int THD_datablock_from_atr( THD_datablock *dblk, char *dirname, char *headname )
{
THD_diskptr *dkptr ;
ATR_int *atr_rank , *atr_dimen , *atr_scene , *atr_btype ;
ATR_float *atr_flt ;
ATR_string *atr_labs ;
int ii , view_type , func_type , dset_type ,
nx,ny,nz,nvox , nvals , ibr,typ ;
Boolean ok ;
char prefix[THD_MAX_NAME]="Unknown" ;
MRI_IMAGE *qim ;
int brick_ccode ;
char name[666] ;
ENTRY("THD_datablock_from_atr") ;
if( dblk == NULL || dblk->natr <= 0 ) RETURN(0) ; /* bad input */
dkptr = dblk->diskptr ;
/*-- get relevant attributes: rank, dimensions, view_type & func_type --*/
atr_rank = THD_find_int_atr( dblk , ATRNAME_DATASET_RANK ) ;
atr_dimen = THD_find_int_atr( dblk , ATRNAME_DATASET_DIMENSIONS ) ;
atr_scene = THD_find_int_atr( dblk , ATRNAME_SCENE_TYPE ) ;
/*-- missing an attribute ==> quit now --*/
if( atr_rank == NULL || atr_dimen == NULL || atr_scene == NULL ) RETURN(0) ;
/*-- load type codes from SCENE attribute --*/
STATUS("loading *_type from SCENE") ;
view_type = atr_scene->in[0] ;
func_type = atr_scene->in[1] ;
dset_type = atr_scene->in[2] ;
/*-- load other values from attributes into relevant places --*/
ok = True ;
nvox = 1 ;
STATUS("loading from RANK") ;
dkptr->rank = atr_rank->in[0] ; /* N.B.: rank isn't used much */
dkptr->nvals = dblk->nvals = nvals = atr_rank->in[1] ; /* but nvals is used */
STATUS("loading from DIMENSIONS") ;
for( ii=0 ; ii < dkptr->rank ; ii++ ){
dkptr->dimsizes[ii] = atr_dimen->in[ii] ;
ok = ( ok && dkptr->dimsizes[ii] >= 1 ) ;
nvox *= dkptr->dimsizes[ii] ;
}
#if 0
if( PRINT_TRACING ){
char str[256] ;
sprintf(str,"rank=%d nvals=%d dim[0]=%d dim[1]=%d dim[2]=%d nvox=%d",
dkptr->rank , dkptr->nvals ,
dkptr->dimsizes[0] , dkptr->dimsizes[1] , dkptr->dimsizes[2] , nvox ) ;
STATUS(str) ;
}
#endif
if( !ok || nvals < 1 ||
dkptr->rank < THD_MIN_RANK || dkptr->rank > THD_MAX_RANK ){
STATUS("bad rank!!??") ;
RETURN(0) ;
}
/*-- create the storage filenames --*/
STATUS("creating storage filenames") ;
if( headname != NULL && strchr(headname,'+') != NULL ){
FILENAME_TO_PREFIX(headname,prefix) ;
THD_init_diskptr_names( dkptr, dirname,NULL,prefix , view_type , True ) ;
} else {
if( headname != NULL ) MCW_strncpy(prefix,headname,THD_MAX_NAME) ;
THD_init_diskptr_names( dkptr, dirname,NULL,prefix , view_type , True ) ;
}
/*-- determine if the BRIK file exists --*/
STATUS("checking if .BRIK file exists") ;
brick_ccode = COMPRESS_filecode(dkptr->brick_name) ;
if (dkptr->storage_mode == STORAGE_UNDEFINED) { /* ZSS: Oct. 2011
the next line was being called all the time before */
if( brick_ccode != COMPRESS_NOFILE )
dkptr->storage_mode = STORAGE_BY_BRICK ; /* a .BRIK file */
}
/*-- if VOLUME_FILENAMES attribute exists, make it so [20 Jun 2002] --*/
if( headname != NULL && dkptr->storage_mode == STORAGE_UNDEFINED ){
atr_labs = THD_find_string_atr(dblk,"VOLUME_FILENAMES") ;
if( atr_labs != NULL ){
dkptr->storage_mode = STORAGE_BY_VOLUMES ;
dblk->malloc_type = DATABLOCK_MEM_MALLOC ;
}
}
/*-- now set the memory allocation codes, etc. --*/
dblk->brick_fac = (float *) XtMalloc( sizeof(float) * nvals ) ;
for( ibr=0 ; ibr < nvals ; ibr++ ) dblk->brick_fac[ibr] = 0.0 ;
/* scaling factors from short type to float type, if nonzero */
if( !AFNI_yesenv("AFNI_IGNORE_BRICK_FLTFAC") ){
atr_flt = THD_find_float_atr( dblk , ATRNAME_BRICK_FLTFAC ) ;
if( atr_flt != NULL ){
for( ibr=0 ; ibr < nvals && ibr < atr_flt->nfl ; ibr++ )
dblk->brick_fac[ibr] = atr_flt->fl[ibr] ;
}
}
/** Now create an empty shell of the "brick" == the data structure
that will hold all the voxel data. Note that all datablocks
will have a brick, even if they never actually contain data
themselves (are only warp-on-demand).
If the BRICK_TYPES input attribute doesn't exist, then all
sub-bricks are shorts. This makes the code work with old-style
datasets, which were always made up of shorts.
