char * THD_find_executable( char *ename )
{
char *etr , *str ;
int ii ;
ENTRY("THD_find_executable") ;
if( !einit ){ einit = 1 ; elist = THD_getpathprogs(NULL, 1) ; }
if( elist == NULL ) RETURN(NULL) ;
etr = THD_trailname( ename , 0 ) ;
for( ii=0 ; ii < elist->num ; ii++ ){
str = THD_trailname( elist->ar[ii] , 0 ) ;
if( strcmp(str,etr) == 0 ) RETURN(elist->ar[ii]) ;
}
RETURN(NULL) ;
}
char *web_prog_help_link(char *prog, int style)
{
char *progname=NULL;
static char weblinka[10][1024]={""}, *weblink;
static int n;
++n; if (n>9) n = 0;
weblink = (char *)weblinka[n]; weblink[0]='\0';
if (!prog) return(weblink);
if (!strcmp(prog,"ALL")) {
if (style == 0) {
snprintf(weblink,1020*sizeof(char),
"https://afni.nimh.nih.gov/pub/dist/doc/program_help/%s.html",
"all-of-them");
} else {
/* Nothing yet, return old */
snprintf(weblink,1020*sizeof(char),
"https://afni.nimh.nih.gov/pub/dist/doc/program_help/%s.html",
"all-of-them");
}
} else {
if (!(progname = THD_find_executable(prog))) {
ERROR_message("Could not find executable %s.\n",
prog);
return(weblink);
}
if (style == 0) {
snprintf(weblink,1020*sizeof(char),
"https://afni.nimh.nih.gov/pub/dist/doc/program_help/%s.html",
THD_trailname(progname,0));
} else {
/* Nothing yet, return old */
snprintf(weblink,1020*sizeof(char),
"https://afni.nimh.nih.gov/pub/dist/doc/program_help/%s.html",
THD_trailname(progname,0));
}
}
return(weblink);
}
int list_afni_files(int type, int withpath, int withnum)
{
int nprogs=0, ii=0;
char *etr=NULL, s[12];
THD_string_array *progs=NULL;
switch (type) {
case 0:
if (!(progs = THD_get_all_afni_executables())) {
ERROR_message(
"Cannot get list of programs from your afni bin directory %s",
THD_abindir(1));
RETURN(0);
}
break;
case 1:
if (!(progs = THD_get_all_afni_readmes())) {
ERROR_message(
"Cannot get list of readmes from your afni bin directory %s",
THD_abindir(1));
RETURN(0);
}
break;
case 2:
if (!(progs = THD_get_all_afni_dsets())) {
ERROR_message(
"Cannot get list of dsets from your afni bin directory %s",
THD_abindir(1));
RETURN(0);
}
break;
default:
ERROR_message("Whatchyoutalkinboutwillis?");
RETURN(0);
break;
}
for (ii=0; ii<progs->num ; ii++ ){
if (withpath) etr = progs->ar[ii];
else etr = THD_trailname( progs->ar[ii] , 0 ) ;
if (withnum) {
sprintf(s,"%d", ii);
fprintf(stdout," %3s. %s\n", s, etr);
} else {
fprintf(stdout,"%s\n", etr);
}
}
nprogs = progs->num;
DESTROY_SARR(progs);
return(nprogs);
}
/*! get all 3D datasets in directory where afni resides */
THD_string_array * THD_get_all_afni_dsets(void )
{
THD_string_array *outar=NULL, *elist=NULL;
char *af=NULL, *etr=NULL;
int N_af, N_afni=strlen("afni"), iaf=0, ii=0, smode, *isrt=NULL;
char scomm[256]={""};
ENTRY("THD_get_all_afni_dsets");
if (!(elist = get_elist()) ||
!(af = THD_abindir(1))) {
ERROR_message("Could not find afni, we're doomed daddy!");
RETURN(outar);
}
N_af = strlen(af);
elist = THD_get_all_files(af,'\0');
/* Now get all dsets under af */
INIT_SARR( outar );
for (ii=0, iaf=0; ii<elist->num ; ii++ ){
smode = storage_mode_from_filename(elist->ar[ii]);
etr = THD_trailname( elist->ar[ii] , 0 ) ;
if (
!THD_is_directory(elist->ar[ii]) &&
!strncmp(af, elist->ar[ii], N_af) &&
(smode > STORAGE_UNDEFINED && smode <= LAST_STORAGE_MODE) &&
(smode != STORAGE_BY_BRICK || /* don't want the .BRICK, just .HEAD */
STRING_HAS_SUFFIX(elist->ar[ii], ".HEAD")) &&
(smode != STORAGE_BY_NIFTI || /* don't want the .img */
!STRING_HAS_SUFFIX(elist->ar[ii], ".img")) &&
strcmp(etr,"AFNI_atlas_spaces.niml")
) {
ADDTO_SARR( outar , elist->ar[ii] ) ; ++iaf;
/*fprintf(stderr," %d- %s smode %d[%d]%d\n", iaf, etr,
STORAGE_UNDEFINED, smode, LAST_STORAGE_MODE); */
} else {
/*fprintf(stderr," skip %s (%s) smode %d[%d]%d\n",
elist->ar[ii], af, STORAGE_UNDEFINED, smode, LAST_STORAGE_MODE); */
}
}
qsort(outar->ar, outar->num, sizeof(char*),
(int(*) (const void *, const void *))compare_string);
if( SARR_NUM(outar) == 0 ) DESTROY_SARR(outar) ;
if (af) free(af); af = NULL;
RETURN( outar );
}
/*! Get all readme files in directory where afni resides */
THD_string_array * THD_get_all_afni_readmes(void )
{
THD_string_array *outar=NULL, *elist=NULL;
char *af=NULL, *etr=NULL, *key="README.";
int N_af, N_afni=strlen("afni"), iaf=0, ii=0, *isrt=NULL, N_key=0;
char scomm[256]={""};
ENTRY("THD_get_all_afni_readmes");
if (!(elist = get_elist()) ||
!(af = THD_abindir(1))) {
ERROR_message("Could not find afni, we're doomed daddy!");
RETURN(outar);
}
/* remove afni from the end to get the path */
N_af = strlen(af);
elist = THD_get_all_files(af,'\0');
/* Now get all readmes under af */
N_key = strlen(key);
INIT_SARR( outar );
for (ii=0, iaf=0; ii<elist->num ; ii++ ){
etr = THD_trailname( elist->ar[ii] , 0 ) ;
if (!THD_is_directory(elist->ar[ii]) &&
!strncmp(af, elist->ar[ii], N_af) &&
!strncmp(key, etr, N_key)
) {
ADDTO_SARR( outar , elist->ar[ii] ) ; ++iaf;
/* fprintf(stderr," %d- %s (%s)\n", iaf, elist->ar[ii], etr); */
} else {
/* fprintf(stderr," skip %s (%s)\n", elist->ar[ii], af); */
}
}
qsort(outar->ar, outar->num, sizeof(char*),
(int(*) (const void *, const void *))compare_string);
if( SARR_NUM(outar) == 0 ) DESTROY_SARR(outar) ;
if (af) free(af); af = NULL;
RETURN( outar );
}
/* Check the static list in prog_opts.c to find whether
or not an option exists for a particular program.
