int main( int argc , char * argv[] )
{
THD_dfvec3 *xx , *yy , dv ;
int nvec=0 , ii,jj, iarg ;
THD_dvecmat rt , rtinv ;
THD_dmat33 pp,ppt , rr ;
THD_dfvec3 tt ;
THD_3dim_dataset *mset=NULL , *dset=NULL ;
double *ww=NULL ;
int nww=0 ;
int keeptags=1 , wtval=0 , verb=0 , dummy=0 ;
char * prefix = "tagalign" , *mfile=NULL ;
float *fvol , cbot,ctop , dsum ;
int nval , nvox , clipit , ival, RMETH=MRI_CUBIC;
float matar[12] ;
int use_3dWarp=1 , matrix_type=ROTATION ;
mainENTRY("3dTagalign main");
/*--- help? ---*/
/*- scan args -*/
iarg = 1 ; RMETH=MRI_CUBIC;
while( iarg < argc && argv[iarg][0] == '-' ){
/*-----*/
if( strcmp(argv[iarg],"-h") == 0 ||
strcmp(argv[iarg],"-help") == 0){ /* 22 Apr 2003 */
usage_3dTagalign(strlen(argv[iarg]) > 3 ? 2:1);
exit(0);
}
/*-----*/
if( strcmp(argv[iarg],"-NN") == 0 ){
RMETH = MRI_NN ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-linear") == 0 ){
RMETH = MRI_LINEAR ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-cubic") == 0 ){
RMETH = MRI_CUBIC ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-quintic") == 0 ){
RMETH = MRI_QUINTIC ; iarg++ ; continue ;
}
/*-----*/
if( strcmp(argv[iarg],"-rotate") == 0 ){ /* 22 Apr 2003 */
matrix_type = ROTATION ; use_3dWarp = 1 ;
iarg++ ; continue ;
}
/*-----*/
if( strcmp(argv[iarg],"-affine") == 0 ){ /* 21 Apr 2003 */
matrix_type = AFFINE ; use_3dWarp = 1 ;
iarg++ ; continue ;
}
/*-----*/
if( strcmp(argv[iarg],"-rotscl") == 0 ){ /* 22 Apr 2003 */
matrix_type = ROTSCL ; use_3dWarp = 1 ;
iarg++ ; continue ;
}
#if 0
/*-----*/
if( strcmp(argv[iarg],"-3dWarp") == 0 ){ /* 21 Apr 2003 */
use_3dWarp = 1 ;
iarg++ ; continue ;
}
#endif
/*-----*/
if( strcmp(argv[iarg],"-master") == 0 ){
if( mset != NULL ) ERREX("Can only have one -master option") ;
if( ++iarg >= argc ) ERREX("Need an argument after -master") ;
mset = THD_open_dataset( argv[iarg] ) ;
if( mset == NULL ) ERREX("Can't open -master dataset") ;
if( mset->tagset == NULL ) ERREX("No tags in -master dataset") ;
if( TAGLIST_COUNT(mset->tagset) < 3 ) ERREX("Not enough tags in -master dataset") ;
for( nvec=ii=0 ; ii < TAGLIST_COUNT(mset->tagset) ; ii++ )
if( TAG_SET(TAGLIST_SUBTAG(mset->tagset,ii)) ) nvec++ ;
if( nvec < 3 ) ERREX("Not enough tags set in -master dataset") ;
if( nvec < TAGLIST_COUNT(mset->tagset) )
fprintf(stderr,"++ WARNING: not all tags are set in -master dataset\n") ;
if( verb ) fprintf(stderr,"++ Found %d tags in -master dataset\n",nvec) ;
iarg++ ; continue ;
}
#if 0
/*-----*/
if( strcmp(argv[iarg],"-wtval") == 0 ){
if( ww != NULL ) ERREX("Can't have -wtval after -wt1D") ;
wtval++ ;
iarg++ ; continue ;
}
/*-----*/
if( strcmp(argv[iarg],"-wt1D") == 0 ){
MRI_IMAGE * wtim ; float * wtar ;
if( wtval ) ERREX("Can't have -wt1D after -wtval") ;
if( ww != NULL ) ERREX("Can't have two -wt1D options!") ;
if( ++iarg >= argc ) ERREX("Need an argument after -wt1D") ;
wtim = mri_read_1D( argv[iarg] ) ;
if( wtim == NULL ) ERREX("Can't read -wtim file") ;
if( wtim->ny > 1 ) ERREX("-wtim file has more than one columm") ;
wtar = MRI_FLOAT_PTR(wtim) ;
ww = (double *) malloc(sizeof(double)*wtim->nx) ; nww = wtim->nx ;
for( ii=0 ; ii < nww ; ii++ ){
ww[ii] = (double) wtar[ii] ;
if( ww[ii] < 0.0 ) ERREX("Negative value found in -wt1D file") ;
}
mri_free(wtim) ;
iarg++ ; continue ;
}
#endif
/*-----*/
if( strcmp(argv[iarg],"-nokeeptags") == 0 ){
keeptags = 0 ;
iarg++ ; continue ;
}
/*-----*/
if( strncmp(argv[iarg],"-verb",5) == 0 ){
verb++ ;
iarg++ ; continue ;
}
/*-----*/
if( strcmp(argv[iarg],"-dummy") == 0 ){
dummy++ ;
iarg++ ; continue ;
}
/*-----*/
if( strcmp(argv[iarg],"-prefix") == 0 ){
if( ++iarg >= argc ) ERREX("Need an argument after -prefix") ;
prefix = argv[iarg] ;
if( !THD_filename_ok(prefix) ) ERREX("-prefix string is illegal") ;
iarg++ ; continue ;
}
/*-----*/
if( strcmp(argv[iarg],"-matvec") == 0 ){
if( ++iarg >= argc ) ERREX("Need an argument after -matvec") ;
mfile = argv[iarg] ;
if( !THD_filename_ok(mfile) ) ERREX("-matvec string is illegal") ;
iarg++ ; continue ;
}
/*-----*/
fprintf(stderr,"** Unknown option: %s\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1) ;
} /* end of scanning command line for options */
if( argc < 2 ){
ERROR_message("Too few options");
usage_3dTagalign(0);
exit(1) ;
}
if( mset == NULL ) ERREX("No -master option found on command line") ;
#if 0
if( ww != NULL && nww < nvec ) ERREX("Not enough weights found in -wt1D file") ;
/*-- if -wtval, setup weights from master tag values --*/
if( wtval ){
ww = (double *) malloc(sizeof(double)*nvec) ; nww = nvec ;
for( ii=jj=0 ; ii < TAGLIST_COUNT(mset->tagset) ; ii++ ){
if( TAG_SET(TAGLIST_SUBTAG(mset->tagset,ii)) ){
ww[jj] = (double) TAG_VAL(TAGLIST_SUBTAG(mset->tagset,ii)) ;
if( ww[jj] < 0.0 ) ERREX("Negative value found in -master tag values") ;
jj++ ;
}
}
}
#endif
/*-- read input dataset (to match to master dataset) --*/
if( iarg >= argc ) ERREX("No input dataset?") ;
dset = THD_open_dataset( argv[iarg] ) ;
if( dset == NULL ) ERREX("Can't open input dataset") ;
if( dset->tagset == NULL ) ERREX("No tags in input dataset") ;
if( TAGLIST_COUNT(dset->tagset) !=
TAGLIST_COUNT(mset->tagset) ) ERREX("Tag counts don't match in -master and input") ;
/* check if set tags match exactly */
for( ii=0 ; ii < TAGLIST_COUNT(mset->tagset) ; ii++ ){
if( TAG_SET(TAGLIST_SUBTAG(mset->tagset,ii)) !=
TAG_SET(TAGLIST_SUBTAG(dset->tagset,ii)) )
ERREX("Set tags don't match in -master and input") ;
}
/*-- load vector lists: xx=master, yy=input --*/
xx = (THD_dfvec3 *) malloc( sizeof(THD_dfvec3) * nvec ) ;
yy = (THD_dfvec3 *) malloc( sizeof(THD_dfvec3) * nvec ) ;
dsum = 0.0 ;
for( ii=jj=0 ; ii < nvec ; ii++ ){
if( TAG_SET(TAGLIST_SUBTAG(mset->tagset,ii)) ){
LOAD_DFVEC3( xx[jj] , /* N.B.: */
TAG_X( TAGLIST_SUBTAG(mset->tagset,ii) ) , /* these are */
TAG_Y( TAGLIST_SUBTAG(mset->tagset,ii) ) , /* in Dicom */
TAG_Z( TAGLIST_SUBTAG(mset->tagset,ii) ) ) ; /* order now */
LOAD_DFVEC3( yy[jj] ,
TAG_X( TAGLIST_SUBTAG(dset->tagset,ii) ) ,
TAG_Y( TAGLIST_SUBTAG(dset->tagset,ii) ) ,
TAG_Z( TAGLIST_SUBTAG(dset->tagset,ii) ) ) ;
dv = SUB_DFVEC3( xx[jj] , yy[jj] ) ;
dsum += dv.xyz[0]*dv.xyz[0] + dv.xyz[1]*dv.xyz[1] + dv.xyz[2]*dv.xyz[2] ;
jj++ ;
}
}
dsum = sqrt(dsum/nvec) ;
fprintf(stderr,"++ RMS distance between tags before = %.2f mm\n" , dsum ) ;
/*-- compute best transformation from mset to dset coords --*/
switch( matrix_type ){
default:
case ROTATION:
rt = DLSQ_rot_trans( nvec , yy , xx , ww ) ; /* in thd_rot3d.c */
break ;
case AFFINE:
rt = DLSQ_affine ( nvec , yy , xx ) ; /* 21 Apr 2003 */
break ;
case ROTSCL:
rt = DLSQ_rotscl ( nvec , yy , xx , (DSET_NZ(dset)==1) ? 2 : 3 ) ;
break ;
}
rtinv = INV_DVECMAT(rt) ;
/*-- check for floating point legality --*/
nval = 0 ;
for( ii=0 ; ii < 3 ; ii++ ){
dsum = rt.vv.xyz[ii] ; nval += thd_floatscan(1,&dsum) ;
for( jj=0 ; jj < 3 ; jj++ ){
dsum = rt.mm.mat[ii][jj] ; nval += thd_floatscan(1,&dsum) ;
}
}
if( nval > 0 ){
fprintf(stderr,"** Floating point errors during calculation\n"
"** of transform matrix and translation vector\n" ) ;
exit(1) ;
}
/*-- check for rotation matrix legality --*/
dsum = DMAT_DET(rt.mm) ;
if( dsum == 0.0 || (matrix_type == ROTATION && fabs(dsum-1.0) > 0.01) ){
fprintf(stderr,"** Invalid transform matrix computed: tags dependent?\n"
"** computed [matrix] and [vector] follow:\n" ) ;
for( ii=0 ; ii < 3 ; ii++ )
fprintf(stderr," [ %10.5f %10.5f %10.5f ] [ %10.5f ] \n",
rt.mm.mat[ii][0],rt.mm.mat[ii][1],rt.mm.mat[ii][2],rt.vv.xyz[ii] );
exit(1) ;
}
/*-- print summary --*/
if( verb ){
fprintf(stderr,"++ Matrix & Vector [Dicom: x=R-L; y=A-P; z=I-S]\n") ;
for( ii=0 ; ii < 3 ; ii++ )
fprintf(stderr," %10.5f %10.5f %10.5f %10.5f\n",
rt.mm.mat[ii][0],rt.mm.mat[ii][1],rt.mm.mat[ii][2],rt.vv.xyz[ii] );
}
if( matrix_type == ROTATION || matrix_type == ROTSCL ){
double theta, costheta , dist , fac=1.0 ;
if( matrix_type == ROTSCL ){
fac = DMAT_DET(rt.mm); fac = fabs(fac);
if( DSET_NZ(dset) == 1 ) fac = sqrt(fac) ;
else fac = cbrt(fac) ;
}
costheta = 0.5 * sqrt(1.0 + DMAT_TRACE(rt.mm)/fac ) ;
theta = 2.0 * acos(costheta) * 180/3.14159265 ;
dist = SIZE_DFVEC3(rt.vv) ;
fprintf(stderr,"++ Total rotation=%.2f degrees; translation=%.2f mm; scaling=%.2f\n",
theta,dist,fac) ;
}
if( mfile ){
FILE * mp ;
if( THD_is_file(mfile) )
fprintf(stderr,"++ Warning: -matvec will overwrite file %s\n",mfile) ;
mp = fopen(mfile,"w") ;
if( mp == NULL ){
fprintf(stderr,"** Can't write to -matvec %s\n",mfile) ;
} else {
for( ii=0 ; ii < 3 ; ii++ )
fprintf(mp," %10.5f %10.5f %10.5f %10.5f\n",
rt.mm.mat[ii][0],rt.mm.mat[ii][1],rt.mm.mat[ii][2],rt.vv.xyz[ii] );
fclose(mp) ;
if( verb ) fprintf(stderr,"++ Wrote matrix+vector to %s\n",mfile) ;
}
}
if( dummy ){
fprintf(stderr,"++ This was a -dummy run: no output dataset\n") ; exit(0) ;
}
/*-- 21 Apr 2003: transformation can be done the old way (a la 3drotate),
or the new way (a la 3dWarp). --*/
#if 0
if( !use_3dWarp ){ /**** the old way ****/
/*-- now must scramble the rotation matrix and translation
vector from Dicom coordinate order to dataset brick order --*/
pp = DBLE_mat_to_dicomm( dset ) ;
ppt = TRANSPOSE_DMAT(pp) ;
rr = DMAT_MUL(ppt,rt.mm) ; rr = DMAT_MUL(rr,pp) ; tt = DMATVEC(ppt,rt.vv) ;
/*-- now create the output dataset by screwing with the input dataset
(this code is adapted from 3drotate.c) --*/
DSET_mallocize(dset) ;
DSET_load( dset ) ; CHECK_LOAD_ERROR(dset) ;
dset->idcode = MCW_new_idcode() ;
dset->dblk->diskptr->storage_mode = STORAGE_BY_BRICK ; /* 14 Jan 2004 */
EDIT_dset_items( dset ,
ADN_prefix , prefix ,
ADN_label1 , prefix ,
ADN_none ) ;
if( !THD_ok_overwrite() &&
(THD_deathcon() && THD_is_file(dset->dblk->diskptr->header_name) )){
fprintf(stderr,
"** Output file %s already exists -- cannot continue!\n",
dset->dblk->diskptr->header_name ) ;
exit(1) ;
}
tross_Make_History( "3dTagalign" , argc,argv , dset ) ;
/*-- if desired, keep old tagset --*/
if( keeptags ){
THD_dfvec3 rv ;
dsum = 0.0 ;
for( jj=ii=0 ; ii < TAGLIST_COUNT(dset->tagset) ; ii++ ){
if( TAG_SET(TAGLIST_SUBTAG(dset->tagset,ii)) ){
rv = DMATVEC( rt.mm , yy[jj] ) ; /* operating on */
rv = ADD_DFVEC3( rt.vv , rv ) ; /* Dicom order */
dv = SUB_DFVEC3( xx[jj] , rv ) ;
dsum += dv.xyz[0]*dv.xyz[0] + dv.xyz[1]*dv.xyz[1]
+ dv.xyz[2]*dv.xyz[2] ;
UNLOAD_DFVEC3( rv , TAG_X( TAGLIST_SUBTAG(dset->tagset,ii) ) ,
TAG_Y( TAGLIST_SUBTAG(dset->tagset,ii) ) ,
TAG_Z( TAGLIST_SUBTAG(dset->tagset,ii) ) ) ;
jj++ ;
}
}
dsum = sqrt(dsum/nvec) ;
fprintf(stderr,"++ RMS distance between tags after = %.2f mm\n" , dsum ) ;
} else {
myXtFree(dset->tagset) ; /* send it to the dustbin */
}
/*-- rotate sub-bricks --*/
if( verb ) fprintf(stderr,"++ computing output BRIK") ;
nvox = DSET_NVOX(dset) ;
nval = DSET_NVALS(dset) ;
fvol = (float *) malloc( sizeof(float) * nvox ) ;
THD_rota_method( MRI_HEPTIC ) ;
clipit = 1 ;
for( ival=0 ; ival < nval ; ival++ ){
/*- get sub-brick out of dataset -*/
EDIT_coerce_type( nvox ,
DSET_BRICK_TYPE(dset,ival),DSET_ARRAY(dset,ival) ,
MRI_float,fvol ) ;
if( clipit ){
register int ii ; register float bb,tt ;
bb = tt = fvol[0] ;
for( ii=1 ; ii < nvox ; ii++ ){
if( fvol[ii] < bb ) bb = fvol[ii] ;
else if( fvol[ii] > tt ) tt = fvol[ii] ;
}
cbot = bb ; ctop = tt ;
}
if( verb && nval < 5 ) fprintf(stderr,".") ;
/*- rotate it -*/
THD_rota_vol_matvec( DSET_NX(dset) , DSET_NY(dset) , DSET_NZ(dset) ,
fabs(DSET_DX(dset)) , fabs(DSET_DY(dset)) ,
fabs(DSET_DZ(dset)) ,
fvol , rr , tt ) ;
if( verb ) fprintf(stderr,".") ;
if( clipit ){
register int ii ; register float bb,tt ;
bb = cbot ; tt = ctop ;
for( ii=0 ; ii < nvox ; ii++ ){
if( fvol[ii] < bb ) fvol[ii] = bb ;
else if( fvol[ii] > tt ) fvol[ii] = tt ;
}
}
if( verb && nval < 5 ) fprintf(stderr,".") ;
/*- put it back into dataset -*/
EDIT_coerce_type( nvox, MRI_float,fvol ,
DSET_BRICK_TYPE(dset,ival),DSET_ARRAY(dset,ival) );
} /* end of loop over sub-brick index */
if( verb ) fprintf(stderr,":") ;
/* save matrix+vector into dataset, too */
UNLOAD_DMAT(rt.mm,matar[0],matar[1],matar[2],
matar[4],matar[5],matar[6],
matar[8],matar[9],matar[10] ) ;
UNLOAD_DFVEC3(rt.vv,matar[3],matar[7],matar[11]) ;
THD_set_atr( dset->dblk, "TAGALIGN_MATVEC", ATR_FLOAT_TYPE, 12, matar ) ;
/* write dataset to disk */
dset->dblk->master_nvals = 0 ; /* in case this was a mastered dataset */
DSET_write(dset) ;
if( verb ) fprintf(stderr,"\n") ;
} else
#endif
{ /**** the new way: use 3dWarp type transformation ****/
THD_3dim_dataset *oset ;
THD_vecmat tran ;
#if 0
DFVEC3_TO_FVEC3( rt.vv , tran.vv ) ;
DMAT_TO_MAT ( rt.mm , tran.mm ) ;
#else
DFVEC3_TO_FVEC3( rtinv.vv , tran.vv ) ;
DMAT_TO_MAT ( rtinv.mm , tran.mm ) ;
#endif
mri_warp3D_method( RMETH ) ;
oset = THD_warp3D_affine( dset, tran, mset, prefix, 0, WARP3D_NEWDSET ) ;
if( oset == NULL ){
fprintf(stderr,"** ERROR: THD_warp3D() fails!\n"); exit(1);
}
tross_Copy_History( dset , oset ) ;
tross_Make_History( "3dTagalign" , argc,argv , oset ) ;
UNLOAD_DMAT(rt.mm,matar[0],matar[1],matar[2],
matar[4],matar[5],matar[6],
matar[8],matar[9],matar[10] ) ;
UNLOAD_DFVEC3(rt.vv,matar[3],matar[7],matar[11]) ;
THD_set_atr( oset->dblk, "TAGALIGN_MATVEC", ATR_FLOAT_TYPE, 12, matar ) ;
/*-- if desired, keep old tagset --*/
if( keeptags ){
THD_dfvec3 rv ;
oset->tagset = myXtNew(THD_usertaglist) ;
*(oset->tagset) = *(dset->tagset) ;
dsum = 0.0 ;
for( jj=ii=0 ; ii < TAGLIST_COUNT(oset->tagset) ; ii++ ){
if( TAG_SET(TAGLIST_SUBTAG(oset->tagset,ii)) ){
rv = DMATVEC( rt.mm , yy[jj] ) ;
rv = ADD_DFVEC3( rt.vv , rv ) ;
dv = SUB_DFVEC3( xx[jj] , rv ) ;
dsum += dv.xyz[0]*dv.xyz[0] + dv.xyz[1]*dv.xyz[1]
+ dv.xyz[2]*dv.xyz[2] ;
UNLOAD_DFVEC3( rv , TAG_X( TAGLIST_SUBTAG(oset->tagset,ii) ) ,
TAG_Y( TAGLIST_SUBTAG(oset->tagset,ii) ) ,
TAG_Z( TAGLIST_SUBTAG(oset->tagset,ii) ) ) ;
jj++ ;
}
}
dsum = sqrt(dsum/nvec) ;
fprintf(stderr,"++ RMS distance between tags after = %.2f mm\n" , dsum ) ;
}
DSET_write(oset) ;
} /* end of 3dWarp-like work */
exit(0) ;
}
int main( int argc , char *argv[] )
{
NI_stream ns ;
void *nini = NULL, *vel=NULL;
NI_element *nel=NULL;
char *strm=NULL, *attr=NULL;
int nn, mode = NI_TEXT_MODE, shhh=0, exact=1;
FILE *outf = stdout;
char *aa=NULL, *select_attr=NULL, *select_attr_val=NULL;
int dodup = 0, nodata=0, dostderr=1, isfile=0;
int stat = 0, excl = 0;
nn = 1;
while (nn < argc && argv[nn][0] == '-') {
if (!strcmp(argv[nn], "-help") || !strcmp(argv[nn], "-h")) {
usage_niccc(strlen(argv[nn]) > 3 ? 2:1);
exit(0);
}
if (!strcmp(argv[nn],"-dup")) {
dodup = 1; ++nn; continue;
}
if (!strcmp(argv[nn],"-nodata")) {
nodata = 0; ++nn; continue;
}
if (!strcmp(argv[nn],"-stdout")) {
dostderr = 0; ++nn; continue;
}
if (!strcmp(argv[nn],"-#")) {
mode = mode|NI_HEADERSHARP_FLAG;
++nn; continue;
}
if (!strcmp(argv[nn],"-quiet")) {
shhh=1;
++nn; continue;
}
if (!strcmp(argv[nn],"-f")) {
isfile=1;
++nn; continue;
}
if (!strcmp(argv[nn],"-s")) {
isfile=2;
++nn; continue;
}
if (!strcmp(argv[nn],"-attribute")) {
++nn;
if (nn >= argc) {
fprintf(stderr,"Need attribute after -attribute\n");
exit(1);
}
attr=argv[nn];
++nn; continue;
}
if (!strcmp(argv[nn],"-nel_from_string")) {
++nn;
if (nn >= argc) {
fprintf(stderr,"Need string after -nel_from_string\n");
exit(1);
}
nini = (NI_element *)NI_read_element_fromstring(argv[nn]);
++nn; continue;
}
if (!strcmp(argv[nn],"-skip_nel_with_attr") ||
!strcmp(argv[nn],"-find_nel_with_attr")) {
if (strstr(argv[nn],"-find")) {
excl=0;
} else {
excl=1;
}
++nn;
if (nn+1 >= argc) {
fprintf(stderr,
"Need attribute and value after -skip_nel_with_attr\n");
exit(1);
}
select_attr=argv[nn++];
select_attr_val = argv[nn];
++nn; continue;
}
if (!strcmp(argv[nn],"-match")) {
++nn;
if (nn >= argc) {
fprintf(stderr,"Need parameter after -match\n");
exit(1);
}
if (!strcmp(argv[nn],"exact")) exact = 1;
else if (!strcmp(argv[nn],"partial")) exact = 0;
else {
fprintf(stderr,"%s is not a valid value for -match. \n"
"Use either exact or partial\n", argv[nn]);
exit(1);
}
++nn; continue;
}
ERROR_message("Bad option %s. See niccc -help for details.\n",
argv[nn]);
suggest_best_prog_option(argv[0], argv[nn]);
exit(1);
}
if( argc < 2 ){
ERROR_exit("Too few options");
}
if (nodata) mode = mode&NI_HEADERONLY_FLAG;
if (nn >= argc) {
fprintf(stderr,"Usage: niccc [-dup] streamspec\n");exit(1);
}
strm = (char *) realloc(strm, (strlen(argv[nn])+32)*sizeof(char));
if (isfile == 2) {
sprintf(strm,"str:");
ns = NI_stream_open( strm , "r" ) ;
NI_stream_setbuf( ns , argv[nn] ) ;
} else {
if (isfile == 1) {
sprintf(strm,"file:%s",argv[nn]);
} else {
strcpy(strm, argv[nn]);
}
ns = NI_stream_open( strm, "r" ) ;
if( ns == NULL ){
fprintf(stderr,"*** niccc: NI_stream_open fails for %s\n", strm) ;
if (THD_is_file(strm)) {
fprintf(stderr,
" It looks like %s is a file.\n"
" Make sure you use option -f before it\n",
strm) ;
}
exit(1) ;
}
}
/*** NI_stream_setbufsize( ns , 6666 ) ; ***/
while(1){
nn = NI_stream_goodcheck( ns , 1 ) ;
if( nn < 0 ){
if (strncmp(strm,"file:",5) && strncmp(strm,"str:",4)) {
fprintf(stderr,"\n*** niccc: Stream %s fails\n", strm); exit(1);
} else {
exit(stat);
}
}
if( nn == 0 ){ NI_sleep(5); continue; } /* waiting for Godot */
if (dostderr) outf = stderr;
if ( (nn = NI_stream_readcheck( ns , 1 ) ) > 0) { /* check for data */
if (!excl) {
stat = 1; /* using -find, exit with status if not found */
} else {
stat = 0; /* you got something, exit well */
}
while( (nini = NI_read_element( ns , 2 )) ) {
if (select_attr) {
if ((aa = NI_get_attribute(nini, select_attr))) {
if (!strcmp(aa,select_attr_val)) { /* match */
if (excl) goto NEXT;
else stat = 0; /* found something */
} else if (!excl) goto NEXT; /* no match */
}
}
if (attr) {
if (exact) {
aa = NI_get_attribute(nini, attr);
if (aa) {
if (shhh) fprintf(outf,"%s\n", aa);
else fprintf(outf,"%s: %s\n",attr, aa);
exit(0);
} else {
if (!shhh) fprintf(stderr,"%s: Not found.\n", attr);
exit(1);
}
} else {
int tt=NI_element_type(nini) ;
int nn, nfound=0;
if( tt == NI_ELEMENT_TYPE ){
nel=(NI_element *)nini;
for( nn=0 ; nn < nel->attr_num ; nn++ ) {
if( strncmp(nel->attr_lhs[nn],attr,
strlen(attr)) == 0 ) {
if (shhh) fprintf(outf,"%s\n", nel->attr_rhs[nn]);
else fprintf(outf,"%s: %s\n",
nel->attr_lhs[nn], nel->attr_rhs[nn]);
++nfound;
}
}
if (nfound) exit(0);
else {
if (!shhh) fprintf(stderr,"%s: Not found.\n", attr);
exit(1);
}
} else {
if (strncmp(strm,"file:",5)) {
fprintf(stderr,"\n*** niccc: not ready for non elements\n");
exit(1);
} else {
exit(1);
}
}
}
}
if (dodup) {
if (!shhh) fprintf(stderr,
"*** niccc: duplication returned element:\n");
vel = NI_duplicate(nini, 1);
NI_free_element( nini ) ; nini=NULL;
NIML_to_terminal( vel, mode, dostderr ) ;
} else {
if (!shhh) fprintf(stderr,"*** niccc: reading returned element:\n") ;
NIML_to_terminal( nini, mode, dostderr ) ;
}
NEXT:
if (nini) NI_free_element( nini ) ; nini=NULL;
if (vel) NI_free_element( vel ); vel = NULL;
}
}
} /* while stream is good */
}
int main( int argc , char *argv[] )
{
THD_3dim_dataset *inset=NULL , *outset ;
THD_3dim_dataset **insar=NULL ; int nsar=0 ;
int iarg=1 , ii,kk , ids ;
MCW_cluster *nbhd=NULL ;
char *prefix="./localhistog" ;
int ntype=0 ; float na=0.0f,nb=0.0f,nc=0.0f ;
int verb=1 , do_prob=0 ;
int nx=0,ny=0,nz=0,nvox=0, rbot,rtop ;
char *labfile=NULL ; NI_element *labnel=NULL ;
int nlab=0 , *labval=NULL ; char **lablab=NULL ; char buf[THD_MAX_SBLABEL] ;
UINT32 *ohist , *mhist=NULL ; char *ohist_name=NULL ; int ohzadd=0 ;
int *rlist , numval ; float mincount=0.0f ; int mcc ;
int *exlist=NULL, numex=0 ;
int do_excNONLAB=0 ;
/*---- for the clueless who wish to become clued-in ----*/
if( argc == 1 ){ usage_3dLocalHistog(1); exit(0); } /* Bob's help shortcut */
/*---- official startup ---*/
#if defined(USING_MCW_MALLOC) && !defined(USE_OMP)
enable_mcw_malloc() ;
#endif
PRINT_VERSION("3dLocalHistog"); mainENTRY("3dLocalHistog main"); machdep();
AFNI_logger("3dLocalHistog",argc,argv);
if( getpid()%2 ) AUTHOR("Bilbo Baggins"); else AUTHOR("Thorin Oakenshield");
AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */
/*---- loop over options ----*/
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0){
usage_3dLocalHistog(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
if( strncmp(argv[iarg],"-qu",3) == 0 ){
verb = 0 ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-verb",5) == 0 ){
verb++ ; iarg++ ; continue ;
}
#ifdef ALLOW_PROB
if( strncmp(argv[iarg],"-prob",5) == 0 ){
do_prob = 1 ; iarg++ ; continue ;
}
#endif
if( strcmp(argv[iarg],"-exclude") == 0 ){
int ebot=-6666666,etop=-6666666 , ee ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '-exclude'") ;
sscanf(argv[iarg],"%d..%d",&ebot,&etop) ;
if( ebot >= -TWO15 && ebot <= TWO15 ){
if( etop < -TWO15 || etop > TWO15 || etop < ebot ) etop = ebot ;
exlist = (int *)realloc(exlist,sizeof(int)*(etop-ebot+1+numex+1)) ;
for( ee=ebot ; ee <= etop ; ee++ ){ if( ee != 0 ) exlist[numex++] = ee ; }
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-excNONLAB") == 0 ){
do_excNONLAB = 1 ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-prefix") == 0 ){
if( ++iarg >= argc ) ERROR_exit("Need argument after '-prefix'") ;
prefix = strdup(argv[iarg]) ;
if( !THD_filename_ok(prefix) ) ERROR_exit("Bad -prefix!") ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-hsave") == 0 ){
if( ++iarg >= argc ) ERROR_exit("Need argument after '-hsave'") ;
ohist_name = strdup(argv[iarg]) ;
if( !THD_filename_ok(ohist_name) ) ERROR_exit("Bad -hsave!") ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-mincount") == 0 ){
char *cpt ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '-mincount'") ;
mincount = (float)strtod(argv[iarg],&cpt) ;
#if 0
if( mincount > 0.0f && mincount < 50.0f && *cpt == '%' ) /* percentage */
mincount = -0.01f*mincount ;
#endif
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-nbhd") == 0 ){
char *cpt ;
if( ntype > 0 ) ERROR_exit("Can't have 2 '-nbhd' options") ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '-nbhd'") ;
cpt = argv[iarg] ;
if( strncasecmp(cpt,"SPHERE",6) == 0 ){
sscanf( cpt+7 , "%f" , &na ) ;
ntype = NTYPE_SPHERE ;
} else if( strncasecmp(cpt,"RECT",4) == 0 ){
sscanf( cpt+5 , "%f,%f,%f" , &na,&nb,&nc ) ;
if( na == 0.0f && nb == 0.0f && nc == 0.0f )
ERROR_exit("'RECT(0,0,0)' is not a legal neighborhood") ;
ntype = NTYPE_RECT ;
} else if( strncasecmp(cpt,"RHDD",4) == 0 ){
sscanf( cpt+5 , "%f" , &na ) ;
if( na == 0.0f ) ERROR_exit("Can't have a RHDD of radius 0") ;
ntype = NTYPE_RHDD ;
} else if( strncasecmp(cpt,"TOHD",4) == 0 ){
sscanf( cpt+5 , "%f" , &na ) ;
if( na == 0.0f ) ERROR_exit("Can't have a TOHD of radius 0") ;
ntype = NTYPE_TOHD ;
} else {
ERROR_exit("Unknown -nbhd shape: '%s'",cpt) ;
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-lab_file") == 0 || strcmp(argv[iarg],"-labfile") == 0 ){
char **labnum ; int nbad=0 ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]) ;
if( labfile != NULL ) ERROR_exit("Can't use '%s' twice!",argv[iarg-1]) ;
labfile = strdup(argv[iarg]) ;
labnel = THD_string_table_read(labfile,0) ;
if( labnel == NULL || labnel->vec_num < 2 )
ERROR_exit("Can't read label file '%s'",labfile) ;
nlab = labnel->vec_len ;
labnum = (char **)labnel->vec[0] ;
lablab = (char **)labnel->vec[1] ;
labval = (int *)calloc(sizeof(int),nlab) ;
for( ii=0 ; ii < nlab ; ii++ ){
if( labnum[ii] != NULL ){
labval[ii] = (int)strtod(labnum[ii],NULL) ;
if( labval[ii] < -TWO15 || labval[ii] > TWO15 ){ labval[ii] = 0; nbad++; }
}
}
if( nbad > 0 )
ERROR_message("%d label values are outside the range %d..%d :-(" ,
nbad , -TWO15 , TWO15 ) ;
iarg++ ; continue ;
}
ERROR_message("** 3dLocalHistog: Illegal option: '%s'",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1) ;
} /*--- end of loop over options ---*/
/*---- check for stupid user inputs ----*/
if( iarg >= argc ) ERROR_exit("No datasets on command line?") ;
if( ohist_name == NULL && strcmp(prefix,"NULL") == 0 )
ERROR_exit("-prefix NULL is only meaningful if you also use -hsave :-(") ;
/*------------ scan input datasets, built overall histogram ------------*/
nsar = argc - iarg ;
insar = (THD_3dim_dataset **)malloc(sizeof(THD_3dim_dataset *)*nsar) ;
if( verb ) fprintf(stderr,"Scanning %d datasets ",nsar) ;
ohist = (UINT32 *)calloc(sizeof(UINT32),TWO16) ;
for( ids=iarg ; ids < argc ; ids++ ){ /* dataset loop */
insar[ids-iarg] = inset = THD_open_dataset(argv[ids]) ;
CHECK_OPEN_ERROR(inset,argv[ids]) ;
if( ids == iarg ){
nx = DSET_NX(inset); ny = DSET_NY(inset); nz = DSET_NZ(inset); nvox = nx*ny*nz;
} else if( nx != DSET_NX(inset) ||
ny != DSET_NY(inset) || nz != DSET_NZ(inset) ){
ERROR_exit("Dataset %s grid doesn't match!",argv[ids]) ;
}
if( !THD_datum_constant(inset->dblk) )
ERROR_exit("Dataset %s doesn't have a fixed data type! :-(",argv[ids]) ;
if( THD_need_brick_factor(inset) )
ERROR_exit("Dataset %s has scale factors! :-(",argv[ids]) ;
if( DSET_BRICK_TYPE(inset,0) != MRI_byte &&
DSET_BRICK_TYPE(inset,0) != MRI_short &&
DSET_BRICK_TYPE(inset,0) != MRI_float )
ERROR_exit("Dataset %s is not byte- or short-valued! :-(",argv[ids]) ;
DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ;
for( ii=0 ; ii < DSET_NVALS(inset) ; ii++ ){ /* add to overall histogram */
if( verb ) fprintf(stderr,".") ;
switch( DSET_BRICK_TYPE(inset,ii) ){
case MRI_short:{
short *sar = (short *)DSET_BRICK_ARRAY(inset,ii) ;
for( kk=0 ; kk < nvox ; kk++ ) ohist[ sar[kk]+TWO15 ]++ ;
}
break ;
case MRI_byte:{
byte *bar = (byte *)DSET_BRICK_ARRAY(inset,ii) ;
for( kk=0 ; kk < nvox ; kk++ ) ohist[ bar[kk]+TWO15 ]++ ;
}
break ;
case MRI_float:{
float *far = (float *)DSET_BRICK_ARRAY(inset,ii) ; short ss ;
for( kk=0 ; kk < nvox ; kk++ ){ ss = SHORTIZE(far[kk]); ohist[ss+TWO15]++; }
}
break ;
}
} /* end of sub-brick loop */
DSET_unload(inset) ; /* will re-load later, as needed */
} /* end of dataset loop */
if( verb ) fprintf(stderr,"\n") ;
/*-------------- process overall histogram for fun and profit -------------*/
/* if we didn't actually find 0, put it in the histogram now */
if( ohist[0+TWO15] == 0 ){ ohist[0+TWO15] = 1 ; ohzadd = 1 ; }
/* excNONLAB? */
if( nlab > 0 && do_excNONLAB ){
byte *klist = (byte *)calloc(sizeof(byte),TWO16) ; int nee ;
for( ii=0 ; ii < nlab ; ii++ ){ if( labval[ii] != 0 ) klist[labval[ii]+TWO15] = 1 ; }
for( nee=ii=0 ; ii < TWO16 ; ii++ ){ if( !klist[ii] ) nee++ ; }
exlist = (int *)realloc(exlist,sizeof(int)*(numex+nee+1)) ;
for( ii=0 ; ii < TWO16 ; ii++ ){ if( ii != TWO15 && !klist[ii] ) exlist[numex++] = ii-TWO15 ; }
free(klist) ;
}
/* make a copy of ohist and edit it for mincount, etc */
mhist = (UINT32 *)malloc(sizeof(UINT32)*TWO16) ;
memcpy(mhist,ohist,sizeof(UINT32)*TWO16) ;
mcc = (mincount < 0.0f) ? (int)(-mincount*nvox) : (int)mincount ;
if( mcc > 1 ){
for( ids=ii=0 ; ii < TWO16 ; ii++ ){
if( ii != TWO15 && mhist[ii] > 0 && mhist[ii] < mcc ){ mhist[ii] = 0; ids++; }
}
if( ids > 0 && verb )
INFO_message("Edited out %d values with overall histogram counts less than %d",ids,mcc) ;
}
if( numex > 0 ){
int ee ;
for( ids=0,ii=0 ; ii < numex ; ii++ ){
ee = exlist[ii] ;
if( mhist[ee+TWO15] > 0 ){ mhist[ee+TWO15] = 0; ids++; }
}
free(exlist) ;
if( ids > 0 && verb )
INFO_message("Edited out %d values from the exclude list",ids) ;
}
/* count number of values with nonzero (edited) counts */
numval = 0 ;
for( ii=0 ; ii < TWO16 ; ii++ ) if( mhist[ii] != 0 ) numval++ ;
if( numval == 0 ) ERROR_exit("Nothing found! WTF?") ; /* should not happen */
/* make list of all values with nonzero (edited) count */
rlist = (int *)malloc(sizeof(int)*numval) ;
if( verb > 1 ) fprintf(stderr,"++ Include list:") ;
for( ii=kk=0 ; ii < TWO16 ; ii++ ){
if( mhist[ii] != 0 ){
rlist[kk++] = ii-TWO15 ;
if( verb > 1 ) fprintf(stderr," %d[%u]",ii-TWO15,mhist[ii]) ;
}
}
if( verb > 1 ) fprintf(stderr,"\n") ;
rbot = rlist[0] ; rtop = rlist[numval-1] ; /* smallest and largest values found */