**/
atr_btype = THD_find_int_atr( dblk , ATRNAME_BRICK_TYPES ) ;
if( atr_btype == NULL ){
THD_init_datablock_brick( dblk , MRI_short , NULL ) ;
} else {
THD_init_datablock_brick( dblk , atr_btype->nin , atr_btype->in ) ;
}
if( !THD_datum_constant(dblk) ){ /* 15 Sep 2004 */
fprintf(stderr,
"\n** WARNING: File %s has mixed-type sub-bricks. ", MYHEAD ) ;
}
/* 25 April 1998: check if the byte order is stored inside */
atr_labs = THD_find_string_atr( dblk , ATRNAME_BYTEORDER ) ;
if( atr_labs != NULL && atr_labs->nch > 0 ){
if( strncmp(atr_labs->ch,LSB_FIRST_STRING,ORDER_LEN) == 0 )
dkptr->byte_order = LSB_FIRST ;
else if( strncmp(atr_labs->ch,MSB_FIRST_STRING,ORDER_LEN) == 0 )
dkptr->byte_order = MSB_FIRST ;
else
fprintf(stderr,"*** Unknown %s found in dataset %s\n",
ATRNAME_BYTEORDER , MYHEAD ) ;
} else if( !no_ordwarn &&
DBLK_BRICK_TYPE(dblk,0) != MRI_byte &&
dblk->diskptr->storage_mode == STORAGE_BY_BRICK ){ /* 20 Sep 1999 */
static int first=1 ;
if( first ){
fprintf(stderr,
"\n*** The situation below can be rectified with program '3drefit -byteorder':\n");
first = 0 ;
}
fprintf(stderr," ** Dataset %s: assuming byteorder %s\n",
MYHEAD , BYTE_ORDER_STRING(dkptr->byte_order) ) ;
}
/* if the data is not on disk, the flag remains at DATABLOCK_MEM_UNDEFINED,
otherwise the flag says how the memory for the bricks is to be created. */
if( dkptr->storage_mode == STORAGE_BY_BRICK ){
#if MMAP_THRESHOLD > 0
dblk->malloc_type = (dblk->total_bytes > MMAP_THRESHOLD)
? DATABLOCK_MEM_MMAP : DATABLOCK_MEM_MALLOC ;
DBLK_mmapfix(dblk) ; /* 18 Mar 2005 */
#else
dblk->malloc_type = DATABLOCK_MEM_MALLOC ;
#endif
/* must be malloc-ed if:
data is compressed,
data is not in native byte order, or
user explicity forbids use of mmap */
if( brick_ccode >= 0 || dkptr->byte_order != native_order || no_mmap )
dblk->malloc_type = DATABLOCK_MEM_MALLOC ;
}
/* 30 Nov 1997: create the labels for sub-bricks */
THD_init_datablock_labels( dblk ) ;
atr_labs = THD_find_string_atr( dblk , ATRNAME_BRICK_LABS ) ;
if( atr_labs != NULL && atr_labs->nch > 0 ){ /* create labels from attribute */
int ipos = -1 , ipold , ngood ;
for( ibr=0 ; ibr < nvals ; ibr++ ){ /* loop over bricks */
for( ipold = ipos++ ; /* skip to */
ipos < atr_labs->nch && atr_labs->ch[ipos] != '\0' ; /* next \0 */
ipos++ ) /* nada */ ; /* or end. */
ngood = ipos - ipold - 1 ; /* number of good chars */
if( ngood > 0 ){
XtFree(dblk->brick_lab[ibr]) ;
/* 27 Oct 2011 - increase to 64 */
if( ngood > THD_MAX_SBLABEL ) ngood = THD_MAX_SBLABEL;
dblk->brick_lab[ibr] = (char *) XtMalloc(sizeof(char)*(ngood+2)) ;
memcpy( dblk->brick_lab[ibr] , atr_labs->ch+(ipold+1) , ngood ) ;
dblk->brick_lab[ibr][ngood] = '\0' ;
}
if( ipos >= atr_labs->nch ) break ; /* nothing more to do */
} /* end of loop over sub-bricks */
}
/* create the keywords for sub-bricks */
THD_init_datablock_keywords( dblk ) ;
atr_labs = THD_find_string_atr( dblk , ATRNAME_BRICK_KEYWORDS ) ;
if( atr_labs != NULL && atr_labs->nch > 0 ){ /* create keywords from attribute */
int ipos = -1 , ipold , ngood ;
for( ibr=0 ; ibr < nvals ; ibr++ ){ /* loop over bricks */
for( ipold = ipos++ ; /* skip to */
ipos < atr_labs->nch && atr_labs->ch[ipos] != '\0' ; /* next \0 */
ipos++ ) /* nada */ ; /* or end. */
ngood = ipos - ipold - 1 ; /* number of good chars */
if( ngood > 0 ){
XtFree(dblk->brick_keywords[ibr]) ;
dblk->brick_keywords[ibr] = (char *) XtMalloc(sizeof(char)*(ngood+2)) ;
memcpy( dblk->brick_keywords[ibr] , atr_labs->ch+(ipold+1) , ngood ) ;
dblk->brick_keywords[ibr][ngood] = '\0' ;
}
if( ipos >= atr_labs->nch ) break ; /* nothing more to do */
} /* end of loop over sub-bricks */
}
/* create the auxiliary statistics stuff for each brick, if present */
atr_labs = THD_find_string_atr( dblk , "BRICK_STATSYM" ) ; /* 01 Jun 2005 */
if( atr_labs != NULL && atr_labs->nch > 0 ){
NI_str_array *sar ; int scode,np ; float parm[3] ;
sar = NI_decode_string_list( atr_labs->ch , ";" ) ;
if( sar != NULL && sar->num > 0 ){
for( ibr=0 ; ibr < nvals && ibr < sar->num ; ibr++ ){
NI_stat_decode( sar->str[ibr] , &scode , parm,parm+1,parm+2 ) ;