Return 1: If program is found and the option exists
0: If program found and option does not exist
-1: If program was not in the list
-2: If the caller needs brains.
*/
int check_for_opt_in_prog_opts(char *prog, char *opt)
{
PROG_OPTS PO;
int i=0;
char sbuf[64]={""}, *found;
if (!prog || !opt) return(-2);
PO = poptslist[i++];
while (PO.program) {
if (!strcmp(THD_trailname(prog, 0),PO.program)) {
snprintf(sbuf, 64, "%s;", opt);
/* fprintf(stderr,"%s, %s-->%s, %s\n",
prog, sbuf, PO.program, PO.options); */
if ((found=strstr(PO.options,sbuf))) {
return(1);
} else {
return(0);
}
}
PO = poptslist[i++];
}
/* program not found */
return(-1);
}
THD_session * THD_init_session( char *sessname )
{
THD_session *sess ;
XtPointer_array *dblk_arrarr ;
THD_datablock_array *dblk_arr ;
THD_3dim_dataset *dset=NULL , *temp_dset;
THD_3dim_dataset_array *dset_arr ;
int ibar , idset , iview , nds , qview=-666 ;
ENTRY("THD_init_session") ;
/*-- sanity check --*/
if( sessname == NULL || strlen(sessname) == 0 || !THD_is_directory(sessname) )
RETURN( NULL ) ;
/*-- initialize session --*/
sess = myXtNew( THD_session ) ;
sess->type = SESSION_TYPE ;
sess->parent = NULL ;
#ifdef DEBUG_SESSIONS
fprintf(stderr, "blanking session\n");
#endif
BLANK_SESSION(sess) ; /* null out all entries */
/* save directory name, with a trailing slash */
MCW_strncpy( sess->sessname , sessname , THD_MAX_NAME ) ;
iview = strlen(sess->sessname) ;
if( sess->sessname[iview-1] != '/' ) { /* tack trailing / onto sessname */
sess->sessname[iview] = '/' ;
sess->sessname[iview+1] = '\0' ;
} else {
iview-- ; /* iview now points to last non-NUL character in string */
}
/* save last name from sessname */
#if 1
{ char *env = my_getenv( "AFNI_SESSTRAIL" ) ;
int tt = 0 ;
if( env != NULL ) tt = strtol(env,NULL,10) ;
env = THD_trailname(sess->sessname,tt) ;
tt = 1+strlen(env) - THD_MAX_NAME ;
if( tt < 0 ) tt = 0 ;
strcpy( sess->lastname , env+tt ) ;
}
#else
for( iview-- ; iview >= 0 ; iview-- )
if( sess->sessname[iview] == '/' ) break ;
MCW_strncpy( sess->lastname, &(sess->sessname[iview+1]), THD_MAX_NAME ) ;
#endif
/*-- override dataset 'view'?? [30 May 2013] --*/
{ char *env = my_getenv("AFNI_OVERRIDE_VIEW") ;
if( env != NULL ) {
if( toupper(*env) == 'T' ) qview = VIEW_TALAIRACH_TYPE ;
else if( toupper(*env) == 'O' ) qview = VIEW_ORIGINAL_TYPE ;
else
WARNING_message("AFNI_OVERRIDE_VIEW=%s is not understood",env) ;
}
}
/*-- read all datablocks --*/
dblk_arrarr = THD_init_alldir_datablocks( sess->sessname ) ;
/*-- for each datablock array ... --*/
for( ibar=0 ; ibar < dblk_arrarr->num ; ibar++ ) {
/*-- get the current array of datablocks --*/
dblk_arr = (THD_datablock_array *) dblk_arrarr->ar[ibar] ;
if( dblk_arr == NULL || dblk_arr->num <= 0 ) continue ; /* huh? */
/*-- convert it into an array of datasets --*/
dset_arr = THD_array_3dim_from_block( dblk_arr ) ;
if( dset_arr == NULL || dset_arr->num <= 0 ) continue ;
/*-- place it into the next row of the THD_session [28 Jul 2003] --*/
nds = sess->num_dsset ;
if( nds >= THD_MAX_SESSION_SIZE ) { /* bad! */
fprintf(stderr,
"\n*** Session %s table overflow with dataset %s ***\n",
sessname , dset_arr->ar[0]->self_name) ;
for( idset=0 ; idset < dset_arr->num ; idset++ )
THD_delete_3dim_dataset( dset_arr->ar[idset] , False ) ;
FREE_3DARR(dset_arr) ;
continue ; /* skip to next dblk_arr (ibar loop) */
}
/*-- put each dataset into this row in its view place --*/
for( idset=0 ; idset < dset_arr->num ; idset++ ) {
dset = dset_arr->ar[idset] ;
iview = dset->view_type ;
if( qview >= 0 ) iview = qview ; /* 30 May 2013 */
if( GET_SESSION_DSET(sess,nds,iview) != NULL ) { /* should never happen */
fprintf(stderr,
"\n*** Session %s has duplicate dataset views of %s ***\n",
sessname , dset->self_name) ;
THD_delete_3dim_dataset( dset , False ) ;
} else {
#ifdef DEBUG_SESSIONS
fprintf(stderr,"\nputting datasets into initial view \n");
#endif
SET_SESSION_DSET(dset, sess, nds, iview); /* should always happen */
/* sess->dsset_xform_table[nds][iview] = dset ; */ /* should always happen */
}
}
sess->num_dsset ++ ; /* one more row */
FREE_3DARR(dset_arr) ;
} /* end of loop over each datablock array (ibar) */
/*-- throw away the datablock arrays at this point --*/
