i<Dim[0] ; i++)
free(INDEX[i]);
free(INDEX);
free(temp_arr); // need to free
for( i=0 ; i<2*ArrMax ; i++)
free(Ttot[i]);
free(Ttot);
//free(mode);
return 0;
}
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) ;
}
/*!
A function to call SUMA_qhull_wrap or SUMA_qdelaunay_wrap
*/
SUMA_SurfaceObject *SUMA_ConvexHullSurface(
SUMA_GENERIC_PROG_OPTIONS_STRUCT * Opt)
{
static char FuncName[]={"SUMA_ConvexHullSurface"};
SUMA_SurfaceObject *SO=NULL;
float *xyz=NULL, *xyzp=NULL, *txyz=NULL;
int npt, *ijk=NULL, nf=0, cnt, i, j, k, nxx, nyy, nzz,N_txyz=-1;
FILE *fid=NULL;
THD_fvec3 fv, iv;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
npt = 0;
N_txyz=-1;
if (Opt->UseThisBrain) {
MRI_IMAGE *im = NULL;
float *far=NULL;
int nx2, i3;
/* load the 1D file */
im = mri_read_1D (Opt->UseThisBrain);
if (!im) {
SUMA_S_Err("Failed to read file");
SUMA_RETURN(NULL);
}
far = MRI_FLOAT_PTR(im);
if (im->nx == 0) {
SUMA_S_Errv("Empty file %s.\n", Opt->UseThisBrain);
SUMA_RETURN(NULL);
}
if (im->ny != 3) {
SUMA_S_Errv("Found %d columns in %s. Expecting 3\n",
im->ny, Opt->UseThisBrain);
SUMA_RETURN(NULL);
}
/* copy the columns */
N_txyz = im->nx;
txyz = (float *)SUMA_malloc(im->nx*im->ny*sizeof(float));
if (!txyz) {
SUMA_S_Crit("Failed to allocate.");
SUMA_RETURN(NULL);
}
nx2 = 2*im->nx;
for (i=0; i<N_txyz; ++i) {
i3 = 3*i;
txyz[i3 ] = far[i];
txyz[i3+1] = far[i+im->nx];
txyz[i3+2] = far[i+nx2];
}
/* done, clean up and out you go */
if (im) mri_free(im); im = NULL;
}
if (Opt->in_vol) {
cnt = 0; npt = 0;
nxx = (DSET_NX(Opt->in_vol));
nyy = (DSET_NY(Opt->in_vol));
nzz = (DSET_NZ(Opt->in_vol));
if (Opt->debug) fprintf(SUMA_STDERR,"%s:\nRunning qhull...\n", FuncName);
xyz = (float *)SUMA_malloc(3*nxx*nyy*nzz*sizeof(float));
if (!xyz) {
SUMA_S_Err("Failed to allocate"); SUMA_RETURN(NULL);
}
for( k = 0 ; k < nzz ; k++ ) {
for( j = 0 ; j < nyy ; j++ ) {
for( i = 0 ; i < nxx ; i++ ) {
if (Opt->mcdatav[cnt] == 1) {
fv.xyz[0] = DSET_XORG(Opt->in_vol) + i * DSET_DX(Opt->in_vol);
fv.xyz[1] = DSET_YORG(Opt->in_vol) + j * DSET_DY(Opt->in_vol);
fv.xyz[2] = DSET_ZORG(Opt->in_vol) + k * DSET_DZ(Opt->in_vol);
/* change mm to RAI coords */
iv = SUMA_THD_3dmm_to_dicomm( Opt->in_vol->daxes->xxorient,
Opt->in_vol->daxes->yyorient,
Opt->in_vol->daxes->zzorient,
fv );
xyz[3*npt] = iv.xyz[0];
xyz[3*npt+1] = iv.xyz[1]; xyz[3*npt+2] = iv.xyz[2];
npt++;
}
++cnt;
}
}
}
} else if (Opt->XYZ) {
xyz = (float *)SUMA_malloc(3*Opt->N_XYZ*sizeof(float));
if (!xyz) {
SUMA_S_Err("Failed to allocate"); SUMA_RETURN(NULL);
}
for( k = 0 ; k < 3*Opt->N_XYZ ; k++ ) {
xyz[k] = Opt->XYZ[k]; npt = Opt->N_XYZ;
}
} else {
SUMA_S_Err("No input");
goto CLEANUP;
}