if( scode >= AFNI_FIRST_STATCODE && scode <= AFNI_LAST_STATCODE ){
np = NI_stat_numparam(scode) ;
THD_store_datablock_stataux( dblk , ibr,scode,np,parm ) ;
}
}
NI_delete_str_array(sar) ;
}
} else { /*--- the olde way to get ye brick stataux parameters ---*/
atr_flt = THD_find_float_atr( dblk , ATRNAME_BRICK_STATAUX ) ;
if( atr_flt != NULL && atr_flt->nfl >= 3 ){
int ipos=0 , iv,nv,jv ;
/* attribute stores all stataux stuff as follows:
sub-brick-index statcode no.-of-values value ... value
sub-brick-index statcode no.-of-values value ... value, etc. */
while( ipos <= atr_flt->nfl - 3 ){
iv = (int) ( atr_flt->fl[ipos++] ) ; /* which sub-brick */
jv = (int) ( atr_flt->fl[ipos++] ) ; /* statcode */
nv = (int) ( atr_flt->fl[ipos++] ) ; /* # of values that follow */
if( nv > atr_flt->nfl - ipos ) nv = atr_flt->nfl - ipos ;
THD_store_datablock_stataux( dblk , iv , jv , nv , atr_flt->fl + ipos ) ;
ipos += nv ;
}
}
}
#if 0
if( PRINT_TRACING ){
char str[256] ;
sprintf(str,"rank=%d nvals=%d dim[0]=%d dim[1]=%d dim[2]=%d",
dkptr->rank , dkptr->nvals ,
dkptr->dimsizes[0] , dkptr->dimsizes[1] , dkptr->dimsizes[2] ) ;
STATUS(str) ;
}
#endif
/*-- FDR curves [23 Jan 2008] --*/
for( ibr=0 ; ibr < dblk->nvals ; ibr++ ){
sprintf(name,"FDRCURVE_%06d",ibr) ;
atr_flt = THD_find_float_atr( dblk , name ) ;
if( atr_flt != NULL && atr_flt->nfl > 3 ){
int nv = atr_flt->nfl - 2 ; floatvec *fv ;
MAKE_floatvec(fv,nv) ;
fv->x0 = atr_flt->fl[0] ; fv->dx = atr_flt->fl[1] ;
memcpy( fv->ar , atr_flt->fl + 2 , sizeof(float)*nv ) ;
if( dblk->brick_fdrcurve == NULL )
dblk->brick_fdrcurve = (floatvec **)calloc(sizeof(floatvec *),dblk->nvals);
dblk->brick_fdrcurve[ibr] = fv ;
}
}
for( ibr=0 ; ibr < dblk->nvals ; ibr++ ){
sprintf(name,"MDFCURVE_%06d",ibr) ;
atr_flt = THD_find_float_atr( dblk , name ) ;
if( atr_flt != NULL && atr_flt->nfl > 3 ){
int nv = atr_flt->nfl - 2 ; floatvec *fv ;
MAKE_floatvec(fv,nv) ;
fv->x0 = atr_flt->fl[0] ; fv->dx = atr_flt->fl[1] ;
memcpy( fv->ar , atr_flt->fl + 2 , sizeof(float)*nv ) ;
if( dblk->brick_mdfcurve == NULL )
dblk->brick_mdfcurve = (floatvec **)calloc(sizeof(floatvec *),dblk->nvals);
dblk->brick_mdfcurve[ibr] = fv ;
}
}
RETURN(1) ;
}
THD_3dim_dataset * THD_open_nifti( char *pathname )
{
THD_3dim_dataset *dset=NULL ;
nifti_image *nim ;
int ntt , nbuc , nvals ;
int use_qform = 0 , use_sform = 0, form_code = 0 ;
int statcode = 0 , datum , iview , ibr ;
int scale_data = 0 ; /* flag based on scl_slope and inter 20 Jun 2008 */
int xform_data = 0;
THD_ivec3 orixyz , nxyz ;
THD_fvec3 dxyz , orgxyz ;
THD_mat33 R ;
mat44 ijk_to_dicom44 ;
char *ppp , prefix[THD_MAX_PREFIX] ;
char form_priority = 'S' ; /* 23 Mar 2006 */
static int n_xform_warn=0;
ENTRY("THD_open_nifti") ;
/*-- open input file --*/
{ /* set the nifti_io debug level 8 Apr 2005 [rickr] */
char * ept = my_getenv("AFNI_NIFTI_DEBUG");
if( ept != NULL ) nifti_set_debug_level(atoi(ept));
}
nifti_set_alter_cifti(1) ; /* if CIFTI, shift dims 23 Jul 2015 [rickr] */
nim = nifti_image_read( pathname, 0 ) ;
if( nim == NULL || nim->nifti_type == 0 ) RETURN(NULL) ;
/*-- extract some useful AFNI-ish information from the nim struct --*/
/* we must have at least 2 spatial dimensions */
/* this should be okay 11 Jun 2007 */
/* if( nim->nx < 2 || nim->ny < 2 ) RETURN(NULL) ; */
/* 4th dimension = time; 5th dimension = bucket:
these are mutually exclusive in AFNI at present */
ntt = nim->nt ; nbuc = nim->nu ;
/* nt and nu might be 0 now (see irritating niftilib 1.17 update) */
/* so ensure that ntt and nbuc are positive 02 Mar 2006 [rickr] */
if( ntt <= 0 ) ntt = 1;
if( nbuc <= 0 ) nbuc = 1;
if( nim->nz <= 0 ) nim->nz = 1 ; /* 03 Mar 2006: RWCox */
if( ntt > 1 && nbuc > 1 ){
fprintf(stderr,
"** AFNI can't deal with 5 dimensional NIfTI(%s)\n",
pathname ) ;
RETURN(NULL) ;
}
nvals = MAX(ntt,nbuc) ;
/* collapse higher-dimensional datasets 23 Jul 2015 [rickr] */
/* (this includes CIFTI) */
if( nim->nv > 1 ) nvals *= nim->nv;
if( nim->nw > 1 ) nvals *= nim->nw;
if( ntt > 1 ) ntt = nvals;
else nbuc = nvals;
/* determine type of dataset values:
if we are scaling, or if the data type in the NIfTI file
is something AFNI can't handle, then the result will be floats */
/* do not scale if slope is 0 or if slope is 1 and inter is 0 */
if( !isfinite(nim->scl_slope) || !isfinite(nim->scl_inter) ){
fprintf(stderr,"** bad scl_slope and inter = %f, %f, ignoring...\n",
nim->scl_slope, nim->scl_inter);
} else {
scale_data = nim->scl_slope != 0.0 &&
(nim->scl_slope != 1.0 || nim->scl_inter != 0.0) ;
}
{ char *eee = getenv("AFNI_NIFTI_SCALE") ;
if( eee != NULL && toupper(*eee) == 'N' ) scale_data = 0 ;
}
switch( nim->datatype ){
default:
fprintf(stderr,
"** AFNI can't handle NIFTI datatype=%d (%s) in file %s\n",
nim->datatype, nifti_datatype_string(nim->datatype), pathname );
RETURN(NULL) ;
break ;
case DT_UINT8: datum = scale_data ? MRI_float : MRI_byte ;
xform_data = scale_data;
break ;
case DT_INT16: datum = scale_data ? MRI_float : MRI_short ;
xform_data = scale_data;
break ;
case DT_FLOAT32: datum = MRI_float ; break ;
case DT_COMPLEX64: datum = MRI_complex ; break ;
case DT_RGB24: datum = MRI_rgb ; break ;
case DT_INT8: /* NIfTI-1 data types that AFNI can't handle directly */
case DT_UINT16:
case DT_INT32:
case DT_UINT32:
case DT_FLOAT64: datum = MRI_float ; xform_data = 1 ; break ;
#if 0
case DT_COMPLEX128: /* this case would be too much like real work */
fprintf(stderr,
"** AFNI convert NIFTI_datatype=%d (%s) in file %s to COMPLEX64\n",
nim->datatype, nifti_datatype_string(nim->datatype), pathname );
datum = MRI_complex ;
break ;
#endif
}
if( xform_data && !AFNI_noenv("AFNI_NIFTI_TYPE_WARN")) {
if (!n_xform_warn || AFNI_yesenv("AFNI_NIFTI_TYPE_WARN")) {/* ZSS 04/11 */
fprintf(stderr,
"** AFNI converts NIFTI_datatype=%d (%s) in file %s to FLOAT32\n",
nim->datatype, nifti_datatype_string(nim->datatype), pathname );
if (!AFNI_yesenv("AFNI_NIFTI_TYPE_WARN")) {
fprintf(stderr,
" Warnings of this type will be muted for this session.\n"
" Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.\n");
}
}
++n_xform_warn;
}
/* check for statistics code */
if( nim->intent_code >= NIFTI_FIRST_STATCODE &&
nim->intent_code <= NIFTI_LAST_STATCODE ){
if( nim->intent_code > FUNC_PT_TYPE ){
fprintf(stderr,
"** AFNI doesn't understand NIFTI statistic type %d (%s) in file %s\n",
nim->intent_code , nifti_intent_string(nim->intent_code) , pathname ) ;
} else {
statcode = nim->intent_code ;
if( nbuc > 1 ){
fprintf(stderr,
"** AFNI doesn't support NIFTI voxel-dependent statistic parameters"
" in file %s\n" , pathname ) ;
statcode = 0 ;
}
}
}
/* 23 Mar 2006: set qform or sform as having priority -- RWCox */
ppp = my_getenv("NIFTI_FORM_PRIORITY") ;
if( ppp == NULL ) ppp = getenv("AFNI_FORM_PRIORITY") ;
if( ppp == NULL ) ppp = getenv("AFNI_NIFTI_PRIORITY") ;
if( ppp == NULL ) ppp = getenv("AFNI_NIFTI_FORM") ;
if( ppp == NULL ) ppp = getenv("AFNI_NIFTI_FORM_PRIORITY") ;
if( ppp != NULL ){
char fp = toupper(*ppp) ;
if( fp == 'S' || fp == 'Q' ) form_priority = fp ;
else WARNING_message("Illegal NIFTI_FORM_PRIORITY='%s'",ppp) ;
}
/** 24 Mar 2006: check determs of qform and sform, if have both **/
if( nim->qform_code > 0 && nim->sform_code > 0 ){
float qdet , sdet ;
LOAD_MAT(R, nim->qto_xyz.m[0][0] ,
nim->qto_xyz.m[0][1] ,
nim->qto_xyz.m[0][2] ,
nim->qto_xyz.m[1][0] ,
nim->qto_xyz.m[1][1] ,
nim->qto_xyz.m[1][2] ,
nim->qto_xyz.m[2][0] ,
nim->qto_xyz.m[2][1] ,
nim->qto_xyz.m[2][2] ) ; qdet = MAT_DET(R) ;
LOAD_MAT(R, nim->sto_xyz.m[0][0] ,
nim->sto_xyz.m[0][1] ,
nim->sto_xyz.m[0][2] ,
nim->sto_xyz.m[1][0] ,
nim->sto_xyz.m[1][1] ,
nim->sto_xyz.m[1][2] ,
nim->sto_xyz.m[2][0] ,
nim->sto_xyz.m[2][1] ,
nim->sto_xyz.m[2][2] ) ; sdet = MAT_DET(R) ;
if( qdet*sdet < 0.0f )
WARNING_message("NIfTI('%s'): Qform/Sform handedness differ; %c wins!",
pathname , form_priority ) ;
}
/* KRH 07/11/05 -- adding ability to choose spatial transform
from the options of qform, sform, bothform, or noform.
If qform is present, it will be used.
If qform is absent, but sform present, then the sform
will be modified to be an orthogonal rotation and used.
If both qform and sform are absent, then we will have
an error.