STATUS("trashing dblk_arrarr") ;
for( ibar=0 ; ibar < dblk_arrarr->num ; ibar++ ) {
dblk_arr = (THD_datablock_array *) dblk_arrarr->ar[ibar] ;
FREE_DBARR( dblk_arr ) ;
}
FREE_XTARR( dblk_arrarr ) ;
/*-- 29 Oct 2001: try to read .mnc "datasets" --*/
if( !AFNI_noenv("AFNI_MINC_DATASETS") ) {
char ename[THD_MAX_NAME] , **fn_minc , *eee ;
int num_minc , ii ;
STATUS("looking for MINC files") ;
strcpy(ename,sess->sessname) ;
strcat(ename,"*.mnc") ;
eee = ename ;
MCW_file_expand( 1,&eee , &num_minc,&fn_minc ) ; /* find files */
if( num_minc > 0 ) { /* got some! */
STATUS("opening MINC files") ;
for( ii=0 ; ii < num_minc ; ii++ ) { /* loop over files */
dset = THD_open_minc( fn_minc[ii] ) ; /* try it on */
if( !ISVALID_DSET(dset) ) continue ; /* doesn't fit? */
nds = sess->num_dsset ;
if( nds >= THD_MAX_SESSION_SIZE ) {
fprintf(stderr,
"\n*** Session %s table overflow with MINC dataset %s ***\n",
sessname , fn_minc[ii] ) ;
THD_delete_3dim_dataset( dset , False ) ;
break ; /* out of for loop */
}
iview = dset->view_type ;
SET_SESSION_DSET(dset, sess, nds, iview);
/* sess->dsset_xform_table[nds][iview] = dset ;*/
sess->num_dsset ++ ;
} /* end of loop over files */
MCW_free_expand( num_minc , fn_minc ) ;
} /* end of if we found MINC files */
}
/*-- 06 Apr 2005: try to read NIfTI-1 files [KRH and RWC] --*/
if( !AFNI_noenv("AFNI_NIFTI_DATASETS") ) {
char *ename[2] , **fn_nifti ;
int num_nifti , ii ;
STATUS("looking for NIFTI files") ;
ename[0] = AFMALL(char, THD_MAX_NAME) ;
ename[1] = AFMALL(char, THD_MAX_NAME) ;
strcpy(ename[0],sess->sessname) ;
strcat(ename[0],"*.nii") ;
strcpy(ename[1],sess->sessname) ;
strcat(ename[1],"*.nii.gz") ;
MCW_file_expand( 2,ename , &num_nifti,&fn_nifti ) ; /* find files */
free(ename[0]) ;
free(ename[1]) ;
if( num_nifti > 0 ) { /* got some! */
STATUS("opening NIFTI files") ;
for( ii=0 ; ii < num_nifti ; ii++ ) { /* loop over files */
dset = THD_open_nifti( fn_nifti[ii] ) ; /* try it on */
if( !ISVALID_DSET(dset) ) continue ; /* doesn't fit? */
nds = sess->num_dsset ;
if( nds >= THD_MAX_SESSION_SIZE ) {
fprintf(stderr,
"\n*** Session %s table overflow with NIfTI dataset %s ***\n",
sessname , fn_nifti[ii] ) ;
THD_delete_3dim_dataset( dset , False ) ;
break ; /* out of for loop */
}
iview = dset->view_type ;
SET_SESSION_DSET(dset, sess, nds, iview);
/* sess->dsset_xform_table[nds][iview] = dset ;*/
sess->num_dsset ++ ;
} /* end of loop over files */
MCW_free_expand( num_nifti , fn_nifti ) ;
} /* end of if we found NIFTI files */
}
MRI_shindss * GRINCOR_read_input( char *fname )
{
NI_element *nel=NULL ;
char *dfname=NULL , *atr ;
NI_float_array *facar ; NI_int_array *nvar, *nnode=NULL, *ninmask=NULL;
MRI_shindss *shd ;
long long nbytes_needed , nbytes_dfname=0 ; int fdes ;
void *var ; int ids , nvmax , nvtot ;
int datum , datum_size ;
char *geometry_string=NULL ;
THD_3dim_dataset *tdset=NULL; int nvox;
int no_ivec=0 , *ivec=NULL , *nvals=NULL , nvec,ndset ; float *fac=NULL ;
NI_str_array *slabar=NULL ;
if( fname == NULL || *fname == '\0' ) GQUIT(NULL) ;
/* get data element */
if (!THD_is_ondisk(fname))
GQUIT("not on disk") ;
nelshd = nel = NI_read_element_fromfile(fname) ;
if( nel == NULL || nel->type != NI_ELEMENT_TYPE )
GQUIT("not properly formatted") ;
if( strcmp(nel->name,"3dGroupInCorr") != 0 )
GQUIT("data element name is not '3dGroupInCorr'") ;
/* no data vector ==> using all voxels */
no_ivec = ( nel->vec_num < 1 ||
nel->vec_len < 1 || nel->vec_typ[0] != NI_INT ) ;
/* number of vectors in each dataset */
atr = NI_get_attribute(nel,"nvec");
if( atr == NULL ) GQUIT("nvec attribute missing?") ;
nvec = (int)strtod(atr,NULL) ;
if( nvec < 2 || (!no_ivec && nel->vec_len != nvec) )
GQUIT("nvec attribute has illegal value") ;
/* number of datasets */
atr = NI_get_attribute(nel,"ndset");
if( atr == NULL ) GQUIT("ndset attribute missing") ;
ndset = (int)strtod(atr,NULL) ;
if( ndset < 1 ) GQUIT("ndset attribute has illegal value") ;
/* number of time points in each dataset (varies with dataset) */
atr = NI_get_attribute(nel,"nvals");
if( atr == NULL ) GQUIT("nvals attribute missing") ;
nvar = NI_decode_int_list(atr,",") ;
if( nvar == NULL || nvar->num < ndset )