if( rbot == rtop ) ERROR_exit("Only one value (%d) found in all inputs!",rbot) ;
/* if 0 isn't first in rlist, then
put it in first place and move negative values up by one spot */
if( rbot < 0 ){
for( kk=0 ; kk < numval && rlist[kk] != 0 ; kk++ ) ; /*nada*/
if( kk < numval ){ /* should always be true */
for( ii=kk-1 ; ii >= 0 ; ii-- ) rlist[ii+1] = rlist[ii] ;
rlist[0] = 0 ;
}
}
if( verb )
INFO_message("Value range = %d..%d (%d distinct values)",rbot,rtop,numval );
/* save overall histogram? */
if( ohist_name != NULL ){
FILE *fp = fopen(ohist_name,"w") ; int nl=0 ;
if( fp == NULL ) ERROR_exit("Can't open -hsave '%s' for output!",ohist_name) ;
if( ohzadd ) ohist[0+TWO15] = 0 ;
for( ii=0 ; ii < TWO16 ; ii++ ){
if( ohist[ii] != 0 ){ fprintf(fp,"%6d %u\n",ii-TWO15,ohist[ii]); nl++; }
}
fclose(fp) ;
if( verb ) INFO_message("Wrote %d lines to -hsave file %s",nl,ohist_name) ;
}
free(ohist) ; free(mhist) ; mhist = ohist = NULL ; /* done with this */
if( strcmp(prefix,"NULL") == 0 ) exit(0) ; /* special case */
/*----------- build the neighborhood mask -----------*/
if( ntype <= 0 ){ /* default neighborhood */
ntype = NTYPE_SPHERE ; na = 0.0f ;
if( verb ) INFO_message("Using default neighborhood = self") ;
}
switch( ntype ){
default:
ERROR_exit("WTF? ntype=%d",ntype) ; /* should not happen */
case NTYPE_SPHERE:{
float dx , dy , dz ;
if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; }
else { dx = fabsf(DSET_DX(insar[0])) ;
dy = fabsf(DSET_DY(insar[0])) ;
dz = fabsf(DSET_DZ(insar[0])) ; }
nbhd = MCW_spheremask( dx,dy,dz , na ) ;
}
break ;
case NTYPE_RECT:{
float dx , dy , dz ;
if( na < 0.0f ){ dx = 1.0f; na = -na; } else dx = fabsf(DSET_DX(insar[0]));
if( nb < 0.0f ){ dy = 1.0f; nb = -nb; } else dy = fabsf(DSET_DY(insar[0]));
if( nc < 0.0f ){ dz = 1.0f; nc = -nc; } else dz = fabsf(DSET_DZ(insar[0]));
nbhd = MCW_rectmask( dx,dy,dz , na,nb,nc ) ;
}
break ;
case NTYPE_RHDD:{
float dx , dy , dz ;
if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; }
else { dx = fabsf(DSET_DX(insar[0])) ;
dy = fabsf(DSET_DY(insar[0])) ;
dz = fabsf(DSET_DZ(insar[0])) ; }
nbhd = MCW_rhddmask( dx,dy,dz , na ) ;
}
break ;
case NTYPE_TOHD:{
float dx , dy , dz ;
if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; }
else { dx = fabsf(DSET_DX(insar[0])) ;
dy = fabsf(DSET_DY(insar[0])) ;
dz = fabsf(DSET_DZ(insar[0])) ; }
nbhd = MCW_tohdmask( dx,dy,dz , na ) ;
}
break ;
}
if( verb ) INFO_message("Neighborhood comprises %d voxels",nbhd->num_pt) ;
/*------- actually do some work for a change (is it lunchtime yet?) -------*/
if( verb ) fprintf(stderr,"Voxel-wise histograms ") ;
outset = THD_localhistog( nsar,insar , numval,rlist , nbhd , do_prob,verb ) ;
if( outset == NULL ) ERROR_exit("Function THD_localhistog() fails?!") ;
/*---- save resulting dataset ----*/
EDIT_dset_items( outset , ADN_prefix,prefix , ADN_none ) ;
tross_Copy_History( insar[0] , outset ) ;
tross_Make_History( "3dLocalHistog" , argc,argv , outset ) ;
/* but first attach labels to sub-bricks */
EDIT_BRICK_LABEL(outset,0,"0:Other") ;
for( kk=1 ; kk < numval ; kk++ ){
sprintf(buf,"%d:",rlist[kk]) ;
for( ii=0 ; ii < nlab ; ii++ ){
if( labval[ii] == rlist[kk] && lablab[ii] != NULL ){
ids = strlen(buf) ;
MCW_strncpy(buf+ids,lablab[ii],THD_MAX_SBLABEL-ids) ;
break ;
}
}
EDIT_BRICK_LABEL(outset,kk,buf) ;
}
DSET_write( outset ) ;
if( verb ) WROTE_DSET( outset ) ;
exit(0) ;
}
int main( int argc , char *argv[] )
{
MRI_IMAGE *imin, *imout , *imout_orig;
THD_3dim_dataset *iset, *oset , *ooset;
char *prefix = "SpatNorm", *bottom_cuts = NULL;
int iarg , verb=0, OrigSpace = 0 , specie = HUMAN;
float SpatNormDxyz= 0.0, iset_scaled=1.0;
THD_ivec3 orixyz , nxyz ;
THD_fvec3 dxyz , orgxyz, originRAIfv, fv2;
mainENTRY("3dSpatNorm main") ; machdep() ;
if (argc == 1) { usage_3dSpatNorm(1); exit(0); }
/*--- options ---*/
iarg = 1 ;
OrigSpace = 0;
while( iarg < argc && argv[iarg][0] == '-' ){
if (strcmp(argv[iarg],"-h") == 0 || strcmp(argv[iarg],"-help") == 0 ) {
usage_3dSpatNorm(strlen(argv[iarg]) > 3 ? 2:1);
exit(0);
}
/* -prefix */
if( strcmp(argv[iarg],"-prefix") == 0 ){
if( ++iarg >= argc ){
fprintf(stderr,"**ERROR: -prefix requires another argument!\n") ;
exit(1) ;
}
prefix = strdup(argv[iarg]) ;
if( !THD_filename_ok(prefix) ){
fprintf(stderr,"**ERROR: -prefix value contains forbidden characters!\n") ;
exit(1) ;
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-dxyz") == 0 ){
if( ++iarg >= argc ){
fprintf(stderr,"**ERROR: -dxyz requires another argument!\n") ;
exit(1) ;
}
SpatNormDxyz = atof(argv[iarg]) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-bottom_cuts") == 0 ){
if( ++iarg >= argc ){
fprintf(stderr,"**ERROR: -bottom_cuts requires another argument!\n") ;
exit(1) ;
}
bottom_cuts = argv[iarg] ;
iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-verb",5) == 0 ){
verb++ ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-human",5) == 0 ){
specie = HUMAN ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-monkey",5) == 0 ){
specie = MONKEY ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-marmoset",5) == 0 ){
specie = MARMOSET ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-rat",5) == 0 ){
specie = RAT ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-orig_space",10) == 0 ){
OrigSpace = 1 ; iarg++ ; continue ;
}
fprintf(stderr,"**ERROR: %s is unknown option!\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1) ;
}
if( iarg >= argc ){
fprintf(stderr,"**ERROR: no input dataset name on command line?!\n") ;
exit(1) ;
}
/*--- read dataset ---*/
iset = THD_open_dataset( argv[iarg] ) ;
if( !ISVALID_DSET(iset) ){
fprintf(stderr,"**ERROR: can't open dataset %s\n",argv[iarg]) ;
exit(1) ;
}
/*--- get median brick --*/
if( verb ) fprintf(stderr,"++3dSpatNorm: loading dataset\n") ;
if (specie == MARMOSET) {
iset_scaled = 2.5;
THD_volDXYZscale(iset->daxes, iset_scaled, 0);
specie = MONKEY;
}
imin = THD_median_brick( iset ) ;
if( imin == NULL ){
fprintf(stderr,"**ERROR: can't load dataset %s\n",argv[iarg]) ;
exit(1) ;
}
imin->dx = fabs(iset->daxes->xxdel) ;
imin->dy = fabs(iset->daxes->yydel) ;
imin->dz = fabs(iset->daxes->zzdel) ;
mri_speciebusiness(specie);
mri_brain_normalize_cuts(bottom_cuts);
if (SpatNormDxyz) {
if (verb) fprintf(stderr,"Overriding default resampling\n");
mri_brainormalize_initialize(SpatNormDxyz, SpatNormDxyz, SpatNormDxyz);
} else {
float xxdel, yydel, zzdel, minres;
if (specie == MONKEY) minres = 0.5;
else if (specie == MARMOSET) minres = 0.2;
else if (specie == RAT) minres = 0.1;
else minres = 0.5;
/* don't allow for too low a resolution, please */
if (imin->dx < minres) xxdel = minres;
else xxdel = imin->dx;
if (imin->dy < minres) yydel = minres;
else yydel = imin->dy;
if (imin->dz < minres) zzdel = minres;
else zzdel = imin->dz;
if (verb) {
fprintf(stderr,
"%s:\n"
" Original resolution %f, %f, %f\n"
" SpatNorm resolution %f, %f, %f\n",
"3dSpatnorm", imin->dx, imin->dy, imin->dz,
xxdel, yydel, zzdel);
}
mri_brainormalize_initialize(xxdel, yydel, zzdel);
}
/* To get around the #define for voxel counts and dimensions */
mri_brainormalize_initialize(imin->dz, imin->dy, imin->dz);
/* me needs the origin of this dset in RAI world */
LOAD_FVEC3( originRAIfv ,
iset->daxes->xxorg , iset->daxes->yyorg , iset->daxes->zzorg) ;
originRAIfv = THD_3dmm_to_dicomm( iset , originRAIfv ) ;
LOAD_FVEC3(fv2, iset->daxes->xxorg + (iset->daxes->nxx-1)*iset->daxes->xxdel ,
iset->daxes->yyorg + (iset->daxes->nyy-1)*iset->daxes->yydel ,
iset->daxes->zzorg + (iset->daxes->nzz-1)*iset->daxes->zzdel);
fv2 = THD_3dmm_to_dicomm( iset , fv2 ) ;
if( originRAIfv.xyz[0] > fv2.xyz[0] ) {
float tf; tf = originRAIfv.xyz[0];
originRAIfv.xyz[0] = fv2.xyz[0]; fv2.xyz[0] = tf; }
if( originRAIfv.xyz[1] > fv2.xyz[1] ) {
float tf; tf = originRAIfv.xyz[1];
originRAIfv.xyz[1] = fv2.xyz[1]; fv2.xyz[1] = tf; }
if( originRAIfv.xyz[2] > fv2.xyz[2] ) {
float tf; tf = originRAIfv.xyz[2];
originRAIfv.xyz[2] = fv2.xyz[2]; fv2.xyz[2] = tf; }
if (verb) {
fprintf(stderr,"++3dSpatNorm (ZSS): RAI origin info: %f %f %f\n",
originRAIfv.xyz[0], originRAIfv.xyz[1], originRAIfv.xyz[2]);
}
DSET_unload( iset ) ; /* don't need this data no more */
/*-- convert image to shorts, if appropriate --*/
if( DSET_BRICK_TYPE(iset,0) == MRI_short ||
DSET_BRICK_TYPE(iset,0) == MRI_byte ){
imout = mri_to_short(0.0,imin) ; /* ZSS Oct 2012: Let function set scaling*/
mri_free(imin) ; imin = imout ;
}
/*--- normalize image spatially ---*/
mri_brainormalize_verbose( verb ) ;
if (OrigSpace) {
imout = mri_brainormalize( imin , iset->daxes->xxorient,
iset->daxes->yyorient,
iset->daxes->zzorient , &imout_orig, NULL) ;
} else {
imout = mri_brainormalize( imin , iset->daxes->xxorient,
iset->daxes->yyorient,
iset->daxes->zzorient , NULL, NULL) ;
}
mri_free( imin ) ;
if( imout == NULL ){
fprintf(stderr,"**ERROR: normalization fails!?\n"); exit(1);
}
if (OrigSpace) {
if( verb ) fprintf(stderr,"++3dSpatNorm: Output in Orignal space\n") ;
mri_free( imout ) ;
imout = imout_orig;
imout->xo = originRAIfv.xyz[0];
imout->yo = originRAIfv.xyz[1];
imout->zo = originRAIfv.xyz[2];
imout_orig = NULL;
} else {
if( verb ) fprintf(stderr,"++3dSpatNorm: Output in SpatNorm space\n") ;
}
#if 0
if( AFNI_yesenv("WATERSHED") ){
imin = mri_watershedize( imout , 0.10 ) ;
if( imin != NULL ){ mri_free(imout); imout = imin; }
}
#endif
/*--- create output dataset ---*/
if( verb )
fprintf(stderr,"++3dSpatNorm: Creating output dset\n") ;
oset = EDIT_empty_copy( NULL ) ;
tross_Copy_History( iset , oset ) ;
tross_Make_History( "3dSpatNorm" , argc,argv , oset ) ;
LOAD_IVEC3( nxyz , imout->nx , imout->ny , imout->nz ) ;
LOAD_FVEC3( dxyz , imout->dx , imout->dy , imout->dz ) ;
LOAD_FVEC3( orgxyz , imout->xo , imout->yo , imout->zo ) ;
LOAD_IVEC3( orixyz , ORI_R2L_TYPE , ORI_A2P_TYPE , ORI_I2S_TYPE ) ;
if( verb )
fprintf(stderr,"++3dSpatNorm: EDIT_dset_items\n") ;
EDIT_dset_items( oset ,
ADN_prefix , prefix ,
ADN_datum_all , imout->kind ,
ADN_nxyz , nxyz ,
ADN_xyzdel , dxyz ,
ADN_xyzorg , orgxyz ,
ADN_xyzorient , orixyz ,
ADN_malloc_type , DATABLOCK_MEM_MALLOC ,
ADN_view_type , VIEW_ORIGINAL_TYPE ,
ADN_type , HEAD_ANAT_TYPE ,
ADN_func_type , ANAT_BUCK_TYPE ,
ADN_none ) ;
if( verb )
fprintf(stderr,"++3dSpatNorm: EDIT_substitute_brick\n") ;
EDIT_substitute_brick( oset , 0 , imout->kind , mri_data_pointer(imout) ) ;
if (OrigSpace) {
if( verb )
fprintf(stderr,"++3dSpatNorm: Changing orientation from RAI\n") ;
ooset = r_new_resam_dset ( oset, iset, 0, 0, 0, NULL, MRI_NN, NULL, 1, 0);
if (!ooset) {
fprintf(stderr,"**ERROR: Failed to reslice!?\n"); exit(1);
}
/* put prefix back, r_new_resam_dset puts dummy prefix */
EDIT_dset_items( ooset ,
ADN_prefix , prefix,
ADN_none ) ;
DSET_delete(oset); oset = ooset; ooset = NULL;
}
if (iset_scaled != 1.0f)
THD_volDXYZscale(oset->daxes,
1/iset_scaled, 0);
DSET_write(oset) ;
if( verb )
fprintf(stderr,"++3dSpatNorm: wrote dataset %s\n",DSET_BRIKNAME(oset)) ;
exit(0) ;
}
int main( int argc , char *argv[] )
{
int iarg=1 , ii , do_iwarp=0 ;
char *prefix = "NwarpCat" ;
mat44 wmat , smat , qmat ;
THD_3dim_dataset *oset=NULL ;
char *cwarp_all=NULL ; int ntot=0 ;
AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */
if( argc < 2 || strcasecmp(argv[1],"-help") == 0 ) NWC_help() ;
/*-- bureaucracy --*/
mainENTRY("3dNwarpCat"); machdep();
AFNI_logger("3dNwarpCat",argc,argv);
PRINT_VERSION("3dNwarpCat"); AUTHOR("Zhark the Warper");
(void)COX_clock_time() ;
putenv("AFNI_WSINC5_SILENT=YES") ;
/*-- initialization --*/
CW_no_expad = 1 ; /* don't allow automatic padding of input warp */
Hverb = 0 ; /* don't be verbose inside mri_nwarp.c */
for( ii=0 ; ii < NWMAX ; ii++ ) cwarp[ii] = NULL ;
/*-- scan args --*/
while( iarg < argc && argv[iarg][0] == '-' ){
/*---------------*/
if( strcasecmp(argv[iarg],"-iwarp") == 0 ){
do_iwarp = 1 ; iarg++ ; continue ;
}
/*---------------*/
if( strcasecmp(argv[iarg],"-space") == 0 ){
sname = strdup(argv[++iarg]) ; iarg++ ; continue ;
}
/*---------------*/
if( strcasecmp(argv[iarg],"-NN") == 0 || strncasecmp(argv[iarg],"-nearest",6) == 0 ){
WARNING_message("NN interpolation not legal here -- switched to linear") ;
interp_code = MRI_LINEAR ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-linear",4)==0 || strncasecmp(argv[iarg],"-trilinear",6)==0 ){
interp_code = MRI_LINEAR ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-cubic",4)==0 || strncasecmp(argv[iarg],"-tricubic",6)==0 ){
WARNING_message("cubic interplation not legal here -- switched to quintic") ;
interp_code = MRI_QUINTIC ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-quintic",4)==0 || strncasecmp(argv[iarg],"-triquintic",6)==0 ){
interp_code = MRI_QUINTIC ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-wsinc",5) == 0 ){
interp_code = MRI_WSINC5 ; iarg++ ; continue ;
}
/*---------------*/
if( strcasecmp(argv[iarg],"-expad") == 0 ){
int expad ;
if( ++iarg >= argc ) ERROR_exit("no argument after '%s' :-(",argv[iarg-1]) ;
expad = (int)strtod(argv[iarg],NULL) ;
if( expad < 0 ){
WARNING_message("-expad %d is illegal and is set to zero",expad) ;
expad = 0 ;
}
CW_extra_pad = expad ; /* this is how we force extra padding */
iarg++ ; continue ;
}
/*---------------*/
if( strncasecmp(argv[iarg],"-interp",5)==0 ){
char *inam ;
if( ++iarg >= argc ) ERROR_exit("no argument after '%s' :-(",argv[iarg-1]) ;
inam = argv[iarg] ; if( *inam == '-' ) inam++ ;
if( strcasecmp(inam,"NN")==0 || strncasecmp(inam,"nearest",5)==0 ){
WARNING_message("NN interpolation not legal here -- changed to linear") ;
interp_code = MRI_LINEAR ;
} else if( strncasecmp(inam,"linear",3)==0 || strncasecmp(inam,"trilinear",5)==0 ){
interp_code = MRI_LINEAR ;
} else if( strncasecmp(inam,"cubic",3)==0 || strncasecmp(inam,"tricubic",5)==0 ){
WARNING_message("cubic interplation not legal here -- changed to quintic") ;
interp_code = MRI_QUINTIC ;
} else if( strncasecmp(inam,"quintic",3)==0 || strncasecmp(inam,"triquintic",5)==0 ){
interp_code = MRI_QUINTIC ;
} else if( strncasecmp(inam,"wsinc",4)==0 ){
interp_code = MRI_WSINC5 ;
} else {
ERROR_exit("Unknown code '%s' after '%s' :-(",argv[iarg],argv[iarg-1]) ;
}
iarg++ ; continue ;
}
/*---------------*/
if( strcasecmp(argv[iarg],"-verb") == 0 ){
verb++ ; NwarpCalcRPN_verb(verb) ; iarg++ ; continue ;
}
/*---------------*/
if( strcasecmp(argv[iarg],"-prefix") == 0 ){
if( ++iarg >= argc ) ERROR_exit("no argument after '%s' :-(",argv[iarg-1]) ;
prefix = argv[iarg] ;
if( !THD_filename_ok(prefix) ) ERROR_exit("Illegal name after '%s'",argv[iarg-1]) ;
iarg++ ; continue ;
}
/*---------------*/
if( strncasecmp(argv[iarg],"-warp",5) == 0 ){
int nn ;
if( iarg >= argc-1 ) ERROR_exit("no argument after '%s' :-(",argv[iarg]) ;
if( !isdigit(argv[iarg][5]) ) ERROR_exit("illegal format for '%s' :-(",argv[iarg]) ;
nn = (int)strtod(argv[iarg]+5,NULL) ;
if( nn <= 0 || nn > NWMAX )
ERROR_exit("illegal warp index in '%s' :-(",argv[iarg]) ;
if( cwarp[nn-1] != NULL )
ERROR_exit("'%s': you can't specify warp #%d more than once :-(",argv[iarg],nn) ;
cwarp[nn-1] = strdup(argv[++iarg]) ;
if( nn > nwtop ) nwtop = nn ;
iarg++ ; continue ;
}
/*---------------*/
ERROR_message("Confusingly Unknown option '%s' :-(",argv[iarg]) ;
suggest_best_prog_option(argv[0],argv[iarg]) ;
exit(1) ;
}
/*-- load any warps left on the command line, after options --*/
for( ; iarg < argc && nwtop < NWMAX-1 ; iarg++ )
cwarp[nwtop++] = strdup(argv[iarg]) ;
/*-- check if all warp strings are affine matrices --*/
#undef AFFINE_WARP_STRING
#define AFFINE_WARP_STRING(ss) \
( strstr((ss)," ") == NULL && \
( strcasestr((ss),".1D") != NULL || strcasestr((ss),".txt") != NULL ) )
for( ntot=ii=0 ; ii < nwtop ; ii++ ){
if( cwarp[ii] == NULL ) continue ;
ntot += strlen(cwarp[ii]) ;
if( ! AFFINE_WARP_STRING(cwarp[ii]) ) break ; /* not affine */
}
if( ntot == 0 ) ERROR_exit("No warps on command line?!") ;
if( ii == nwtop ){ /* all are affine (this is for Ziad) */
char *fname = malloc(sizeof(char)*(strlen(prefix)+16)) ; FILE *fp ;
float a11,a12,a13,a14,a21,a22,a23,a24,a31,a32,a33,a34 ;
LOAD_IDENT_MAT44(wmat) ;
for( ii=0 ; ii < nwtop ; ii++ ){
if( cwarp[ii] == NULL ) continue ;
smat = CW_read_affine_warp_OLD(cwarp[ii]) ;
qmat = MAT44_MUL(smat,wmat) ; wmat = qmat ;
}
if( strcmp(prefix,"-") == 0 || strncmp(prefix,"stdout",6) == 0 ){
fp = stdout ; strcpy(fname,"stdout") ;
} else {
strcpy(fname,prefix) ;
if( strstr(fname,".1D") == NULL ) strcat(fname,".aff12.1D") ;
fp = fopen(fname,"w") ;
if( fp == NULL ) ERROR_exit("Can't open output matrix file %s",fname) ;
}
if( do_iwarp ){
qmat = MAT44_INV(wmat) ; wmat = qmat ;
}
UNLOAD_MAT44(wmat,a11,a12,a13,a14,a21,a22,a23,a24,a31,a32,a33,a34) ;
fprintf(fp,
" %13.6g %13.6g %13.6g %13.6g %13.6g %13.6g %13.6g %13.6g %13.6g %13.6g %13.6g %13.6g\n",
a11,a12,a13,a14,a21,a22,a23,a24,a31,a32,a33,a34 ) ;
if( verb && fp != stdout ) INFO_message("Wrote matrix to %s",fname) ;
if( fp != stdout ) fclose(fp) ;
exit(0) ;
}
/*** at least one nonlinear warp ==> cat all strings, use library function to read ***/
cwarp_all = (char *)calloc(sizeof(char),(ntot+NWMAX)*2) ;
for( ii=0 ; ii < nwtop ; ii++ ){
if( cwarp[ii] != NULL ){ strcat(cwarp_all,cwarp[ii]) ; strcat(cwarp_all," ") ; }
}
oset = IW3D_read_catenated_warp( cwarp_all ) ; /* process all of them at once */
if( do_iwarp ){ /* 18 Jul 2014 */
THD_3dim_dataset *qwarp ;
if( verb ) fprintf(stderr,"Applying -iwarp option") ;
qwarp = THD_nwarp_invert(oset) ;
DSET_delete(oset) ;
oset = qwarp ;
if( verb ) fprintf(stderr,"\n") ;
}
tross_Make_History( "3dNwarpCat" , argc,argv , oset ) ;
if( sname != NULL ) MCW_strncpy( oset->atlas_space , sname , THD_MAX_NAME ) ;
EDIT_dset_items( oset , ADN_prefix,prefix , ADN_none ) ;
DSET_write(oset) ; WROTE_DSET(oset) ;
/*--- run away screaming into the night, never to be seen again ---*/
INFO_message("total CPU time = %.1f sec Elapsed = %.1f\n",
COX_cpu_time() , COX_clock_time() ) ;
exit(0) ;
}
/*!\**
File : SUMA.c
\author : Ziad Saad
Date : Thu Dec 27 16:21:01 EST 2001
Purpose :
Input paramters :
\param
\param
Usage :
SUMA ( )
Returns :
\return
\return
Support :
\sa OpenGL prog. Guide 3rd edition
\sa varray.c from book's sample code
Side effects :
***/
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"suma"};
int kar, i;
SUMA_SFname *SF_name;
SUMA_Boolean brk, SurfIn;
char *NameParam, *AfniHostName = NULL, *s = NULL, *pdspec=NULL, *pdsv=NULL;
char *specfilename[SUMA_MAX_N_GROUPS], *VolParName[SUMA_MAX_N_GROUPS];
byte InMem[SUMA_MAX_N_GROUPS];
SUMA_SurfSpecFile *Specp[SUMA_MAX_N_GROUPS];
SUMA_Axis *EyeAxis;
SUMA_EngineData *ED= NULL;
DList *list = NULL;
DListElmt *Element= NULL;
int iv15[15], N_iv15, ispec, nspec;
struct stat stbuf;
float fff=0.0;
int Start_niml = 0;
SUMA_Boolean Domemtrace = YUP;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_Boolean LocalHead = NOPE;
SUMA_STANDALONE_INIT;
SUMA_mainENTRY;
SUMAg_CF->isGraphical = YUP;
ps = SUMA_Parse_IO_Args(argc, argv, "-i;-t;-dset;-do;");
/* initialize Volume Parent and AfniHostName to nothing */
for (ispec=0; ispec < SUMA_MAX_N_GROUPS; ++ispec) {
specfilename[ispec] = NULL;
VolParName[ispec] = NULL;
Specp[ispec] = NULL;
InMem[ispec] = 0;
}
AfniHostName = NULL;
/* Allocate space for DO structure */
SUMAg_DOv = SUMA_Alloc_DisplayObject_Struct (SUMA_MAX_DISPLAYABLE_OBJECTS);
/* call the function to parse the other surface mode inputs */
ispec = 0;
if (LocalHead) SUMA_Show_IO_args(ps);
if (ps->i_N_surfnames || ps->t_N_surfnames || ps->N_DO) {
SUMA_LH("-i and/or -t surfaces on command line!");
Specp[ispec] = SUMA_IO_args_2_spec (ps, &nspec);
if (Specp[ispec]) {
++ispec;
if (nspec != 1) {
SUMA_S_Errv("-spec is being parsed separately here, "
"expecting one spec only from SUMA_IO_args_2_spec, \n"
"got %d\n", nspec);
exit (1);
}
} else {
SUMA_S_Err("Failed to load -i/-t surfaces");
exit(1);
}
}
/* Work the options */
kar = 1;
brk = NOPE;
SurfIn = NOPE;
Domemtrace = YUP;
while (kar < argc) { /* loop accross command ine options */
/*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
SUMA_usage (ps, strlen(argv[kar]) > 3 ? 2:1);
exit (0); /* return a good status on -help 12 Jul 2013 [rickr] */
}
/* -list_ports list and quit */
if( strncmp(argv[kar],"-list_ports", 8) == 0) {
show_ports_list(); exit(0);
}
/* -port_number and quit */
if( strncmp(argv[kar],"-port_number", 8) == 0) {
int pp = 0;
if( ++kar >= argc )
ERROR_exit("need an argument after -port_number!");
pp = get_port_named(argv[kar]);
if (strcmp(argv[kar-1], "-port_number_quiet")) {
fprintf(stdout, "\nPort %s: %d\n", argv[kar], pp);
} else {
fprintf(stdout, "%d\n", pp);
}
if (pp < 1) exit(1);
else exit(0);
}
if (strcmp(argv[kar], "-visuals") == 0) {
SUMA_ShowAllVisuals ();
exit (0);
}
if (strcmp(argv[kar], "-brethren_windows") == 0) {
Display *dd=NULL; Window ww;
if (!(dd = XOpenDisplay(NULL))) {
SUMA_S_Err("No display "); exit(1);
}
ww = XDefaultRootWindow(dd);
SUMA_WindowsOnRootDisplay(dd, ww , 0);
exit (0);
}
if (strcmp(argv[kar], "-version") == 0) {
s = SUMA_New_Additions (0.0, 1);
fprintf (SUMA_STDOUT,"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-sources") == 0) {
s = SUMA_sources_Info();
fprintf (SUMA_STDOUT,"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-help_nido") == 0) {
s = SUMA_NIDO_Info();
fprintf (SUMA_STDOUT,"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-all_latest_news") == 0) {
s = SUMA_New_Additions (-1.0, 0);
fprintf (SUMA_STDOUT,"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-help_sphinx_interactive") == 0) {
FILE *fout = NULL;
if( ++kar >= argc )
ERROR_exit("need a file name after -help_sphinx_interactive!");
fout = fopen(argv[kar],"w");
if (!fout) {
SUMA_S_Err("Failed to open %s for writing", argv[kar]);
exit(1);
}
SUMA_help_message(fout,SPX);
fclose(fout); fout = NULL;
exit (0);
}
if (strcmp(argv[kar], "-help_interactive") == 0) {
FILE *fout = fopen("Mouse_Keyboard_Controls.txt","w");
if (!fout) {
SUMA_S_Err("Failed to open Mouse_Keyboard_Controls.txt for writing");
exit(1);
}
SUMA_help_message(fout,TXT);
fclose(fout); fout = NULL;
exit (0);
}
if (strcmp(argv[kar], "-test_help_string_edit") == 0) {
SUMA_Sphinx_String_Edit_Help(SUMA_STDOUT, 0);
exit(0);
}
if (strcmp(argv[kar], "-test_help_string_edit_web") == 0) {
SUMA_Sphinx_String_Edit_Help(SUMA_STDOUT, 1);
exit(0);
}
if (strcmp(argv[kar], "-environment") == 0) {
s = SUMA_env_list_help (0, TXT);
fprintf (SUMA_STDOUT,
"#SUMA ENVIRONMENT \n"
"# If you do not have a ~/.sumarc file, cannot find a SUMA\n"
"# environment variable that's been mentioned in documentation,\n"
"# or fervently desire to update your current ~/.sumarc with \n"
"# all the latest variables that SUMA uses, you should run: \n"
"# \n"
"# suma -update_env\n"
"# \n"
"# Unless you have setup SUMA environment variables outside of\n"
"# your ~/.sumarc file, updating your ~/.sumarc file with \n"
"# 'suma -update_env' WILL NOT ALTER changes you have already\n"
"# made to the variables in your current ~/.sumarc. \n"
"# For this reason consider running the update command after each \n"
"# upgrade of your AFNI/SUMA binaries.\n"
"***ENVIRONMENT\n"
"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-default_env") == 0) {
s = SUMA_env_list_help (1, NO_FORMAT);
fprintf (SUMA_STDOUT,
"#SUMA DEFAULT ENVIRONMENT (user settings ignored)\n"
"# see also suma -udate_env or suma -environment\n"
"# \n"
"***ENVIRONMENT\n"
"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-update_env") == 0) {
if (system("suma -environment > ___sumarc")) {
SUMA_S_Err("Failed to create env file.");
exit(1);
}
if (SUMA_filexists("~/.sumarc")) {
if (system("\\cp -f ~/.sumarc ~/.sumarc-bak")) {
SUMA_S_Err("Failed to backup ~/.sumarc to ~/.sumarc-bak.");
exit(1);
}
}
if (system("\\mv ___sumarc ~/.sumarc")) {
SUMA_S_Err("Failed to copy newrc (___sumarc) to ~/.sumarc");
exit(1);
}
SUMA_S_Note("Environment update done.");
exit(0);
}
if (strcmp(argv[kar], "-latest_news") == 0) {
s = SUMA_New_Additions (0.0, 0);
fprintf (SUMA_STDOUT,"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-progs") == 0) {
s = SUMA_All_Programs();
fprintf (SUMA_STDOUT,"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-motif_ver") == 0) { /* 9 Mar 2009 [rickr] */
show_motif_version_string();
exit (0);
}
if (!brk && (strcmp(argv[kar], "-iodbg") == 0)) {
fprintf(SUMA_STDERR,"Error %s: Obsolete, use -trace\n", FuncName);
exit (0);
/*
fprintf(SUMA_STDOUT,
"Warning %s: SUMA running in in/out debug mode.\n", FuncName);
SUMA_INOUT_NOTIFY_ON;
brk = YUP;
*/
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
#if SUMA_MEMTRACE_FLAG
if (!brk && (strcmp(argv[kar], "-memdbg") == 0)) {
fprintf(SUMA_STDOUT,"Error %s: -memdbg is obsolete, use -trace\n",
FuncName);
exit (0);
fprintf( SUMA_STDOUT,
"Warning %s: SUMA running in memory trace mode.\n",
FuncName);
SUMAg_CF->MemTrace = YUP;
#ifdef USING_MCW_MALLOC
#endif
brk = YUP;
}
#endif
if (!brk && (strcmp(argv[kar], "-dev") == 0)) {
fprintf(SUMA_STDOUT,
"Warning %s: SUMA running in developer mode, "
"some options may malfunction.\n", FuncName);
SUMAg_CF->Dev = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-fake_cmap") == 0)) {
SUMA_S_Warn("-fake_cmap is for automatic selfies of the widgets.\n"
"You should not use this option for any other reason\n");
SUMAg_CF->Fake_Cmap = YUP;
brk = YUP;
}
if (!brk && SUMAg_CF->Dev && (strcmp(argv[kar], "-truth_table") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need expression after -truth_table \n");
exit (1);
}
SUMA_bool_eval_truth_table(argv[kar], 0); exit(0);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-niml") == 0)) {
Start_niml = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-noniml") == 0)) {
Start_niml = -1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-vp") == 0 ||
strcmp(argv[kar], "-sa") == 0 ||
strcmp(argv[kar], "-sv") == 0))
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -vp|-sa|-sv \n");
exit (1);
}
if (ispec < 1) {
fprintf (SUMA_STDERR,
"a -spec option must precede the first -sv option\n");
exit (1);
}
if (!specfilename[ispec-1] && !Specp[ispec-1]) {
fprintf (SUMA_STDERR,
"a -spec option must precede each -sv option\n");
exit (1);
}
VolParName[ispec-1] = argv[kar];
if (LocalHead) {
fprintf(SUMA_STDOUT, "Found: %s\n", VolParName[ispec]);
}
brk = YUP;
}
if (!brk && strcmp(argv[kar], "-drive_com") == 0)
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -drive_com\n");
exit (1);
}
SUMAg_CF->dcom = (char **)SUMA_realloc(SUMAg_CF->dcom,
(SUMAg_CF->N_dcom+1)*sizeof(char *));
SUMAg_CF->dcom[SUMAg_CF->N_dcom] = SUMA_copy_string(argv[kar]);
++SUMAg_CF->N_dcom;
brk = YUP;
}
if (!brk && strcmp(argv[kar], "-ah") == 0)
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -ah\n");
exit (1);
}
if (strcmp(argv[kar],"localhost") != 0) {
AfniHostName = argv[kar];
}else {
fprintf (SUMA_STDERR,
"localhost is the default for -ah\n"
"No need to specify it.\n");
}
/*fprintf(SUMA_STDOUT, "Found: %s\n", AfniHostName);*/
brk = YUP;
}
if (!brk && strcmp(argv[kar], "-spec") == 0)
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -spec \n");
exit (1);
}
if (ispec >= SUMA_MAX_N_GROUPS) {
fprintf (SUMA_STDERR,
"Cannot accept more than %d spec files.\n",
SUMA_MAX_N_GROUPS);
exit(1);
}
if (SUMA_is_predefined_SO_name(argv[kar], NULL,
&pdspec, &pdsv, NULL) == 3) {
specfilename[ispec] = pdspec; pdspec = NULL; /* Memory leak! */
VolParName[ispec] = pdsv; pdsv = NULL; /* Memory leak! */
} else {
specfilename[ispec] = argv[kar];
}
if (LocalHead) {
fprintf(SUMA_STDOUT, "Found: %s\n", specfilename[ispec]);
}
++ispec;
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
if ( !strcmp(argv[kar], "-i") ||
!strncmp(argv[kar], "-i_",3) ) {
fprintf (SUMA_STDERR,
"Error %s: Option %s not understood. \n"
" Make sure parameter after -i or -i_ is the full name of a surface.\n"
"%s",
FuncName, argv[kar],
strlen(argv[kar])==2 ?