Previously assumed qform present. */
/* 23 Mar 2006: use form_priority to choose between them */
if ((nim->qform_code > 0) && (nim->sform_code > 0) ) {
if( form_priority == 'Q' ) { use_qform = 1 ; use_sform = 0 ; }
else { use_qform = 0 ; use_sform = 1 ; }
} else if (nim->qform_code > 0){ use_qform = 1 ; use_sform = 0 ; }
else if (nim->sform_code > 0){ use_qform = 0 ; use_sform = 1 ; }
else {
use_qform = 0 ; use_sform = 0 ;
WARNING_message(
"NO spatial transform (neither qform nor sform), in NIfTI file '%s'" ,
pathname ) ;
}
/** now take NIfTI-1.1 coords and transform to AFNI codes **/
if (use_qform) {
float orgx, orgy, orgz ;
form_code = nim->qform_code;
/* determine orientation from the qto_xyz matrix,
which transforms (i,j,k) voxel indexes to (x,y,z) LPI coordinates */
LOAD_MAT(R, -nim->qto_xyz.m[0][0] , /* negate x and y */
-nim->qto_xyz.m[0][1] , /* coefficients, */
-nim->qto_xyz.m[0][2] , /* since AFNI works */
-nim->qto_xyz.m[1][0] , /* with RAI coords, */
-nim->qto_xyz.m[1][1] , /* but NIFTI uses */
-nim->qto_xyz.m[1][2] , /* LPI coordinates. */
nim->qto_xyz.m[2][0] , /* [Which is my own] */
nim->qto_xyz.m[2][1] , /* [damn fault!!!!!] */
nim->qto_xyz.m[2][2] ) ;
LOAD_MAT44(ijk_to_dicom44,
-nim->qto_xyz.m[0][0] , /* negate x and y */
-nim->qto_xyz.m[0][1] , /* coefficients, */
-nim->qto_xyz.m[0][2] , /* since AFNI works */
-nim->qto_xyz.m[0][3] ,
-nim->qto_xyz.m[1][0] , /* with RAI coords, */
-nim->qto_xyz.m[1][1] , /* but NIFTI uses */
-nim->qto_xyz.m[1][2] , /* LPI coordinates. */
-nim->qto_xyz.m[1][3] ,
nim->qto_xyz.m[2][0] , /* [Which is my own] */
nim->qto_xyz.m[2][1] , /* [damn fault!!!!!] */
nim->qto_xyz.m[2][2] ,
nim->qto_xyz.m[2][3] ) ;
orixyz = THD_matrix_to_orientation( R ) ; /* compute orientation codes */
iview = NIFTI_code_to_view(nim->qform_code);
/* load the offsets and the grid spacings */
if (ORIENT_xyz[orixyz.ijk[0]] == 'z' ) {
orgx = nim->qto_xyz.m[ORIENT_xyzint[orixyz.ijk[0]] - 1][3] ;
} else {
orgx = - nim->qto_xyz.m[ORIENT_xyzint[orixyz.ijk[0]] - 1][3] ;
}
if (ORIENT_xyz[orixyz.ijk[1]] == 'z' ) {
orgy = nim->qto_xyz.m[ORIENT_xyzint[orixyz.ijk[1]] - 1][3] ;
} else {
orgy = - nim->qto_xyz.m[ORIENT_xyzint[orixyz.ijk[1]] - 1][3] ;
}
if (ORIENT_xyz[orixyz.ijk[2]] == 'z' ) {
orgz = nim->qto_xyz.m[ORIENT_xyzint[orixyz.ijk[2]] - 1][3] ;
} else {
orgz = - nim->qto_xyz.m[ORIENT_xyzint[orixyz.ijk[2]] - 1][3] ;
}
LOAD_FVEC3( orgxyz , orgx ,
orgy ,
orgz ) ;
#if 0
LOAD_FVEC3( orgxyz , -nim->qto_xyz.m[0][3] , /* again, negate */
-nim->qto_xyz.m[1][3] , /* x and y coords */
nim->qto_xyz.m[2][3] ) ;
#endif
/* AFNI space units are always mm */
if( nim->xyz_units == NIFTI_UNITS_METER ){
nim->dx *= 1000.0 ; nim->dy *= 1000.0 ; nim->dz *= 1000.0 ;
} else if( nim->xyz_units == NIFTI_UNITS_MICRON ){
nim->dx *= 0.001 ; nim->dy *= 0.001 ; nim->dz *= 0.001 ;
}
LOAD_FVEC3( dxyz , (ORIENT_sign[orixyz.ijk[0]]=='+') ? nim->dx : -nim->dx ,
(ORIENT_sign[orixyz.ijk[1]]=='+') ? nim->dy : -nim->dy ,
(ORIENT_sign[orixyz.ijk[2]]=='+') ? nim->dz : -nim->dz ) ;
} else if (use_sform) {
int orimap[7] = { 6 , 1 , 0 , 2 , 3 , 4 , 5 } ;
int oritmp[3] ;
float dxtmp, dytmp, dztmp ;
float xmax, ymax, zmax ;
float orgx, orgy, orgz ;
float fig_merit, ang_merit ;
form_code = nim->sform_code;
/* convert sform to nifti orientation codes */
/* n2 10 Jul, 2015 [rickr] */
nifti_dmat44_to_orientation(nim->sto_xyz,
&oritmp[0], &oritmp[1], &oritmp[2] ) ;
/* convert nifti orientation codes to AFNI codes and store in vector */
LOAD_IVEC3( orixyz , orimap[oritmp[0]] ,
orimap[oritmp[1]] ,
orimap[oritmp[2]] ) ;
/* assume original view if there's no talairach id present */
iview = NIFTI_code_to_view(nim->sform_code);
/* load the offsets and the grid spacings */
if (ORIENT_xyz[orixyz.ijk[0]] == 'z' ) {
orgx = nim->sto_xyz.m[ORIENT_xyzint[orixyz.ijk[0]] - 1][3] ;
} else {
orgx = - nim->sto_xyz.m[ORIENT_xyzint[orixyz.ijk[0]] - 1][3] ;