GQUIT("nvals attribute doesn't match ndset") ;
nvals = nvar->ar ; nvar->ar = NULL ; NI_delete_int_array(nvar) ;
nvmax = nvtot = nvals[0] ;
for( ids=1 ; ids < ndset ; ids++ ){ /* Feb 2011 */
nvtot += nvals[ids] ;
if( nvals[ids] > nvmax ) nvmax = nvals[ids] ;
}
/* dataset labels [23 May 2010] */
atr = NI_get_attribute(nel,"dset_labels") ;
if( atr != NULL ){
slabar = NI_decode_string_list(atr,";,") ;
if( slabar == NULL || slabar->num < ndset )
GQUIT("dset_labels attribute invalid") ;
}
/* datum of datasets */
atr = NI_get_attribute(nel,"datum") ;
if( atr != NULL && strcasecmp(atr,"byte") == 0 ){
datum = 1 ; datum_size = sizeof(sbyte) ;
} else {
datum = 2 ; datum_size = sizeof(short) ;
}
/* number of bytes needed:
sizeof(datum) * number of vectors per dataset
* number of datasets
* sum of per dataset vector lengths */
nbytes_needed = 0 ;
for( ids=0 ; ids < ndset ; ids++ ) nbytes_needed += nvals[ids] ;
nbytes_needed *= ((long long)nvec) * datum_size ;
if( nbytes_needed >= twogig &&
( sizeof(void *) < 8 || sizeof(size_t) < 8 ) ) /* too much for 32-bit */
GQUIT("datafile size exceeds 2 GB -- you need a 64-bit computer!") ;
/* scale factor for each dataset */
atr = NI_get_attribute(nel,"fac") ;
if( atr == NULL ) GQUIT("fac attribute missing") ;
facar = NI_decode_float_list(atr,",") ;
if( facar == NULL || facar->num < ndset )
GQUIT("can't decode fac attribute") ;
fac = facar->ar ; facar->ar = NULL ; NI_delete_float_array(facar) ;
for( ids=0 ; ids < ndset ; ids++ ) if( fac[ids] <= 0.0f ) fac[ids] = 1.0f ;
/* grid definition */
atr = NI_get_attribute(nel,"geometry") ;
if( atr == NULL ) GQUIT("geometry attribute missing") ;
geometry_string = strdup(atr) ;
tdset = EDIT_geometry_constructor( geometry_string , "GrpInCorr" ) ;
if( tdset == NULL ) GQUIT("can't decode geometry attribute") ;
nvox = DSET_NVOX(tdset) ;
if( no_ivec && nvox != nvec )
GQUIT("geometry attribute doesn't match nvec attribute") ;
if( !no_ivec && nvox < nvec )
GQUIT("geometry attribute specifies too few voxels") ;
/* name of data file: check its size against what's needed */
#if 0
atr = NI_get_attribute(nel,"datafile") ;
if( atr != NULL ){
dfname = strdup(atr) ; nbytes_dfname = THD_filesize(dfname) ;
if( nbytes_dfname <= 0 && strstr(dfname,"/") != NULL ){
char *tnam = THD_trailname(atr,0) ;
nbytes_dfname = THD_filesize(tnam) ;
if( nbytes_dfname > 0 ){ free(dfname); dfname = strdup(tnam); }
}
}
#endif
if( nbytes_dfname <= 0 && strstr(fname,".niml") != NULL ){
if( dfname != NULL ) free(dfname) ;
dfname = strdup(fname) ; strcpy(dfname+strlen(dfname)-5,".data") ;
nbytes_dfname = THD_filesize(dfname) ;
}
if( nbytes_dfname <= 0 ){
char mess[THD_MAX_NAME+256] ;
sprintf(mess,"datafile is missing (%s)",dfname) ; GQUIT(mess) ;
} else if( nbytes_dfname < nbytes_needed ){
char mess[THD_MAX_NAME+1024] ;
sprintf(mess,"datafile %s has %s bytes but needs at least %s",
dfname ,
commaized_integer_string(nbytes_dfname) ,
commaized_integer_string(nbytes_needed) ) ;
GQUIT(mess) ;
} else {
INFO_message("EIC: data file %s found with %s bytes of data",
dfname , commaized_integer_string(nbytes_dfname) ) ;
}
fdes = open( dfname , O_RDWR ) ;
if( fdes < 0 ){
char mess[THD_MAX_NAME+256] ;
sprintf(mess,"can't open datafile (%s)",dfname) ; GQUIT(mess) ;
}
NI_set_attribute( nelshd , "datafile" , dfname ) ;
/* ivec[i] is the voxel spatial index of the i-th vector */
if( no_ivec ){
ivec = NULL ; /* means all voxels: ivec[i] == i */
} else {
ivec = (int *)nel->vec[0] ; /* copy pointer */
nel->vec[0] = NULL ; /* NULL out in element so won't be free-ed */
}
/* And stuff for LR surface pairs ZSS Jan 09*/
if ((atr=NI_get_attribute(nel,"LRpair_nnode"))) {
nnode = NI_decode_int_list(atr,",") ;
}
if ((atr=NI_get_attribute(nel,"LRpair_ninmask"))) {
ninmask = NI_decode_int_list(atr,",") ;
}
/* create output struct */
shd = (MRI_shindss *)malloc(sizeof(MRI_shindss)) ;
shd->nvals = nvals ; shd->nvals_max = nvmax ; shd->nvals_tot = nvtot ;
shd->nvec = nvec ;
shd->ndset = ndset ;
shd->geometry_string = geometry_string ;
shd->tdset = tdset ;
shd->dfname = dfname ;
shd->nvox = nvox ;
shd->nx = DSET_NX(tdset); shd->ny = DSET_NY(tdset); shd->nz = DSET_NZ(tdset);
shd->ivec = ivec ;
shd->fac = fac ;
/* and surface fields... ZSS Jan 09 */