"For -i to work, SUMA needs to guess at the surface type from\n"
" the filename extensions. If SUMA fails try the full -i_* option"
" instead.\n" : ""
);
} else {
fprintf (SUMA_STDERR,
"Error %s: Option %s not understood. Try -help for usage\n",
FuncName, argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
}
exit (1);
} else {
brk = NOPE;
kar ++;
}
}/* loop accross command ine options */
/* -ah option now checked for in ps */
if (ps->cs->afni_host_name && !AfniHostName) {
AfniHostName = SUMA_copy_string(ps->cs->afni_host_name);
}
#if 0
SUMA_S_Note("KILL ME");
{
int i,j, nl;
SUMA_TextBoxSize("Hello", &i,&j,&nl,NULL);
SUMA_TextBoxSize("",
&i,&j,&nl,GLUT_BITMAP_8_BY_13);
SUMA_TextBoxSize("O",
&i,&j,&nl,GLUT_BITMAP_8_BY_13);
SUMA_TextBoxSize(NULL,
&i,&j,&nl,GLUT_BITMAP_8_BY_13);
}
SUMA_ReadNIDO("/Users/ziad/SUMA_test_dirs/DO/TextDO/sample.niml.do", NULL);
exit(1);
#endif
/* Make surface loading pacifying */
SetLoadPacify(1);
#if 0
if (ps->N_DO) { /* Have DOs on command line */
if (Specp[0]) { /* Add to Specp[0] */
if (ps->N_DO + Specp[0]->N_DO > SUMA_MAX_DO_SPEC) {
SUMA_S_Warn("Too many DOs, increase static limit..");
/* ignore extras for now */
ps->N_DO = SUMA_MAX_DO_SPEC - Specp[0]->N_DO;
}
for (i=0; i<ps->N_DO; ++i) {
strcpy(Specp[0]->DO_name[Specp[0]->N_DO], ps->DO_name[i]);
Specp[0]->DO_type[Specp[0]->N_DO] = ps->DO_type[i];
++Specp[0]->N_DO;
}
} else {
Specp[0]
}
}
#endif
/* any Specp to be found ?*/
if (specfilename[0] == NULL && Specp[0] == NULL) {
SUMA_SurfaceObject **SOv=NULL;
int N_SOv = 0;
fprintf (SUMA_STDERR,
"\n"
"%s: \n"
" No input specified, loading some toy surfaces...\n"
" Use '.' and ',' to cycle between them.\n"
" See suma -help for assistance.\n"
"\n", FuncName);
/* create your own surface and put it in a spec file */
SOv = SUMA_GimmeSomeSOs(&N_SOv);
Specp[ispec] = SUMA_SOGroup_2_Spec (SOv, N_SOv);
SUMA_free(SOv); SOv = NULL;
InMem[ispec] = 1;
++ispec;
}
if(!SUMA_Assign_HostName (SUMAg_CF, AfniHostName, -1)) {
fprintf (SUMA_STDERR,
"Error %s: Failed in SUMA_Assign_HostName\n", FuncName);
exit (1);
}
#ifdef SUMA_DISASTER
/* a function to test Memtracing */
{
int *jnk;
jnk = SUMA_disaster();
SUMA_free(jnk); /* without the -trace, you'll get a
warning here if jnk is corrupted */
}
#endif
/* create an Eye Axis DO */
EyeAxis = SUMA_Alloc_Axis ("Eye Axis", AO_type);
if (EyeAxis == NULL) {
SUMA_error_message (FuncName,"Error Creating Eye Axis",1);
exit(1);
}
/* Store it into SUMAg_DOv */
if (!SUMA_AddDO( SUMAg_DOv, &SUMAg_N_DOv,
(void *)EyeAxis, AO_type, SUMA_SCREEN)) {
SUMA_error_message (FuncName,"Error Adding DO", 1);
exit(1);
}
/*fprintf (SUMA_STDERR, "SUMAg_N_DOv = %d created\n", SUMAg_N_DOv);
SUMA_Show_DOv(SUMAg_DOv, SUMAg_N_DOv, NULL);*/
/* Allocate space (and initialize) Surface Viewer Structure */
SUMAg_SVv = SUMA_Alloc_SurfaceViewer_Struct (SUMA_MAX_SURF_VIEWERS);
/* SUMAg_N_SVv gets updated in SUMA_X_SurfaceViewer_Create
and reflects not the number of elements in SUMAg_SVv which is
SUMA_MAX_SURF_VIEWERS, but the number of viewers that were realized
by X */
/* Check on initialization */
/*SUMA_Show_SurfaceViewer_Struct (SUMAg_cSV, stdout);*/
/* Create the Surface Viewer Window */
if (!SUMA_X_SurfaceViewer_Create ()) {
fprintf(stderr,"Error in SUMA_X_SurfaceViewer_Create. Exiting\n");
return 1;
}
for (i=0; i<ispec; ++i) {
if (!list) list = SUMA_CreateList();
ED = SUMA_InitializeEngineListData (SE_Load_Group);
if (!( Element = SUMA_RegisterEngineListCommand ( list, ED,
SEF_cp, (void *)specfilename[i],
SES_Suma, NULL, NOPE,
SEI_Head, NULL ))) {
fprintf(SUMA_STDERR,"Error %s: Failed to register command\n", FuncName);
exit (1);
}
if (!( Element = SUMA_RegisterEngineListCommand ( list, ED,
SEF_ip, (void *)Specp[i],
SES_Suma, NULL, NOPE,
SEI_In, Element ))) {
fprintf(SUMA_STDERR,"Error %s: Failed to register command\n", FuncName);
exit (1);
}
fff = (float) InMem[i];
if (!( Element = SUMA_RegisterEngineListCommand ( list, ED,
SEF_f, (void *)&fff,
SES_Suma, NULL, NOPE,
SEI_In, Element ))) {
fprintf(SUMA_STDERR,"Error %s: Failed to register command\n", FuncName);
exit (1);
}
if (!( Element = SUMA_RegisterEngineListCommand ( list, ED,
SEF_vp, (void *)VolParName[i],
SES_Suma, NULL, NOPE,
SEI_In, Element ))) {
fprintf(SUMA_STDERR,"Error %s: Failed to register command\n", FuncName);
exit (1);
}
N_iv15 = SUMA_MAX_SURF_VIEWERS;
if (N_iv15 > 15) {
fprintf( SUMA_STDERR,
"Error %s: trying to register more than 15 viewers!\n",
FuncName);
exit(1);
}
for (kar=0; kar<N_iv15; ++kar) iv15[kar] = kar;
if (!( Element = SUMA_RegisterEngineListCommand ( list, ED,
SEF_iv15, (void *)iv15,
SES_Suma, NULL, NOPE,
SEI_In, Element ))) {
fprintf(SUMA_STDERR,"Error %s: Failed to register command\n", FuncName);
exit (1);
}
if (!( Element = SUMA_RegisterEngineListCommand ( list, ED,
SEF_i, (void *)&N_iv15,
SES_Suma, NULL, NOPE,
SEI_In, Element ))) {
fprintf(SUMA_STDERR,"Error %s: Failed to register command\n", FuncName);
exit (1);
}
}
if (ispec > 0 && !SUMA_Engine (&list)) {
fprintf(SUMA_STDERR,"Error %s: Failed in SUMA_Engine\n", FuncName);
exit (1);
}
/* For some reason, I had to add the glLightfv line below
to force the lightflipping done in SUMA_SetupSVforDOs to take place
in the A viewer when first opened. I don't know why that is, especially
since other controllers would show up lit correctly without this
glLightfv line below.
To make matters worse, the A controller's light0_position is correctly
flipped.
It is just that the shading is done as if the position was never flipped.
Actually, without the line below, the first time you hit the F key (to
manually flip the light), nothing changes, that's because the light's position is unflipped, which is supposed to show the incorrect lighting.
You'll have to hit F again to have the lighting correctly flipped
and the shading reflecting it.... ZSS, Aug. 05 04 */
glLightfv(GL_LIGHT0, GL_POSITION, SUMAg_SVv[0].light0_position);
if (Start_niml != -1 && (Start_niml == 1|| AFNI_yesenv("SUMA_START_NIML"))) {
if (!list) list = SUMA_CreateList();
SUMA_REGISTER_HEAD_COMMAND_NO_DATA( list, SE_StartListening,
SES_Suma, NULL);
if (!SUMA_Engine (&list)) {
fprintf(SUMA_STDERR, "Error %s: SUMA_Engine call failed.\n", FuncName);
exit (1);
}
}
/* load the datasets onto the first SO, if any, else hope that dset
is some form of DO */
if (ps->N_dsetname>0) {
SUMA_SurfaceObject *SO = SUMA_findanySOp_inDOv(SUMAg_DOv,
SUMAg_N_DOv, NULL);
if (!SO) {
SUMA_LH("Could not find any SO, here is hoping dset is a DO");
}
for (i=0; i<ps->N_dsetname; ++i) {
if (!(SUMA_LoadDsetOntoSO_eng(ps->dsetname[i], SO, 1, 1, 1, NULL))) {
SUMA_S_Errv("Failed to load %s onto %s\n",
ps->dsetname[i], SO?SO->Label:"NULL");
}
}
}
SUMA_FreeGenericArgParse(ps); ps = NULL;
/* A Warning about no sumarc */
if (NoSumaRcFound()) {
SUMA_S_Warn(
"\n"
" No sumarc file found. You should create one by running the following:\n"
"\n"
" suma -update_env\n"
"\n"
" I also recommend you run 'suma -update_env' whenever you update AFNI.\n"
"\n"
" See details for -environment and -update_env options in suma -help's output.\n"
"\n");
}
/*Main loop */
XtAppMainLoop(SUMAg_CF->X->App);
/* Done, clean up time */
if (ispec) {
int k=0;
for (k=0; k<ispec; ++k) {
if (!SUMA_FreeSpecFields((Specp[k]))) {
SUMA_S_Err("Failed to free spec fields");
}
Specp[k] = NULL;
}
} ispec = 0;
if (!SUMA_Free_Displayable_Object_Vect (SUMAg_DOv, SUMAg_N_DOv))
SUMA_error_message(FuncName,"DO Cleanup Failed!",1);
if (!SUMA_Free_SurfaceViewer_Struct_Vect (SUMAg_SVv, SUMA_MAX_SURF_VIEWERS))
SUMA_error_message(FuncName,"SUMAg_SVv Cleanup Failed!",1);
if (!SUMA_Free_CommonFields(SUMAg_CF))
SUMA_error_message(FuncName,"SUMAg_CF Cleanup Failed!",1);
SUMA_RETURN(0); /* ANSI C requires main to return int. */
}/* Main */
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) ;
}
int main( int argc , char * argv[] )
{
THD_3dim_dataset *mask_dset=NULL, *iset=NULL,
*sset=NULL, *xset=NULL, *vset=NULL;
char *prefix="toy";
int iarg=1 , mcount, udatum = MRI_float;
byte *maskvox=NULL;
mainENTRY("3dToyProg main"); machdep(); AFNI_logger("3dToyProg",argc,argv);
#ifdef USING_MCW_MALLOC
enable_mcw_malloc() ;
#endif
/*-- options --*/
set_obliquity_report(0); /* silence obliquity */
while( iarg < argc && argv[iarg][0] == '-' ){
CHECK_HELP(argv[iarg], help_3dToyProg);
if( strncmp(argv[iarg],"-mask",5) == 0 ){
if (iarg >= argc) ERROR_exit("Need dset after -mask");
mask_dset = THD_open_dataset( argv[++iarg] ) ;
if( mask_dset == NULL )
ERROR_exit("Cannot open mask dataset!\n") ;
if( DSET_BRICK_TYPE(mask_dset,0) == MRI_complex )
ERROR_exit("Cannot deal with complex-valued mask dataset!\n");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-input") == 0) {
if (iarg >= argc) ERROR_exit("Need dset after -mask");
if (!(iset = THD_open_dataset( argv[++iarg]))) {
ERROR_exit("Cannot open input dataset %s!\n", argv[iarg]) ;
}
DSET_mallocize(iset); DSET_load(iset); /* load data part of dataset */
iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-prefix",6) == 0) {
if (iarg >= argc) ERROR_exit("Need name after -prefix");
prefix = argv[++iarg];
iarg++ ; continue ;
continue ;
}
if( strcmp(argv[iarg],"-datum") == 0) {
if (iarg >= argc) ERROR_exit("Need datum type after -datum");
++iarg;
if (!strcmp(argv[iarg],"float")) udatum = MRI_float;
else if (!strcmp(argv[iarg],"short")) udatum = MRI_short;
else {
ERROR_exit(
"For the purpose of this demo, only float and short are allowed");
}
iarg++ ; continue ;
continue ;
}
ERROR_message("ILLEGAL option: %s\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
if( argc < 2 ){
help_3dToyProg(TXT, 0);
PRINT_COMPILE_DATE ; exit(0) ;
}
if( !iset )
ERROR_exit("No dataset on command line!?") ;
if (mask_dset) {
if (THD_dataset_mismatch(mask_dset, iset))
ERROR_exit("grid mismatch between input dset and mask dset");
maskvox = THD_makemask( mask_dset , 0 , 1.0, -1.0 ) ;
mcount = THD_countmask( DSET_NVOX(mask_dset) , maskvox ) ;
if( mcount <= 0 ) ERROR_exit("No voxels in the mask!\n") ;
INFO_message("%d voxels in the mask dset %s\n",
mcount, DSET_PREFIX(mask_dset)) ;
DSET_delete(mask_dset) ; mask_dset=NULL; /* Done with the mask dset */
}
/* An illustration of how volume navigation works */
Dataset_Navigation(iset);
/* Let us create a dataset from scratch */
sset = New_Dataset_From_Scratch(prefix);
/* Now for the output, add history, check for overwrite and write away */
tross_Copy_History( iset , sset );/* Copy the old history (not mandatory). */
tross_Make_History("3dToyProg", argc, argv ,sset) ; /* add the new */
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(sset)) ) {
ERROR_message(
"Output %s already exists, use -overwrite to do you know what",
DSET_HEADNAME(sset));
} else DSET_write(sset);
/* Now we'll do some voxelwise computations */
xset = Voxelwise_Operations(sset, maskvox, prefix);
tross_Copy_History( iset , xset ) ; /* Copy the old */
tross_Make_History("3dToyProg", argc, argv ,xset) ; /* add the new */
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(xset)) ) {
ERROR_message(
"Output %s already exists, use -overwrite to do you know what",
DSET_HEADNAME(xset));
} else DSET_write(xset);
/* Or some volumewise operations */
vset = Volumewise_Operations(sset, prefix, udatum);
tross_Copy_History( iset , vset ) ; /* Copy the old */
tross_Make_History("3dToyProg", argc, argv ,vset) ; /* add the new */
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(vset)) ) {
ERROR_message(
"Output %s already exists, use -overwrite to do you know what",
DSET_HEADNAME(vset));
} else DSET_write(vset);
/* cleanup */
DSET_delete(xset); xset = NULL;
DSET_delete(vset); vset = NULL;
DSET_delete(sset); sset = NULL;
exit(0) ;
}
/*!
\brief parse the arguments for SurfQual program
\param argv (char *)
\param argc (int)
\return Opt (SUMA_SURFQUAL_OPTIONS *) options structure.
To free it, use
SUMA_free(Opt->out_prefix);
SUMA_free(Opt);
*/
SUMA_SURFQUAL_OPTIONS *SUMA_SurfQual_ParseInput (char *argv[], int argc,
SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]= {"SUMA_SurfQual_ParseInput"};
SUMA_SURFQUAL_OPTIONS *Opt=NULL;
int kar, i, ind;
char *outprefix;
SUMA_Boolean brk = NOPE;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = (SUMA_SURFQUAL_OPTIONS *)SUMA_malloc(sizeof(SUMA_SURFQUAL_OPTIONS));
kar = 1;
Opt->out_prefix = NULL;
Opt->surftype = NULL;
Opt->self_intersect = 0;
Opt->DoSum = 0;
brk = NOPE;
while (kar < argc) { /* loop accross command ine options */
/*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
usage_SUMA_SurfQual(ps, strlen(argv[kar]) > 3 ? 2:1);
exit (0);
}
/* skip the options parsed in SUMA_ParseInput_basics_s */
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-sphere") == 0)) {
if (Opt->surftype) {
SUMA_S_Err( "Surface type already specified.\n"
"Only one type allowed.");
exit(1);
}
Opt->surftype = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-self_intersect") == 0)) {
Opt->self_intersect = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-summary") == 0)) {
Opt->DoSum = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -prefix \n");
exit (1);
}
Opt->out_prefix = SUMA_copy_string(argv[kar]);
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
fprintf (SUMA_STDERR,
"Error %s:\nOption %s not understood. Try -help for usage\n",
FuncName, argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}
#if 0
if (Spec->N_Surfs < 1) {
SUMA_SL_Err("No surface specified.");
exit(1);
}
#endif
SUMA_RETURN (Opt);
}
/*!
\brief parse the arguments for SurfSmooth program
\param argv (char *)
\param argc (int)
\return Opt (SUMA_GETPATCH_OPTIONS *) options structure.
To free it, use
SUMA_free(Opt->out_prefix);
SUMA_free(Opt);
*/
SUMA_GETPATCH_OPTIONS *SUMA_GetPatch_ParseInput (char *argv[], int argc,
SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_GetPatch_ParseInput"};
SUMA_GETPATCH_OPTIONS *Opt=NULL;
int kar, i, ind;
char *outprefix;
SUMA_Boolean brk = NOPE;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = (SUMA_GETPATCH_OPTIONS *)SUMA_malloc(sizeof(SUMA_GETPATCH_OPTIONS));
kar = 1;
Opt->iType = SUMA_FT_NOT_SPECIFIED;
Opt->out_prefix = NULL;
Opt->out_volprefix = NULL;
Opt->in_name = NULL;
Opt->minhits = 2;
Opt->labelcol = -1;
Opt->nodecol = -1;
Opt->thislabel = -1;
Opt->DoVol = 0;
Opt->VolOnly = 0;
Opt->coordgain = 0.0;
Opt->Do_p2s = NOPE;
Opt->FixBowTie = -1;
Opt->adjust_contour = -1;
Opt->oType = SUMA_FT_NOT_SPECIFIED;
Opt->verb = 1;
Opt->flip = 0;
brk = NOPE;
while (kar < argc) { /* loop accross command ine options */
/*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
usage_SUMA_getPatch(ps, strlen(argv[kar]) > 3 ? 2:1);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-hits") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -hits \n");
exit (1);
}
Opt->minhits = atoi(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-coord_gain") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -coord_gain \n");
exit (1);
}
Opt->coordgain = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-masklabel") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -masklabel \n");
exit (1);
}
Opt->thislabel = atoi(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-patch2surf") == 0)) {
Opt->Do_p2s = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-vol") == 0)) {
Opt->DoVol = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-flip_orientation") == 0)) {
Opt->flip = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-vol_only") == 0)) {
Opt->DoVol = 1;
Opt->VolOnly = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-adjust_contour") == 0)) {
Opt->adjust_contour = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-do-not-adjust_contour") == 0)) {
Opt->adjust_contour = 0;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-check_bowtie") == 0)) {
Opt->FixBowTie = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-fix_bowtie") == 0)) {
Opt->FixBowTie = 2;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-ok_bowtie") == 0)) {
Opt->FixBowTie = 0;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -prefix \n");
exit (1);
}
Opt->out_prefix = SUMA_copy_string(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-verb") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -verb \n");
exit (1);
}
Opt->verb = atoi(argv[kar]);
if (Opt->verb < 0 || Opt->verb > 10) {
SUMA_S_Errv("Something fishy with -verb value of %s\n"
"Need integer from 0 to 2\n", argv[kar]);
exit(1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-stiched_surface") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -stiched_surface \n");
exit (1);
}
Opt->out_volprefix = SUMA_copy_string(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-out_type") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -out_type \n");
exit (1);
}
Opt->oType = SUMA_guess_surftype_argv(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-input") == 0)) {
kar ++;
if (kar+2 >= argc) {
fprintf (SUMA_STDERR, "need 3 arguments after -input \n");
exit (1);
}
Opt->in_name = argv[kar]; kar ++;
Opt->nodecol = atoi(argv[kar]); kar ++;
Opt->labelcol = atoi(argv[kar]);
brk = YUP;
}
#if 0
if (!brk && (strcmp(argv[kar], "-spec") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -spec \n");
exit (1);
}
Opt->spec_file = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sv") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -sv \n");
exit (1);
}
Opt->sv_name = argv[kar];
brk = YUP;
}
if (!brk && (strncmp(argv[kar], "-surf_", 6) == 0)) {
if (kar + 1>= argc) {
fprintf (SUMA_STDERR, "need argument after -surf_X SURF_NAME \n");
exit (1);
}
ind = argv[kar][6] - 'A';
if (ind < 0 || ind >= SURFPATCH_MAX_SURF) {
fprintf (SUMA_STDERR, "-surf_X SURF_NAME option is out of range.\n");
exit (1);
}
kar ++;
Opt->surf_names[ind] = argv[kar];
Opt->N_surf = ind+1;
brk = YUP;
}
#endif
if (!brk && !ps->arg_checked[kar]) {
fprintf (SUMA_STDERR,
"Error %s:\nOption %s not understood. Try -help for usage\n",
FuncName, argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}
/* sanity checks */
if (Opt->FixBowTie < 0) {
if (Opt->DoVol) Opt->FixBowTie = 1; /* important to check in this case */
else Opt->FixBowTie = 0;
}
if (Opt->adjust_contour < 0) {
if (Opt->DoVol) Opt->adjust_contour = 0;
else Opt->adjust_contour = 0;
}
if (!Opt->out_prefix) Opt->out_prefix = SUMA_copy_string("SurfPatch");
if (Opt->thislabel >= 0 && Opt->labelcol < 0) {
SUMA_SL_Err("Cannot use -masklabel without specifying "
"ilabel in -input option");
exit(1);
}
if (Opt->minhits < 1 || Opt->minhits > 3) {
SUMA_SL_Err("minhits must be > 0 and < 3");
exit(1);
}
if (!Opt->in_name) {
SUMA_SL_Err("No input specified.");
exit(1);
}
SUMA_RETURN (Opt);
}
int main( int argc , char *argv[] )
{
int iarg , ii,jj,kk,mm , nvec , do_one=0 , nx=0,ny , ff, doterse = 0 ;
MRI_IMAGE *tim ;
MRI_IMARR *tar ;
double sum , *eval , *amat , **tvec , *bmat , *svec ;
float *far ;
int demean=0 , docov=0 ;
char *matname ;
int okzero = 0;
mainENTRY("1ddot main"); machdep();
/* options */
iarg = 1 ; nvec = 0 ;
while( iarg < argc && argv[iarg][0] == '-' ){
if (strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0){
usage_1ddot(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
if( strcmp(argv[iarg],"-one") == 0 ){
demean = 0 ; do_one = 1 ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-okzero") == 0 ){
okzero = 1 ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-dem",4) == 0 ){
demean = 1 ; do_one = 0 ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-cov",4) == 0 ){
docov = 1 ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-inn",4) == 0 ){
docov = 2 ; iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-rank") == 0 ||
strcasecmp(argv[iarg],"-spearman") == 0 ){
do_one = 0; docov = 3; demean = 0; doterse = 1; iarg++; continue;
}
if( strncmp(argv[iarg],"-terse",4) == 0 ){
doterse = 1 ; iarg++ ; continue ;
}
fprintf(stderr,"** Unknown option: %s\n",argv[iarg]);
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
if( argc < 2 ){ usage_1ddot(1); exit(0) ; }
if( iarg == argc ) ERROR_exit("No 1D files on command line!?") ;
/* input 1D files */
ff = iarg ;
INIT_IMARR(tar) ; if( do_one ) nvec = 1 ;
for( ; iarg < argc ; iarg++ ){
tim = mri_read_1D( argv[iarg] ) ;
if( tim == NULL ){
fprintf(stderr,"** Can't read 1D file %s\n",argv[iarg]); exit(1);
}
if( nx == 0 ){
nx = tim->nx ;
} else if( tim->nx != nx ){
fprintf(stderr,"** 1D file %s doesn't match first file in length!\n",
argv[iarg]); exit(1);
}
nvec += tim->ny ;
ADDTO_IMARR(tar,tim) ;
}
if (!doterse) {
printf("\n") ;
printf("++ 1ddot input vectors:\n") ;
}
jj = 0 ;
if( do_one ){
if (!doterse) printf("00..00: all ones\n") ;
jj = 1 ;
}
for( mm=0 ; mm < IMARR_COUNT(tar) ; mm++ ){
tim = IMARR_SUBIM(tar,mm) ;
if (!doterse) printf("%02d..%02d: %s\n", jj,jj+tim->ny-1, argv[ff+mm] ) ;
jj += tim->ny ;
}
/* create vectors from 1D files */
tvec = (double **) malloc( sizeof(double *)*nvec ) ;
svec = (double * ) malloc( sizeof(double )*nvec ) ;
for( jj=0 ; jj < nvec ; jj++ )
tvec[jj] = (double *) malloc( sizeof(double)*nx ) ;
kk = 0 ;
if( do_one ){
svec[0] = 1.0 / sqrt((double)nx) ;
for( ii=0 ; ii < nx ; ii++ ) tvec[0][ii] = 1.0 ;
kk = 1 ;
}
for( mm=0 ; mm < IMARR_COUNT(tar) ; mm++ ){
tim = IMARR_SUBIM(tar,mm) ;
far = MRI_FLOAT_PTR(tim) ;
for( jj=0 ; jj < tim->ny ; jj++,kk++ ){
for( ii=0 ; ii < nx ; ii++ ) tvec[kk][ii] = far[ii+jj*nx] ;
if( demean ){
sum = 0.0 ;
for( ii=0 ; ii < nx ; ii++ ) sum += tvec[kk][ii] ;
sum /= nx ;
for( ii=0 ; ii < nx ; ii++ ) tvec[kk][ii] -= sum ;
}
sum = 0.0 ;
for( ii=0 ; ii < nx ; ii++ ) sum += tvec[kk][ii] * tvec[kk][ii] ;
if( sum == 0.0 ) {
if (okzero) svec[kk] = 0.0;
else ERROR_exit("Input column %02d is all zero!",kk) ;
} else {
svec[kk] = 1.0 / sqrt(sum) ;
}
}
}
DESTROY_IMARR(tar) ;
/* normalize vectors? (for ordinary correlation) */
if( !docov ){
for( kk=0 ; kk < nvec ; kk++ ){
sum = svec[kk] ;
for( ii=0 ; ii < nx ; ii++ ) tvec[kk][ii] *= sum ;
}
}
switch(docov){
default:
case 3: matname = "Spearman" ; break ;
case 2: matname = "InnerProduct" ; break ;
case 1: matname = "Covariance" ; break ;
case 0: matname = "Correlation" ; break ;
}
/* create matrix from dot product of vectors */
amat = (double *) calloc( sizeof(double) , nvec*nvec ) ;
if( docov != 3 ){
for( kk=0 ; kk < nvec ; kk++ ){
for( jj=0 ; jj <= kk ; jj++ ){
sum = 0.0 ;
for( ii=0 ; ii < nx ; ii++ ) sum += tvec[jj][ii] * tvec[kk][ii] ;
amat[jj+nvec*kk] = sum ;
if( jj < kk ) amat[kk+nvec*jj] = sum ;
}
}
} else { /* Spearman */
for( kk=0 ; kk < nvec ; kk++ ){
for( jj=0 ; jj <= kk ; jj++ ){
amat[jj+nvec*kk] = THD_spearman_corr_dble( nx , tvec[jj] , tvec[kk] ) ;
if( jj < kk ) amat[kk+nvec*jj] = amat[jj+nvec*kk] ;
}
}
}
/* normalize */
if (docov==1) {
for( kk=0 ; kk < nvec ; kk++ ){
for( jj=0 ; jj <= kk ; jj++ ){
sum = amat[jj+nvec*kk] / (double) (nx-1);
amat[jj+nvec*kk] = sum;
if( jj < kk ) amat[kk+nvec*jj] = sum ;
}
}
}
/* print matrix out */
if (!doterse) {
printf("\n"
"++ %s Matrix:\n ",matname) ;
for( jj=0 ; jj < nvec ; jj++ ) printf(" %02d ",jj) ;
printf("\n ") ;
for( jj=0 ; jj < nvec ; jj++ ) printf(" ---------") ;
printf("\n") ;
}
for( kk=0 ; kk < nvec ; kk++ ){
if (!doterse) printf("%02d:",kk) ;
for( jj=0 ; jj < nvec ; jj++ ) printf(" %9.5f",amat[jj+kk*nvec]) ;
printf("\n") ;
}
if (doterse) exit(0) ; /* au revoir */
/* compute eigendecomposition */
eval = (double *) malloc( sizeof(double)*nvec ) ;
symeig_double( nvec , amat , eval ) ;
printf("\n"
"++ Eigensolution of %s Matrix:\n " , matname ) ;
for( jj=0 ; jj < nvec ; jj++ ) printf(" %9.5f",eval[jj]) ;
printf("\n ") ;
for( jj=0 ; jj < nvec ; jj++ ) printf(" ---------") ;
printf("\n") ;
for( kk=0 ; kk < nvec ; kk++ ){
printf("%02d:",kk) ;
for( jj=0 ; jj < nvec ; jj++ ) printf(" %9.5f",amat[kk+jj*nvec]) ;
printf("\n") ;
}
/* compute matrix inverse */
if ( eval[0]/eval[nvec-1] < 1.0e-10) {
printf("\n"
"-- WARNING: Matrix is near singular,\n"
" rubbish likely for inverses ahead.\n");
}
for( jj=0 ; jj < nvec ; jj++ ) eval[jj] = 1.0 / eval[jj] ;
bmat = (double *) calloc( sizeof(double) , nvec*nvec ) ;
for( ii=0 ; ii < nvec ; ii++ ){
for( jj=0 ; jj < nvec ; jj++ ){
sum = 0.0 ;
for( kk=0 ; kk < nvec ; kk++ )
sum += amat[ii+kk*nvec] * amat[jj+kk*nvec] * eval[kk] ;
bmat[ii+jj*nvec] = sum ;
}
}
printf("\n") ;
printf("++ %s Matrix Inverse:\n " , matname ) ;
for( jj=0 ; jj < nvec ; jj++ ) printf(" %02d ",jj) ;
printf("\n ") ;
for( jj=0 ; jj < nvec ; jj++ ) printf(" ---------") ;
printf("\n") ;
for( kk=0 ; kk < nvec ; kk++ ){
printf("%02d:",kk) ;
for( jj=0 ; jj < nvec ; jj++ ) printf(" %9.5f",bmat[jj+kk*nvec]) ;
printf("\n") ;
}
/* square roots of diagonals of the above */
printf("\n") ;
printf("++ %s sqrt(diagonal)\n ",matname) ;
for( jj=0 ; jj < nvec ; jj++ ) printf(" %9.5f",sqrt(bmat[jj+jj*nvec])) ;
printf("\n") ;
/* normalize matrix inverse */
for( ii=0 ; ii < nvec ; ii++ ){
for( jj=0 ; jj < nvec ; jj++ ){
sum = bmat[ii+ii*nvec] * bmat[jj+jj*nvec] ;
if( sum > 0.0 )
amat[ii+jj*nvec] = bmat[ii+jj*nvec] / sqrt(sum) ;
else
amat[ii+jj*nvec] = 0.0 ;
}
}
printf("\n") ;
printf("++ %s Matrix Inverse Normalized:\n " , matname ) ;
for( jj=0 ; jj < nvec ; jj++ ) printf(" %02d ",jj) ;
printf("\n ") ;
for( jj=0 ; jj < nvec ; jj++ ) printf(" ---------") ;
printf("\n") ;
for( kk=0 ; kk < nvec ; kk++ ){
printf("%02d:",kk) ;
for( jj=0 ; jj < nvec ; jj++ ) printf(" %9.5f",amat[jj+kk*nvec]) ;
printf("\n") ;
}
/* done */
exit(0) ;
}
int main( int argc , char *argv[] )
{
int iarg=1 , verb=0 , interp_code=MRI_QUINTIC , ainterp_code=-666 ;
char *expr ; int nexpr , narg ;
THD_3dim_dataset *oset ;
AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */
if( argc < 2 || strcasecmp(argv[1],"-help") == 0 ) NWC_help() ;
mainENTRY("3dNwarpCalc"); machdep();
AFNI_logger("3dNwarpCalc",argc,argv);
PRINT_VERSION("3dNwarpCalc"); AUTHOR("Bob the Warped");
(void)COX_clock_time() ;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcasecmp(argv[iarg],"-NN") == 0 || strncasecmp(argv[iarg],"-nearest",6) == 0 ){
WARNING_message("NN interpolation not legal here -- switched to linear") ;
interp_code = MRI_LINEAR ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-linear",4)==0 || strncasecmp(argv[iarg],"-trilinear",6)==0 ){
interp_code = MRI_LINEAR ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-cubic",4)==0 || strncasecmp(argv[iarg],"-tricubic",6)==0 ){
WARNING_message("cubic interplation not legal here -- switched to quintic") ;
interp_code = MRI_QUINTIC ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-quintic",4)==0 || strncasecmp(argv[iarg],"-triquintic",6)==0 ){
interp_code = MRI_QUINTIC ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-wsinc",5) == 0 ){
interp_code = MRI_WSINC5 ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-interp",5)==0 ){
char *inam ;
if( ++iarg >= argc ) ERROR_exit("no argument after '%s' :-(",argv[iarg-1]) ;
inam = argv[iarg] ; if( *inam == '-' ) inam++ ;
if( strcasecmp(inam,"NN")==0 || strncasecmp(inam,"nearest",5)==0 ){
WARNING_message("NN interpolation not legal here -- changed to linear") ;
interp_code = MRI_LINEAR ;
} else if( strncasecmp(inam,"linear",3)==0 || strncasecmp(inam,"trilinear",5)==0 ){
interp_code = MRI_LINEAR ;
} else if( strncasecmp(inam,"cubic",3)==0 || strncasecmp(inam,"tricubic",5)==0 ){
WARNING_message("cubic interplation not legal here -- changed to quintic") ;
interp_code = MRI_QUINTIC ;
} else if( strncasecmp(inam,"quintic",3)==0 || strncasecmp(inam,"triquintic",5)==0 ){
interp_code = MRI_QUINTIC ;
} else if( strncasecmp(inam,"wsinc",4)==0 ){
interp_code = MRI_WSINC5 ;
} else {
ERROR_exit("Unknown code '%s' after '%s' :-(",argv[iarg],argv[iarg-1]) ;
}
iarg++ ; continue ;
}
/*---------------*/
if( strncasecmp(argv[iarg],"-ainterp",6)==0 ){
char *inam ;
if( ++iarg >= argc ) ERROR_exit("no argument after '%s' :-(",argv[iarg-1]) ;
inam = argv[iarg] ; if( *inam == '-' ) inam++ ;
if( strcasecmp(inam,"NN")==0 || strncasecmp(inam,"nearest",5)==0 ){
ainterp_code = MRI_NN ;
} else if( strncasecmp(inam,"linear",3)==0 || strncasecmp(inam,"trilinear",5)==0 ){
ainterp_code = MRI_LINEAR ;
} else if( strncasecmp(inam,"cubic",3)==0 || strncasecmp(inam,"tricubic",5)==0 ){
ainterp_code = MRI_CUBIC ;
} else if( strncasecmp(inam,"quintic",3)==0 || strncasecmp(inam,"triquintic",5)==0 ){
ainterp_code = MRI_QUINTIC ;
} else if( strncasecmp(inam,"wsinc",4)==0 ){
ainterp_code = MRI_WSINC5 ;
} else {
ERROR_exit("Unknown code '%s' after '%s' :-(",argv[iarg],argv[iarg-1]) ;
}
iarg++ ; continue ;
}
/*---------------*/
if( strcasecmp(argv[iarg],"-verb") == 0 ){
verb++ ; iarg++ ; continue ;
}
/*---------------*/
ERROR_message("Bizarre and Unknown option '%s' :-(",argv[iarg]) ;
suggest_best_prog_option(argv[0],argv[iarg]) ;
exit(1) ;
}
if( iarg >= argc ) ERROR_exit("No command line expression :-(") ;
/*--- Assemble all remaining args into the expression ---*/
expr = strdup(argv[iarg++]) ;
for( ; iarg < argc ; iarg++ ){
nexpr = strlen(expr) ;
narg = strlen(argv[iarg]) ; if( narg == 0 ) continue ;
expr = (char *)realloc( expr , sizeof(char)*(nexpr+narg+4) ) ;
strcat(expr," ") ; strcat(expr,argv[iarg]) ;
}
if( ainterp_code < 0 ) ainterp_code = interp_code ;
/*--- All the work is done herein ---*/
NwarpCalcRPN_verb(verb) ;
oset = NwarpCalcRPN( expr , NULL , interp_code , ainterp_code ) ;
/*--- run away screaming into the night, never to be seen again ---*/
free(expr) ; if( oset != NULL ) DSET_delete(oset) ;
INFO_message("total CPU time = %.1f sec Elapsed = %.1f\n",
COX_cpu_time() , COX_clock_time() ) ;
exit(0) ;
}
int main(int argc, char *argv[]) {
int i,j,k,m,n,mm;
int iarg;
THD_3dim_dataset *insetTIME = NULL;
THD_3dim_dataset *MASK=NULL;
THD_3dim_dataset *ROIS=NULL;
char *prefix="NETCORR" ;
char in_name[300];
char in_mask[300];
char in_rois[300];
char OUT_grid[300];
char OUT_indiv[300];
char OUT_indiv0[300];
// int *SELROI=NULL; // if selecting subset of ROIs
// int HAVE_SELROI=0;
int NIFTI_OUT = 0;
byte ***mskd=NULL; // define mask of where time series are nonzero
byte *mskd2=NULL; // not great, but another format of mask
int HAVE_MASK=0;
int HAVE_ROIS=0;
int FISH_OUT=0;
int PART_CORR=0;
int TS_OUT=0;
int TS_LABEL=0;
int TS_INDIV=0;
int TS_WBCORR_r=0;
int TS_WBCORR_Z=0;
int *NROI_REF=NULL,*INVROI_REF=NULL;
int **ROI_LABELS_REF=NULL, **INV_LABELS_REF=NULL,**ROI_COUNT=NULL;
int ***ROI_LISTS=NULL;
double ***ROI_AVE_TS=NULL; // double because of GSL
float ***Corr_Matr=NULL;
float ***PCorr_Matr=NULL, ***PBCorr_Matr=NULL;
int Nvox=-1; // tot number vox
int *Dim=NULL;
int *Nlist=NULL;
Dtable *roi_dtable=NULL;
char *LabTabStr=NULL;
char ***ROI_STR_LABELS=NULL;
// for niml.dset -> graph viewing in SUMA
char ***gdset_roi_names=NULL;
SUMA_DSET *gset=NULL;
float ***flat_matr=NULL;
float *xyz=NULL;
char OUT_gdset[300];
NI_group *GDSET_netngrlink=NULL;
char *NAME_gdset=NULL;
int Noutmat = 1; // num of matr to output: start with CC for sure
char **ParLab=NULL;
int FM_ctr = 0; // for counting through flatmatr entries
int OLD_LABEL=0; // ooollld style format of regions: Nnumber:Rnumber
int IGNORE_LT=0; // ignore label table
int idx = 0;
int Nmask = 0;
FILE *fout1,*fin,*fout2;
AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */
mainENTRY("3dNetCorr"); machdep();
// ****************************************************************
// ****************************************************************
// load AFNI stuff
// ****************************************************************
// ****************************************************************
// INFO_message("version: BETA");
/** scan args **/
if (argc == 1) { usage_NetCorr(1); exit(0); }
iarg = 1;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 ||
strcmp(argv[iarg],"-h") == 0 ) {
usage_NetCorr(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
if( strcmp(argv[iarg],"-prefix") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-prefix'");
prefix = strdup(argv[iarg]) ;
if( !THD_filename_ok(prefix) )
ERROR_exit("Illegal name after '-prefix'");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-inset") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-input'");
sprintf(in_name,"%s", argv[iarg]);
insetTIME = THD_open_dataset(in_name) ;
if( (insetTIME == NULL ))
ERROR_exit("Can't open time series dataset '%s'.",in_name);
// just 0th time point for output...