}
if (ORIENT_xyz[orixyz.ijk[1]] == 'z' ) {
orgy = nim->sto_xyz.m[ORIENT_xyzint[orixyz.ijk[1]] - 1][3] ;
} else {
orgy = - nim->sto_xyz.m[ORIENT_xyzint[orixyz.ijk[1]] - 1][3] ;
}
if (ORIENT_xyz[orixyz.ijk[2]] == 'z' ) {
orgz = nim->sto_xyz.m[ORIENT_xyzint[orixyz.ijk[2]] - 1][3] ;
} else {
orgz = - nim->sto_xyz.m[ORIENT_xyzint[orixyz.ijk[2]] - 1][3] ;
}
LOAD_FVEC3( orgxyz , orgx ,
orgy ,
orgz ) ;
#if 0
LOAD_FVEC3( orgxyz , -nim->sto_xyz.m[0][3] , /* again, negate */
-nim->sto_xyz.m[1][3] , /* x and y coords */
nim->sto_xyz.m[2][3] ) ;
#endif
#define MAXNUM(a,b) ( (a) > (b) ? (a):(b))
#define MAX3(a,b,c) ( (MAXNUM(a,b)) > (MAXNUM(a,c)) ? (MAXNUM(a,b)):(MAXNUM(a,c)))
#define MINNUM(a,b) ( (a) < (b) ? (a):(b))
#define MIN3(a,b,c) ( (MINNUM(a,b)) < (MINNUM(a,c)) ? (MINNUM(a,b)):(MINNUM(a,c)))
dxtmp = sqrt ( nim->sto_xyz.m[0][0] * nim->sto_xyz.m[0][0] +
nim->sto_xyz.m[1][0] * nim->sto_xyz.m[1][0] +
nim->sto_xyz.m[2][0] * nim->sto_xyz.m[2][0] ) ;
xmax = MAX3(fabs(nim->sto_xyz.m[0][0]),fabs(nim->sto_xyz.m[1][0]),fabs(nim->sto_xyz.m[2][0])) / dxtmp ;
dytmp = sqrt ( nim->sto_xyz.m[0][1] * nim->sto_xyz.m[0][1] +
nim->sto_xyz.m[1][1] * nim->sto_xyz.m[1][1] +
nim->sto_xyz.m[2][1] * nim->sto_xyz.m[2][1] ) ;
ymax = MAX3(fabs(nim->sto_xyz.m[0][1]),fabs(nim->sto_xyz.m[1][1]),fabs(nim->sto_xyz.m[2][1])) / dytmp ;
dztmp = sqrt ( nim->sto_xyz.m[0][2] * nim->sto_xyz.m[0][2] +
nim->sto_xyz.m[1][2] * nim->sto_xyz.m[1][2] +
nim->sto_xyz.m[2][2] * nim->sto_xyz.m[2][2] ) ;
zmax = MAX3(fabs(nim->sto_xyz.m[0][2]),fabs(nim->sto_xyz.m[1][2]),fabs(nim->sto_xyz.m[2][2])) / dztmp ;
fig_merit = MIN3(xmax,ymax,zmax) ;
ang_merit = acos (fig_merit) * 180.0 / 3.141592653 ;
#if 0
if (fabs(ang_merit) > .01) {
WARNING_message (
"qform not present in:\n"
" '%s'\n"
" oblique sform used, and the worst axis is\n"
" %f degrees from plumb.\n"
" If you are performing spatial transformations on this dset, \n"
" or viewing/combining it with volumes of differing obliquity,\n"
" you should consider running: \n"
" 3dWarp -deoblique \n"
" on this and other oblique datasets in the same session.\n"
,pathname, ang_merit ) ;
}
#endif
if( nim->xyz_units == NIFTI_UNITS_METER ){
dxtmp *= 1000.0 ; dytmp *= 1000.0 ; dztmp *= 1000.0 ;
} else if( nim->xyz_units == NIFTI_UNITS_MICRON ){
dxtmp *= 0.001 ; dytmp *= 0.001 ; dztmp *= 0.001 ;
}
LOAD_FVEC3( dxyz , (ORIENT_sign[orixyz.ijk[0]]=='+') ? dxtmp : -dxtmp ,
(ORIENT_sign[orixyz.ijk[1]]=='+') ? dytmp : -dytmp ,
(ORIENT_sign[orixyz.ijk[2]]=='+') ? dztmp : -dztmp ) ;
LOAD_MAT44(ijk_to_dicom44, -nim->sto_xyz.m[0][0] , /* negate x and y */
-nim->sto_xyz.m[0][1] , /* coefficients, */
-nim->sto_xyz.m[0][2] , /* since AFNI works */
-nim->sto_xyz.m[0][3] ,
-nim->sto_xyz.m[1][0] , /* with RAI coords, */
-nim->sto_xyz.m[1][1] , /* but NIFTI uses */
-nim->sto_xyz.m[1][2] , /* LPI coordinates. */
-nim->sto_xyz.m[1][3] ,
nim->sto_xyz.m[2][0] , /* [Which is my own] */
nim->sto_xyz.m[2][1] , /* [damn fault!!!!!] */
nim->sto_xyz.m[2][2] ,
nim->sto_xyz.m[2][3] ) ;
} else { /* NO SPATIAL XFORM. BAD BAD BAD BAD BAD BAD. */
float dxtmp, dytmp, dztmp ;
/* if pixdim data are present, use them in order to set pixel
dimensions. otherwise, set the dimensions to 1 unit. */
dxtmp = ((nim->pixdim[1] > 0) ? nim->pixdim[1] : 1) ;
dytmp = ((nim->pixdim[2] > 0) ? nim->pixdim[2] : 1) ;
dztmp = ((nim->pixdim[3] > 0) ? nim->pixdim[3] : 1) ;
if( nim->xyz_units == NIFTI_UNITS_METER ){
dxtmp *= 1000.0 ; dytmp *= 1000.0 ; dztmp *= 1000.0 ;
} else if( nim->xyz_units == NIFTI_UNITS_MICRON ){
dxtmp *= 0.001 ; dytmp *= 0.001 ; dztmp *= 0.001 ;
}
/* set orientation to LPI by default */
LOAD_IVEC3( orixyz , 1 ,
2 ,
4 ) ;
LOAD_FVEC3( dxyz , (ORIENT_sign[orixyz.ijk[0]]=='+') ? dxtmp : -dxtmp ,
(ORIENT_sign[orixyz.ijk[1]]=='+') ? dytmp : -dytmp ,
(ORIENT_sign[orixyz.ijk[2]]=='+') ? dztmp : -dztmp ) ;
iview = NIFTI_default_view();