if (nnode) {
if (nnode->num != 2) GQUIT("LRpair_nnode must have 2 values");
shd->nnode[0] = nnode->ar[0];
shd->nnode[1] = nnode->ar[1];
NI_delete_int_array(nnode); nnode=NULL;
} else {
shd->nnode[0] = shd->nnode[1] = -1 ;
}
if (ninmask) {
if (ninmask->num != 2) GQUIT("LRpair_ninmask must have 2 values");
shd->ninmask[0] = ninmask->ar[0];
shd->ninmask[1] = ninmask->ar[1];
NI_delete_int_array(ninmask); ninmask=NULL;
} else {
shd->ninmask[0] = shd->ninmask[1] = -1 ;
}
/*--- 07 Apr 2010: setup default use list (all of them) ---*/
shd->nuse = ndset ;
shd->use = (int *)malloc(sizeof(int)*ndset) ;
for( ids=0 ; ids < ndset ; ids++ ) shd->use[ids] = ids ;
shd->dslab = (slabar != NULL) ? slabar->str : NULL ; /* 23 May 2010 */
/*--- now have to map data from disk ---*/
var = mmap( 0 , (size_t)nbytes_needed ,
PROT_WRITE , THD_MMAP_FLAG , fdes , 0 ) ;
close(fdes) ; /* close file descriptor does not unmap data */
if( var == (void *)(-1) ){ /* this is bad */
ERROR_message(
"EIC: file %s: can't mmap() datafile -- memory space exhausted?" , dfname ) ;
free(shd) ; return NULL ;
}
/*-- create array of pointers to each dataset's data array --*/
shd->datum = datum ;
if( datum == 2 ){ /* shorts */
shd->sv = (short **)malloc(sizeof(short *)*ndset) ;
shd->bv = NULL ;
shd->sv[0] = (short *)var ;
for( ids=1 ; ids < ndset ; ids++ )
shd->sv[ids] = shd->sv[ids-1] + nvals[ids-1]*nvec ;
} else { /* sbytes */
shd->sv = NULL ;
shd->bv = (sbyte **)malloc(sizeof(sbyte *)*ndset) ;
shd->bv[0] = (sbyte *)var ;
for( ids=1 ; ids < ndset ; ids++ )
shd->bv[ids] = shd->bv[ids-1] + nvals[ids-1]*nvec ;
}
shd->nbytes = nbytes_needed ;
return shd ;
}
char * AFNI_make_update_script(void)
{
char *pg_ftp , *pg_afni , *pg_gzip , *pg_tar ;
char hbuf[4096], fname[128], adir[4096], *cpt, cwd[4096] ;
FILE *fp ;
static char sname[4096] ;
pg_ftp = THD_find_executable("ftp" ); if( pg_ftp == NULL ) return NULL;
pg_afni = THD_find_executable("afni"); if( pg_afni == NULL ) return NULL;
pg_gzip = THD_find_executable("gzip");
if( pg_gzip == NULL ) pg_gzip = THD_find_executable("pigz") ;
if( pg_gzip == NULL ) return NULL;
pg_tar = THD_find_executable("tar" ); if( pg_tar == NULL ) return NULL;
strcpy(adir,pg_afni) ; /* extract name of AFNI directory */
cpt = THD_trailname(adir,0) ;
*cpt = '\0' ;
if( strlen(adir) <= 0 ) return NULL ; /* no AFNI directory? */
strcpy( cwd , adir ) ; /* try to write a test file there */
strcat( cwd , "afni_qadgop" ) ;
fp = fopen( cwd , "a" ) ;
if( fp == NULL ) return NULL ; /* can't write to AFNI directory? */
fclose(fp) ; remove(cwd) ;
getcwd( cwd , 4096 ) ; /* get current directory for later use */
chdir( adir ) ; /* switch to AFNI directory for this work */
/* write a script to get and install the binary archive via FTP */
gethostname( hbuf , 4096 ) ;
strcpy( fname , SHSHSH(SHOWOFF) ) ; strcat( fname , ".tgz" ) ;
fp = fopen( SNAME , "w" ) ; if( fp == NULL ){ chdir(cwd); return NULL; }
fprintf( fp ,
"#!/bin/sh\n"
"echo '++ FTP-ing %s from afni.nimh.nih.gov'\n"
"%s -n afni.nimh.nih.gov << EEEEE\n" /* FTP to get file */
"user anonymous AFNI_UPDATER@%s\n"
"binary\n"
"passive\n"
"cd tgz\n"
"get %s\n"
"bye\n"
"EEEEE\n"
"echo '++ Unpacking %s'\n"
"%s -dc %s | %s xf -\n" /* uncompress and untar .tgz file */
"/bin/rm -f %s\n" /* delete .tgz file */
"echo '++ Moving files'\n"
"/bin/mv -f %s/* .\n" /* move untar-ed files up to here */
"/bin/rm -rf %s\n" /* remove any directory leftovers */
"echo '++ Finished'\n" ,
fname , /* filename to get (for 'FTP-ing' echo) */
pg_ftp , /* FTP program */
hbuf , /* hostname, for FTP password */
fname , /* filename to get (for FTP) */
fname , /* ditto (for 'Unpacking' echo) */
pg_gzip, fname, pg_tar, /* GZIP program, filename, TAR program */
fname , /* filename to delete */
SHSHSH(SHOWOFF) , /* directory to copy up */
SHSHSH(SHOWOFF) /* directory to delete */
) ;
fclose( fp ) ;
chmod( SNAME , S_IRUSR | S_IWUSR | S_IXUSR ) ; /* mark as executable */
/* get back to current working directory, then leave */
chdir(cwd) ;
sprintf(sname,"%s%s",adir,SNAME) ; return sname ;
}
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) ;
}
MRI_IMARR * THD_get_all_timeseries( char * dname )
{
THD_string_array * flist , * rlist ;