Dim = (int *)calloc(4,sizeof(int));
DSET_load(insetTIME); CHECK_LOAD_ERROR(insetTIME);
Nvox = DSET_NVOX(insetTIME) ;
Dim[0] = DSET_NX(insetTIME); Dim[1] = DSET_NY(insetTIME);
Dim[2] = DSET_NZ(insetTIME); Dim[3]= DSET_NVALS(insetTIME);
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-mask") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-mask'");
HAVE_MASK= 1;
sprintf(in_mask,"%s", argv[iarg]);
MASK = THD_open_dataset(in_mask) ;
if( (MASK == NULL ))
ERROR_exit("Can't open time series dataset '%s'.",in_mask);
DSET_load(MASK); CHECK_LOAD_ERROR(MASK);
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_rois") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-in_rois'");
sprintf(in_rois,"%s", argv[iarg]);
ROIS = THD_open_dataset(in_rois) ;
if( (ROIS == NULL ))
ERROR_exit("Can't open time series dataset '%s'.",in_rois);
DSET_load(ROIS); CHECK_LOAD_ERROR(ROIS);
HAVE_ROIS=DSET_NVALS(ROIS); //number of subbricks
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-fish_z") == 0) {
FISH_OUT=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-nifti") == 0) {
NIFTI_OUT=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-part_corr") == 0) {
PART_CORR=2; // because we calculate two matrices here
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-ts_out") == 0) {
TS_OUT=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-ts_label") == 0) {
TS_LABEL=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-ts_indiv") == 0) {
TS_INDIV=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-ts_wb_corr") == 0) {
TS_WBCORR_r=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-ts_wb_Z") == 0) {
TS_WBCORR_Z=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-old_labels") == 0) {
OLD_LABEL=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-ignore_LT") == 0) {
IGNORE_LT=1;
iarg++ ; continue ;
}
/* if( strcmp(argv[iarg],"-sel_roi") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-in_rois'");
SELROI = (int *)calloc(MAX_SELROI,sizeof(int));
if( (fin = fopen(argv[iarg], "r")) == NULL) {
fprintf(stderr, "Error opening file %s.",argv[iarg]);
exit(1);
}
idx=0;
while( !feof(fin) && (idx<MAX_SELROI-1) ){
fscanf(fin, "%d",&SELROI[idx]);
fscanf(fin," ");
idx++;
}
HAVE_SELROI=idx;
printf("HAVE_SELROI=%d\n",HAVE_SELROI);
if(HAVE_SELROI<=0) {
ERROR_message("Error reading in `-sel_roi'-- appears to have no ROIs listed.\n");
exit(1);
}
iarg++ ; continue ;
}*/
ERROR_message("Bad option '%s'\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
INFO_message("Reading in.");
if( !TS_OUT && TS_LABEL) {
ERROR_message("with '-ts_label', you also need '-ts_out'.\n");
exit(1);
}
if (iarg < 3) {
ERROR_message("Too few options. Try -help for details.\n");
exit(1);
}
if(!HAVE_ROIS) {
ERROR_message("Need to load ROIs with >=1 subbrick...\n");
exit(1);
}
if(Nvox != DSET_NVOX(ROIS)) {
ERROR_message("Data sets of `-inset' and `in_rois' have "
"different numbers of voxels per brik!\n");
exit(1);
}
if( (HAVE_MASK>0) && (Nvox != DSET_NVOX(MASK)) ) {
ERROR_message("Data sets of `-inset' and `mask' have "
"different numbers of voxels per brik!\n");
exit(1);
}
// ****************************************************************
// ****************************************************************
// make storage
// ****************************************************************
// ****************************************************************
Nlist = (int *)calloc(1,sizeof(int));
mskd2 = (byte *)calloc(Nvox,sizeof(byte));
mskd = (byte ***) calloc( Dim[0], sizeof(byte **) );
for ( i = 0 ; i < Dim[0] ; i++ )
mskd[i] = (byte **) calloc( Dim[1], sizeof(byte *) );
for ( i = 0 ; i < Dim[0] ; i++ )
for ( j = 0 ; j < Dim[1] ; j++ )
mskd[i][j] = (byte *) calloc( Dim[2], sizeof(byte) );
if( (mskd == NULL) || (Nlist == NULL) || (mskd2 == NULL)) {
fprintf(stderr, "\n\n MemAlloc failure (masks).\n\n");
exit(122);
}
// *************************************************************
// *************************************************************
// Beginning of main loops
// *************************************************************
// *************************************************************
INFO_message("Allocating...");
// go through once: define data vox, and calc rank for each
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ ) {
if( HAVE_MASK ) {
if( THD_get_voxel(MASK,idx,0)>0 ) {
mskd[i][j][k] = 1;
mskd2[idx] = 1;
Nmask++;
}
}
else // simple automask attempt
if( fabs(THD_get_voxel(insetTIME,idx,0))+
fabs(THD_get_voxel(insetTIME,idx,1))+
fabs(THD_get_voxel(insetTIME,idx,2))+
fabs(THD_get_voxel(insetTIME,idx,3))+
fabs(THD_get_voxel(insetTIME,idx,4)) > EPS_V) {
mskd[i][j][k] = 1;
mskd2[idx] = 1;
Nmask++;
}
idx+= 1; // skip, and mskd and KW are both still 0 from calloc
}
if (HAVE_MASK) {
DSET_delete(MASK);
free(MASK);
}
// obviously, this should always be TRUE at this point...
if(HAVE_ROIS>0) {
NROI_REF = (int *)calloc(HAVE_ROIS, sizeof(int));
INVROI_REF = (int *)calloc(HAVE_ROIS, sizeof(int));
if( (NROI_REF == NULL) || (INVROI_REF == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(122);
}
for( i=0 ; i<HAVE_ROIS ; i++)
INVROI_REF[i] = (int) THD_subbrick_max(ROIS, i, 1);
ROI_LABELS_REF = calloc( HAVE_ROIS,sizeof(ROI_LABELS_REF));
for(i=0 ; i<HAVE_ROIS ; i++)
ROI_LABELS_REF[i] = calloc(INVROI_REF[i]+1,sizeof(int));
INV_LABELS_REF = calloc( HAVE_ROIS,sizeof(INV_LABELS_REF));
for(i=0 ; i<HAVE_ROIS ; i++)
INV_LABELS_REF[i] = calloc(INVROI_REF[i]+1,sizeof(int));
if( (ROI_LABELS_REF == NULL) || (INV_LABELS_REF == NULL)
) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(123);
}
INFO_message("Labelling regions internally.");
// Step 3A-2: find out the labels in the ref, organize them
// both backwards and forwards.
i = ViveLeRoi(ROIS,
ROI_LABELS_REF, // ordered list of ROILABEL ints, [1..M];
// maxval is N.
INV_LABELS_REF, // ith values at the actual input locs;
// maxval is M.
NROI_REF, // M: # of ROIs per brik
INVROI_REF); // N: max ROI label per brik
if( i != 1)
ERROR_exit("Problem loading/assigning ROI labels");
ROI_STR_LABELS = (char ***) calloc( HAVE_ROIS, sizeof(char **) );
for ( i=0 ; i<HAVE_ROIS ; i++ )
ROI_STR_LABELS[i] = (char **) calloc( NROI_REF[i]+1, sizeof(char *) );
for ( i=0 ; i<HAVE_ROIS ; i++ )
for ( j=0 ; j<NROI_REF[i]+1 ; j++ )
ROI_STR_LABELS[i][j] = (char *) calloc( 100 , sizeof(char) );
if( (ROI_STR_LABELS == NULL)) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(123);
}
// Sept 2014: Labeltable stuff
if( IGNORE_LT ) {
INFO_message("Ignoring any '-in_rois' label table (if there is one).");
}
else{
if ((ROIS->Label_Dtable = DSET_Label_Dtable(ROIS))) {
if ((LabTabStr = Dtable_to_nimlstring( DSET_Label_Dtable(ROIS),
"VALUE_LABEL_DTABLE"))) {
//fprintf(stdout,"%s", LabTabStr);
if (!(roi_dtable = Dtable_from_nimlstring(LabTabStr))) {
ERROR_exit("Could not parse labeltable.");
}
}
else {
INFO_message("No label table from '-in_rois'.");
}
}
}
i = Make_ROI_Output_Labels( ROI_STR_LABELS,
ROI_LABELS_REF,
HAVE_ROIS,
NROI_REF,
roi_dtable,
1 );//!!!opts.DUMP_with_LABELS
ROI_COUNT = calloc( HAVE_ROIS,sizeof(ROI_COUNT));
for(i=0 ; i<HAVE_ROIS ; i++)
ROI_COUNT[i] = calloc(NROI_REF[i],sizeof(int));
if( (ROI_COUNT == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(123);
}
// find num of vox per ROI
for( m=0 ; m<HAVE_ROIS ; m++ ) {
idx=0;
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ ) {
if( (THD_get_voxel(ROIS,idx,m) > 0 ) && mskd[i][j][k] ) {
ROI_COUNT[m][INV_LABELS_REF[m][(int)
THD_get_voxel(ROIS,idx,m)]-1]++;
}
idx++;
}
}
// make list of vox per ROI
ROI_LISTS = (int ***) calloc( HAVE_ROIS, sizeof(int **) );
for ( i=0 ; i<HAVE_ROIS ; i++ )
ROI_LISTS[i] = (int **) calloc( NROI_REF[i], sizeof(int *) );
for ( i=0 ; i <HAVE_ROIS ; i++ )
for ( j=0 ; j<NROI_REF[i] ; j++ )
ROI_LISTS[i][j] = (int *) calloc( ROI_COUNT[i][j], sizeof(int) );
// make average time series per voxel
ROI_AVE_TS = (double ***) calloc( HAVE_ROIS, sizeof(double **) );
for ( i=0 ; i<HAVE_ROIS ; i++ )
ROI_AVE_TS[i] = (double **) calloc( NROI_REF[i], sizeof(double *) );
for ( i=0 ; i <HAVE_ROIS ; i++ )
for ( j=0 ; j<NROI_REF[i] ; j++ )
ROI_AVE_TS[i][j] = (double *) calloc( Dim[3], sizeof(double) );
// store corr coefs
Corr_Matr = (float ***) calloc( HAVE_ROIS, sizeof(float **) );
for ( i=0 ; i<HAVE_ROIS ; i++ )
Corr_Matr[i] = (float **) calloc( NROI_REF[i], sizeof(float *) );
for ( i=0 ; i <HAVE_ROIS ; i++ )
for ( j=0 ; j<NROI_REF[i] ; j++ )
Corr_Matr[i][j] = (float *) calloc( NROI_REF[i], sizeof(float) );
if( (ROI_LISTS == NULL) || (ROI_AVE_TS == NULL)
|| (Corr_Matr == NULL)) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(123);
}
if(PART_CORR) {
PCorr_Matr = (float ***) calloc( HAVE_ROIS, sizeof(float **) );
for ( i=0 ; i<HAVE_ROIS ; i++ )
PCorr_Matr[i] = (float **) calloc( NROI_REF[i], sizeof(float *) );
for ( i=0 ; i <HAVE_ROIS ; i++ )
for ( j=0 ; j<NROI_REF[i] ; j++ )
PCorr_Matr[i][j] = (float *) calloc( NROI_REF[i], sizeof(float));
PBCorr_Matr = (float ***) calloc( HAVE_ROIS, sizeof(float **) );
for ( i=0 ; i<HAVE_ROIS ; i++ )
PBCorr_Matr[i] = (float **) calloc( NROI_REF[i], sizeof(float *) );
for ( i=0 ; i <HAVE_ROIS ; i++ )
for ( j=0 ; j<NROI_REF[i] ; j++ )
PBCorr_Matr[i][j] = (float *) calloc( NROI_REF[i], sizeof(float));
if( (PCorr_Matr == NULL) || (PBCorr_Matr == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(123);
}
}
// reuse this to help place list indices
for( i=0 ; i<HAVE_ROIS ; i++ )
for( j=0 ; j<NROI_REF[i] ; j++ )
ROI_COUNT[i][j] = 0;
INFO_message("Getting volumes.");
for( m=0 ; m<HAVE_ROIS ; m++ ) {
idx=0;
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ ) {
if( (THD_get_voxel(ROIS,idx,m) > 0) && mskd[i][j][k] ) {
mm = INV_LABELS_REF[m][(int) THD_get_voxel(ROIS,idx,m)]-1;
ROI_LISTS[m][mm][ROI_COUNT[m][mm]] = idx;
ROI_COUNT[m][mm]++;
}
idx++;
}
}
}
// bit of freeing
for( i=0 ; i<Dim[0] ; i++)
for( j=0 ; j<Dim[1] ; j++) {
free(mskd[i][j]);
}
for( i=0 ; i<Dim[0] ; i++) {
free(mskd[i]);
}
free(mskd);
INFO_message("Calculating average time series.");
// ROI values
for(i=0 ; i<HAVE_ROIS ; i++)
for( j=0 ; j<NROI_REF[i] ; j++ ) {
Nlist[0]=ROI_COUNT[i][j];
k = CalcAveRTS(ROI_LISTS[i][j], ROI_AVE_TS[i][j],
insetTIME, Dim, Nlist);
}
INFO_message("Calculating correlation matrix.");
if(PART_CORR)
INFO_message("... and calculating partial correlation matrix.");
for(i=0 ; i<HAVE_ROIS ; i++) {
for( j=0 ; j<NROI_REF[i] ; j++ )
for( k=j ; k<NROI_REF[i] ; k++ ) {
Corr_Matr[i][j][k] = Corr_Matr[i][k][j] = (float)
CORR_FUN(ROI_AVE_TS[i][j], ROI_AVE_TS[i][k], Dim[3]);
}
if(PART_CORR)
mm = CalcPartCorrMatr(PCorr_Matr[i], PBCorr_Matr[i],
Corr_Matr[i], NROI_REF[i]);
}
// **************************************************************
// **************************************************************
// Store and output
// **************************************************************
// **************************************************************
INFO_message("Writing output: %s ...", prefix);
// - - - - - - - - NIML prep - - - - - - - - - - - - - -
if(FISH_OUT)
Noutmat++;
if(PART_CORR)
Noutmat+=2;
ParLab = (char **)calloc(Noutmat, sizeof(char *));
for (j=0; j<Noutmat; ++j)
ParLab[j] = (char *)calloc(32, sizeof(char));
if( (ParLab == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(121);
}
// NIML output
flat_matr = (float ***) calloc( HAVE_ROIS, sizeof(float **) );
for ( i = 0 ; i < HAVE_ROIS ; i++ )
flat_matr[i] = (float **) calloc( Noutmat, sizeof(float *) );
for ( i = 0 ; i < HAVE_ROIS ; i++ )
for ( j = 0 ; j < Noutmat ; j++ )
flat_matr[i][j] = (float *) calloc( NROI_REF[i]*NROI_REF[i],
sizeof(float));
gdset_roi_names = (char ***)calloc(HAVE_ROIS, sizeof(char **));
for (i=0; i< HAVE_ROIS ; i++ ) {
gdset_roi_names[i] = (char **)calloc(NROI_REF[i], sizeof(char *));
for (j=0; j<NROI_REF[i]; ++j) {
gdset_roi_names[i][j] = (char *)calloc(32, sizeof(char));
if( OLD_LABEL )
snprintf(gdset_roi_names[i][j],31,"N%03d:R%d", i,
ROI_LABELS_REF[i][j]);
else{
snprintf(gdset_roi_names[i][j],31,"%s",
ROI_STR_LABELS[i][j+1]);
//fprintf(stderr," %s ",
// ROI_STR_LABELS[i][j+1]);
}
}
}
if( (flat_matr == NULL) || ( gdset_roi_names == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(14);
}
for( k=0 ; k<HAVE_ROIS ; k++) { // each netw gets own file
sprintf(OUT_grid,"%s_%03d.netcc",prefix,k); // zero counting now
if( (fout1 = fopen(OUT_grid, "w")) == NULL) {
fprintf(stderr, "Error opening file %s.",OUT_grid);
exit(19);
}
// same format as .grid files now
fprintf(fout1,"# %d # Number of network ROIs\n",NROI_REF[k]); // NROIs
fprintf(fout1,"# %d # Number of netcc matrices\n",
FISH_OUT+PART_CORR+1); // Num of params
// Sept 2014: label_table stuff
// don't need labeltable to make them, can do anyways
fprintf(fout1, "# WITH_ROI_LABELS\n");
for( i=1 ; i<NROI_REF[k] ; i++ )
fprintf(fout1," %10s \t",ROI_STR_LABELS[k][i]);
fprintf(fout1," %10s\n",ROI_STR_LABELS[k][i]);
// THIS IS FOR KNOWING WHICH MATR WE'RE AT
// it's always zero for CC; they match one-to-one with later vars
FM_ctr = 0;
ParLab[FM_ctr] = strdup("CC");
for( i=1 ; i<NROI_REF[k] ; i++ ) // labels of ROIs
fprintf(fout1," %10d \t",ROI_LABELS_REF[k][i]);// at =NROI, have '\n'
fprintf(fout1," %10d\n# %s\n",ROI_LABELS_REF[k][i],"CC");
for( i=0 ; i<NROI_REF[k] ; i++ ) {
for( j=0 ; j<NROI_REF[k]-1 ; j++ ) {// b/c we put '\n' after last one.
fprintf(fout1,"%12.4f\t",Corr_Matr[k][i][j]);
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] = Corr_Matr[k][i][j];
}
fprintf(fout1,"%12.4f\n",Corr_Matr[k][i][j]);
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] = Corr_Matr[k][i][j];
}
if(FISH_OUT) {
FM_ctr++;
ParLab[FM_ctr] = strdup("FZ");
fprintf(fout1,"# %s\n", "FZ");
for( i=0 ; i<NROI_REF[k] ; i++ ) {
for( j=0 ; j<NROI_REF[k]-1 ; j++ ) {// b/c we put '\n' after last
fprintf(fout1,"%12.4f\t",BOBatanhf(Corr_Matr[k][i][j]));
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] =
BOBatanhf(Corr_Matr[k][i][j]);
/* fprintf(fout1,"%12.4f\t",FisherZ(Corr_Matr[k][i][j]));
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] =
FisherZ(Corr_Matr[k][i][j]);*/
}
fprintf(fout1,"%12.4f\n",BOBatanhf(Corr_Matr[k][i][j]));
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] =
BOBatanhf(Corr_Matr[k][i][j]);
/*fprintf(fout1,"%12.4f\n",FisherZ(Corr_Matr[k][i][j]));
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] =
FisherZ(Corr_Matr[k][i][j]);*/
}
}
if(PART_CORR) {
FM_ctr++;
ParLab[FM_ctr] = strdup("PC");
fprintf(fout1,"# %s\n", "PC");
for( i=0 ; i<NROI_REF[k] ; i++ ) {
for( j=0 ; j<NROI_REF[k]-1 ; j++ ) {// b/c we put '\n' after last
fprintf(fout1,"%12.4f\t",PCorr_Matr[k][i][j]);
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] = PCorr_Matr[k][i][j];
}
fprintf(fout1,"%12.4f\n",PCorr_Matr[k][i][j]);
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] = PCorr_Matr[k][i][j];
}
FM_ctr++;
ParLab[FM_ctr] = strdup("PCB");
fprintf(fout1,"# %s\n", "PCB");
for( i=0 ; i<NROI_REF[k] ; i++ ) {
for( j=0 ; j<NROI_REF[k]-1 ; j++ ) {// b/c we put '\n' after last
fprintf(fout1,"%12.4f\t",PBCorr_Matr[k][i][j]);
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] = PBCorr_Matr[k][i][j];
}
fprintf(fout1,"%12.4f\n",PBCorr_Matr[k][i][j]);
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] = PBCorr_Matr[k][i][j];
}
}
fclose(fout1);
// more nimling
gset = SUMA_FloatVec_to_GDSET(flat_matr[k], Noutmat,
NROI_REF[k]*NROI_REF[k],
"full", ParLab,
NULL, NULL, NULL);
if( xyz = THD_roi_cmass(ROIS, k, ROI_LABELS_REF[k]+1, NROI_REF[k]) ) {
if (!(SUMA_AddGDsetNodeListElement(gset, NULL,
xyz, NULL, NULL,
gdset_roi_names[k],
NULL, NULL,
NROI_REF[k]))) {
ERROR_message("Failed to add node list");
exit(1);
}
free(xyz);
}
else {
ERROR_message("Failed in THD_roi_cmass"); exit(1);
}
sprintf(OUT_gdset,"%s_%03d",prefix,k);
GDSET_netngrlink =
Network_link(SUMA_FnameGet( OUT_gdset, "f",NULL));
NI_add_to_group(gset->ngr, GDSET_netngrlink);
NAME_gdset = SUMA_WriteDset_ns( OUT_gdset,
gset, SUMA_ASCII_NIML, 1, 0);
if (!NAME_gdset && !SUMA_IS_DSET_STDXXX_FORMAT(SUMA_ASCII_NIML)) {
ERROR_message("Failed to write dataset."); exit(1);
} else {
if (NAME_gdset) SUMA_free(NAME_gdset); NAME_gdset = NULL;
}
SUMA_FreeDset(gset);
gset=NULL;
}
if(TS_OUT) {
for( k=0 ; k<HAVE_ROIS ; k++) { // each netw gets own file
sprintf(OUT_grid,"%s_%03d.netts",prefix,k);
if( (fout1 = fopen(OUT_grid, "w")) == NULL) {
fprintf(stderr, "Error opening file %s.",OUT_grid);
exit(19);
}
for( i=0 ; i<NROI_REF[k] ; i++ ) {
if(TS_LABEL)
fprintf(fout1,"%d\t",ROI_LABELS_REF[k][i+1]); // labels go 1...M
for( j=0 ; j<Dim[3]-1 ; j++ ) // b/c we put '\n' after last one.
fprintf(fout1,"%.3e\t",ROI_AVE_TS[k][i][j]);
fprintf(fout1,"%.3e\n",ROI_AVE_TS[k][i][j]);
}
fclose(fout1);
}
}
if( TS_INDIV ) {
for( k=0 ; k<HAVE_ROIS ; k++) { // each netw gets own file
sprintf(OUT_indiv0,"%s_%03d_INDIV", prefix, k);
mkdir(OUT_indiv0, 0777);
for( i=0 ; i<NROI_REF[k] ; i++ ) {
sprintf(OUT_indiv,"%s/ROI_%03d.netts",
OUT_indiv0,ROI_LABELS_REF[k][i+1]);
if( (fout2 = fopen(OUT_indiv, "w")) == NULL) {
fprintf(stderr, "\nError opening file '%s'.\n",OUT_indiv);
exit(19);
}
for( j=0 ; j<Dim[3]-1 ; j++ ) // b/c we put '\n' after last one.
fprintf(fout2,"%.3e\t",ROI_AVE_TS[k][i][j]);
fprintf(fout2,"%.3e\n",ROI_AVE_TS[k][i][j]);
fclose(fout2);
}
}
}
if( TS_WBCORR_r || TS_WBCORR_Z ) {
INFO_message("Starting whole brain correlations.");
i = WB_netw_corr( TS_WBCORR_r,
TS_WBCORR_Z,
HAVE_ROIS,
prefix,
NIFTI_OUT,
NROI_REF,
Dim,
ROI_AVE_TS,
ROI_LABELS_REF,
insetTIME,
mskd2,
Nmask,
argc,
argv);
}
// ************************************************************
// ************************************************************
// Freeing
// ************************************************************
// ************************************************************
DSET_delete(ROIS);
free(ROIS);
for ( i = 0 ; i < HAVE_ROIS ; i++ ) {
for (j = 0; j < NROI_REF[i]; ++j)
free(gdset_roi_names[i][j]);
free(gdset_roi_names[i]);
}
free(gdset_roi_names);
for ( i = 0 ; i < HAVE_ROIS ; i++ )
for ( j = 0 ; j < Noutmat ; j++ )
free(flat_matr[i][j]);
for ( i = 0 ; i < HAVE_ROIS ; i++ )
free(flat_matr[i]);
free(flat_matr);
for( i=0 ; i<Noutmat ; i++)
free(ParLab[i]);
free(ParLab);
if(LabTabStr)
free(LabTabStr);
if(roi_dtable)
free(roi_dtable);
for ( i=0 ; i<HAVE_ROIS ; i++ )
for ( j=0 ; j<NROI_REF[i]+1 ; j++ )
free(ROI_STR_LABELS[i][j]);
for ( i=0 ; i<HAVE_ROIS ; i++ )
free(ROI_STR_LABELS[i]);
free(ROI_STR_LABELS);
DSET_delete(insetTIME);
free(insetTIME);
free(mskd2);
free(Nlist);
free(Dim); // need to free last because it's used for other arrays...
free(prefix);
// if(HAVE_SELROI)
// free(SELROI);
if(HAVE_ROIS >0) {
for( i=0 ; i<HAVE_ROIS ; i++) {
for( j=0 ; j<NROI_REF[i] ; j++) {
free(ROI_LISTS[i][j]);
free(ROI_AVE_TS[i][j]);
free(Corr_Matr[i][j]);
if(PART_CORR) {
free(PCorr_Matr[i][j]);
free(PBCorr_Matr[i][j]);
}
}
free(ROI_LISTS[i]);
free(ROI_AVE_TS[i]);
free(Corr_Matr[i]);
if(PART_CORR){
free(PCorr_Matr[i]);
free(PBCorr_Matr[i]);
}
free(ROI_LABELS_REF[i]);
free(INV_LABELS_REF[i]);
free(ROI_COUNT[i]);
}
free(ROI_LISTS);
free(ROI_AVE_TS);
free(Corr_Matr);
if(PART_CORR) {
free(PCorr_Matr);
free(PBCorr_Matr);
}
free(ROI_LABELS_REF);
free(INV_LABELS_REF);
free(ROI_COUNT);
free(NROI_REF);
free(INVROI_REF);
}
return 0;
}
int main( int argc , char * argv[] )
{
THD_3dim_dataset *dset, *outset=NULL;
int iarg=1, npad = 0, extent=0;
char *prefix=NULL, *iname=NULL;
char *oijkext = NULL;
FILE *fout_ijkext=NULL;
int extent_ijk=0;
int extent_ijk_midslice=0;
int imid=0, jmid=0, kmid=0;
int extent_xyz_midslice=0;
float xmid=0, ymid=0, zmid=0;
/*-- startup bureaucracy --*/
mainENTRY("3dAutobox main"); machdep(); AFNI_logger("3dAutobox",argc,argv);
PRINT_VERSION("3dAutobox") ;
/*-- read command line options --*/
iarg = 1 ;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0){
help_autobox();
exit(0) ;
}
if( strcmp(argv[iarg],"-prefix") == 0 ){
prefix = argv[++iarg] ;
if( !THD_filename_ok(prefix) ){
fprintf(stderr,"** 3dAutobox: Illegal string after -prefix!\n");
exit(1) ;
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-input") == 0 ){
iname = argv[++iarg] ;
// This is a bad check, because it doesn't permit subbrick
// selection! Will do check later.