/* set origin to 0,0,0 */
LOAD_FVEC3( orgxyz , 0 ,
0 ,
0 ) ;
/* put scaled identity matrix by default */
LOAD_MAT44(ijk_to_dicom44, dxtmp, 0.0, 0.0, 0.0,
0.0, dytmp, 0.0, 0.0,
0.0, 0.0, dztmp, 0.0 );
}
/*-- make an AFNI dataset! --*/
dset = EDIT_empty_copy(NULL) ;
ppp = THD_trailname(pathname,0) ; /* strip directory */
MCW_strncpy( prefix , ppp , THD_MAX_PREFIX ) ; /* to make prefix */
/* You need to set the path too
before, if you loaded ~/tmp/joe.nii the path appeared
to be ./joe.nii, troubling in multiple instances.
ZSS Dec 2011 */
THD_init_diskptr_names( dset->dblk->diskptr ,
THD_filepath(pathname) ,
NULL , prefix ,
dset->view_type , True );
nxyz.ijk[0] = nim->nx ; /* grid dimensions */
nxyz.ijk[1] = nim->ny ;
nxyz.ijk[2] = nim->nz ;
dset->idcode.str[0] = 'N' ; /* overwrite 1st 3 bytes with something special */
dset->idcode.str[1] = 'I' ;
dset->idcode.str[2] = 'I' ;
MCW_hash_idcode( pathname , dset ) ; /* 06 May 2005 */
EDIT_dset_items( dset ,
ADN_prefix , prefix ,
ADN_datum_all , datum ,
ADN_nxyz , nxyz ,
ADN_xyzdel , dxyz ,
ADN_xyzorg , orgxyz ,
ADN_xyzorient , orixyz ,
ADN_malloc_type , DATABLOCK_MEM_MALLOC ,
ADN_view_type , iview ,
ADN_type , (statcode != 0) ? HEAD_FUNC_TYPE
: HEAD_ANAT_TYPE ,
ADN_none ) ;
/* copy transformation matrix to dataset structure */
/* moved after setting grid 4 Apr 2014 [rickr,drg] */
dset->daxes->ijk_to_dicom_real = ijk_to_dicom44;
/* not a time dependent dataset */
if( ntt < 2 ){
EDIT_dset_items( dset ,
ADN_nvals , nbuc ,
ADN_datum_all , datum ,
ADN_func_type , (statcode != 0) ? FUNC_BUCK_TYPE
: ANAT_BUCK_TYPE ,
ADN_none ) ;
} else { /* is a time dependent dataset */
if( nim->time_units == NIFTI_UNITS_MSEC ){
nim->dt *= 0.001 ;
nim->toffset *= 0.001 ;
} else if( nim->time_units == NIFTI_UNITS_USEC ){
nim->dt *= 1.e-6 ;
nim->toffset *= 1.e-6 ;
}
EDIT_dset_items( dset ,
ADN_nvals , ntt ,
ADN_ntt , ntt ,
ADN_datum_all , datum ,
ADN_ttorg , nim->toffset , /* 12 Oct 2007 [rickr] */
ADN_ttdel , nim->dt ,
ADN_ttdur , 0.0 ,
ADN_tunits , UNITS_SEC_TYPE ,
ADN_func_type , (statcode != 0) ? FUNC_FIM_TYPE
: ANAT_EPI_TYPE ,
ADN_none ) ;
/* if present, add stuff about the slice-timing offsets */
if( nim->slice_dim == 3 && /* AFNI can only deal with */
nim->slice_code > 0 && /* slice timing offsets */
nim->slice_duration > 0.0 && /* along the k-axis of */
nim->slice_start >= 0 && /* the dataset volume */
nim->slice_start < nim->nz &&
nim->slice_end > nim->slice_start &&
nim->slice_end < nim->nz ){
float *toff=(float *)calloc(sizeof(float),nim->nz) , tsl ;
int kk ;
if( nim->time_units == NIFTI_UNITS_MSEC ) nim->slice_duration *= 0.001;
else if( nim->time_units == NIFTI_UNITS_USEC ) nim->slice_duration *= 1.e-6;
/* set up slice time offsets in the divers orders */
switch( nim->slice_code ){
case NIFTI_SLICE_SEQ_INC:
tsl = 0.0 ;
for( kk=nim->slice_start ; kk <= nim->slice_end ; kk++ ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
break ;
case NIFTI_SLICE_SEQ_DEC:
tsl = 0.0 ;
for( kk=nim->slice_end ; kk >= nim->slice_end ; kk-- ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
break ;
case NIFTI_SLICE_ALT_INC:
tsl = 0.0 ;
for( kk=nim->slice_start ; kk <= nim->slice_end ; kk+=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
for( kk=nim->slice_start+1 ; kk <= nim->slice_end ; kk+=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
break ;
case NIFTI_SLICE_ALT_INC2:
tsl = 0.0 ;
for( kk=nim->slice_start+1 ; kk <= nim->slice_end ; kk+=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
for( kk=nim->slice_start ; kk <= nim->slice_end ; kk+=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
break ;
case NIFTI_SLICE_ALT_DEC:
tsl = 0.0 ;
for( kk=nim->slice_end ; kk >= nim->slice_start ; kk-=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
for( kk=nim->slice_end-1 ; kk >= nim->slice_start ; kk-=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