int ir , ll , ii ;
char * fname , * tname ;
float * far ;
MRI_IMARR * outar ;
MRI_IMAGE * outim , * flim ;
#ifdef NEWWAY
char * pat ;
#endif
unsigned long max_fsize ; /* 20 Jul 2004: max 1D file size to load */
max_fsize = (unsigned long) AFNI_numenv( "AFNI_MAX_1DSIZE" ) ;
if( max_fsize == 0 ) max_fsize = 123*1024 ;
/*----- sanity check and initialize -----*/
if( dname == NULL || strlen(dname) == 0 ) return NULL ;
INIT_IMARR( outar ) ;
/*----- find all *.1D files -----*/
#ifdef NEWWAY
ii = strlen(dname) ;
pat = (char *) malloc(sizeof(char)*(ii+8)) ;
strcpy(pat,dname) ;
if( pat[ii-1] != '/' ) strcat(pat,"/") ;
strcat(pat,"*.1D*") ;
flist = THD_get_wildcard_filenames( pat ) ;
free(pat) ;
#else
flist = THD_get_all_filenames( dname ) ;
#endif
if( flist == NULL || flist->num <= 0 ){
DESTROY_SARR(flist) ;
DESTROY_IMARR(outar) ;
return NULL ;
}
rlist = THD_extract_regular_files( flist ) ;
DESTROY_SARR(flist) ;
if( rlist == NULL || rlist->num <= 0 ){
DESTROY_SARR(rlist) ;
DESTROY_IMARR(outar) ;
return NULL ;
}
for( ir=0 ; ir < rlist->num ; ir++ ){
fname = rlist->ar[ir] ; if( fname == NULL ) continue ;
ll = strlen(fname) - 3 ; if( ll < 1 ) continue ;
if( strcmp(fname+ll,".1D")==0 ||
strcmp(fname+ll,"1Dx")==0 ||
strcmp(fname+ll,"1Dv")==0 ){
if( THD_filesize(fname) > max_fsize ) continue ; /* 20 Jul 2004 */
flim = mri_read_1D( fname ) ;
if( flim != NULL ){
far = MRI_FLOAT_PTR(flim) ;
for( ii=0 ; ii < flim->nvox ; ii++ )
if( fabs(far[ii]) >= 33333.0 ) far[ii] = WAY_BIG ;
tname = THD_trailname(fname,1) ;
mri_add_name( tname , flim ) ;
ADDTO_IMARR( outar , flim ) ;
}
}
}
DESTROY_SARR(rlist) ;
if( IMARR_COUNT(outar) == 0 ) DESTROY_IMARR(outar) ;
return outar ;
}
int main( int argc , char *argv[] )
{
int iarg , ii,jj,kk,mm , nvec , nx=0,ny , ff , vlen=4 ;
MRI_IMAGE *tim , *vsim=NULL ;
MRI_IMARR *tar ;
char **vecnam , *tnam ;
float *far , **tvec , *vsig=NULL , xsig,ysig ;
float_quad qcor ; float_pair pci ; float corst, cor025, cor500, cor975 ;
char fmt[256] ;
int cormeth=0 ; /* 0=Pearson, 1=Spearman, 2=Quadrant, 3=Kendall tau_b */
float (*corfun)(int,float *,float *) ;
/*-- start the AFNI machinery --*/
mainENTRY("1dCorrelate main") ; machdep() ;
/* check for options */
iarg = 1 ; nvec = 0 ;
while( iarg < argc && argv[iarg][0] == '-' ){
/* I get by with a little help from my friends? */
if( strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0){
usage_1dCorrelate(strlen(argv[iarg])>3 ? 2:1);
exit(0) ;
}
/*--- methods ---*/
if( toupper(argv[iarg][1]) == 'P' ){ cormeth = 0 ; iarg++ ; continue ; }
if( toupper(argv[iarg][1]) == 'S' ){ cormeth = 1 ; iarg++ ; continue ; }
if( toupper(argv[iarg][1]) == 'Q' ){ cormeth = 2 ; iarg++ ; continue ; }
if( toupper(argv[iarg][1]) == 'K' ){ cormeth = 3 ; iarg++ ; continue ; }
if( toupper(argv[iarg][1]) == 'T' ){ cormeth = 4 ; iarg++ ; continue ; }
if( toupper(argv[iarg][1]) == 'U' ){ cormeth = 5 ; iarg++ ; continue ; }
/*--- set nboot ---*/
if( strcasecmp(argv[iarg],"-nboot") == 0 || strcasecmp(argv[iarg],"-num") == 0 ){
iarg++ ; if( iarg >= argc ) ERROR_exit("Need argument after '-nboot'") ;
nboot = (int)strtod(argv[iarg],NULL) ;
if( nboot < NBMIN ){
WARNING_message("Replacing -nboot %d with %d",nboot,NBMIN) ;
nboot = NBMIN ;
}
iarg++ ; continue ;
}
/*--- set alpha ---*/
if( strcasecmp(argv[iarg],"-alpha") == 0 ){
iarg++ ; if( iarg >= argc ) ERROR_exit("Need argument after '-alpha'") ;
alpha = (float)strtod(argv[iarg],NULL) ;
if( alpha < 1.0f ){
WARNING_message("Replacing -alpha %.1f with 1",alpha) ;
alpha = 0.01f ;
} else if( alpha > 20.0f ){
WARNING_message("Replacing -alpha %.1f with 20",alpha) ;
alpha = 0.20f ;
} else {
alpha *= 0.01f ; /* convert from percent to fraction */
}
iarg++ ; continue ;
}
/*--- block resampling ---*/
if( strcasecmp(argv[iarg],"-blk") == 0 || strcasecmp(argv[iarg],"-block") == 0 ){
doblk = 1 ; iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-vsig") == 0 ){
if( vsim != NULL ) ERROR_exit("Can't use -vsig twice!") ;
if( ++iarg >= argc ) ERROR_exit("Need argument after -vsig") ;
vsim = mri_read_1D(argv[iarg]) ;
if( vsim == NULL ) ERROR_exit("Can't read -vsig file '%s'",argv[iarg]) ;
iarg++ ; continue ;
}
/*--- user should be flogged ---*/