/*if( !THD_filename_ok(iname) ){
fprintf(stderr,"** 3dAutobox: Illegal string after -input!\n");
exit(1) ;
}*/
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-noclust") == 0 ){
MRI_autobbox_clust(0) ; /* turn of clustering and clipping */
THD_autobbox_clip(0) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-npad") == 0 ){
npad = (int)strtod(argv[++iarg],NULL) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-extent_ijk") == 0 ){
extent_ijk = 1 ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-extent_ijk_to_file") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-extent_ijk_to_file'\n") ;
oijkext = argv[iarg];
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-extent_ijk_midslice") == 0 ){
extent_ijk_midslice = 1 ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-extent_xyz_midslice") == 0 ){
extent_xyz_midslice = 1 ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-extent") == 0 ){
extent = 1 ;
iarg++ ; continue ;
}
/*- washappenin, dood? -*/
ERROR_message("** 3dAutobox: %s makes no sense here.\n",
argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
if( argc < 2){ help_autobox(); exit(0); }
/* got input ? */
if( iarg == argc-1 )
iname = argv[iarg] ;
else if (iarg != argc)
ERROR_exit("** 3dAutobox: %s is nonsense on the line \n"
" I know you're John; stop pretending you have an accent!",
argv[iarg]) ;
if( !iname )
ERROR_exit("** 3dAutobox: Where is my input?") ;
/*-- read data --*/
dset = THD_open_dataset(iname);
// Check here instead of after -input.
if( dset == NULL )
ERROR_exit("Can't open time series dataset '%s'.",iname);
CHECK_OPEN_ERROR(dset,iname);
if( DSET_BRICK_TYPE(dset,0) != MRI_short &&
DSET_BRICK_TYPE(dset,0) != MRI_byte &&
DSET_BRICK_TYPE(dset,0) != MRI_float )
ERROR_exit("** ILLEGAL dataset type: %s :-(",
MRI_type_name[DSET_BRICK_TYPE(dset,0)]) ;
DSET_load(dset) ; CHECK_LOAD_ERROR(dset) ;
{
int nx=DSET_NX(dset), ny=DSET_NY(dset), nz=DSET_NZ(dset), nxy=nx*ny ;
int xm=-1,xp=-1,ym=-1,yp=-1,zm=-1,zp=-1;
THD_autobbox( dset , &xm,&xp , &ym,&yp , &zm,&zp, NULL ) ;
xm -= npad; ym -= npad; zm -= npad; /* for LRF */
xp += npad; yp += npad; zp += npad;
INFO_message("Auto bbox: x=%d..%d y=%d..%d z=%d..%d\n",
xm,xp,ym,yp,zm,zp ) ;
// [PT: Oct 18, 2018] New output text file, if desired
if( oijkext ) {
if( (fout_ijkext = fopen(oijkext, "w")) == NULL ) {
fprintf(stderr, "\n\nError opening file %s.\n", oijkext);
exit(1);
}
fprintf( fout_ijkext, "%8d %8d %8d %8d %8d %8d\n",
xm, xp, ym, yp, zm, zp );
fclose(fout_ijkext);
INFO_message("Wrote ijk extents file: %s", oijkext);
}
if( extent_ijk )
printf( "%8d %8d %8d %8d %8d %8d\n",
xm, xp, ym, yp, zm, zp );
if( extent_ijk_midslice ) {
imid = (xm + xp) / 2; // integer division fine, b/c we need ints
jmid = (ym + yp) / 2;
kmid = (zm + zp) / 2;
printf( "%8d %8d %8d\n", imid, jmid, kmid );
}
if ( (extent && !prefix) || (extent_xyz_midslice && !prefix) )
prefix = "EXTENT_ONLY";
if( prefix ){
outset = THD_zeropad( dset ,
-xm, xp-nx+1,
-ym, yp-ny+1,
-zm, zp-nz+1,
prefix , ZPAD_IJK ) ;
if( THD_deathcon() && THD_is_file(DSET_HEADNAME(outset)) )
ERROR_exit("3dAutobox: output file %s already exists :-(",
DSET_HEADNAME(outset) ) ;
if( outset == NULL )
ERROR_exit("3dAutobox: Some error occurred in processing :-(") ;
tross_Copy_History( dset , outset ) ; /* 31 Jan 2001 - RWCox */
tross_Make_History( "3dAutobox" , argc,argv , outset ) ;
if (!strstr(prefix,"EXTENT_ONLY")) {
DSET_write(outset) ;
INFO_message("3dAutobox: output dataset = %s",
DSET_BRIKNAME(outset)) ;
}
if (extent) {
float RL_AP_IS[6];
THD_dset_extent(outset, '-', RL_AP_IS);
printf("Extent auto bbox: R=%f L=%f A=%f P=%f I=%f S=%f\n",
RL_AP_IS[0],RL_AP_IS[1],
RL_AP_IS[2],RL_AP_IS[3],
RL_AP_IS[4],RL_AP_IS[5] ) ;
}
if( extent_xyz_midslice ) {
INFO_message("aaa" );
float RL_AP_IS2[6];
THD_dset_extent(outset, '-', RL_AP_IS2);
xmid = (RL_AP_IS2[0] + RL_AP_IS2[1]) / 2.;
ymid = (RL_AP_IS2[2] + RL_AP_IS2[3]) / 2.;
zmid = (RL_AP_IS2[4] + RL_AP_IS2[5]) / 2.;
printf( "%10.5f %10.5f %10.5f\n", xmid, ymid, zmid );
}
}
}
exit(0) ;
}
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) ;
}
int main(int argc, char *argv[]) {
int i, k, ii;
int iarg;
char *prefix=NULL;
char *maskname=NULL;
char *gradsname=NULL;
char *dtsname=NULL;
THD_3dim_dataset *MASK=NULL;
THD_3dim_dataset *DTS=NULL;
MRI_IMAGE *GRADS=NULL, *GRADS_IN=NULL;
int Ngrads=0, Nfull=0;
int Nvox=-1; // tot number vox
int Dim[3]={0,0,0}; // dim in each dir
float NOISESCALE_DWI = -1.;
float NOISESCALE_B0 = -1;
float S0 = 1000.;
float bval = 1.;
int NOISE_IN_S0 = 0;
byte *mskd2=NULL; // not great, but another format of mask
float **dwi=NULL;
THD_3dim_dataset *DWI_OUT=NULL;
const gsl_rng_type * T;
gsl_rng *r;
long seed;
srand(time(0));
seed = time(NULL) ;
gsl_rng_env_setup();
T = gsl_rng_default;
r = gsl_rng_alloc (T);
gsl_rng_set (r, seed);
// ###################################################################
// ######################### load ##################################
// ###################################################################
mainENTRY("3dDTtoNoisyDWI"); machdep();
if (argc == 1) { usage_DTtoNoisyDWI(1); exit(0); }
iarg = 1;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 ||
strcmp(argv[iarg],"-h") == 0 ) {
usage_DTtoNoisyDWI(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
if( strcmp(argv[iarg],"-dt_in") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-eig_vecs'");
dtsname = strdup(argv[iarg]) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-prefix") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-prefix'");
prefix = strdup(argv[iarg]) ;
if( !THD_filename_ok(prefix) )
ERROR_exit("Illegal name after '-prefix'");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-mask") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-mask'");
maskname = strdup(argv[iarg]) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-grads") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-mask'");
gradsname = strdup(argv[iarg]) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-noise_DWI") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need numerical argument after '-noise_DWI'");
NOISESCALE_DWI = atof(argv[iarg]);
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-noise_B0") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need numerical argument after '-noise_B0'");
NOISESCALE_B0 = atof(argv[iarg]);
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-S0") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need numerical argument after '-S0'");
S0 = atof(argv[iarg]);
if(S0 <= 0 )
ERROR_exit("The '-S0' value must be >0.");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-bval") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need numerical argument after '-bval'");
bval = atof(argv[iarg]);
if(bval <= 0 )
ERROR_exit("The '-bval' value must be >0.");
iarg++ ; continue ;
}
ERROR_message("Bad option '%s'\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
// ###################################################################
// #################### some checks ###############################
// ###################################################################
if(!prefix)
ERROR_exit("Need to give a '-prefix'.");
if(!dtsname)
ERROR_exit("Need to input diffusion tensor file after '-dt_in'.");
if(!gradsname)
ERROR_exit("Need to input gradient file after '-grads'.");
if( NOISESCALE_DWI<0 )
ERROR_exit("Fractional noise value after '-snr0' needs to be >0. "
"It sets the noise scale of ref signal S0.");
if(NOISESCALE_DWI > 0)
INFO_message("You have chosen an SNR0 of approximately %.2f for DWIs",
1./NOISESCALE_DWI);
else
INFO_message("You have noiseless (i.e., infinite SNR) set of DWIs");
if( NOISESCALE_B0 < 0 )
NOISESCALE_B0 = NOISESCALE_DWI;
if(NOISESCALE_B0 > 0)
INFO_message("You have chosen an SNR0 of approximately %.2f for the B0",
1./NOISESCALE_B0);
else
INFO_message("You have noiseless (i.e., infinite SNR) reference B0.");
// ###################################################################
if(dtsname) {
DTS = THD_open_dataset(dtsname);
DSET_load(DTS); CHECK_LOAD_ERROR(DTS);
if( 6 != DSET_NVALS(DTS) )
ERROR_exit("DT file '%s' must have 6 bricks-- "
"it has %d bricks!",
dtsname, DSET_NVALS(DTS));
}
Nvox = DSET_NVOX(DTS);
Dim[0] = DSET_NX(DTS);
Dim[1] = DSET_NY(DTS);
Dim[2] = DSET_NZ(DTS);
if(Nvox<0)
ERROR_exit("Error reading Nvox from eigenvalue file.");
mskd2 = (byte *)calloc(Nvox,sizeof(byte));
if( (mskd2 == NULL)) {
fprintf(stderr, "\n\n MemAlloc failure (masks).\n\n");
exit(122);
}
if(maskname) {
MASK = THD_open_dataset(maskname);
DSET_load(MASK); CHECK_LOAD_ERROR(MASK);
if( 1 != DSET_NVALS(MASK) )
ERROR_exit("Mask file '%s' is not scalar-- "
"it has %d bricks!",
maskname, DSET_NVALS(MASK));
for( k=0 ; k<Nvox ; k++ )
if (THD_get_voxel(MASK, k, 0) > 0 )
mskd2[k] = 1;
DSET_delete(MASK);
free(MASK);
free(maskname);
}
else {
for( k=0 ; k<Nvox ; k++ )
if( fabs(THD_get_voxel(DTS,k,0) > EPS_V) )
mskd2[k] = 1;
}
GRADS_IN = mri_read_1D (gradsname);
GRADS = mri_transpose(GRADS_IN); // get rid of autotranspose...
if (GRADS == NULL)
ERROR_exit("Error reading gradient vector file");
mri_free(GRADS_IN);
Ngrads = GRADS->ny;
if(Ngrads < 6)
ERROR_exit("Too few grads (there appear to be only %d).",Ngrads);
if(GRADS->nx !=3 )
ERROR_exit("Wrong number of columns in the grad file: "
" am reading %d instead of 3.",GRADS->nx);
Nfull = Ngrads+1;
INFO_message("Have surmised there are %d total grads; "
"output file will have %d bricks", Ngrads,Nfull);
dwi = calloc(Nfull,sizeof(dwi));
for(i=0 ; i<Nfull ; i++)
dwi[i] = calloc( Nvox,sizeof(float));
INFO_message("Calculating the DWIs.");
i = RicianNoiseDWIs( dwi, Nvox, Ngrads, DTS,
NOISESCALE_DWI, NOISESCALE_B0,
GRADS, mskd2,
S0, bval, r);
INFO_message("Writing the DWIs.");
DWI_OUT = EDIT_empty_copy( DTS );
EDIT_dset_items(DWI_OUT,
ADN_nvals, Nfull,
ADN_datum_all, MRI_float ,
ADN_prefix, prefix,
ADN_none );
for( i=0; i<Nfull ; i++) {
EDIT_substitute_brick(DWI_OUT, i, MRI_float, dwi[i]);
dwi[i]=NULL;
}
THD_load_statistics( DWI_OUT );
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(DWI_OUT)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(DWI_OUT));
tross_Make_History("3dDTtoNoisyDWI", argc, argv, DWI_OUT);
THD_write_3dim_dataset(NULL, NULL, DWI_OUT, True);
DSET_delete(DWI_OUT);
free(DWI_OUT);
// #################################################################
// ########################## free ###############################
// #################################################################
DSET_delete(DTS);
free(DTS);
for( i=0 ; i<Nfull ; i++)
free(dwi[i]);
free(dwi);
free(prefix);
free(gradsname);
free(dtsname);
mri_free(GRADS);
return 0;
}
int main( int argc , char *argv[] )
{
THD_3dim_dataset *old_dset , *new_dset ; /* input and output datasets */
THD_3dim_dataset *mask_dset=NULL ;
float mask_bot=666.0 , mask_top=-666.0 ;
byte *cmask=NULL ; int ncmask=0 ;
byte *mmm = NULL ;
int mcount=0, verb=0;
int nopt, nbriks, ii ;
int addBriks = 0 ; /* n-1 sub-bricks out */
int fullBriks = 0 ; /* n sub-bricks out */
int tsout = 0 ; /* flag to output a time series (not a stat bucket) */
int numMultBriks,methIndex,brikIndex;
/*----- Help the pitiful user? -----*/
/* bureaucracy */
mainENTRY("3dTstat main"); machdep(); AFNI_logger("3dTstat",argc,argv);
PRINT_VERSION("3dTstat"); AUTHOR("KR Hammett & RW Cox");
/*--- scan command line for options ---*/
if (argc == 1) { usage_3dTstat(1); exit(0); } /* Bob's help shortcut */
nopt = 1 ;
nbriks = 0 ;
nmeths = 0 ;
verb = 0;
while( nopt < argc && argv[nopt][0] == '-' ){
if (strcmp(argv[nopt], "-h") == 0 || strcmp(argv[nopt], "-help") == 0) {
usage_3dTstat(strlen(argv[nopt]) > 3 ? 2:1);
exit(0);
}
if( strcmp(argv[nopt],"-verb") == 0 ){
verb++ ; nopt++ ; continue ;
}
/*-- methods --*/
if( strcasecmp(argv[nopt],"-centromean") == 0 ){ /* 01 Nov 2010 */
meth[nmeths++] = METH_CENTROMEAN ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-bmv") == 0 ){
meth[nmeths++] = METH_BMV ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-median") == 0 ){
meth[nmeths++] = METH_MEDIAN ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-nzmedian") == 0 ){
meth[nmeths++] = METH_NZMEDIAN ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-DW") == 0 ){
meth[nmeths++] = METH_DW ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-zcount") == 0 ){
meth[nmeths++] = METH_ZCOUNT ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-nzcount") == 0 ){
meth[nmeths++] = METH_NZCOUNT ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-MAD") == 0 ){
meth[nmeths++] = METH_MAD ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-mean") == 0 ){
meth[nmeths++] = METH_MEAN ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-sum") == 0 ){
meth[nmeths++] = METH_SUM ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-sos") == 0 ){
meth[nmeths++] = METH_SUM_SQUARES ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-abssum") == 0 ){
meth[nmeths++] = METH_ABSSUM ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-slope") == 0 ){
meth[nmeths++] = METH_SLOPE ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-stdev") == 0 ||
strcasecmp(argv[nopt],"-sigma") == 0 ){
meth[nmeths++] = METH_SIGMA ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-cvar") == 0 ){
meth[nmeths++] = METH_CVAR ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-cvarinv") == 0 ){
meth[nmeths++] = METH_CVARINV ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-stdevNOD") == 0 ||
strcasecmp(argv[nopt],"-sigmaNOD") == 0 ){ /* 07 Dec 2001 */
meth[nmeths++] = METH_SIGMA_NOD ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-cvarNOD") == 0 ){ /* 07 Dec 2001 */
meth[nmeths++] = METH_CVAR_NOD ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-cvarinvNOD") == 0 ){
meth[nmeths++] = METH_CVARINVNOD ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-min") == 0 ){
meth[nmeths++] = METH_MIN ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-max") == 0 ){
meth[nmeths++] = METH_MAX ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-absmax") == 0 ){
meth[nmeths++] = METH_ABSMAX ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-signed_absmax") == 0 ){
meth[nmeths++] = METH_SIGNED_ABSMAX ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-argmin") == 0 ){
meth[nmeths++] = METH_ARGMIN ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-argmin1") == 0 ){
meth[nmeths++] = METH_ARGMIN1 ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-argmax") == 0 ){
meth[nmeths++] = METH_ARGMAX ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-argmax1") == 0 ){
meth[nmeths++] = METH_ARGMAX1 ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-argabsmax") == 0 ){
meth[nmeths++] = METH_ARGABSMAX ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-argabsmax1") == 0 ){
meth[nmeths++] = METH_ARGABSMAX1;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-duration") == 0 ){
meth[nmeths++] = METH_DURATION ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-onset") == 0 ){
meth[nmeths++] = METH_ONSET ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-offset") == 0 ){
meth[nmeths++] = METH_OFFSET ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-centroid") == 0 ){
meth[nmeths++] = METH_CENTROID ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-centduration") == 0 ){
meth[nmeths++] = METH_CENTDURATION ;
nbriks++ ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-nzmean") == 0 ){
meth[nmeths++] = METH_NZMEAN ;
nbriks++ ;
nopt++ ; continue ;
}
if( strncmp(argv[nopt],"-mask",5) == 0 ){
if( mask_dset != NULL )
ERROR_exit("Cannot have two -mask options!\n") ;
if( nopt+1 >= argc )
ERROR_exit("-mask option requires a following argument!\n");
mask_dset = THD_open_dataset( argv[++nopt] ) ;
if( mask_dset == NULL )
ERROR_exit("Cannot open mask dataset!\n") ;
if( DSET_BRICK_TYPE(mask_dset,0) == MRI_complex )
ERROR_exit("Cannot deal with complex-valued mask dataset!\n");
nopt++ ; continue ;
}
if( strncmp(argv[nopt],"-mrange",5) == 0 ){
if( nopt+2 >= argc )
ERROR_exit("-mrange option requires 2 following arguments!\n");
mask_bot = strtod( argv[++nopt] , NULL ) ;
mask_top = strtod( argv[++nopt] , NULL ) ;
if( mask_top < mask_top )
ERROR_exit("-mrange inputs are illegal!\n") ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-cmask") == 0 ){ /* 16 Mar 2000 */
if( nopt+1 >= argc )
ERROR_exit("-cmask option requires a following argument!\n");
cmask = EDT_calcmask( argv[++nopt] , &ncmask, 0 ) ;
if( cmask == NULL ) ERROR_exit("Can't compute -cmask!\n");
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-autocorr") == 0 ){
meth[nmeths++] = METH_AUTOCORR ;
if( ++nopt >= argc ) ERROR_exit("-autocorr needs an argument!\n");
meth[nmeths++] = atoi(argv[nopt++]);
if (meth[nmeths - 1] == 0) {
addBriks++;
} else {
nbriks+=meth[nmeths - 1] ;
}
continue ;
}
if( strcasecmp(argv[nopt],"-autoreg") == 0 ){
meth[nmeths++] = METH_AUTOREGP ;
if( ++nopt >= argc ) ERROR_exit("-autoreg needs an argument!\n");
meth[nmeths++] = atoi(argv[nopt++]);
if (meth[nmeths - 1] == 0) {
addBriks++;
} else {
nbriks+=meth[nmeths - 1] ;
}
continue ;
}
if( strcasecmp(argv[nopt],"-accumulate") == 0 ){ /* 4 Mar 2008 [rickr] */
meth[nmeths++] = METH_ACCUMULATE ;
meth[nmeths++] = -1; /* flag to add N (not N-1) output bricks */
fullBriks++;
tsout = 1; /* flag to output a timeseries */
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-l2norm") == 0 ){ /* 07 Jan 2013 [rickr] */
meth[nmeths++] = METH_L2_NORM ;
nbriks++ ;
nopt++ ; continue ;
}
/*-- prefix --*/
if( strcasecmp(argv[nopt],"-prefix") == 0 ){
if( ++nopt >= argc ) ERROR_exit("-prefix needs an argument!\n");
MCW_strncpy(prefix,argv[nopt],THD_MAX_PREFIX) ;
if( !THD_filename_ok(prefix) )
ERROR_exit("%s is not a valid prefix!\n",prefix);
nopt++ ; continue ;
}
/*-- tdiff --*/
if( strcasecmp(argv[nopt],"-tdiff") == 0 ){ /* 25 May 2011 */
do_tdiff = 1 ; nopt++ ; continue ;
}
/*-- nscale --*/
if( strcasecmp(argv[nopt],"-nscale") == 0 ){ /* 25 May 2011 */
nscale = 1 ; nopt++ ; continue ;
}
/*-- datum --*/
if( strcasecmp(argv[nopt],"-datum") == 0 ){
if( ++nopt >= argc ) ERROR_exit("-datum needs an argument!\n");
if( strcasecmp(argv[nopt],"short") == 0 ){
datum = MRI_short ;
} else if( strcasecmp(argv[nopt],"float") == 0 ){
datum = MRI_float ;
} else if( strcasecmp(argv[nopt],"byte") == 0 ){
datum = MRI_byte ;
} else {
ERROR_exit("-datum of type '%s' is not supported!\n",
argv[nopt] ) ;
}
nopt++ ; continue ;
}
/* base percentage for duration calcs */
if (strcasecmp (argv[nopt], "-basepercent") == 0) {
if( ++nopt >= argc ) ERROR_exit("-basepercent needs an argument!\n");
basepercent = strtod(argv[nopt], NULL);
if(basepercent>1) basepercent /= 100.0; /* assume integer percent if >1*/
nopt++; continue;
}
/*-- Quien sabe'? --*/
ERROR_message("Unknown option: %s\n",argv[nopt]) ;
suggest_best_prog_option(argv[0], argv[nopt]);
exit(1);
}
if (argc < 2) {
ERROR_message("Too few options, use -help for details");
exit(1);
}
/*--- If no options selected, default to single stat MEAN -- KRH ---*/
if (nmeths == 0) nmeths = 1;
if (nbriks == 0 && addBriks == 0 && fullBriks == 0) nbriks = 1;
/*----- read input dataset -----*/
if( nopt >= argc ) ERROR_exit(" No input dataset!?") ;
old_dset = THD_open_dataset( argv[nopt] ) ;
if( !ISVALID_DSET(old_dset) )
ERROR_exit("Can't open dataset %s\n",argv[nopt]);
nopt++ ;
if( nopt < argc )
WARNING_message("Trailing datasets on command line ignored: %s ...",argv[nopt]) ;
if( DSET_NVALS(old_dset) == 1 ){
WARNING_message("Input dataset has 1 sub-brick ==> -tdiff is turned off") ;
do_tdiff = 0 ;
}
/* no input volumes is bad, 1 volume applies to only certain methods */
/* 2 Nov 2010 [rickr] */
if( DSET_NVALS(old_dset) == 0 ) {
ERROR_exit("Time series is of length 0?\n") ;
}
else if( DSET_NVALS(old_dset) == 1 || (do_tdiff && DSET_NVALS(old_dset)==2) ) {
int methOK, OK = 1;
/* see if each method is valid for nvals == 1 */
for( methIndex = 0; methIndex < nmeths; methIndex++ ) {
methOK = 0;
for( ii = 0; ii < NUM_1_INPUT_METHODS; ii++ ) {
if( meth[methIndex] == valid_1_input_methods[ii] ) {
methOK = 1;
break;
}
}
if( ! methOK )
ERROR_exit("Can't use dataset with %d values per voxel!" ,
DSET_NVALS(old_dset) ) ;
}
/* tell the library function that this case is okay */
g_thd_maker_allow_1brick = 1;
}
if( DSET_NUM_TIMES(old_dset) < 2 ){
WARNING_message("Input dataset is not 3D+time; assuming TR=1.0") ;
EDIT_dset_items( old_dset ,
ADN_ntt , DSET_NVALS(old_dset) ,
ADN_ttorg , 0.0 ,
ADN_ttdel , 1.0 ,
ADN_tunits , UNITS_SEC_TYPE ,
NULL ) ;
}
/* If one or more of the -autocorr/-autoreg options was called with */
/* an argument of 0, then I'll now add extra BRIKs for the N-1 data */
/* output points for each. */
nbriks += ((DSET_NVALS(old_dset)-1) * addBriks);
nbriks += ((DSET_NVALS(old_dset) ) * fullBriks);
/* ------------- Mask business -----------------*/
if( mask_dset == NULL ){
mmm = NULL ;
if( verb )
INFO_message("%d voxels in the entire dataset (no mask)\n",
DSET_NVOX(old_dset)) ;
} else {
if( DSET_NVOX(mask_dset) != DSET_NVOX(old_dset) )
ERROR_exit("Input and mask datasets are not same dimensions!\n");
mmm = THD_makemask( mask_dset , 0 , mask_bot, mask_top ) ;
mcount = THD_countmask( DSET_NVOX(old_dset) , mmm ) ;
if( mcount <= 0 ) ERROR_exit("No voxels in the mask!\n") ;
if( verb ) INFO_message("%d voxels in the mask\n",mcount) ;
DSET_delete(mask_dset) ;
}
if( cmask != NULL ){
if( ncmask != DSET_NVOX(old_dset) )
ERROR_exit("Input and cmask datasets are not same dimensions!\n");
if( mmm != NULL ){
for( ii=0 ; ii < DSET_NVOX(old_dset) ; ii++ )
mmm[ii] = (mmm[ii] && cmask[ii]) ;
free(cmask) ;
mcount = THD_countmask( DSET_NVOX(old_dset) , mmm ) ;
if( mcount <= 0 ) ERROR_exit("No voxels in the mask+cmask!\n") ;
if( verb ) INFO_message("%d voxels in the mask+cmask\n",mcount) ;
} else {
mmm = cmask ;
mcount = THD_countmask( DSET_NVOX(old_dset) , mmm ) ;
if( mcount <= 0 ) ERROR_exit("No voxels in the cmask!\n") ;
if( verb ) INFO_message("%d voxels in the cmask\n",mcount) ;
}
}
/*------------- ready to compute new dataset -----------*/
new_dset = MAKER_4D_to_typed_fbuc(
old_dset , /* input dataset */
prefix , /* output prefix */
datum , /* output datum */
0 , /* ignore count */
0 , /* can't detrend in maker function KRH 12/02*/
nbriks , /* number of briks */
STATS_tsfunc , /* timeseries processor */
NULL, /* data for tsfunc */
mmm,
nscale
) ;
if( new_dset != NULL ){
tross_Copy_History( old_dset , new_dset ) ;
tross_Make_History( "3dTstat" , argc,argv , new_dset ) ;
for (methIndex = 0,brikIndex = 0; methIndex < nmeths;
methIndex++, brikIndex++) {
if ((meth[methIndex] == METH_AUTOCORR) ||
(meth[methIndex] == METH_ACCUMULATE) ||
(meth[methIndex] == METH_AUTOREGP)) {
numMultBriks = meth[methIndex+1];
/* note: this looks like it should be NV-1 4 Mar 2008 [rickr] */
if (numMultBriks == 0) numMultBriks = DSET_NVALS(old_dset)-1;
/* new flag for NVALS [rickr] */
if (numMultBriks == -1) numMultBriks = DSET_NVALS(old_dset);
for (ii = 1; ii <= numMultBriks; ii++) {
char tmpstr[25];
if (meth[methIndex] == METH_AUTOREGP) {
sprintf(tmpstr,"%s[%d](%d)",meth_names[meth[methIndex]],
numMultBriks,ii);
} else {
sprintf(tmpstr,"%s(%d)",meth_names[meth[methIndex]],ii);
}
EDIT_BRICK_LABEL(new_dset, (brikIndex + ii - 1), tmpstr) ;
}
methIndex++;
brikIndex += numMultBriks - 1;
} else {
EDIT_BRICK_LABEL(new_dset, brikIndex, meth_names[meth[methIndex]]) ;
}
}
if( tsout ) /* then change output to a time series */
EDIT_dset_items( new_dset ,
ADN_ntt , brikIndex ,
ADN_ttorg , DSET_TIMEORIGIN(old_dset) ,
ADN_ttdel , DSET_TIMESTEP(old_dset) ,
ADN_tunits , DSET_TIMEUNITS(old_dset) ,
NULL ) ;
DSET_write( new_dset ) ;
WROTE_DSET( new_dset ) ;
} else {
ERROR_exit("Unable to compute output dataset!\n") ;
}
exit(0) ;
}
/*! compute the overall minimum and maximum voxel values for a dataset */
int main( int argc , char * argv[] )
{
THD_3dim_dataset * old_dset , * new_dset ; /* input and output datasets */
int nopt, nbriks;
int slow_flag, quick_flag, min_flag, max_flag, mean_flag,
automask,count_flag, sum_flag, var_flag, absolute_flag;
int positive_flag, negative_flag, zero_flag, nan_flag, perc_flag, vol_flag;
byte * mmm=NULL ;
int mmvox=0 ;
int nxyz, i;
float *dvec = NULL, mmin=0.0, mmax=0.0;
int N_mp;
double *mpv=NULL, *perc = NULL;
double mp =0.0f, mp0 = 0.0f, mps = 0.0f, mp1 = 0.0f, di =0.0f ;
byte *mmf = NULL;
MRI_IMAGE *anat_im = NULL;
char *mask_dset_name=NULL;
/*----- Read command line -----*/
mainENTRY("3dBrickStat main"); machdep(); AFNI_logger("3dBrickStat",argc,argv);
nopt = 1 ;
min_flag = 0;
max_flag = -1;
mean_flag = 0;
sum_flag = 0;
var_flag = 0;
slow_flag = 0;
quick_flag = -1;
automask = 0;
count_flag = 0;
vol_flag = 0;
positive_flag = -1;
negative_flag = -1;
absolute_flag = 0;
zero_flag = -1;
nan_flag = -1;
perc_flag = 0;
mmin = 1.0;
mmax = -1.0;
mask_dset_name = NULL;
datum = MRI_float;
while( nopt < argc && argv[nopt][0] == '-' ){
if( strcmp(argv[nopt],"-help") == 0 ||
strcmp(argv[nopt],"-h") == 0){
usage_3dBrickStat(strlen(argv[nopt])> 3 ? 2:1);
exit(0);
}
if( strcmp(argv[nopt],"-ver") == 0 ){
PRINT_VERSION("3dBrickStat"); AUTHOR("Daniel Glen");
nopt++; continue;
}
if( strcmp(argv[nopt],"-quick") == 0 ){
quick_flag = 1;
nopt++; continue;
}
if( strcmp(argv[nopt],"-percentile") == 0 ){
perc_flag = 1;
++nopt;
if (nopt + 2 >= argc) {
ERROR_exit( "** Error: Need 3 parameter after -percentile\n");
}
mp0 = atof(argv[nopt])/100.0f; ++nopt;
mps = atof(argv[nopt])/100.0f; ++nopt;
mp1 = atof(argv[nopt])/100.0f;
if (mps == 0.0f) {
ERROR_exit( "** Error: step cannot be 0" );
}
if (mp0 < 0 || mp0 > 100 || mp1 < 0 || mp1 > 100) {
ERROR_exit( "** Error: p0 and p1 must be >=0 and <= 100" );
}
nopt++; continue;
}
if( strcmp(argv[nopt],"-median") == 0 ){
perc_flag = 1;
mp0 = 0.50f;
mps = 0.01f;
mp1 = 0.50f;
nopt++; continue;
}
if( strcmp(argv[nopt],"-slow") == 0 ){
slow_flag = 1;
nopt++; continue;
}
if( strcmp(argv[nopt],"-min") == 0 ){
min_flag = 1;
nopt++; continue;
}
if( strcmp(argv[nopt],"-max") == 0 ){
max_flag = 1;
nopt++; continue;
}
if( strcmp(argv[nopt],"-sum") == 0 ){
sum_flag = 1;
nopt++; continue;
}
if( strcmp(argv[nopt],"-mean") == 0 ){
mean_flag = 1;
nopt++; continue;
}
if( strcmp(argv[nopt],"-var") == 0 ){
if (var_flag) {
ERROR_message("Looks like -stdev is already used.\n"
"-var and -stdev are mutually exclusive");
exit (1);
}
var_flag = 1;
nopt++; continue;
}
if( strcmp(argv[nopt],"-stdev") == 0 ){
if (var_flag) {
ERROR_message("Looks like -var is already used.\n"
"-var and -stdev are mutually exclusive");
exit (1);
}
var_flag = 2;
nopt++; continue;
}
if( strcmp(argv[nopt],"-count") == 0 ){
count_flag = 1;
nopt++; continue;
}
if( strcmp(argv[nopt],"-volume") == 0 ){
vol_flag = 1;
nopt++; continue;
}
if( strcmp(argv[nopt],"-positive") == 0 ){
if(positive_flag!=-1) {
ERROR_exit( "Can not use multiple +/-/0 options");
}
positive_flag = 1;
negative_flag = 0;
zero_flag = 0;
nopt++; continue;
}
if( strcmp(argv[nopt],"-negative") == 0 ){
if(positive_flag!=-1) {
ERROR_exit( "Can not use multiple +/-/0 options");
}
positive_flag = 0;
negative_flag = 1;
zero_flag = 0;
nopt++; continue;
}
if( strcmp(argv[nopt],"-zero") == 0 ){
if(positive_flag!=-1) {
ERROR_exit( "Can not use multiple +/-/0 options");
}
positive_flag = 0;
negative_flag = 0;
zero_flag = 1;
nopt++; continue;
}
if( strcmp(argv[nopt],"-non-positive") == 0 ){
if(positive_flag!=-1) {
ERROR_exit( "Can not use multiple +/-/0 options");
}
positive_flag = 0;
negative_flag = 1;
zero_flag = 1;
nopt++; continue;
}
if( strcmp(argv[nopt],"-non-negative") == 0 ){
if(positive_flag!=-1) {
ERROR_exit( "Can not use multiple +/-/0 options");
}
positive_flag = 1;
negative_flag = 0;
zero_flag = 1;
nopt++; continue;
}
if( strcmp(argv[nopt],"-non-zero") == 0 ){
if(positive_flag!=-1) {
ERROR_exit( "Can not use multiple +/-/0 options");
}
positive_flag = 1;
negative_flag = 1;
zero_flag = 0;
nopt++; continue;
}
if( strcmp(argv[nopt],"-absolute") == 0 ){
absolute_flag = 1;
nopt++; continue;
}
if( strcmp(argv[nopt],"-nan") == 0 ){
if(nan_flag!=-1) {
ERROR_exit( "Can not use both -nan -nonan options");
}
nan_flag = 1;
nopt++; continue;
}
if( strcmp(argv[nopt],"-nonan") == 0 ){
if(nan_flag!=-1) {
ERROR_exit( "Can not use both -nan -nonan options");
}
nan_flag = 0;
nopt++; continue;
}
if( strcmp(argv[nopt],"-autoclip") == 0 ||
strcmp(argv[nopt],"-automask") == 0 ){
if( mmm != NULL ){
ERROR_exit(" ERROR: can't use -autoclip/mask with -mask!");
}
automask = 1 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-mrange") == 0 ){
if (nopt+2 >= argc) {
ERROR_exit(" ERROR: Need two values after -mrange");
}
mmin = atof(argv[++nopt]);
mmax = atof(argv[++nopt]);
if (mmax < mmin) {
ERROR_exit(
"1st value in -mrange %s %s should be the smallest one",
argv[nopt-1], argv[nopt]);
}
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-mvalue") == 0 ){
if (nopt+1 >= argc) {
ERROR_exit(" ERROR: Need 1 value after -mvalue");
}
mmin = atof(argv[++nopt]);
mmax = mmin ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-mask") == 0 ){
if( mask_dset_name != NULL )
ERROR_exit(" ERROR: can't have 2 -mask options!");
mask_dset_name = argv[++nopt];
nopt++ ; continue ;
}
ERROR_message( " Error - unknown option %s", argv[nopt]);
suggest_best_prog_option(argv[0], argv[nopt]);
exit(1);
}
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
ERROR_message("Too few options");
usage_3dBrickStat(0);
exit(1) ;
}
if (mask_dset_name) {
int ninmask = 0;
THD_3dim_dataset * mask_dset ;
if( automask ){
ERROR_exit(" ERROR: can't use -mask with -automask!");
}
mask_dset = THD_open_dataset(mask_dset_name) ;
CHECK_OPEN_ERROR(mask_dset,mask_dset_name) ;
mmm = THD_makemask( mask_dset , 0 , mmin, mmax ) ;
mmvox = DSET_NVOX( mask_dset ) ;
ninmask = THD_countmask (mmvox, mmm);
if (!ninmask) {
ERROR_exit(" No voxels in mask !");
}
/* text output program, so avoid extras 26 Dec 2013 [rickr] */
/* INFO_message("%d voxels in mask\n", ninmask); */
DSET_delete(mask_dset) ;
}
if(((mmm!=NULL) && (quick_flag))||(automask &&quick_flag)) {
if(quick_flag==1)
WARNING_message( "+++ Warning - can't have quick option with mask");
quick_flag = 0;
slow_flag = 1;
}
/* if max_flag is not set by user, check if other user options set */
if(max_flag==-1) {
if(min_flag || mean_flag || count_flag || vol_flag || sum_flag
|| perc_flag || var_flag)
max_flag = 0;
else
max_flag = 1; /* otherwise check only for max */
}
if((var_flag==1)||(mean_flag==1)||(count_flag==1)||
(vol_flag==1)||(absolute_flag==1) ||
(positive_flag!=-1)||(nan_flag!=-1)||
(sum_flag == 1)||(perc_flag == 1) || (var_flag==2)) {
/* mean flag or count_flag implies slow */
slow_flag = 1;
}
/* check slow and quick options */
if((slow_flag)&&(quick_flag!=1)) /* if user asked for slow give it to him */
quick_flag = 0;
else
quick_flag = 1;
if((max_flag==0)&&(min_flag==0)) /* if the user only asked for mean */
quick_flag = 0; /* no need to do quick way */
if((quick_flag) &&
((absolute_flag==1)||(positive_flag==1)||(negative_flag==1)||(zero_flag==1)))
WARNING_message( " Warning - ignoring +/-/0/abs flags for quick computations");
if(positive_flag==-1) { /* if no +/-/0 options set, allow all voxels */
positive_flag = 1;
negative_flag = 1;
zero_flag = 1;
}
/*----- read input dataset -----*/
if( nopt >= argc ){
ERROR_exit(" No input dataset!?");
}
old_dset = THD_open_dataset( argv[nopt] ) ;
CHECK_OPEN_ERROR(old_dset,argv[nopt]) ;
nxyz = DSET_NVOX(old_dset) ;
if( mmm != NULL && mmvox != nxyz ){
ERROR_exit(" Mask and input datasets not the same size!") ;
}
if(automask && mmm == NULL ){
mmm = THD_automask( old_dset ) ;
for(i=0;i<nxyz;i++) {
if(mmm[i]!=0) ++mmvox;
}
}
if(quick_flag)
Print_Header_MinMax(min_flag, max_flag, old_dset);
if(slow_flag!=1)
exit(0);
/* ZSS do some diddlyiddly sorting - DO not affect Daniel's function later on*/
if (perc_flag == 1) {
DSET_mallocize (old_dset);
DSET_load (old_dset);