if (Opt->corder) {
SUMA_PC_XYZ_PROJ *pcp=NULL;
if (Opt->geom==1) {
SUMA_S_Warn("PCA projection makes no sense for usual convex hull");
}
if (!(pcp = SUMA_Project_Coords_PCA (xyz, npt, npt/2, NULL,
E3_PLN_PRJ, ROT_2_Z,0))) {
SUMA_S_Err("Failed to project");
goto CLEANUP;
}
xyzp = pcp->xyzp; pcp->xyzp = NULL;
pcp = SUMA_Free_PC_XYZ_Proj(pcp);
} else {
xyzp = xyz;
}
if (N_txyz >= 0 && N_txyz != npt) {
SUMA_S_Errv("Mismatch between number of coordinates for convex hull\n"
"and number of coordinates to adopt in the end.\n"
" %d, versus %d in -these_coords\n",
npt, N_txyz);
goto CLEANUP;
}
if (Opt->geom == 1) { /* convex hull */
if (! (nf = SUMA_qhull_wrap(npt, xyzp, &ijk, 1, Opt->s)) ) {
fprintf(SUMA_STDERR,"%s:\nFailed in SUMA_qhull_wrap\n", FuncName);
goto CLEANUP;
}
/* Other than unif==0 make no sense here, but leave it to the user */
switch (Opt->unif) {
case 0: /* coordinates as passed to qhull,
could be projected ones*/
SO = SUMA_Patch2Surf(xyzp, npt, ijk, nf, 3);
break;
case 1: /* Original corrdinates passed to qhull
(pre-projections, if any) */
SO = SUMA_Patch2Surf(xyz, npt, ijk, nf, 3);
break;
case 2: /* special coordinates passed by user,
never passed in any form to qhull */
SUMA_S_Warn("Makes no sense to mess with coords for convex hull...");
SO = SUMA_Patch2Surf(txyz, npt, ijk, nf, 3);
break;
default:
SUMA_S_Err("pit of despair");
goto CLEANUP;
}
if (Opt->debug) fprintf(SUMA_STDERR,"%s:\n%d triangles.\n", FuncName, nf);
} else if (Opt->geom == 2) { /* triangulation */
if (! (nf = SUMA_qdelaunay_wrap(npt, xyzp, &ijk, 1, Opt->s)) ) {
fprintf(SUMA_STDERR,"%s:\nFailed in SUMA_qdelaunay_wrap\n", FuncName);
goto CLEANUP;
}
switch (Opt->unif) {
case 0: /* coordinates as passed to qdelaunay,
could be projected ones*/
if (xyz == xyzp) xyz=NULL; /* xyzp will be set to
null in next call,
so xyz is treated
the same here */
SO = SUMA_NewSO(&xyzp, npt, &ijk, nf, NULL);
SUMA_LHv("xyzp %p, ijk %p\n", txyz, ijk);
break;
case 1: /* Original corrdinates passed to qdelaunay
(pre-projections, if any) */
SO = SUMA_NewSO(&xyz, npt, &ijk, nf, NULL);
SUMA_LHv("xyz %p, ijk %p\n", txyz, ijk);
break;
case 2: /* special coordinates passed by user,
never passed in any form to qdelaunay */
SO = SUMA_NewSO(&txyz, npt, &ijk, nf, NULL);
SUMA_LHv("txyz %p, ijk %p\n", txyz, ijk);
break;
default:
SUMA_S_Err("pit of despair, again");
goto CLEANUP;
}
} else {
SUMA_S_Errv("Opt->geom = %d not valid\n", Opt->geom);
goto CLEANUP;
}
CLEANUP:
if (ijk) SUMA_free(ijk); ijk=NULL;
if(txyz) SUMA_free(txyz); txyz=NULL;
if (xyzp != xyz && xyzp != NULL) SUMA_free(xyzp); xyzp = NULL;
if (xyz) SUMA_free(xyz); xyz = NULL;
SUMA_RETURN(SO);
}