ERROR_message("Monstrously illegal option '%s'",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
/*--- user should be flogged twice ---*/
if( argc < 2 ){
usage_1dCorrelate(1) ; exit(0) ;
}
if( iarg == argc )
ERROR_exit("No 1D files on command line!?\n") ;
/* the function to compute the correlation */
corfun = cor_func[cormeth] ;
/* check and assemble list of input 1D files */
ff = iarg ;
INIT_IMARR(tar) ;
for( ; iarg < argc ; iarg++ ){
tim = mri_read_1D( argv[iarg] ) ;
if( tim == NULL ) ERROR_exit("Can't read 1D file '%s'",argv[iarg]) ;
if( nx == 0 ){
nx = tim->nx ;
if( nx < 3 )
ERROR_exit("1D file '%.77s' length=%d is less than 3",argv[iarg],nx) ;
else if( nx < 7 )
WARNING_message("1D file '%.77s' length=%d is less than 7",argv[iarg],nx) ;
} else if( tim->nx != nx ){
ERROR_exit("Length of 1D file '%.77s' [%d] doesn't match first file [%d]",
argv[iarg] , tim->nx , nx );
}
nvec += tim->ny ;
ADDTO_IMARR(tar,tim) ;
}
/* user is really an idiot -- flogging's too good for him */
if( nvec < 2 ) ERROR_exit("Must have at least 2 input columns!") ;
if( nx < 20 && doblk ){
doblk = 0 ;
WARNING_message("Column length %d < 20 ==> cannot use block resampling",nx) ;
}
if( vsim != NULL ){
if( vsim->nvox < nvec )
ERROR_exit("-vsig file only has %d entries, but needs at least %d",vsim->nvox,nvec) ;
vsig = MRI_FLOAT_PTR(vsim) ;
}
/* create vectors from 1D files */
tvec = (float **)malloc( sizeof(float *)*nvec ) ;
vecnam = (char **)malloc( sizeof(char *)*nvec ) ;
for( jj=0 ; jj < nvec ; jj++ ){
tvec[jj] = (float *)malloc( sizeof(float)*nx ) ;
vecnam[jj] = (char *)malloc(sizeof(char)*THD_MAX_NAME) ;
}
/* copy data into new space, create output labels, check for stoopiditees */
for( kk=mm=0 ; mm < IMARR_COUNT(tar) ; mm++ ){
tim = IMARR_SUBIM(tar,mm) ;
far = MRI_FLOAT_PTR(tim) ;
tnam = tim->name ; if( tnam == NULL ) tnam = "File" ;
for( jj=0 ; jj < tim->ny ; jj++,kk++ ){
for( ii=0 ; ii < nx ; ii++ ) tvec[kk][ii] = far[ii+jj*nx] ;
sprintf(vecnam[kk],"%s[%d]",THD_trailname(tnam,0),jj) ; /* vector name */
iarg = strlen(vecnam[kk]) ; vlen = MAX(vlen,iarg) ;
if( THD_is_constant(nx,tvec[kk]) )
ERROR_exit("Column %s is constant!",vecnam[kk]) ;
}
}
DESTROY_IMARR(tar) ;
/*--- Print a beeyootiful header ---*/
printf("# %s correlation [n=%d #col=%d]\n",cor_name[cormeth],nx,nvec) ;
sprintf(fmt,"# %%-%ds %%-%ds",vlen,vlen) ;
printf(fmt,"Name","Name") ;
printf(" Value BiasCorr %5.2f%% %5.2f%%",50.0f*alpha,100.0f-50.0f*alpha) ;
if( cormeth == 0 ) /* Pearson */
printf(" N:%5.2f%% N:%5.2f%%",50.0f*alpha,100.0f-50.0f*alpha) ;
printf("\n") ;
printf("# ") ;
for( ii=0 ; ii < vlen ; ii++ ) printf("-") ;
printf(" ") ;
for( ii=0 ; ii < vlen ; ii++ ) printf("-") ;
printf(" ") ;
printf(" --------") ;
printf(" --------") ;
printf(" --------") ;
printf(" --------") ;
if( cormeth == 0 ){ printf(" --------") ; printf(" --------") ; }
printf("\n") ;
if( cormeth != 0 ) /* non-Pearson */
sprintf(fmt," %%-%ds %%-%ds %%+8.5f %%+8.5f %%+8.5f %%+8.5f\n",vlen,vlen) ;
else /* Pearson */
sprintf(fmt," %%-%ds %%-%ds %%+8.5f %%+8.5f %%+8.5f %%+8.5f %%+8.5f %%+8.5f\n",vlen,vlen) ;
/*--- Do some actual work for a suprising change ---*/
for( jj=0 ; jj < nvec ; jj++ ){ /* loops over column pairs */
for( kk=jj+1 ; kk < nvec ; kk++ ){
if( vsig != NULL ){ xsig = vsig[jj]; ysig = vsig[kk]; } else { xsig = ysig = 0.0f; }
qcor = Corrboot( nx, tvec[jj], tvec[kk], xsig, ysig, corfun ) ; /* outsourced */
corst = qcor.a ; cor025 = qcor.b ; cor500 = qcor.c ; cor975 = qcor.d ;
if( cormeth == 0 ){ /* Pearson */
pci = PCorrCI( nx , corst , alpha ) ;
printf(fmt, vecnam[jj], vecnam[kk], corst, cor500, cor025, cor975, pci.a,pci.b ) ;
} else { /* all other methods */
printf(fmt, vecnam[jj], vecnam[kk], corst, cor500, cor025, cor975 ) ;
}
}
}
/* Finished -- go back to watching Star Trek reruns -- Tribbles ahoy, Cap'n! */
exit(0) ;
}
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) ;
}
/*
Generate C array that lists all afni programs and their options
There is a most unholy relationship between this function and
the include line: #include "prog_opts.c"
This function is for internal machinations having to do with
automatic generation of help web pages. It is not for mass
consumption.