if (DSET_NVALS(old_dset) != 1) {
ERROR_exit( "-percentile can only be used on one sub-brick only.\n"
"Use sub-brick selectors '[.]' to specify sub-brick of interest.\n");
}
/* prep for input and output of percentiles */
if (mp0 > mp1) {
N_mp = 1;
} else {
/* allocate one above ceiling to prevent truncation error (and crash),
N_mp is recomputed anyway 16 Mar 2009 [rickr] */
N_mp = (int)((double)(mp1-mp0)/(double)mps) + 2;
}
mpv = (double *)malloc(sizeof(double)*N_mp);
perc = (double *)malloc(sizeof(double)*N_mp);
if (!mpv || !perc) {
ERROR_message("Failed to allocate for mpv or perc");
exit(1);
}
N_mp = 0;
mp = mp0;
do {
mpv[N_mp] = mp; ++N_mp; mp += mps;
} while (mp <= mp1+.00000001);
if (!Percentate (DSET_ARRAY(old_dset, 0), mmm, nxyz,
DSET_BRICK_TYPE(old_dset,0), mpv, N_mp,
0, perc,
zero_flag, positive_flag, negative_flag )) {
ERROR_message("Failed to compute percentiles.");
exit(1);
}
/* take care of brick factor */
if (DSET_BRICK_FACTOR(old_dset,0)) {
for (i=0; i<N_mp; ++i) {
perc[i] = perc[i]*DSET_BRICK_FACTOR(old_dset,0);
}
}
for (i=0; i<N_mp; ++i) {
fprintf(stdout,"%.1f %f ", mpv[i]*100.0f, perc[i]);
}
free(mpv); mpv = NULL;
free(perc); perc = NULL;
}
Max_func(min_flag, max_flag, mean_flag,count_flag,
positive_flag, negative_flag, zero_flag, absolute_flag,
nan_flag, sum_flag, var_flag, vol_flag,old_dset, mmm, mmvox);
if(mmm!=NULL)
free(mmm);
exit(0);
/* unused code time series method for extracting data */
#if 0
EDIT_dset_items( old_dset ,
ADN_ntt , DSET_NVALS(old_dset) ,
ADN_ttorg , 0.0 ,
ADN_ttdel , 1.0 ,
ADN_tunits , UNITS_SEC_TYPE ,
NULL ) ;
nbriks = 1;
/*------------- ready to compute new min, max -----------*/
new_dset = MAKER_4D_to_typed_fbuc(
old_dset , /* input dataset */
"temp" , /* output prefix */
datum , /* output datum */
0 , /* ignore count */
0 , /* can't detrend in maker function KRH 12/02*/
nbriks , /* number of briks */
Max_tsfunc , /* timeseries processor */
NULL, /* data for tsfunc */
NULL, /* mask */
0 /* Allow auto scaling of output */
) ;
if(min_flag)
printf("%-13.6g ", minvalue);
if(max_flag)
printf("%-13.6g", maxvalue);
printf("\n");
exit(0) ;
#endif
}
int AFNI_prefilter_args( int *argc , char **argv )
{
int narg=*argc , ii,jj , nused , ttt ;
char *used , *eee ;
if( narg <= 1 || argv == NULL ) return(0) ;
used = (char *)calloc((size_t)narg,sizeof(char)) ;
eee = getenv("AFNI_TRACE") ; ttt = YESSISH(eee) ;
if( ttt )
fprintf( stderr,
"++ AFNI_prefilter_args() processing argv[1..%d]\n",narg-1) ;
/*--- scan thru argv[];
see if any should be processed now and marked as 'used up' ---*/
for( ii=1 ; ii < narg ; ii++ ){
/*** empty argument (should never happen in Unix) ***/
if( argv[ii] == NULL ){
if( ttt ) fprintf(stderr,"++ argv[%d] is NULL\n",ii) ;
used[ii] = 1 ; continue ;
}
/*** -Dname=val to set environment variable ***/
if( strncmp(argv[ii],"-D",2) == 0 && strchr(argv[ii],'=') != NULL ){
if( ttt ) fprintf(stderr,"++ argv[%d] does setenv %s\n",ii,argv[ii]) ;
(void)AFNI_setenv(argv[ii]+2) ; used[ii] = 1 ; continue ;
}
/*** -Vname to get environment variable ***/
if( strncmp(argv[ii],"-V",2) == 0 && strchr(argv[ii],'=') != NULL ){
if( ttt ) fprintf(stderr,"++ argv[%d] does getenv %s\n",ii,argv[ii]) ;
fprintf(stdout,"%s\n",
(eee = my_getenv(argv[ii]+2)) ? eee:"") ;
used[ii] = 1 ; exit(0) ;
}
/*** -overwrite to set AFNI_DECONFLICT ***/
if( strcmp(argv[ii],"-overwrite") == 0 ){
if( ttt ) fprintf(stderr,"++ argv[%d] is -overwrite\n",ii) ;
AFNI_setenv("AFNI_DECONFLICT=OVERWRITE") ;
THD_set_quiet_overwrite(1); /* no need to kvetch */
used[ii] = 1 ; continue ;
}
/*** echo command ***/
if( strcmp(argv[ii],"-echo_edu") == 0 ){
if( ttt ) fprintf(stderr,"++ argv[%d] is -echo_edu\n",ii) ;
{
int jjj=0;
fprintf(stdout,"\n+++ Command Echo:\n ");
for (jjj=0; jjj<narg; ++jjj) {
if (jjj != ii) {
fprintf(stdout,"%s ", argv[jjj]);
}
}
fprintf(stdout,"\n\n");
used[ii] = 1 ; continue ;
}
}
if( strcmp(argv[ii],"-all_opts") == 0 ){
if( ttt ) fprintf(stderr,"++ argv[%d] is -all_opts\n",ii) ;
print_prog_options(argv[0]); used[ii] = 1 ;
exit(0);
/* better exit, otherwise output get burried by program's own -help */
}
if( strcmp(argv[ii],"-h_find") == 0 ){
if( ttt ) fprintf(stderr,"++ argv[%d] is -h_find\n",ii) ;
if (ii+1 >= narg) {
fprintf(stderr,"** -h_find needs a string.\n");
exit(1);
}
used[ii] = 1 ; ii++;
suggest_best_prog_option(argv[0], argv[ii]);
used[ii] = 1 ;
exit(0);
/* better exit, otherwise output get burried by program's own -help */
}
if( strcmp(argv[ii],"-h_aspx") == 0 && ii == 1){
char *s=NULL;
if( ttt ) fprintf(stderr,"++ argv[%d] is -h_apsx\n",ii) ;
if (!(s = sphinxize_prog_help(argv[0], 0))) {
fprintf(stderr,"** Failed to get auto-sphinxized string\n");
exit(1);
}
fprintf(stdout,"%s", s); free(s);
used[ii] = 1 ;
exit(0);
}
if( strcmp(argv[ii],"-h_view") == 0 ){
if( ttt ) fprintf(stderr,"++ argv[%d] is -h_view\n",ii) ;
view_prog_help(argv[0]);
used[ii] = 1 ;
exit(0);
/* better exit, otherwise output get burried by program's own -help */
}
if( strcmp(argv[ii],"-h_web") == 0 ){
if( ttt ) fprintf(stderr,"++ argv[%d] is -h_web\n",ii) ;
web_prog_help(argv[0],0);
used[ii] = 1 ;
exit(0);
/* better exit, otherwise output get burried by program's own -help */
}
/*** -ok_1D_text to set AFNI_1D_ZERO_TEXT ZSS Dec 09 ***/
if( strcmp(argv[ii],"-ok_1D_text") == 0 ){
if( ttt ) fprintf(stderr,"++ argv[%d] is -ok_1D_text\n",ii) ;
AFNI_setenv("AFNI_1D_ZERO_TEXT=YES") ; used[ii] = 1 ; continue ;
}
/*** -skip_afnirc to avoid .afnirc file ***/
if( strcmp(argv[ii],"-skip_afnirc") == 0 ){
if( ttt ) fprintf(stderr,"++ argv[%d] is -skip_afnirc\n",ii) ;
AFNI_mark_environ_done() ; used[ii] = 1 ; continue ;
}
/*** -pad_to_node to force sparse data to a particular size ***/
if( strcmp(argv[ii],"-pad_to_node") == 0 ){
if( ttt ) fprintf(stderr,"++ argv[%d] is -pad_to_node\n",ii) ;
if (ii+1 >= narg) {
fprintf(stderr,"** -pad_to_node needs a positive integer,\n"
" or standard mesh description such as ld120\n");
exit(1);
}
used[ii] = 1 ; ii++;
if (!strncasecmp(argv[ii],"ld",2)) {
if (strlen(argv[ii]) < 3) {
fprintf(stderr,"** need a number right after ld (like ld120)\n");
exit(1);
}
MRILIB_DomainMaxNodeIndex = SUMA_IcoNums(atoi(argv[ii]+2), 0, 'n')-1;
if( ttt ) fprintf(stderr, "ld pad_to_node %d\n",
MRILIB_DomainMaxNodeIndex);
} else if (!strncasecmp(argv[ii],"rd",2)) {
if (strlen(argv[ii]) < 3) {
fprintf(stderr,"** need a number right after rd (like rd6)\n");
exit(1);
}
MRILIB_DomainMaxNodeIndex = SUMA_IcoNums(atoi(argv[ii]+2), 1, 'n')-1;
if( ttt ) fprintf(stderr, "rd pad_to_node %d\n",
MRILIB_DomainMaxNodeIndex);
} else if (!strncasecmp(argv[ii],"d:",2)) {
THD_3dim_dataset *dset=NULL;
if (strlen(argv[ii]) < 3) {
fprintf(stderr,
"** need a dataset right after d: (like d:hello.niml.dset)\n");
exit(1);
}
dset = THD_open_dataset(argv[ii]+2);
if (dset) {
DSET_MAX_NODE(dset, MRILIB_DomainMaxNodeIndex);
DSET_delete(dset); dset = NULL;
if( ttt ) fprintf(stderr, "d: pad_to_node %d\n",
MRILIB_DomainMaxNodeIndex);
} else {
fprintf(stderr,"** Could not load dset %s to determine padding\n",
argv[ii]+2);
}
} else {
MRILIB_DomainMaxNodeIndex = atoi(argv[ii]);
if( ttt ) fprintf(stderr, "pad_to_node %d\n",
MRILIB_DomainMaxNodeIndex);
}
if (MRILIB_DomainMaxNodeIndex < 0) {
fprintf(stderr,"** parameter for -pad_to_node (%d) is negative!\n",
MRILIB_DomainMaxNodeIndex);
exit(1);
}else if (MRILIB_DomainMaxNodeIndex > 500000) {
fprintf(stderr,
"** parameter for -pad_to_node (%d) is suspiciously large.\n"
" I hope you know what you're doing.\n",
MRILIB_DomainMaxNodeIndex );
}
used[ii] = 1;
continue ;
}
if( strcmp(argv[ii],"-np") == 0 ||
strcmp(argv[ii],"-npq") == 0 ){ /* ZSS, June 2011 */
if( ttt ) fprintf(stderr,"++ argv[%d] is -np\n",ii) ;
if (ii+1 >= narg) {
fprintf(stderr,
"** -np needs an integer NP such that 1024 <= NP <= 65500\n");
exit(1);
}
used[ii] = 1 ; ii++;
if (set_user_np(atoi(argv[ii]))<1) {
if (strcmp(argv[ii-1],"-npq")) { /* not quiet mode? */
fprintf(stderr,
"** -np is not an integer such that 1024 <= NP <= 65500\n"
" -np was ignored\n");
}
} else {
if (strcmp(argv[ii-1],"-npq"))
fprintf(stderr,"++ -np set to %d\n", get_user_np());
}
used[ii] = 1;
continue ;
}
if( strcmp(argv[ii],"-npb") == 0 ){ /* ZSS, June 2011 */
if( ttt ) fprintf(stderr,"++ argv[%d] is -npb\n",ii) ;
if (ii+1 >= narg) {
fprintf(stderr,
"** -npb needs an integer NPB such that 0 <= NPB <= %d\n",
get_max_port_bloc());
exit(1);
}
used[ii] = 1 ; ii++;
if (set_user_np_bloc(atoi(argv[ii]))<1) {
fprintf(stderr,
"** -npb is not an integer such that 0 <= NPB <= %d\n"
" -npb was ignored\n", get_max_port_bloc());
}
used[ii] = 1;
continue ;
}
if( strcmp(argv[ii],"-pif") == 0 ){ /* ZSS, June 2011 */
if( ttt ) fprintf(stderr,"++ argv[%d] is -pif\n",ii) ;
if (ii+1 >= narg) {
fprintf(stderr,
"** -pif needs a string value\n");
exit(1);
}
used[ii] = 1 ; ii++;
set_user_pif(argv[ii]);
used[ii] = 1;
continue ;
}
/* -max_port_bloc number and quit */
if( strncmp(argv[ii],"-max_port_bloc", 8) == 0) {
int pp = 0;
pp = get_max_port_bloc();
if (strcmp(argv[ii-1], "-max_port_bloc_quiet")) {
fprintf(stdout, "Maximum port bloc number: %d\n",
pp);
} else {
fprintf(stdout, "%d\n", pp);
}
exit(0);
}
/* -num_assigned port number and quit */
if( strncmp(argv[ii],"-num_assigned_ports", 8) == 0) {
int pp = 0;
pp = get_max_port_bloc();
if (strcmp(argv[ii-1], "-num_assigned_ports_quiet")) {
fprintf(stdout, "Number of assigned ports: %d\n",
pp);
} else {
fprintf(stdout, "%d\n", pp);
}
exit(0);
}
/*** if get to here, argv[ii] is nothing special ***/
} /* end of loop over argv[] */
/*--- compress out used up argv[] entries ---*/
for( nused=0,ii=narg-1 ; ii >= 1 ; ii-- ){
if( !used[ii] ) continue ;
for( jj=ii+1 ; jj < narg ; jj++ ) argv[jj-1] = argv[jj] ;
argv[narg-1] = NULL ; narg-- ; nused++ ;
}
if( ttt && nused > 0 )
fprintf(stderr,"++ 'used up' %d argv[] entries, leaving %d\n",nused,narg) ;
free((void *)used) ; *argc = narg ; return(nused);
}
SEG_OPTS *GenFeatureDist_ParseInput (SEG_OPTS *Opt, char *argv[], int argc)
{
static char FuncName[]={"GenFeatureDist_ParseInput"};
int kar, i, ind, exists;
char *outname, cview[10], *sbuf=NULL;
int brk = 0;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_ENTRY;
brk = 0;
kar = 1;
while (kar < argc) { /* loop accross command ine options */
/*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
Opt->helpfunc(0);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
#ifdef USE_TRACING
if( strncmp(argv[kar],"-trace",5) == 0 ){
DBG_trace = 1 ;
brk = 1 ;
}
if( strncmp(argv[kar],"-TRACE",5) == 0 ){
DBG_trace = 2 ;
brk = 1 ;
}
#endif
if (!brk && (strcmp(argv[kar], "-debug") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -debug \n");
exit (1);
}
Opt->debug = atoi(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-talk_afni") == 0)) {
Opt->ps->cs->talk_suma = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-openmp") == 0)) {
Opt->openmp = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-no_openmp") == 0)) {
Opt->openmp = 0;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-vox_debug") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need 1D vox index after -vox_debug \n");
exit (1);
}
if (kar+2<argc) { /* see if we have ijk */
int iii, jjj, kkk;
if (argv[kar][0]!='-' && argv[kar][1]!='-' && argv[kar][2]!='-' &&
(iii = atoi(argv[kar ])) >= 0 &&
(jjj = atoi(argv[kar+1])) >= 0 &&
(kkk = atoi(argv[kar+2])) >= 0 ) {
Opt->VoxDbg3[0]=iii;
Opt->VoxDbg3[1]=jjj;
Opt->VoxDbg3[2]=kkk;
++kar; ++kar;
}
}
if (Opt->VoxDbg3[0] < 0) {
Opt->VoxDbg = atoi(argv[kar]);
}
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-vox_debug_file") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need filename after -vox_debug_file \n");
exit (1);
}
if (!strcmp(argv[kar],"-")) {
Opt->VoxDbgOut = stdout;
} else if (!strcmp(argv[kar],"+")) {
Opt->VoxDbgOut = stderr;
} else {
Opt->VoxDbgOut = fopen(argv[kar],"w");
}
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-cmask") == 0)) {
kar ++;
if (kar >= argc) {
ERROR_exit("-cmask option requires a following argument!\n");
}
Opt->cmask = EDT_calcmask( argv[kar] , &(Opt->dimcmask), 0 ) ;
if( Opt->cmask == NULL ) ERROR_exit("Can't compute -cmask!\n");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-mask") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -mask \n");
exit (1);
}
Opt->mset_name = argv[kar];
brk = 1;
}
if( !brk && (strncmp(argv[kar],"-mrange",5) == 0) ){
if( kar+2 >= argc )
ERROR_exit("-mrange option requires 2 following arguments!\n");
Opt->mask_bot = strtod( argv[++kar] , NULL ) ;
Opt->mask_top = strtod( argv[++kar] , NULL ) ;
if( Opt->mask_top < Opt->mask_bot )
ERROR_exit("-mrange inputs are illegal!\n") ;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-anat") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -anat \n");
exit (1);
}
Opt->aset_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-sig") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -sig \n");
exit (1);
}
while (kar < argc && argv[kar][0] != '-') {
sbuf =
SUMA_append_replace_string(sbuf, argv[kar], " ", 1);
++kar;
}
if (kar < argc && argv[kar][0] == '-') --kar; /* unwind */
Opt->sig_names = SUMA_NI_str_array(Opt->sig_names, sbuf, "add");
SUMA_free(sbuf); sbuf = NULL;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-samp") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -samp \n");
exit (1);
}
while (kar < argc && argv[kar][0] != '-') {
sbuf =
SUMA_append_replace_string(sbuf, argv[kar], " ", 1);
++kar;
}
if (kar < argc && argv[kar][0] == '-') --kar; /* unwind */
Opt->samp_names = SUMA_NI_str_array(Opt->samp_names, sbuf, "add");
SUMA_free(sbuf); sbuf = NULL;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-hspec") == 0)) {
kar ++;
if (kar+3 >= argc) {
fprintf (stderr, "need 4 arguments after -hspec \n");
exit (1);
}
Opt->hspec = (SUMA_HIST **)
SUMA_realloc(Opt->hspec, (Opt->N_hspec+1)*sizeof(SUMA_HIST *));
Opt->hspec[Opt->N_hspec] = (SUMA_HIST*)SUMA_calloc(1,sizeof(SUMA_HIST));
Opt->hspec[Opt->N_hspec]->label = SUMA_copy_string(argv[kar++]);
Opt->hspec[Opt->N_hspec]->min = (float)strtod(argv[kar++],NULL);
Opt->hspec[Opt->N_hspec]->max = (float)strtod(argv[kar++],NULL);
Opt->hspec[Opt->N_hspec]->K = (float)strtod(argv[kar],NULL);
++Opt->N_hspec;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -prefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->proot = argv[kar];
Opt->prefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->crefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->pgrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->cgrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->frefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->xrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->prefix,"%s.p", argv[kar]);
sprintf(Opt->pgrefix,"%s.pg", argv[kar]);
sprintf(Opt->crefix,"%s.c", argv[kar]);
sprintf(Opt->cgrefix,"%s.cg", argv[kar]);
sprintf(Opt->frefix,"%s.f", argv[kar]);
sprintf(Opt->xrefix,"%s.x", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-classes") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -classes \n");
exit (1);
}
Opt->clss = NI_strict_decode_string_list(argv[kar] ,";, ");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-features") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -features \n");
exit (1);
}
Opt->feats = NI_strict_decode_string_list(argv[kar] ,";, ");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-keys") == 0)) {
NI_str_array *nstr=NULL; int ii;
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -keys \n");
exit (1);
}
if (!(nstr = NI_strict_decode_string_list(argv[kar] ,";, "))){
ERROR_exit("Bad option %s after -keys", argv[kar]);
}
Opt->keys = (int *)calloc(nstr->num, sizeof(int));
for (ii=0;ii<nstr->num; ++ii)
Opt->keys[ii] = strtol(nstr->str[ii],NULL,10);
NI_delete_str_array(nstr);nstr=NULL;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-labeltable") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -labeltable \n");
exit (1);
}
Opt->labeltable_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-uid") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -uid \n");
exit (1);
}
snprintf(Opt->uid,128,"%s",argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-ShowTheseHists") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -ShowTheseHists \n");
exit (1);
}
{
NI_str_array *hisnames=NULL;
SUMA_HIST *hh=NULL;
int ii=0;
hisnames = NI_strict_decode_string_list(argv[kar],";, ");
for (ii=0; ii<hisnames->num; ++ii) {
if ((hh = SUMA_read_hist(hisnames->str[ii]))) {
SUMA_Show_hist(hh, 1, NULL);
hh = SUMA_Free_hist(hh);
} else {
SUMA_S_Errv("Hist %s not found.\n", hisnames->str[ii]);
exit(1);
}
}
hisnames = SUMA_free_NI_str_array(hisnames);
}
exit(0);
brk = 1;
}
if (!brk) {
fprintf (stderr,"Option #%d %s not understood. \n"
"Try -help for usage\n", kar, argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = 0;
kar ++;
}
}
if (!Opt->prefix) Opt->prefix = strdup("./GenFeatureDistOut.p");
if (!Opt->frefix) Opt->frefix = strdup("./GenFeatureDistOut.f");
if (!Opt->xrefix) Opt->xrefix = strdup("./GenFeatureDistOut.x");
if (!Opt->crefix) Opt->crefix = strdup("./GenFeatureDistOut.c");
if (Opt->uid[0]=='\0') UNIQ_idcode_fill(Opt->uid);
if (Opt->VoxDbg > -1 && !Opt->VoxDbgOut) {
char stmp[256];
sprintf(stmp,"%d.GFD.dbg", Opt->VoxDbg);
Opt->VoxDbgOut = fopen(stmp,"w");
}
SUMA_RETURN(Opt);
}
SUMA_GENERIC_PROG_OPTIONS_STRUCT *
SUMA_SurfMatch_ParseInput( char *argv[], int argc,
SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_SurfMatch_ParseInput"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt=NULL;
int kar;
SUMA_Boolean brk;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = SUMA_Alloc_Generic_Prog_Options_Struct();
Opt->s=NULL;
Opt->flt1 = 1.0;
Opt->b1 = 0;
Opt->efrac = 0.0;
kar = 1;
brk = NOPE;
while (kar < argc) { /* loop accross command ine options */
/*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
usage_SurfMatch(ps, strlen(argv[kar])>3?1:0);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-warp") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a string after -warp \n");
exit (1);
}
++kar;
if (!strcmp(argv[kar],"shift_only") ||
!strcmp(argv[kar],"sho")) {
Opt->s = SUMA_copy_string("shft");
} else if (!strcmp(argv[kar],"shift_rotate") ||
!strcmp(argv[kar],"sro")) {
Opt->s = SUMA_copy_string("shft+rot");
} else if (!strcmp(argv[kar],"shift_rotate_scale") ||
!strcmp(argv[kar],"srs")) {
Opt->s = SUMA_copy_string("shft+rot+scl");
} else if (!strcmp(argv[kar],"affine_general") ||
!strcmp(argv[kar],"aff")) {
Opt->s = SUMA_copy_string("shft+rot+scl+shr");
} else {
SUMA_S_Errv("Bad -warp parameter of %s\n"
"Choose from sho, sro, srs, or aff\n",
argv[kar]);
exit(1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-city") == 0))
{
Opt->b1 = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -prefix \n");
exit (1);
}
Opt->out_prefix = SUMA_copy_string(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-depthlimit") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -depthlimit \n");
exit (1);
}
Opt->flt1 = atof(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-reduce_ref") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -reduce_ref \n");
exit (1);
}
Opt->efrac = atof(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-debug") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -debug \n");
exit (1);
}
Opt->debug = atoi(argv[++kar]);
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
fprintf (SUMA_STDERR,
"Error SurfMatch: Option %s not understood\n", argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}
if (!Opt->out_prefix) {
Opt->out_prefix = SUMA_copy_string("SurfMatch.gii");
THD_force_ok_overwrite(1) ;
}
if (!Opt->s) {
Opt->s = SUMA_copy_string("shft");
}
SUMA_RETURN(Opt);
}
void BUCK_read_opts( int argc , char * argv[] )
{
int nopt = 1 , ii ;
char dname[THD_MAX_NAME] ;
char subv[THD_MAX_NAME] ;
char *cpt ;
THD_3dim_dataset *dset , *fset=NULL ;
int *svar ;
char *str;
int ok, ilen, nlen;
INIT_3DARR(BUCK_dsar) ;
INIT_XTARR(BUCK_subv) ;
while( nopt < argc ){
if( strcmp(argv[nopt],"-help") == 0 ||
strcmp(argv[nopt],"-h") == 0) {
BUCK_Syntax(strlen(argv[nopt])>3?2:1) ;
exit(0);
}
/**** -prefix prefix ****/
if( strncmp(argv[nopt],"-prefix",6) == 0 ||
strncmp(argv[nopt],"-output",6) == 0 ){
if (BUCK_glue){
fprintf(stderr,"-prefix and -glueto options are not compatible\n");
exit(1) ;
}
nopt++ ;
if( nopt >= argc ){
fprintf(stderr,"need argument after -prefix!\n") ; exit(1) ;
}
MCW_strncpy( BUCK_output_prefix , argv[nopt++] , THD_MAX_PREFIX ) ;
continue ;
}
/**** -session directory ****/
if( strncmp(argv[nopt],"-session",6) == 0 ){
if (BUCK_glue){
fprintf(stderr,
"-session and -glueto options are not compatible\n");
exit(1) ;
}
nopt++ ;
if( nopt >= argc ){
fprintf(stderr,"need argument after -session!\n") ; exit(1) ;
}
MCW_strncpy( BUCK_session , argv[nopt++] , THD_MAX_NAME ) ;
continue ;
}
if( strncmp(argv[nopt],"-dry",3) == 0 ){
BUCK_dry = BUCK_verb = 1 ;
nopt++ ; continue ;
}
if( strncmp(argv[nopt],"-fbuc",4) == 0 ){
BUCK_type = HEAD_FUNC_TYPE ;
nopt++ ; continue ;
}
if( strncmp(argv[nopt],"-abuc",4) == 0 ){
BUCK_type = HEAD_ANAT_TYPE ;
nopt++ ; continue ;
}
if( strncmp(argv[nopt],"-verb",5) == 0 ){
BUCK_verb = 1 ;
nopt++ ; continue ;
}
if( strncmp(argv[nopt],"-glueto",5) == 0 ||
strncmp(argv[nopt],"-aglueto",5) == 0){ /* ZSS April 16 2010 */
if( strncmp(BUCK_output_prefix, "buck", 5) != 0 ){
fprintf(stderr,
"-prefix, -glueto, and -aglueto options are not compatible\n");
exit(1) ;
}
if( strncmp(BUCK_session, "./", 5) != 0 ){
fprintf(stderr,
"-session, -glueto, and -aglueto options are not compatible\n");
exit(1) ;
}
nopt++ ;
if( nopt >= argc ){
fprintf(stderr,"need argument after -glueto or -aglueto!\n") ;
exit(1) ;
}
if (strncmp(argv[nopt-1],"-aglueto",5) == 0) { /* ZSS April 16 2010 */
THD_3dim_dataset *ddd = THD_open_dataset( argv[nopt] );
if( !ISVALID_DSET(ddd) ){
/* treat as -prefix */
MCW_strncpy( BUCK_output_prefix , argv[nopt++] , THD_MAX_PREFIX ) ;
continue ;
} else {
/* go on as standard -glueto option */
}
}
BUCK_glue = 1 ;
/*----- Verify that file name ends in View Type -----*/
ok = 1;
nlen = strlen(argv[nopt]);
if (nlen <= 5) ok = 0;
if (ok)
{
#if 0 /* old code - scan from end, instead */
for (ilen = 0; ilen < nlen; ilen++)
{
str = argv[nopt] + ilen;
if (str[0] == '+') break;
}
if (ilen == nlen) ok = 0;
#endif
/* scan from end for view type extension, require one char */
/* 30 Oct 2003 [rickr] */
for (ilen = nlen - 1; ilen > 0; ilen--)
{
str = argv[nopt] + ilen;
if (str[0] == '+') break;
}
if (ilen == 0) ok = 0;
}
if (ok)
{
str = argv[nopt] + ilen + 1;
for (ii=FIRST_VIEW_TYPE ; ii <= LAST_VIEW_TYPE ; ii++)
if (! strncmp(str,VIEW_codestr[ii],4)) break ;
if( ii > LAST_VIEW_TYPE ) ok = 0;
}
if (! ok)
{
fprintf(stderr,
"File name must end in +orig, +acpc, or +tlrc after -glueto\n"
"(consider: 3dbucket -prefix dsetA -overwrite dsetA dsetB ...)\n");
exit(1);
}
/*----- Remove View Type from string to make output prefix -----*/
MCW_strncpy( BUCK_output_prefix , argv[nopt] , ilen+1) ;
/*----- Note: no "continue" statement here. File name will now
be processed as an input dataset -----*/
}
if( strncmp(argv[nopt],"-aglueto",5) == 0 ){
if( strncmp(BUCK_output_prefix, "buck", 5) != 0 ){
fprintf(stderr,"-prefix and -aglueto options are not compatible.\n"
"Make sure you do not have two -agluto options on command.\n");
exit(1) ;
}
if( strncmp(BUCK_session, "./", 5) != 0 ){
fprintf(stderr,
"-session and -aglueto options are not compatible\n");
exit(1) ;
}
BUCK_glue = 1 ;
nopt++ ;
if( nopt >= argc ){
fprintf(stderr,"need argument after -glueto!\n") ; exit(1) ;
}
/*----- Verify that file name ends in View Type -----*/
ok = 1;
nlen = strlen(argv[nopt]);
if (nlen <= 5) ok = 0;
if (ok)
{
#if 0 /* old code - scan from end, instead */
for (ilen = 0; ilen < nlen; ilen++)
{
str = argv[nopt] + ilen;
if (str[0] == '+') break;
}
if (ilen == nlen) ok = 0;
#endif
/* scan from end for view type extension, require one char */
/* 30 Oct 2003 [rickr] */
for (ilen = nlen - 1; ilen > 0; ilen--)
{
str = argv[nopt] + ilen;
if (str[0] == '+') break;
}
if (ilen == 0) ok = 0;
}
if (ok)
{
str = argv[nopt] + ilen + 1;
for (ii=FIRST_VIEW_TYPE ; ii <= LAST_VIEW_TYPE ; ii++)
if (! strncmp(str,VIEW_codestr[ii],4)) break ;
if( ii > LAST_VIEW_TYPE ) ok = 0;
}
if (! ok)
{
fprintf(stderr,
"File name must end in +orig, +acpc, or +tlrc after -glueto\n"
"(consider: 3dbucket -prefix dsetA -overwrite dsetA dsetB ...)\n");
exit(1);
}
/*----- Remove View Type from string to make output prefix -----*/
MCW_strncpy( BUCK_output_prefix , argv[nopt] , ilen+1) ;
/*----- Note: no "continue" statement here. File name will now
be processed as an input dataset -----*/
}
if( argv[nopt][0] == '-' ){
fprintf(stderr,"Unknown option: %s\n",argv[nopt]) ;
suggest_best_prog_option(argv[0], argv[nopt]);
exit(1) ;
}
/**** read dataset ****/
cpt = strstr(argv[nopt],"[") ;
if( cpt == NULL ){
if (strlen(argv[nopt]) > THD_MAX_NAME-1) {
ERROR_exit( "Too long a filename for '%s'\n"
"Maximum limit is %d\n", argv[nopt], THD_MAX_NAME-1);
}
strcpy(dname,argv[nopt]) ;
subv[0] = '\0' ; /* make sure subv is reset ZSS Nov. 2010*/
} else if( cpt == argv[nopt] ){
fprintf(stderr,"illegal dataset specifier: %s\n",argv[nopt]) ;
exit(1) ;
} else {
ii = cpt - argv[nopt] ;
if (ii > THD_MAX_NAME-1) {
ERROR_exit( "Too long a filename for '%s'\n"
"Maximum character limit is %d, have %d\\n",
argv[nopt], THD_MAX_NAME-1, ii);
}
if (strlen(argv[nopt])-ii > THD_MAX_NAME-1) {
ERROR_exit( "Too long a sub-brick selection for '%s'\n"
"Maximum limit is %d, have %d\n"
"Consider using '[1dcat FF.1D]' or '[count ...]' methods\n"
"for sub-brick selection. See 3dTcat -help for details.\n",
argv[nopt], THD_MAX_NAME-1, strlen(argv[nopt])-ii);
}
memcpy(dname,argv[nopt],ii) ; dname[ii] = '\0' ;
strcpy(subv,cpt) ;
}
nopt++ ;
dset = THD_open_one_dataset( dname ) ;
if( dset == NULL ){
fprintf(stderr,"can't open dataset %s\n",dname) ; exit(1) ;
}
THD_force_malloc_type( dset->dblk , DATABLOCK_MEM_MALLOC ) ;
if( BUCK_type < 0 ) BUCK_type = dset->type ;
BUCK_ccode = COMPRESS_filecode(dset->dblk->diskptr->brick_name) ;
/* 16 Mar 2010 */
ii = dset->daxes->nxx * dset->daxes->nyy * dset->daxes->nzz ;
if( BUCK_nvox < 0 ){
BUCK_nvox = ii ; fset = dset ;
} else if( ii != BUCK_nvox ){
ERROR_exit("Dataset %s differs in size from first one",dname);
} else if( !EQUIV_GRIDS(dset,fset) ){
WARNING_message("Dataset %s grid differs from first one",dname) ;
}
ADDTO_3DARR(BUCK_dsar,dset) ;
if (subv == NULL || subv[0] == '\0') { /* lazy way for 3dbucket special */
svar = BUCK_get_subv( DSET_NVALS(dset) , subv ) ; /* ZSS Dec 09 */
} else {
svar = MCW_get_thd_intlist (dset, subv); /* ZSS Dec 09 */
}
if( svar == NULL || svar[0] <= 0 ){
fprintf(stderr,"can't decipher index codes from %s%s\n",dname,subv) ;
exit(1) ;
}
ADDTO_XTARR(BUCK_subv,svar) ;
} /* end of loop over command line arguments */
if( argc < 2) {
ERROR_message("Too few options");
BUCK_Syntax(0) ;
exit(1);
}
return ;
}
int main( int argc , char *argv[] )
{
int vstep=0 , ii,nvox , ntin , ntout , do_one=0 , nup=-1 ;
THD_3dim_dataset *inset=NULL , *outset ;
char *prefix="Upsam", *dsetname=NULL ;
int verb=0 , iarg=1, datum = MRI_float;
float *ivec , *ovec , trin , trout, *fac=NULL, *ofac=NULL,
top=0.0, maxtop=0.0;
/*------- help the pitifully ignorant user? -------*/
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf(
"Usage: 3dUpsample [options] n dataset\n"
"\n"
"* Upsamples a 3D+time dataset, in the time direction,\n"
" by a factor of 'n'.\n"
"* The value of 'n' must be between 2 and 320 (inclusive).\n"
"* The output dataset is in float format by default.\n"
"\n"
"Options:\n"
"--------\n"
" -1 or -one = Use linear interpolation. Otherwise,\n"
" or -linear 7th order polynomial interpolation is used.\n"
"\n"
" -prefix pp = Define the prefix name of the output dataset.\n"
" [default prefix is 'Upsam']\n"
"\n"
" -verb = Be eloquently and mellifluosly verbose.\n"
"\n"
" -n n = An alternate way to specify n\n"
" -input dataset = An alternate way to specify dataset\n"
"\n"
" -datum ddd = Use datatype ddd at output. Choose from\n"
" float (default), short, byte.\n"
"Example:\n"
"--------\n"
" 3dUpsample -prefix LongFred 5 Fred+orig\n"
"\n"
"Nota Bene:\n"
"----------\n"
"* You should not use this for files that were 3dTcat-ed across\n"
" imaging run boundaries, since that will result in interpolating\n"
" between non-contiguous time samples!\n"
"* If the input has M time points, the output will have n*M time\n"
" points. The last n-1 of them will be past the end of the original\n"
" time series.\n"
"* This program gobbles up memory and diskspace as a function of n.\n"
" You can reduce output file size with -datum option.\n"
"\n"
"--- RW Cox - April 2008\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
mainENTRY("3dUpsample"); machdep();
PRINT_VERSION("3dUpsample"); AUTHOR("RWCox") ;
AFNI_logger("3dUpsample",argc,argv);
/*------- read command line args -------*/
datum = MRI_float;
iarg = 1 ;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strncasecmp(argv[iarg],"-prefix",5) == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '%s'",argv[iarg-1]);
prefix = argv[iarg] ;
if( !THD_filename_ok(prefix) )
ERROR_exit("Illegal string after -prefix: '%s'",prefix) ;
iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-one",4) == 0 ||
strcmp (argv[iarg],"-1" ) == 0 ||
strncasecmp(argv[iarg],"-lin",4) == 0 ){
do_one = 1 ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-verb",3) == 0 ){
verb = 1 ; iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-n") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '%s'",argv[iarg-1]);
nup = (int)strtod(argv[iarg],NULL) ;
if( nup < 2 || nup > 320 )
ERROR_exit("3dUpsample rate '%d' is outside range 2..320",nup) ;
iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-input") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '%s'",argv[iarg-1]);
dsetname = argv[iarg];
iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-datum") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '%s'",argv[iarg-1]);
if( strcmp(argv[iarg],"short") == 0 ){
datum = MRI_short ;
} else if( strcmp(argv[iarg],"float") == 0 ){
datum = MRI_float ;
} else if( strcmp(argv[iarg],"byte") == 0 ){
datum = MRI_byte ;
} else {
ERROR_message("-datum of type '%s' not supported in 3dUpsample!\n",
argv[iarg] ) ;
exit(1) ;
}
iarg++ ; continue ;
}
ERROR_message("Unknown argument on command line: '%s'",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit (1);
}
/*------- check options for completeness and consistency -----*/
if (nup == -1) {
if( iarg+1 >= argc )
ERROR_exit("need 'n' and 'dataset' on command line!") ;
nup = (int)strtod(argv[iarg++],NULL) ;
if( nup < 2 || nup > 320 )
ERROR_exit("3dUpsample rate '%d' is outside range 2..320",nup) ;
}
if (!dsetname) {
if( iarg >= argc )
ERROR_exit("need 'dataset' on command line!") ;
dsetname = argv[iarg];
}
inset = THD_open_dataset(dsetname) ;
if( !ISVALID_DSET(inset) )
ERROR_exit("3dUpsample can't open dataset '%s'", dsetname) ;
ntin = DSET_NVALS(inset) ; trin = DSET_TR(inset) ;
if( ntin < 2 )
ERROR_exit("dataset '%s' has only 1 value per voxel?!",dsetname) ;
nvox = DSET_NVOX(inset) ;
if( verb ) INFO_message("loading input dataset into memory") ;
DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ;
/*------ create output dataset ------*/
ntout = ntin * nup ; trout = trin / nup ;
/* scaling factor for output */
fac = NULL; maxtop = 0.0;
if (MRI_IS_INT_TYPE(datum)) {
fac = (float *)calloc(DSET_NVALS(inset), sizeof(float));
ofac = (float *)calloc(ntout, sizeof(float));
for (ii=0; ii<DSET_NVALS(inset); ++ii) {
top = MCW_vol_amax( DSET_NVOX(inset),1,1 ,
DSET_BRICK_TYPE(inset,ii),
DSET_BRICK_ARRAY(inset,ii) ) ;
if (DSET_BRICK_FACTOR(inset, ii))
top = top * DSET_BRICK_FACTOR(inset,ii);
fac[ii] = (top > MRI_TYPE_maxval[datum]) ?