break ;
case NIFTI_SLICE_ALT_DEC2:
tsl = 0.0 ;
for( kk=nim->slice_end-1 ; kk >= nim->slice_start ; kk-=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
for( kk=nim->slice_end ; kk >= nim->slice_start ; kk-=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
break ;
}
EDIT_dset_items( dset ,
ADN_nsl , nim->nz ,
ADN_zorg_sl , orgxyz.xyz[2] ,
ADN_dz_sl , dxyz.xyz[2] ,
ADN_toff_sl , toff ,
ADN_none ) ;
free(toff) ;
} /* end of slice timing stuff */
} /* end of 3D+time dataset stuff */
/* set atlas space based on NIFTI s/qform code */
NIFTI_code_to_space(form_code,dset);
/* add statistics, if present */
if( statcode != 0 ){
for( ibr=0 ; ibr < nvals ; ibr++ )
EDIT_STATAUX4(dset,ibr,statcode,nim->intent_p1,nim->intent_p2,nim->intent_p3,0) ;
}
/*-- flag to read data from disk using NIFTI functions --*/
dset->dblk->diskptr->storage_mode = STORAGE_BY_NIFTI ;
strcpy( dset->dblk->diskptr->brick_name , pathname ) ;
dset->dblk->diskptr->byte_order = nim->byteorder ;
#if 0
for( ibr=0 ; ibr < nvals ; ibr++ ){ /* make sub-brick labels */
sprintf(prefix,"%s[%d]",tname,ibr) ;
EDIT_BRICK_LABEL( dset , ibr , prefix ) ;
}
#endif
/** 10 May 2005: see if there is an AFNI extension;
if so, load attributes from it and
then edit the dataset appropriately **/
{ int ee ; /* extension index */
/* scan extension list to find the first AFNI extension */
for( ee=0 ; ee < nim->num_ext ; ee++ )
if( nim->ext_list[ee].ecode == NIFTI_ECODE_AFNI &&
nim->ext_list[ee].esize > 32 &&
nim->ext_list[ee].edata != NULL ) break ;
/* if found an AFNI extension ... */
if( ee < nim->num_ext ){
char *buf = nim->ext_list[ee].edata , *rhs , *cpt ;
int nbuf = nim->ext_list[ee].esize - 8 ;
NI_stream ns ;
void *nini ;
NI_group *ngr , *nngr ;
/* if have data, it's long enough, and starts properly, then ... */
if( buf != NULL && nbuf > 32 && strncmp(buf,"<?xml",5)==0 ){
if( buf[nbuf-1] != '\0' ) buf[nbuf-1] = '\0' ; /* for safety */
cpt = strstr(buf,"?>") ; /* find XML prolog close */
if( cpt != NULL ){ /* if found it, then ... */
ns = NI_stream_open( "str:" , "r" ) ;
NI_stream_setbuf( ns , cpt+2 ) ; /* start just after prolog */
nini = NI_read_element(ns,1) ; /* get root element */
NI_stream_close(ns) ;
if( NI_element_type(nini) == NI_GROUP_TYPE ){ /* must be a group */
ngr = (NI_group *)nini ;
if( strcmp(ngr->name,"AFNI_attributes") == 0 ){ /* root is OK */
nngr = ngr ;
} else { /* search in group for proper element */
int nn ; void **nnini ;
nn = NI_search_group_deep( ngr , "AFNI_attributes" , &nnini ) ;
if( nn <= 0 ) nngr = NULL ;
else { nngr = (NI_group *)nnini[0]; NI_free(nnini); }
}
if( NI_element_type(nngr) == NI_GROUP_TYPE ){ /* have good name */
rhs = NI_get_attribute( nngr , "self_idcode" ) ;
if( rhs == NULL )
rhs = NI_get_attribute( nngr , "AFNI_idcode" ) ;
if( rhs != NULL ) /* set dataset ID code from XML attribute */
MCW_strncpy( dset->idcode.str , rhs , MCW_IDSIZE ) ;
rhs = NI_get_attribute( nngr , "NIfTI_nums" ) ; /* check if */
if( rhs != NULL ){ /* dataset dimensions */
char buf[128] ; /* were altered */
sprintf(buf,"%ld,%ld,%ld,%ld,%ld,%d" , /* 12 May 2005 */
nim->nx, nim->ny, nim->nz, nim->nt, nim->nu, nim->datatype );
if( strcmp(buf,rhs) != 0 ){
static int nnn=0 ;
if(nnn==0){fprintf(stderr,"\n"); nnn=1;}
fprintf(stderr,
"** WARNING: NIfTI file %s dimensions altered since "
"AFNI extension was added\n",pathname ) ;
}
}
THD_dblkatr_from_niml( nngr , dset->dblk ); /* load attributes */
THD_datablock_apply_atr( dset ) ; /* apply to dataset struct */
}
NI_free_element( ngr ) ; /* get rid of the root element */
} /* end of if found a group element at the root */
} /* end of if extension data array had an XML prolog close */
} /* end of if had a good extension data array */
} /* end of if had an AFNI extension */
} /* end of processing extensions */
/* return unpopulated dataset */
nifti_image_free(nim) ; RETURN(dset) ;
}