\param fout (FILE *): Pointer to output stream
\param verb (int): verbosity
\param thisprog (char *): If not NULL, then update the list of options for
program thisprog. Existing other programs option
are preserved (appendmode is forced to 1)
If NULL, then do this for all programs recognized
by THD_get_all_afni_executables()
\param appendmode (int): 1 --> Keep existing information about programs not
in THD_get_all_afni_executables() or other
than thisprog
0 --> Just output information on programs from
THD_get_all_afni_executables(). This is only
allowed when thisprog == 0
*/
int progopt_C_array(FILE *fout, int verb, char *thisprog, int appendmode)
{
char **ws=NULL, *sout=NULL;
float *ws_score=NULL;
int N_ws=0, ii = 0, jj = 0, found=0;
THD_string_array *progs=NULL;
ENTRY("progopt_C_array");
if (!fout) fout = stdout;
if (thisprog) {
if (!appendmode) {
WARNING_message("Forcing append mode for one program");
appendmode = 1;
}
INIT_SARR( progs );
ADDTO_SARR( progs, thisprog );
} else {
if (!(progs = THD_get_all_afni_executables()) || progs->num < 1) {
ERROR_message("Could not get list of executables");
RETURN(1);
}
}
fprintf(fout,
"#ifndef PROG_OPTS_INCLUDED\n"
"#define PROG_OPTS_INCLUDED\n"
"\n"
"/* \n"
" *********** Manual Edits Can Get CLOBBERED! ***********\n"
" *************** File created automatically ******************\n"
"\n"
" This file was initially created by function progopt_C_array(), \n"
" via program apsearch with:\n"
" apsearch -C_all_prog_opt_array > prog_opts.c\n\n"
" To update entry for just one program (PROG) best use:\n"
" apsearch -C_all_prog_opt_array PROG > prog_opts.c\n\n"
"\n"
"You'll need to also touch thd_getpathprogs.c before rebuilding \n"
"libmri.a, etc.\n"
"*/\n\n"
"#if 0\n"
"static PROG_OPTS poptslist[] = {\n"
" {NULL, NULL, 0}\n"
"}\n"
"#else\n"
"static PROG_OPTS poptslist[] = {\n");
if (appendmode) { /* Keep programs not in list being sent*/
while (poptslist[jj].program != NULL) {
found = 0;
for (ii=0; ii<progs->num && !found; ++ii) {
if (!strcmp(THD_trailname(progs->ar[ii],0), poptslist[jj].program)) {
found = 1;
}
}
if (!found) { /* add it */
if ((sout = form_C_progopt_string_from_struct(poptslist[jj]))){
fprintf(fout, "%s,\n", sout);
free(sout); sout = NULL;
}
}
++jj;
}
}
for (ii=0; ii<progs->num; ++ii) {
if (verb) fprintf(stderr,"Prog %d/%d: %s ", ii+1, progs->num,
THD_trailname(progs->ar[ii],0) );
if ((ws = approx_str_sort_all_popts(progs->ar[ii], 0, &N_ws,
1, &ws_score,
NULL, NULL, 1, 0, '\\'))) {
if (verb) fprintf(stderr,"%d opts\t ", N_ws);
if ((sout = form_C_progopt_string(
THD_trailname(progs->ar[ii], 0), ws, N_ws))){
fprintf(fout, "%s,\n", sout);
free(sout); sout = NULL;
}
for (jj=0; jj<N_ws; ++jj) if (ws[jj]) free(ws[jj]);
free(ws); ws = NULL;
if (ws_score) free(ws_score); ws_score=NULL;
}
}
fprintf(fout, " { NULL, NULL, 0 }\n};\n\n"
"#endif\n\n\n"
"#endif /* For #ifdef PROG_OPTS_INCLUDED */\n");
DESTROY_SARR(progs) ;
RETURN(0);
}
/*! Get all executables in directory where afni resides */
THD_string_array * THD_get_all_afni_executables(void )
{
THD_string_array *outar=NULL, *elist=NULL;
char *af=NULL, *etr=NULL;
int N_af, iaf=0, ii=0, smode, *isrt=NULL;
char scomm[256]={""};
ENTRY("THD_get_all_afni_executables");
if (!(elist = get_elist()) ||
!(af = THD_abindir(1)) ) {
ERROR_message("Could not find afni, we're doomed daddy!");
RETURN(outar);
}
N_af = strlen(af);
/* Now get all executables under af */
INIT_SARR( outar );
for (ii=0, iaf=0; ii<elist->num ; ii++ ){
smode = storage_mode_from_filename(elist->ar[ii]);
etr = THD_trailname( elist->ar[ii] , 0 ) ;
if (
!THD_is_directory(elist->ar[ii]) &&
!strncmp(af, elist->ar[ii], N_af) &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".xml") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".html") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".jpg") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".a") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".c") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".h") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".f") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".xbm") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".tex") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".lib") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".dylib") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".o") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".so") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".la") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".txt") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".R") &&
!(STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".py") &&
/* add a couple of python types to skip 20 Jul 2012 [rickr] */
(!strncmp(etr,"lib_",4) || !strncmp(etr,"gui_",4) ||
!strncmp(etr,"ui_",3)) ) &&
(smode <= STORAGE_UNDEFINED || smode >= LAST_STORAGE_MODE) &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".sumarc") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".afnirc")&&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], "lib.py") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".pyc") &&
!STRING_HAS_SUFFIX_CASE(elist->ar[ii], ".Xdefaults") &&
/* skip README files, processed as scripts 20 Jul 2012 [rickr]
of note: README.atlas_building starts with the line:
README.atlas_building
such process recursion is not good for the system... */
strncmp(etr, "README.", 7)
) {
ADDTO_SARR( outar , elist->ar[ii] ) ; ++iaf;
/* fprintf(stderr," %d- %s\n", iaf, etr); */
} else {
/* fprintf(stderr," skip %s (%s) %d--%d--%d isd %d\n",
elist->ar[ii], af, STORAGE_UNDEFINED, smode, LAST_STORAGE_MODE,
THD_is_directory(elist->ar[ii])); */
}
}
qsort(outar->ar, outar->num, sizeof(char*),
(int(*) (const void *, const void *))compare_string);
if( SARR_NUM(outar) == 0 ) DESTROY_SARR(outar) ;
if (af) free(af); af = NULL;
RETURN( outar );
}