top/MRI_TYPE_maxval[datum] : 0.0 ;
if (top > maxtop) maxtop = top;
}
if (storage_mode_from_filename(prefix) != STORAGE_BY_BRICK) {
fac[0] = (maxtop > MRI_TYPE_maxval[datum]) ?
maxtop/MRI_TYPE_maxval[datum] : 0.0 ;
for (ii=0; ii<ntout; ++ii)
ofac[ii] = fac[0];
if (verb) INFO_message("Forcing global scaling, Max = %f, fac = %f\n",
maxtop, fac[0]);
} else {
if (verb) INFO_message("Reusing scaling factors of input dset\n");
upsample_1( nup, DSET_NVALS(inset), fac, ofac);
}
}
free(fac); fac = NULL;
outset = EDIT_empty_copy(inset) ;
EDIT_dset_items( outset ,
ADN_nvals , ntout ,
ADN_ntt , DSET_NUM_TIMES(inset) > 1 ? ntout : 0 ,
ADN_datum_all , datum ,
ADN_brick_fac , ofac ,
ADN_prefix , prefix ,
ADN_none ) ;
tross_Copy_History( inset , outset ) ;
tross_Make_History( "3dUpsample" , argc,argv , outset ) ;
free(ofac); ofac = NULL;
if( outset->taxis != NULL ){
outset->taxis->ttdel /= nup ;
outset->taxis->ttdur /= nup ;
if( outset->taxis->toff_sl != NULL ){
for( ii=0 ; ii < outset->taxis->nsl ; ii++ )
outset->taxis->toff_sl[ii] /= nup ;
}
}
for( ii=0 ; ii < ntout ; ii++ ){ /* create empty bricks to be filled below */
EDIT_substitute_brick( outset , ii , datum , NULL ) ;
}
/*------- loop over voxels and process them one at a time ---------*/
if( verb )
INFO_message("Upsampling time series from %d to %d: %s interpolation",
ntin , ntout , (do_one) ? "linear" : "heptic" ) ;
if( verb && nvox > 499 ) vstep = nvox / 50 ;
if( vstep > 0 ) fprintf(stderr,"++ voxel loop: ") ;
ivec = (float *)malloc(sizeof(float)*ntin) ;
ovec = (float *)malloc(sizeof(float)*ntout) ;
for( ii=0 ; ii < nvox ; ii++ ){
if( vstep > 0 && ii%vstep==vstep-1 ) vstep_print() ;
THD_extract_array( ii , inset , 0 , ivec ) ;
if( do_one ) upsample_1( nup , ntin , ivec , ovec ) ;
else upsample_7( nup , ntin , ivec , ovec ) ;
THD_insert_series( ii , outset , ntout , MRI_float , ovec ,
datum==MRI_float ? 1:0 ) ;
} /* end of loop over voxels */
if( vstep > 0 ) fprintf(stderr," Done!\n") ;
/*----- clean up and go away -----*/
DSET_write(outset) ;
if( verb ) WROTE_DSET(outset) ;
if( verb ) INFO_message("Total CPU time = %.1f s",COX_cpu_time()) ;
exit(0);
}
/*!
\brief parse the arguments for SurfSmooth program
\param argv (char *)
\param argc (int)
\return Opt (SUMA_SURFCLUST_OPTIONS *) options structure.
To free it, use
SUMA_free(Opt->out_name);
SUMA_free(Opt);
*/
SUMA_SURFCLUST_OPTIONS *SUMA_SurfClust_ParseInput (char *argv[], int argc,
SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_SurfClust_ParseInput"};
SUMA_SURFCLUST_OPTIONS *Opt=NULL;
int kar, i, ind;
char *outname;
SUMA_Boolean brk = NOPE;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = SUMA_create_SurfClust_Opt("SurfClust");
kar = 1;
outname = NULL;
BuildMethod = SUMA_OFFSETS2_NO_REC;
brk = NOPE;
while (kar < argc) { /* loop accross command ine options */
/*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
usage_SUMA_SurfClust(strlen(argv[kar]) > 3 ? 2:1);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-no_cent") == 0)) {
Opt->DoCentrality = 0;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-cent") == 0)) {
Opt->DoCentrality = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-O2") == 0)) {
BuildMethod = SUMA_OFFSETS2;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-O2_NR") == 0)) {
BuildMethod = SUMA_OFFSETS2_NO_REC;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-Oll") == 0)) {
BuildMethod = SUMA_OFFSETS_LL;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-update") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -update \n");
exit (1);
}
Opt->update = atof(argv[kar]);
if (Opt->update < 1 || Opt->update > 100) {
fprintf (SUMA_STDERR,
"-update needs a parameter between "
"1 and 50 (I have %.1f)\n", Opt->update);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -prefix \n");
exit (1);
}
Opt->oform = SUMA_GuessFormatFromExtension(argv[kar], NULL);
if (Opt->oform == SUMA_NO_DSET_FORMAT) Opt->oform = SUMA_ASCII_NIML;
Opt->out_prefix = SUMA_RemoveDsetExtension_s(argv[kar], Opt->oform);
Opt->WriteFile = YUP;
brk = YUP;
}
#if 0
if (!brk && (strcmp(argv[kar], "-spec") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -spec \n");
exit (1);
}
Opt->spec_file = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sv") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -sv \n");
exit (1);
}
Opt->sv_name = argv[kar];
brk = YUP;
}
if (!brk && (strncmp(argv[kar], "-surf_", 6) == 0)) {
if (kar + 1>= argc) {
fprintf (SUMA_STDERR, "need argument after -surf_X SURF_NAME \n");
exit (1);
}
ind = argv[kar][6] - 'A';
if (ind < 0 || ind >= SURFCLUST_MAX_SURF) {
fprintf (SUMA_STDERR,
"-surf_X SURF_NAME option is out of range.\n"
"Only %d surfaces are allowed. \n"
"Must start with surf_A for first surface.\n",
SURFCLUST_MAX_SURF);
exit (1);
}
kar ++;
Opt->surf_names[ind] = argv[kar];
Opt->N_surf = ind+1;
brk = YUP;
}
#endif
if (!brk && (strcmp(argv[kar], "-input") == 0)) {
kar ++;
if (kar+1 >= argc) {
fprintf (SUMA_STDERR, "need 2 arguments after -input \n");
exit (1);
}
Opt->in_name = argv[kar]; kar ++;
/* no need for that one Opt->nodecol = atoi(argv[kar]); kar ++; */
Opt->labelcol = atoi(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-rmm") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -rmm \n");
exit (1);
}
Opt->DistLim = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-in_range") == 0)) {
kar ++;
if (kar+1 >= argc) {
fprintf (SUMA_STDERR, "need two arguments after -in_range \n");
exit (1);
}
Opt->DoThreshold = SUMA_THRESH_INSIDE_RANGE;
Opt->ThreshR[0] = atof(argv[kar]); ++kar;
Opt->ThreshR[1] = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-ex_range") == 0)) {
kar ++;
if (kar+1 >= argc) {
fprintf (SUMA_STDERR, "need two arguments after -ex_range \n");
exit (1);
}
Opt->DoThreshold = SUMA_THRESH_OUTSIDE_RANGE;
Opt->ThreshR[0] = atof(argv[kar]); ++kar;
Opt->ThreshR[1] = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-thresh") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -thresh \n");
exit (1);
}
Opt->DoThreshold = SUMA_LESS_THAN;
Opt->ThreshR[0] = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-athresh") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -athresh \n");
exit (1);
}
Opt->DoThreshold = SUMA_ABS_LESS_THAN;
Opt->ThreshR[0] = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-thresh_col") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -thresh_col \n");
exit (1);
}
Opt->tind = atoi(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-amm2") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -amm2 \n");
exit (1);
}
Opt->AreaLim = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-n") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -n \n");
exit (1);
}
Opt->NodeLim = atoi(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-out_roidset") == 0)) {
Opt->OutROI = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prepend_node_index") == 0)) {
Opt->prepend_node_index = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-out_clusterdset") == 0)) {
Opt->OutClustDset = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-out_fulllist") == 0)) {
Opt->FullROIList = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sort_none") == 0)) {
Opt->SortMode = SUMA_SORT_CLUST_NO_SORT;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sort_n_nodes") == 0)) {
Opt->SortMode = SUMA_SORT_CLUST_BY_NUMBER_NODES;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sort_area") == 0)) {
Opt->SortMode = SUMA_SORT_CLUST_BY_AREA;
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
SUMA_S_Errv("Option %s not understood.\n"
"Try -help for usage\n", argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}
/* sanitorium */
if (Opt->DistLim == -1.5f) {
fprintf (SUMA_STDERR, "must use option -rmm \n");
exit(1);
}
if (!Opt->out_prefix) {
Opt->out_prefix =
SUMA_RemoveDsetExtension_s(Opt->in_name, SUMA_NO_DSET_FORMAT);
}
if (Opt->SortMode == SUMA_SORT_CLUST_NOT_SET) {
Opt->SortMode = SUMA_SORT_CLUST_BY_AREA; }
if (BuildMethod == SUMA_OFFSETS2) { SUMA_S_Note("Using Offsets2"); }
else if (BuildMethod == SUMA_OFFSETS_LL) { SUMA_S_Note("Using Offsets_ll"); }
else if (BuildMethod == SUMA_OFFSETS2_NO_REC) {
if (LocalHead) SUMA_S_Note("Using no recursion"); }
else {
SUMA_SL_Err("Bad BuildMethod");
exit(1);
}
SUMA_SurfClust_Set_Method(BuildMethod);
if (Opt->FullROIList && !(Opt->OutROI || Opt->OutClustDset)) {
SUMA_SL_Err("-out_fulllist must be used in conjunction "
"with -out_ROIdset or -out_clusterdset");
exit(1);
}
SUMA_RETURN(Opt);
}
int main(int argc, char *argv[]) {
int i,j,k,m,n,aa,ii,jj,kk,mm,rr;
int iarg;
int nmask1=0;
int nmask2=0;
THD_3dim_dataset *insetFA = NULL, *insetV1 = NULL,
*insetMD = NULL, *insetL1 = NULL;
THD_3dim_dataset *insetEXTRA=NULL;
THD_3dim_dataset *mset2=NULL;
THD_3dim_dataset *mset1=NULL;
THD_3dim_dataset *outsetMAP=NULL, *outsetMASK=NULL;
char *prefix="tracky";
int LOG_TYPE=0;
char in_FA[300];
char in_V1[300];
char in_MD[300];
char in_L1[300];
int EXTRAFILE=0; // switch for whether other file is input as WM map
char OUT_bin[300];
char OUT_tracstat[300];
char prefix_mask[300];
char prefix_map[300];
// FACT algopts
FILE *fout0;
float MinFA=0.2,MaxAngDeg=45,MinL=20.0;
float MaxAng;
int SeedPerV[3]={2,2,2};
int ArrMax=0;
float tempvmagn;
int Nvox=-1; // tot number vox
int Dim[3]={0,0,0}; // dim in each dir
int Nseed=0,M=30,bval=1000;
int DimSeed[3]; // number of seeds there will be
float Ledge[3]; // voxel edge lengths
int *ROI1, *ROI2;
short int *temp_arr;
char *temp_byte;
int **Tforw, **Tback;
int **Ttot;
float **flTforw, **flTback;
float ****coorded;
int ****INDEX;
int len_forw, len_back; // int count of num of squares through
float phys_forw[1], phys_back[1];
int idx;
float ave_tract_len, ave_tract_len_phys;
int inroi1, inroi2, KEEPIT; // switches for detecting
int in[3]; // to pass to trackit
float physin[3]; // also for trackit, physical loc,
int totlen;
float totlen_phys;
int Numtract;
int READS_in;
float READS_fl;
int end[2][3];
int test_ind[2][3];
int roi3_ct=0, id=0;
float roi3_mu_MD = 0.,roi3_mu_RD = 0.,roi3_mu_L1 = 0.,roi3_mu_FA = 0.;
float roi3_sd_MD = 0.,roi3_sd_RD = 0.,roi3_sd_L1 = 0.,roi3_sd_FA = 0.;
float tempMD,tempFA,tempRD,tempL1;
char dset_or[4] = "RAI";
THD_3dim_dataset *dsetn;
int TV_switch[3] = {0,0,0};
TAYLOR_BUNDLE *tb=NULL;
TAYLOR_TRACT *tt=NULL;
char *mode = "NI_fast_binary";
NI_element *nel=NULL;
int dump_opts=0;
tv_io_header header1 = {.id_string = "TRACK\0",
.origin = {0,0,0},
.n_scalars = 3,
.scal_n[0] = "FA",
.scal_n[1] = "MD",
.scal_n[2] = "L1",
.n_properties = 0,
.vox_to_ras = {{0.,0.,0.,0.},{0.,0.,0.,0.},
{0.,0.,0.,0.},{0.,0.,0.,0.}},
// reset this later based on actual data set
.voxel_order = "RAI\0",
.invert_x = 0,
.invert_y = 0,
.invert_z = 0,
.swap_xy = 0,
.swap_yz = 0,
.swap_zx = 0,
.n_count = 0,
.version = 2,
.hdr_size = 1000};
// for testing names...
char *postfix[4]={"+orig.HEAD\0",".nii.gz\0",".nii\0","+tlrc.HEAD\0"};
int FOUND =-1;
int RECORD_ORIG = 0;
float Orig[3] = {0.0,0.0,0.0};
mainENTRY("3dTrackID"); machdep();
// ****************************************************************
// ****************************************************************
// load AFNI stuff
// ****************************************************************
// ****************************************************************
INFO_message("version: MU");
/** scan args **/
if (argc == 1) { usage_TrackID(1); exit(0); }
iarg = 1;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 ||
strcmp(argv[iarg],"-h") == 0 ) {
usage_TrackID(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
if( strcmp(argv[iarg],"-verb") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need argument after '-verb'") ;
set_tract_verb(atoi(argv[iarg]));
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-write_opts") == 0) {
dump_opts=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-rec_orig") == 0) {
RECORD_ORIG=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-tract_out_mode") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need argument after '-tract_out_mode'") ;
if (strcmp(argv[iarg], "NI_fast_binary") &&
strcmp(argv[iarg], "NI_fast_text") &&
strcmp(argv[iarg], "NI_slow_binary") &&
strcmp(argv[iarg], "NI_slow_text") ) {
ERROR_message("Bad value (%s) for -tract_out_mode",argv[iarg]);
exit(1);
}
mode = argv[iarg];
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-mask1") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-mask1'") ;
mset1 = THD_open_dataset( argv[iarg] ) ;
if( mset1 == NULL )
ERROR_exit("Can't open mask1 dataset '%s'", argv[iarg]) ;
DSET_load(mset1) ; CHECK_LOAD_ERROR(mset1) ;
nmask1 = DSET_NVOX(mset1) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-mask2") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-mask2'") ;
mset2 = THD_open_dataset( argv[iarg] ) ;
if( mset2 == NULL )
ERROR_exit("Can't open mask2 dataset '%s'",
argv[iarg]) ;
DSET_load(mset2) ; CHECK_LOAD_ERROR(mset2) ;
nmask2 = DSET_NVOX(mset2) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-prefix") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-prefix'");
prefix = strdup(argv[iarg]) ;
if( !THD_filename_ok(prefix) )
ERROR_exit("Illegal name after '-prefix'");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-input") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-input'");
for( i=0 ; i<4 ; i++) {
sprintf(in_FA,"%s_FA%s", argv[iarg],postfix[i]);
if(THD_is_ondisk(in_FA)) {
FOUND = i;
break;
}
}
insetFA = THD_open_dataset(in_FA) ;
if( (insetFA == NULL ) || (FOUND==-1))
ERROR_exit("Can't open dataset '%s': for FA.",in_FA);
DSET_load(insetFA) ; CHECK_LOAD_ERROR(insetFA) ;
Nvox = DSET_NVOX(insetFA) ;
Dim[0] = DSET_NX(insetFA); Dim[1] = DSET_NY(insetFA);
Dim[2] = DSET_NZ(insetFA);
Ledge[0] = fabs(DSET_DX(insetFA)); Ledge[1] = fabs(DSET_DY(insetFA));
Ledge[2] = fabs(DSET_DZ(insetFA));
Orig[0] = DSET_XORG(insetFA); Orig[1] = DSET_YORG(insetFA);
Orig[2] = DSET_ZORG(insetFA);
// check tot num vox match (as proxy for dims...)
if( (Nvox != nmask1) || (Nvox != nmask2) )
ERROR_exit("Input dataset does not match both mask volumes!");
// this stores the original data file orientation for later use,
// as well since we convert everything to RAI temporarily, as
// described below
header1.voxel_order[0]=ORIENT_typestr[insetFA->daxes->xxorient][0];
header1.voxel_order[1]=ORIENT_typestr[insetFA->daxes->yyorient][0];
header1.voxel_order[2]=ORIENT_typestr[insetFA->daxes->zzorient][0];
for( i=0 ; i<3 ; i++) {
header1.dim[i] = Dim[i];
header1.voxel_size[i] = Ledge[i];
// will want this when outputting file later for TrackVis.
TV_switch[i] = !(dset_or[i]==header1.voxel_order[i]);
}
dset_or[3]='\0';
FOUND = -1;
for( i=0 ; i<4 ; i++) {
sprintf(in_V1,"%s_V1%s", argv[iarg],postfix[i]);
if(THD_is_ondisk(in_V1)) {
FOUND = i;
break;
}
}
insetV1 = THD_open_dataset(in_V1);
if( insetV1 == NULL )
ERROR_exit("Can't open dataset '%s':V1",in_V1);
DSET_load(insetV1) ; CHECK_LOAD_ERROR(insetV1) ;
FOUND = -1;
for( i=0 ; i<4 ; i++) {
sprintf(in_L1,"%s_L1%s", argv[iarg],postfix[i]);
if(THD_is_ondisk(in_L1)) {
FOUND = i;
break;
}
}
insetL1 = THD_open_dataset(in_L1);
if( insetL1 == NULL )
ERROR_exit("Can't open dataset '%s':L1",in_L1);
DSET_load(insetL1) ; CHECK_LOAD_ERROR(insetL1) ;
FOUND = -1;
for( i=0 ; i<4 ; i++) {
sprintf(in_MD,"%s_MD%s", argv[iarg],postfix[i]);
if(THD_is_ondisk(in_MD)) {
FOUND = i;
break;
}
}
insetMD = THD_open_dataset(in_MD);
if( insetMD == NULL )
ERROR_exit("Can't open dataset '%s':MD",in_MD);
DSET_load(insetMD) ; CHECK_LOAD_ERROR(insetMD) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-algopt") == 0 ){
iarg++ ;
if( iarg >= argc )
ERROR_exit("Need argument after '-algopt'");
if (!(nel = ReadTractAlgOpts(argv[iarg]))) {
ERROR_message("Failed to read options in %s\n", argv[iarg]);
exit(19);
}
if (NI_getTractAlgOpts(nel, &MinFA, &MaxAngDeg, &MinL,
SeedPerV, &M, &bval)) {
ERROR_message("Failed to get options");
exit(1);
}
NI_free_element(nel); nel=NULL;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-logic") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-logic'");
INFO_message("ROI logic type is: %s",argv[iarg]);
if( strcmp(argv[iarg],"AND") == 0 )
LOG_TYPE = 1;
else if( strcmp(argv[iarg],"OR") == 0 )
LOG_TYPE = 0;
else if( strcmp(argv[iarg],"ALL") == 0 )
LOG_TYPE = -1;
else
ERROR_exit("Illegal after '-logic': need 'OR' or 'AND'");
iarg++ ; continue ;
}
//@@
if( strcmp(argv[iarg],"-extra_set") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need argument after '-extra_set'");
EXTRAFILE = 1; // switch on
insetEXTRA = THD_open_dataset(argv[iarg]);
if( (insetEXTRA == NULL ) )
ERROR_exit("Can't open dataset '%s': for extra set.",argv[iarg]);
DSET_load(insetEXTRA) ; CHECK_LOAD_ERROR(insetEXTRA) ;
if( !((Dim[0] == DSET_NX(insetEXTRA)) && (Dim[1] == DSET_NY(insetEXTRA)) && (Dim[2] == DSET_NZ(insetEXTRA))))
ERROR_exit("Dimensions of extra set '%s' don't match those of the DTI prop ones ('%s', etc.).",argv[iarg], in_FA);
iarg++ ; continue ;
}
ERROR_message("Bad option '%s'\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
if (iarg < 4) {
ERROR_message("Too few options. Try -help for details.\n");
exit(1);
}
if (dump_opts) {
nel = NI_setTractAlgOpts(NULL, &MinFA, &MaxAngDeg, &MinL,
SeedPerV, &M, &bval);
WriteTractAlgOpts(prefix, nel);
NI_free_element(nel); nel=NULL;
}
// Process the options a little
for( i=0 ; i<3 ; i++)
DimSeed[i] = Dim[i]*SeedPerV[i];
Nseed = Nvox*SeedPerV[0]*SeedPerV[1]*SeedPerV[2];
// convert to cos of rad value for comparisons, instead of using acos()
MaxAng = cos(CONV*MaxAngDeg);
// switch to add header-- option for now, added Sept. 2012
// for use with map_TrackID to map tracks to different space
if(RECORD_ORIG) {
for( i=0 ; i<3 ; i++)
header1.origin[i] = Orig[i];
}
// at some point, we will have to convert indices into
// pseudo-locations; being forced into this choice means that
// different data set orientations would be represented differently
// and incorrectly in some instances... so, for now, we'll resample
// everything to RAI, and then resample back later. guess this will
// just slow things down slightly.
// have all be RAI for processing here
if(TV_switch[0] || TV_switch[1] || TV_switch[2]) {
dsetn = r_new_resam_dset(insetFA, NULL, 0.0, 0.0, 0.0,
dset_or, RESAM_NN_TYPE, NULL, 1, 0);
DSET_delete(insetFA);
insetFA=dsetn;
dsetn=NULL;
dsetn = r_new_resam_dset(insetMD, NULL, 0.0, 0.0, 0.0,
dset_or, RESAM_NN_TYPE, NULL, 1, 0);
DSET_delete(insetMD);
insetMD=dsetn;
dsetn=NULL;
dsetn = r_new_resam_dset(insetV1, NULL, 0.0, 0.0, 0.0,
dset_or, RESAM_NN_TYPE, NULL, 1, 0);
DSET_delete(insetV1);
insetV1=dsetn;
dsetn=NULL;
dsetn = r_new_resam_dset(insetL1, NULL, 0.0, 0.0, 0.0,
dset_or, RESAM_NN_TYPE, NULL, 1, 0);
DSET_delete(insetL1);
insetL1=dsetn;
dsetn=NULL;
dsetn = r_new_resam_dset(mset1, NULL, 0.0, 0.0, 0.0,
dset_or, RESAM_NN_TYPE, NULL, 1, 0);
DSET_delete(mset1);
mset1=dsetn;
dsetn=NULL;
dsetn = r_new_resam_dset(mset2, NULL, 0.0, 0.0, 0.0,
dset_or, RESAM_NN_TYPE, NULL, 1, 0);
DSET_delete(mset2);
mset2=dsetn;
dsetn=NULL;
if(EXTRAFILE) {
dsetn = r_new_resam_dset(insetEXTRA, NULL, 0.0, 0.0, 0.0,
dset_or, RESAM_NN_TYPE, NULL, 1, 0);
DSET_delete(insetEXTRA);
insetEXTRA=dsetn;
dsetn=NULL;
}
}
// ****************************************************************
// ****************************************************************
// make arrays for tracking
// ****************************************************************
// ****************************************************************
// for temp storage array, just a multiple of longest dimension!
if(Dim[0] > Dim[1])
ArrMax = Dim[0] * 4;
else
ArrMax = Dim[1] * 4;
if(4*Dim[2] > ArrMax)
ArrMax = Dim[2] * 4;
ROI1 = (int *)calloc(Nvox, sizeof(int));
ROI2 = (int *)calloc(Nvox, sizeof(int));
temp_arr = (short int *)calloc(Nvox, sizeof(short int));
temp_byte = (char *)calloc(Nvox, sizeof(char));
// temp storage whilst tracking
Tforw = calloc(ArrMax, sizeof(Tforw));
for(i=0 ; i<ArrMax ; i++)
Tforw[i] = calloc(3, sizeof(int));
Ttot = calloc(2*ArrMax , sizeof(Ttot));
for(i=0 ; i<2*ArrMax ; i++)
Ttot[i] = calloc(3, sizeof(int));
Tback = calloc(ArrMax, sizeof(Tback));
for(i=0 ; i<ArrMax ; i++)
Tback[i] = calloc(3, sizeof(int));
// temp storage whilst tracking, physical loc
flTforw = calloc(ArrMax, sizeof(flTforw));
for(i=0 ; i<ArrMax ; i++)
flTforw[i] = calloc(3, sizeof(int));
flTback = calloc(ArrMax,sizeof(flTback));
for(i=0 ; i<ArrMax ; i++)
flTback[i] = calloc(3, sizeof(int));
if( (ROI1 == NULL) || (ROI2 == NULL) || (temp_arr == NULL)
|| (Tforw == NULL) || (Tback == NULL) || (flTforw == NULL)
|| (flTback == NULL) || (Ttot == NULL)) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(12);
}
coorded = (float ****) calloc( Dim[0], sizeof(float ***) );
for ( i = 0 ; i < Dim[0] ; i++ )
coorded[i] = (float ***) calloc( Dim[1], sizeof(float **) );
for ( i = 0 ; i < Dim[0] ; i++ )
for ( j = 0 ; j < Dim[1] ; j++ )
coorded[i][j] = (float **) calloc( Dim[2], sizeof(float *) );
for ( i=0 ; i<Dim[0] ; i++ )
for ( j=0 ; j<Dim[1] ; j++ )
for ( k= 0 ; k<Dim[2] ; k++ ) //3 comp of V1 and FA
coorded[i][j][k] = (float *) calloc( 4, sizeof(float) );
INDEX = (int ****) calloc( Dim[0], sizeof(int ***) );
for ( i = 0 ; i < Dim[0] ; i++ )
INDEX[i] = (int ***) calloc( Dim[1], sizeof(int **) );
for ( i = 0 ; i < Dim[0] ; i++ )
for ( j = 0 ; j < Dim[1] ; j++ )
INDEX[i][j] = (int **) calloc( Dim[2], sizeof(int *) );
for ( i=0 ; i<Dim[0] ; i++ )
for ( j=0 ; j<Dim[1] ; j++ )
for ( k= 0 ; k<Dim[2] ; k++ )
INDEX[i][j][k] = (int *) calloc( 4, sizeof(int) );
// this statement will never be executed if allocation fails above
if( (INDEX == NULL) || (coorded == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(122);
}
for(i=0 ; i<Nvox ; i++) {
if(THD_get_voxel( mset1, i, 0) >0.5){
ROI1[i] = 1;
}
if(THD_get_voxel( mset2, i, 0) >0.5)
ROI2[i] = 1;
}
// set up eigvecs in 3D coord sys,
// mark off where ROIs are and keep index handy
idx=0;
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ ) {
for( m=0 ; m<3 ; m++ )
coorded[i][j][k][m] = THD_get_voxel(insetV1, idx, m);
if(EXTRAFILE)
coorded[i][j][k][3] = THD_get_voxel(insetEXTRA, idx, 0);
else
coorded[i][j][k][3] = THD_get_voxel(insetFA, idx, 0);
// make sure that |V1| == 1 for all eigenvects, otherwise it's
/// a problem in the tractography; currently, some from
// 3dDWItoDT do not have this property...
tempvmagn = sqrt(coorded[i][j][k][0]*coorded[i][j][k][0]+
coorded[i][j][k][1]*coorded[i][j][k][1]+
coorded[i][j][k][2]*coorded[i][j][k][2]);
if( tempvmagn<0.99 )
for( m=0 ; m<3 ; m++ )
coorded[i][j][k][m]/= tempvmagn;
INDEX[i][j][k][0] =idx; // first value is the index itself
if( ROI1[idx]==1 )
INDEX[i][j][k][1]=1; // second value identifies ROI1 mask
else
INDEX[i][j][k][1]=0;
if( ROI2[idx]==1 )
INDEX[i][j][k][2]=1; // third value identifies ROI2 mask
else
INDEX[i][j][k][2]=0;
// fourth value will be counter for number of kept tracks
// passing through
INDEX[i][j][k][3] = 0;
idx+= 1;
}
// *************************************************************
// *************************************************************
// Beginning of main loop
// *************************************************************
// *************************************************************
Numtract = 0;
ave_tract_len = 0.;
ave_tract_len_phys = 0.;
sprintf(OUT_bin,"%s.trk",prefix);
if( (fout0 = fopen(OUT_bin, "w")) == NULL) {
fprintf(stderr, "Error opening file %s.",OUT_bin);
exit(16);
}
fwrite(&header1,sizeof(tv_io_header),1,fout0);
if (get_tract_verb()) {
INFO_message("Begin tracking...");
}
tb = AppCreateBundle(NULL, 0, NULL, insetFA); // start bundle
id = 0;
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ )
if(coorded[i][j][k][3] >= MinFA) {
for( ii=0 ; ii<SeedPerV[0] ; ii++ )
for( jj=0 ; jj<SeedPerV[1] ; jj++ )
for( kk=0 ; kk<SeedPerV[2] ; kk++ ) {
in[0] = i;
in[1] = j;
in[2] = k;
physin[0] = ((float) in[0] +
(0.5 + (float) ii)/SeedPerV[0])*Ledge[0];
physin[1] = ((float) in[1] +
(0.5 + (float) jj)/SeedPerV[1])*Ledge[1];
physin[2] = ((float) in[2] +
(0.5 + (float) kk)/SeedPerV[2])*Ledge[2];
len_forw = TrackIt(coorded, in, physin, Ledge, Dim,
MinFA, MaxAng, ArrMax, Tforw,
flTforw, 1, phys_forw);
// reset, because it's changed in TrackIt func
in[0] = i;
in[1] = j;
in[2] = k;
physin[0] = ((float) in[0] +
(0.5 + (float) ii)/SeedPerV[0])*Ledge[0];
physin[1] = ((float) in[1] +
(0.5 + (float) jj)/SeedPerV[1])*Ledge[1];
physin[2] = ((float) in[2] +
(0.5 + (float) kk)/SeedPerV[2])*Ledge[2];
len_back = TrackIt(coorded, in, physin, Ledge, Dim,
MinFA, MaxAng, ArrMax, Tback,
flTback, -1, phys_back);
KEEPIT = 0; // a simple switch
totlen = len_forw+len_back-1; // NB: overlap of starts
totlen_phys = phys_forw[0] + phys_back[0];
if( totlen_phys >= MinL ) {
// glue together for simpler notation later
for( n=0 ; n<len_back ; n++) { // all of this
rr = len_back-n-1; // read in backward
for(m=0;m<3;m++)
Ttot[rr][m] = Tback[n][m];
}
for( n=1 ; n<len_forw ; n++){// skip first->overlap
rr = n+len_back-1; // put after
for(m=0;m<3;m++)
Ttot[rr][m] = Tforw[n][m];
}
// <<So close and orthogonal condition>>:
// test projecting ends, to see if they abut ROI.
for(m=0;m<3;m++) {
//actual projected ends
end[1][m] = 2*Ttot[totlen-1][m]-Ttot[totlen-2][m];
end[0][m] = 2*Ttot[0][m]-Ttot[1][m];
// default choice, just retest known ends
// as default
test_ind[1][m] = test_ind[0][m] = Ttot[0][m];
}
tt = Create_Tract(len_back, flTback, len_forw,
flTforw, id, insetFA); ++id;
if (LOG_TYPE == -1) {
KEEPIT = 1;
} else {
inroi1 = 0;
// check forw
for( n=0 ; n<len_forw ; n++) {
if(INDEX[Tforw[n][0]][Tforw[n][1]][Tforw[n][2]][1]==1){
inroi1 = 1;
break;
} else
continue;
}
if( inroi1==0 ){// after 1st half, check 2nd half
for( m=0 ; m<len_back ; m++) {
if(INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][1]==1){
inroi1 = 1;
break;
} else
continue;
}
}
// after 1st&2nd halves, check bound/neigh
if( inroi1==0 ) {
if(INDEX[test_ind[1][0]][test_ind[1][1]][test_ind[1][2]][1]==1)
inroi1 = 1;
if(INDEX[test_ind[0][0]][test_ind[0][1]][test_ind[0][2]][1]==1)
inroi1 = 1;
}
if( ((LOG_TYPE ==0) && (inroi1 ==0)) ||
((LOG_TYPE ==1) && (inroi1 ==1))) {
// have to check in ROI2
inroi2 = 0;
// check forw
for( n=0 ; n<len_forw ; n++) {
if(INDEX[Tforw[n][0]][Tforw[n][1]][Tforw[n][2]][2]==1){
inroi2 = 1;
break;
} else
continue;
}
//after 1st half, check 2nd half
if( inroi2==0 ) {
for( m=0 ; m<len_back ; m++) {
if(INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][2]==1){
inroi2 = 1;
break;
} else
continue;
}
}
// after 1st&2nd halves, check bound/neigh
if( inroi2==0 ) {
if(INDEX[test_ind[1][0]][test_ind[1][1]][test_ind[1][2]][2]==1)
inroi2 = 1;
if(INDEX[test_ind[0][0]][test_ind[0][1]][test_ind[0][2]][2]==1)
inroi2 = 1;
}
// for both cases, need to see it here to keep
if( inroi2 ==1 )
KEEPIT = 1; // otherwise, it's gone
} else if((LOG_TYPE ==0) && (inroi1 ==1))
KEEPIT = 1;
}
}
// by now, we *know* if we're keeping this or not.
if( KEEPIT == 1 ) {
tb = AppCreateBundle(tb, 1, tt, NULL);
tt = Free_Tracts(tt, 1);
READS_in = totlen;
fwrite(&READS_in,sizeof(READS_in),1,fout0);
for( n=0 ; n<len_back ; n++) {
//put this one in backwords, to make it connect
m = len_back - 1 - n;
for(aa=0 ; aa<3 ; aa++) {
// recenter phys loc for trackvis, if nec...
// just works this way (where they define
// origin)
READS_fl = flTback[m][aa];
if(!TV_switch[aa])
READS_fl = Ledge[aa]*Dim[aa]-READS_fl;
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
}
mm = INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][0];
READS_fl =THD_get_voxel(insetFA, mm, 0); // FA
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
READS_fl =THD_get_voxel(insetMD, mm, 0); // MD
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
READS_fl =THD_get_voxel(insetL1, mm, 0); // L1
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
// count this voxel for having a tract
INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][3]+= 1;
}
for( m=1 ; m<len_forw ; m++) {
for(aa=0 ; aa<3 ; aa++) {
// recenter phys loc for trackvis, if nec...
READS_fl = flTforw[m][aa];
if(!TV_switch[aa])
READS_fl = Ledge[aa]*Dim[aa]-READS_fl;
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
}
mm = INDEX[Tforw[m][0]][Tforw[m][1]][Tforw[m][2]][0];
READS_fl =THD_get_voxel(insetFA, mm, 0); // FA
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
READS_fl =THD_get_voxel(insetMD, mm, 0); // MD
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
READS_fl =THD_get_voxel(insetL1, mm, 0); // L1
fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
// count this voxel for having a tract
INDEX[Tforw[m][0]][Tforw[m][1]][Tforw[m][2]][3]+= 1;
}
ave_tract_len+= totlen;
ave_tract_len_phys+= totlen_phys;
Numtract+=1;
}
}
}
fclose(fout0);
if (get_tract_verb()) {
INFO_message("Done tracking, have %d tracks.", tb->N_tracts);
Show_Taylor_Bundle(tb, NULL, 3);
}
if (!Write_Bundle(tb,prefix,mode)) {
ERROR_message("Failed to write the bundle");
}
// **************************************************************
// **************************************************************
// Some simple stats on ROIs and outputs
// **************************************************************
// **************************************************************
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ ) {
if( INDEX[i][j][k][3]>=1 ) {
tempMD = THD_get_voxel(insetMD,INDEX[i][j][k][0],0);
tempFA = THD_get_voxel(insetFA,INDEX[i][j][k][0],0);
tempL1 = THD_get_voxel(insetL1,INDEX[i][j][k][0],0);
tempRD = 0.5*(3*tempMD-tempL1);
roi3_mu_MD+= tempMD;
roi3_mu_FA+= tempFA;
roi3_mu_L1+= tempL1;
roi3_mu_RD+= tempRD;
roi3_sd_MD+= tempMD*tempMD;
roi3_sd_FA+= tempFA*tempFA;
roi3_sd_L1+= tempL1*tempL1;
roi3_sd_RD+= tempRD*tempRD;
roi3_ct+= 1;
}
}
if(roi3_ct > 0 ) { // !!!! make into afni file
roi3_mu_MD/= (float) roi3_ct;
roi3_mu_FA/= (float) roi3_ct;
roi3_mu_L1/= (float) roi3_ct;
roi3_mu_RD/= (float) roi3_ct;
roi3_sd_MD-= roi3_ct*roi3_mu_MD*roi3_mu_MD;
roi3_sd_FA-= roi3_ct*roi3_mu_FA*roi3_mu_FA;
roi3_sd_L1-= roi3_ct*roi3_mu_L1*roi3_mu_L1;
roi3_sd_RD-= roi3_ct*roi3_mu_RD*roi3_mu_RD;
roi3_sd_MD/= (float) roi3_ct-1;
roi3_sd_FA/= (float) roi3_ct-1;
roi3_sd_L1/= (float) roi3_ct-1;
roi3_sd_RD/= (float) roi3_ct-1;
roi3_sd_MD = sqrt(roi3_sd_MD);
roi3_sd_FA = sqrt(roi3_sd_FA);
roi3_sd_L1 = sqrt(roi3_sd_L1);
roi3_sd_RD = sqrt(roi3_sd_RD);
sprintf(OUT_tracstat,"%s.stats",prefix);
if( (fout0 = fopen(OUT_tracstat, "w")) == NULL) {
fprintf(stderr, "Error opening file %s.",OUT_tracstat);
exit(19);
}
fprintf(fout0,"%d\t%d\n",Numtract,roi3_ct);
fprintf(fout0,"%.3f\t%.3f\n",ave_tract_len/Numtract,
ave_tract_len_phys/Numtract);
// as usual, these next values would have to be divided by the
// bval to get their actual value in standard phys units
fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_FA,roi3_sd_FA);
fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_MD,roi3_sd_MD);
fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_RD,roi3_sd_RD);
fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_L1,roi3_sd_L1);
fclose(fout0);
sprintf(prefix_map,"%s_MAP",prefix);
sprintf(prefix_mask,"%s_MASK",prefix);
outsetMAP = EDIT_empty_copy( mset1 ) ;
EDIT_dset_items( outsetMAP ,
ADN_datum_all , MRI_short ,
ADN_prefix , prefix_map ,
ADN_none ) ;
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMAP)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outsetMAP));
outsetMASK = EDIT_empty_copy( mset1 ) ;
EDIT_dset_items( outsetMASK ,
ADN_datum_all , MRI_byte ,
ADN_prefix , prefix_mask ,
ADN_none ) ;
if(!THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMASK)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outsetMASK));
m=0;
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ ) {
temp_arr[m]=INDEX[i][j][k][3];
if(temp_arr[m]>0.5)
temp_byte[m]=1;
else
temp_byte[m]=0;
m++;
}
// re-orient the data as original inputs
// (this function copies the pointer)
EDIT_substitute_brick(outsetMAP, 0, MRI_short, temp_arr);
temp_arr=NULL;
if(TV_switch[0] || TV_switch[1] || TV_switch[2]) {
dsetn = r_new_resam_dset(outsetMAP, NULL, 0.0, 0.0, 0.0,
header1.voxel_order, RESAM_NN_TYPE,
NULL, 1, 0);
DSET_delete(outsetMAP);
outsetMAP=dsetn;
dsetn=NULL;
}
EDIT_dset_items( outsetMAP ,
ADN_prefix , prefix_map ,
ADN_none ) ;
THD_load_statistics(outsetMAP );
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMAP)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outsetMAP));
tross_Make_History( "3dTrackID" , argc , argv , outsetMAP) ;
THD_write_3dim_dataset(NULL, NULL, outsetMAP, True);
// re-orient the data as original inputs
EDIT_substitute_brick(outsetMASK, 0, MRI_byte, temp_byte);
temp_byte=NULL;
if(TV_switch[0] || TV_switch[1] || TV_switch[2]) {
dsetn = r_new_resam_dset(outsetMASK, NULL, 0.0, 0.0, 0.0,
header1.voxel_order, RESAM_NN_TYPE,
NULL, 1, 0);
DSET_delete(outsetMASK);
outsetMASK=dsetn;
dsetn=NULL;
}
EDIT_dset_items( outsetMASK ,
ADN_prefix , prefix_mask ,
ADN_none ) ;
THD_load_statistics(outsetMASK);
if(!THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMASK)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outsetMASK));
tross_Make_History( "3dTrackID" , argc , argv , outsetMASK) ;
THD_write_3dim_dataset(NULL, NULL, outsetMASK, True);
INFO_message("Number of tracts found = %d",Numtract) ;
}
else
INFO_message("\n No Tracts Found!!!\n");
// ************************************************************
// ************************************************************
// Freeing
// ************************************************************
// ************************************************************
// !!! need to free afni-sets?
DSET_delete(insetFA);
DSET_delete(insetMD);
DSET_delete(insetL1);
DSET_delete(insetV1);
DSET_delete(insetEXTRA);
//DSET_delete(outsetMAP);
//DSET_delete(outsetMASK);
DSET_delete(mset2);
DSET_delete(mset1);
free(prefix);
free(insetV1);
free(insetFA);
free(mset1);
free(mset2);
free(insetEXTRA);
free(ROI1);
free(ROI2);
free(temp_byte);
for( i=0 ; i<ArrMax ; i++) {
free(Tforw[i]);
free(Tback[i]);
free(flTforw[i]);
free(flTback[i]);
}
free(Tforw);
free(Tback);
free(flTforw);
free(flTback);
for( i=0 ; i<Dim[0] ; i++)
for( j=0 ; j<Dim[1] ; j++)
for( k=0 ; k<Dim[2] ; k++)
free(coorded[i][j][k]);
for( i=0 ; i<Dim[0] ; i++)
for( j=0 ; j<Dim[1] ; j++)
free(coorded[i][j]);
for( i=0 ; i<Dim[0] ; i++)
free(coorded[i]);
free(coorded);
for( i=0 ; i<Dim[0] ; i++)
for( j=0 ; j<Dim[1] ; j++)
for( k=0 ; k<Dim[2] ; k++)
free(INDEX[i][j][k]);
for( i=0 ; i<Dim[0] ; i++)
for( j=0 ; j<Dim[1] ; j++)
free(INDEX[i][j]);
for( i=0 ; i<Dim[0] ; i++)
free(INDEX[i]);
free(INDEX);
free(temp_arr); // need to free
for( i=0 ; i<2*ArrMax ; i++)
free(Ttot[i]);
free(Ttot);
//free(mode);
return 0;
}
int main( int argc , char *argv[] )
{
int iarg , nerr=0 , nvals,nvox , nx,ny,nz , ii,jj,kk ;
char *prefix="LSSout" , *save1D=NULL , nbuf[256] ;
THD_3dim_dataset *inset=NULL , *outset ;
MRI_vectim *inset_mrv=NULL ;
byte *mask=NULL ; int mask_nx=0,mask_ny=0,mask_nz=0, automask=0, nmask=0 ;
NI_element *nelmat=NULL ; char *matname=NULL ;
char *cgl ;
int Ngoodlist,*goodlist=NULL , nfull , ncmat,ntime ;
NI_int_array *giar ; NI_str_array *gsar ; NI_float_array *gfar ;
MRI_IMAGE *imX, *imA, *imC, *imS ; float *Xar, *Sar ; MRI_IMARR *imar ;
int nS ; float *ss , *oo , *fv , sum ; int nvec , iv ;
int nbstim , nst=0 , jst_bot,jst_top ; char *stlab="LSS" ;
int nodata=1 ;
/*--- help me if you can ---*/
if( argc < 2 || strcasecmp(argv[1],"-HELP") == 0 ) LSS_help() ;
/*--- bureaucratic startup ---*/
PRINT_VERSION("3dLSS"); mainENTRY("3dLSS main"); machdep();
AFNI_logger("3dLSS",argc,argv); AUTHOR("RWCox");
(void)COX_clock_time() ;
/**------- scan command line --------**/
iarg = 1 ;
while( iarg < argc ){
if( strcmp(argv[iarg],"-verb") == 0 ){ verb++ ; iarg++ ; continue ; }
if( strcmp(argv[iarg],"-VERB") == 0 ){ verb+=2 ; iarg++ ; continue ; }
/**========== -mask ==========**/
if( strcasecmp(argv[iarg],"-mask") == 0 ){
THD_3dim_dataset *mset ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '-mask'") ;
if( mask != NULL || automask ) ERROR_exit("Can't have two mask inputs") ;
mset = THD_open_dataset( argv[iarg] ) ;
CHECK_OPEN_ERROR(mset,argv[iarg]) ;
DSET_load(mset) ; CHECK_LOAD_ERROR(mset) ;
mask_nx = DSET_NX(mset); mask_ny = DSET_NY(mset); mask_nz = DSET_NZ(mset);
mask = THD_makemask( mset , 0 , 0.5f, 0.0f ) ; DSET_delete(mset) ;
if( mask == NULL ) ERROR_exit("Can't make mask from dataset '%.33s'",argv[iarg]) ;
nmask = THD_countmask( mask_nx*mask_ny*mask_nz , mask ) ;
if( verb || nmask < 1 ) INFO_message("Number of voxels in mask = %d",nmask) ;
if( nmask < 1 ) ERROR_exit("Mask is too small to process") ;
iarg++ ; continue ;
}
if( strcasecmp(argv[iarg],"-automask") == 0 ){
if( mask != NULL ) ERROR_exit("Can't have -automask and -mask") ;
automask = 1 ; iarg++ ; continue ;
}
/**========== -matrix ==========**/
if( strcasecmp(argv[iarg],"-matrix") == 0 ){
if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]) ;
if( nelmat != NULL ) ERROR_exit("More than 1 -matrix option!?");
nelmat = NI_read_element_fromfile( argv[iarg] ) ; /* read NIML file */
matname = argv[iarg];
if( nelmat == NULL || nelmat->type != NI_ELEMENT_TYPE )
ERROR_exit("Can't process -matrix file '%s'!?",matname) ;
iarg++ ; continue ;
}
/**========== -nodata ===========**/
if( strcasecmp(argv[iarg],"-nodata") == 0 ){
nodata = 1 ; iarg++ ; continue ;
}
/**========== -input ==========**/
if( strcasecmp(argv[iarg],"-input") == 0 ){
if( inset != NULL ) ERROR_exit("Can't have two -input options!?") ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]) ;
inset = THD_open_dataset( argv[iarg] ) ;
CHECK_OPEN_ERROR(inset,argv[iarg]) ;
nodata = 0 ; iarg++ ; continue ;
}
/**========== -prefix =========**/
if( strcasecmp(argv[iarg],"-prefix") == 0 ){
if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]) ;
prefix = strdup(argv[iarg]) ;
if( !THD_filename_ok(prefix) ) ERROR_exit("Illegal string after %s",argv[iarg-1]) ;
if( verb && strcmp(prefix,"NULL") == 0 )
INFO_message("-prefix NULL ==> no dataset will be written") ;
iarg++ ; continue ;
}
/**========== -save1D =========**/
if( strcasecmp(argv[iarg],"-save1D") == 0 ){
if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]) ;
save1D = strdup(argv[iarg]) ;
if( !THD_filename_ok(save1D) ) ERROR_exit("Illegal string after %s",argv[iarg-1]) ;
iarg++ ; continue ;
}
/***** Loser User *****/
ERROR_message("Unknown option: %s",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
} /* end of loop over options */
/*----- check for errors -----*/
if( nelmat == NULL ){ ERROR_message("No -matrix option!?") ; nerr++ ; }
if( nerr > 0 ) ERROR_exit("Can't continue without these inputs!") ;
if( inset != NULL ){
nvals = DSET_NVALS(inset) ; nvox = DSET_NVOX(inset) ;
nx = DSET_NX(inset) ; ny = DSET_NY(inset) ; nz = DSET_NZ(inset) ;
} else {
automask = nvals = 0 ;
nvox = nx = ny = nz = nodata = 1 ; /* nodata */
mask = NULL ;
}
/*----- masque -----*/
if( mask != NULL ){ /* check -mask option for compatibility */
if( mask_nx != nx || mask_ny != ny || mask_nz != nz )
ERROR_exit("-mask dataset grid doesn't match input dataset :-(") ;
} else if( automask ){ /* create a mask from input dataset */
mask = THD_automask( inset ) ;
if( mask == NULL )
ERROR_message("Can't create -automask from input dataset :-(") ;
nmask = THD_countmask( nvox , mask ) ;
if( verb || nmask < 1 )
INFO_message("Number of voxels in automask = %d (out of %d = %.1f%%)",
nmask, nvox, (100.0f*nmask)/nvox ) ;
if( nmask < 1 ) ERROR_exit("Automask is too small to process") ;
} else if( !nodata ) { /* create a 'mask' for all voxels */
if( verb )
INFO_message("No mask ==> computing for all %d voxels",nvox) ;
mask = (byte *)malloc(sizeof(byte)*nvox) ; nmask = nvox ;
memset( mask , 1 , sizeof(byte)*nvox ) ;
}
/*----- get matrix info from the NIML element -----*/
if( verb ) INFO_message("extracting matrix info") ;
ncmat = nelmat->vec_num ; /* number of columns */
ntime = nelmat->vec_len ; /* number of rows */
if( ntime < ncmat+2 )
ERROR_exit("Matrix has too many columns (%d) for number of rows (%d)",ncmat,ntime) ;
/*--- number of rows in the full matrix (without censoring) ---*/
cgl = NI_get_attribute( nelmat , "NRowFull" ) ;
if( cgl == NULL ) ERROR_exit("Matrix is missing 'NRowFull' attribute!") ;
nfull = (int)strtod(cgl,NULL) ;
if( nodata ){
nvals = nfull ;
} else if( nvals != nfull ){
ERROR_exit("-input dataset has %d time points, but matrix indicates %d",
nvals , nfull ) ;
}
/*--- the goodlist = mapping from matrix row index to time index
(which allows for possible time point censoring) ---*/
cgl = NI_get_attribute( nelmat , "GoodList" ) ;
if( cgl == NULL ) ERROR_exit("Matrix is missing 'GoodList' attribute!") ;
giar = NI_decode_int_list( cgl , ";," ) ;
if( giar == NULL || giar->num < ntime )
ERROR_exit("Matrix 'GoodList' badly formatted?!") ;
Ngoodlist = giar->num ; goodlist = giar->ar ;
if( Ngoodlist != ntime )
ERROR_exit("Matrix 'GoodList' incorrect length?!") ;
else if( verb > 1 && Ngoodlist < nfull )
ININFO_message("censoring reduces time series length from %d to %d",nfull,Ngoodlist) ;
/*--- extract the matrix from the NIML element ---*/
imX = mri_new( ntime , ncmat , MRI_float ) ;
Xar = MRI_FLOAT_PTR(imX) ;
if( nelmat->vec_typ[0] == NI_FLOAT ){ /* from 3dDeconvolve_f */
float *cd ;
for( jj=0 ; jj < ncmat ; jj++ ){
cd = (float *)nelmat->vec[jj] ;
for( ii=0 ; ii < ntime ; ii++ ) Xar[ii+jj*ntime] = cd[ii] ;
}
} else if( nelmat->vec_typ[0] == NI_DOUBLE ){ /* from 3dDeconvolve */
double *cd ;
for( jj=0 ; jj < ncmat ; jj++ ){
cd = (double *)nelmat->vec[jj] ;
for( ii=0 ; ii < ntime ; ii++ ) Xar[ii+jj*ntime] = cd[ii] ;
}
} else {
ERROR_exit("Matrix file stored with illegal data type!?") ;
}
/*--- find the stim_times_IM option ---*/
cgl = NI_get_attribute( nelmat , "BasisNstim") ;
if( cgl == NULL ) ERROR_exit("Matrix doesn't have 'BasisNstim' attribute!") ;
nbstim = (int)strtod(cgl,NULL) ;
if( nbstim <= 0 ) ERROR_exit("Matrix 'BasisNstim' attribute is %d",nbstim) ;
for( jj=1 ; jj <= nbstim ; jj++ ){
sprintf(nbuf,"BasisOption_%06d",jj) ;
cgl = NI_get_attribute( nelmat , nbuf ) ;
if( cgl == NULL || strcmp(cgl,"-stim_times_IM") != 0 ) continue ;
if( nst > 0 )
ERROR_exit("More than one -stim_times_IM option was found in the matrix") ;
nst = jj ;
sprintf(nbuf,"BasisColumns_%06d",jj) ;
cgl = NI_get_attribute( nelmat , nbuf ) ;
if( cgl == NULL )
ERROR_exit("Matrix doesn't have %s attribute!",nbuf) ;
jst_bot = jst_top = -1 ;
sscanf(cgl,"%d:%d",&jst_bot,&jst_top) ;
if( jst_bot < 0 || jst_top < 0 )
ERROR_exit("Can't decode matrix attribute %s",nbuf) ;
if( jst_bot == jst_top )
ERROR_exit("Matrix attribute %s shows only 1 column for -stim_time_IM:\n"
" -->> 3dLSS is meant to be used when more than one stimulus\n"
" time was given, and then it computes the response beta\n"
" for each stim time separately. If you have only one\n"
" stim time with -stim_times_IM, you can use the output\n"
" dataset from 3dDeconvolve (or 3dREMLfit) to get that\n"
" single beta directly.\n" , nbuf ) ;
if( jst_bot >= jst_top || jst_top >= ncmat )
ERROR_exit("Matrix attribute %s has illegal value: %d:%d (ncmat=%d)",nbuf,jst_bot,jst_top,ncmat) ;
sprintf(nbuf,"BasisName_%06d",jj) ;
cgl = NI_get_attribute( nelmat , nbuf ) ;
if( cgl != NULL ) stlab = strdup(cgl) ;
if( verb > 1 )
ININFO_message("-stim_times_IM at stim #%d; cols %d..%d",jj,jst_bot,jst_top) ;
}
if( nst == 0 )
ERROR_exit("Matrix doesn't have any -stim_times_IM options inside :-(") ;
/*--- mangle matrix to segregate IM regressors from the rest ---*/
if( verb ) INFO_message("setting up LSS vectors") ;
imar = LSS_mangle_matrix( imX , jst_bot , jst_top ) ;
if( imar == NULL )
ERROR_exit("Can't compute LSS 'mangled' matrix :-(") ;
/*--- setup for LSS computations ---*/
imA = IMARR_SUBIM(imar,0) ;
imC = IMARR_SUBIM(imar,1) ;
imS = LSS_setup( imA , imC ) ; DESTROY_IMARR(imar) ;
if( imS == NULL )
ERROR_exit("Can't complete LSS setup :-((") ;
nS = imS->ny ; Sar = MRI_FLOAT_PTR(imS) ;
if( save1D != NULL ){
mri_write_1D( save1D , imS ) ;
if( verb ) ININFO_message("saved LSS vectors into file %s",save1D) ;
} else if( nodata ){
WARNING_message("-nodata used but -save1D not used ==> you get no output!") ;
}
if( nodata || strcmp(prefix,"NULL") == 0 ){
INFO_message("3dLSS ends since prefix is 'NULL' or -nodata was used") ;
exit(0) ;
}
/*----- create output dataset -----*/
if( verb ) INFO_message("creating output datset in memory") ;
outset = EDIT_empty_copy(inset) ;
EDIT_dset_items( outset ,
ADN_prefix , prefix ,
ADN_datum_all , MRI_float ,
ADN_brick_fac , NULL ,
ADN_nvals , nS ,
ADN_ntt , nS ,
ADN_none ) ;
tross_Copy_History( inset , outset ) ;
tross_Make_History( "3dLSS" , argc,argv , outset ) ;
for( kk=0 ; kk < nS ; kk++ ){
EDIT_substitute_brick( outset , kk , MRI_float , NULL ) ;
sprintf(nbuf,"%s#%03d",stlab,kk) ;
EDIT_BRICK_LABEL( outset , kk , nbuf ) ;
}
/*----- convert input dataset to vectim -----*/
if( verb ) INFO_message("loading input dataset into memory") ;
DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ;
inset_mrv = THD_dset_to_vectim( inset , mask , 0 ) ;
DSET_unload(inset) ;
/*----- compute dot products, store results -----*/
if( verb ) INFO_message("computing away, me buckos!") ;
nvec = inset_mrv->nvec ;
for( kk=0 ; kk < nS ; kk++ ){
ss = Sar + kk*ntime ;
oo = DSET_ARRAY(outset,kk) ;
for( iv=0 ; iv < nvec ; iv++ ){
fv = VECTIM_PTR(inset_mrv,iv) ;
for( sum=0.0f,ii=0 ; ii < ntime ; ii++ )
sum += ss[ii] * fv[goodlist[ii]] ;
oo[inset_mrv->ivec[iv]] = sum ;
}
}
DSET_write(outset) ; WROTE_DSET(outset) ;
/*-------- Hasta la vista, baby --------*/
if( verb )
INFO_message("3dLSS finished: total CPU=%.2f Elapsed=%.2f",
COX_cpu_time() , COX_clock_time() ) ;
exit(0) ;
}
/*!
\brief parse the arguments for SurfSmooth program
\param argv (char *)
\param argc (int)
\return Opt (SUMA_GETPATCH_OPTIONS *) options structure.
To free it, use
SUMA_free(Opt->outfile);
SUMA_free(Opt->histnote);
SUMA_free(Opt);
*/
SUMA_KUBATEST_OPTIONS *SUMA_SampBias_ParseInput(
char *argv[], int argc, SUMA_KUBATEST_OPTIONS* Opt,
SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_SampBias_ParseInput"};
int kar, i, ind;
char *outprefix;
SUMA_Boolean brk = NOPE;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
kar = 1;
brk = NOPE;
Opt->debug = 0;
Opt->plimit = 50;
Opt->dlimit = 1000;
Opt->outfile = NULL;
Opt->prefix = NULL;
Opt->segdo = NULL;
Opt->ps=ps;
while (kar < argc)
{ /* loop accross command ine options */
/*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0)
{
ps->hverb = strlen(argv[kar])>3?2:1;
usage_SUMA_SampBias(ps);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-plimit") == 0))
{
kar++;
if (kar >= argc)
{
fprintf (SUMA_STDERR, "need argument after -plimit \n");
exit (1);
}
Opt->plimit = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-dlimit") == 0))
{
kar++;
if (kar >= argc)
{
fprintf (SUMA_STDERR, "need argument after -dlimit \n");
exit (1);
}
Opt->dlimit = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-out") == 0))
{
kar++;
if (kar >= argc)
{
fprintf (SUMA_STDERR, "need argument after -out \n");
exit (1);
}
Opt->outfile = SUMA_copy_string(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-segdo") == 0))
{
kar++;
if (kar >= argc)
{
fprintf (SUMA_STDERR, "need argument after -segdo \n");
exit (1);
}
Opt->segdo = SUMA_Extension(argv[kar], ".1D.do", NOPE);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0))
{
kar++;
if (kar >= argc)
{
fprintf (SUMA_STDERR, "need argument after -prefix \n");
exit (1);
}
Opt->prefix = SUMA_copy_string(argv[kar]);
brk = YUP;
}
if (!brk && !ps->arg_checked[kar])
{
SUMA_S_Errv("Option %s not understood. Try -help for usage\n",
argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else
{
brk = NOPE;
kar ++;
}
}
/* sanity checks */
if (Opt->outfile == NULL && Opt->prefix == NULL)
{
SUMA_SL_Err("No outfile, or prefix specified.");
exit(1);
}
if (Opt->outfile) {
if (!THD_ok_overwrite() && SUMA_filexists(Opt->outfile)) {
SUMA_S_Errv("Outfile %s already exists\n", Opt->outfile);
exit(1);
}
}
if (Opt->prefix) {
SUMA_DSET_NAME_CHECK(Opt->prefix);
}
Opt->histnote = SUMA_HistString (NULL, argc, argv, NULL);
SUMA_RETURN (Opt);
}
SUMA_GENERIC_PROG_OPTIONS_STRUCT *SUMA_SurfToSurf_ParseInput(
char *argv[], int argc, SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_BrainWrap_ParseInput"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt=NULL;
int kar;
SUMA_Boolean brk, accepting_out;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = SUMA_Alloc_Generic_Prog_Options_Struct();
kar = 1;
brk = NOPE;
Opt->in_1D = NULL;
Opt->NodeDbg = -1;
Opt->debug = 0;
Opt->NearestNode = 0;
Opt->NearestTriangle = 0;
Opt->DistanceToMesh = 0;
Opt->ProjectionOnMesh = 0;
Opt->NearestNodeCoords = 0;
Opt->Data = 0;
Opt->in_name = NULL;
Opt->out_prefix = NULL;
Opt->fix_winding = 0;
Opt->iopt = 0;
Opt->oform = SUMA_NO_DSET_FORMAT;
accepting_out = NOPE;
while (kar < argc) { /* loop accross command ine options */
/*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
if (!brk && accepting_out) {
/* make sure you have not begun with new options */
if (*(argv[kar]) == '-') accepting_out = NOPE;
}
if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
usage_SurfToSurf(ps, strlen(argv[kar]) > 3 ? 2:1);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-debug") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -debug \n");
exit (1);
}
Opt->debug = atoi(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-node_debug") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -node_debug \n");
exit (1);
}
Opt->NodeDbg = atoi(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-node_indices") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a parameter after -node_indices \n");
exit (1);
}
Opt->in_nodeindices = argv[++kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-closest_possible") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -closest_possible \n");
exit (1);
}
Opt->iopt = atoi(argv[++kar]);
if (Opt->iopt != 0 && Opt->iopt != 1 && Opt->iopt != 2 &&
Opt->iopt != 3) {
SUMA_S_Errv("Must choose from 0, 1, 2, or 3 for -closest_possible."
" Have %d\n",
Opt->iopt);
exit (1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-output_params") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR,
"need at least one parameter after output_params \n");
exit (1);
}
accepting_out = YUP;
brk = YUP;
}
if (!brk && accepting_out && (strcmp(argv[kar], "NearestNode") == 0)) {
if (Opt->NearestNode < 1) Opt->NearestNode = 1;
brk = YUP;
}
if (!brk && accepting_out &&
(strcmp(argv[kar], "NearestTriangleNodes") == 0)) {
if (Opt->NearestNode < 3) Opt->NearestNode = 3;
brk = YUP;
}
if (!brk && accepting_out && (strcmp(argv[kar], "NearestTriangle") == 0)) {
if (Opt->NearestTriangle < 1) Opt->NearestTriangle = 1;
brk = YUP;
}
if (!brk && accepting_out && (strcmp(argv[kar], "DistanceToSurf") == 0)) {
Opt->DistanceToMesh = 1;
brk = YUP;
}
if (!brk && accepting_out &&
(strcmp(argv[kar], "ProjectionOnSurf") == 0)) {
Opt->ProjectionOnMesh = 1;
brk = YUP;
}
if (!brk && accepting_out &&
(strcmp(argv[kar], "NearestNodeCoords") == 0)) {
Opt->NearestNodeCoords = 1;
brk = YUP;
}
if (!brk && accepting_out &&
(strcmp(argv[kar], "Data") == 0)) {
if (Opt->Data < 0) {
fprintf (SUMA_STDERR,
"Cannot mix parameter Data with -dset option \n");
exit (1);
}
Opt->Data = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-data") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a name after -data \n");
exit (1);
}
++kar;
if (strcmp(argv[kar],"_XYZ_") == 0) {
/* default Opt->in_name = NULL*/
if (Opt->in_name) {
SUMA_SL_Err("Input already specified."
"Do not mix -data and -dset");
exit (1);
}
} else {
Opt->in_name = SUMA_copy_string(argv[kar]);
}
Opt->Data = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-dset") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a name after -dset \n");
exit (1);
}
++kar;
if (strcmp(argv[kar],"_XYZ_") == 0 || Opt->Data > 0) {
/* default Opt->in_name = NULL*/
if (Opt->in_name || Opt->Data > 0) {
SUMA_SL_Err("Input already specified."
"Do not mix -data and -dset."
"Or use parameter DATA with -dset");
exit (1);
}
} else {
Opt->in_name = SUMA_copy_string(argv[kar]);
}
Opt->Data = -1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a name after -prefix \n");
exit (1);
}
Opt->out_prefix = SUMA_RemoveDsetExtension_eng(argv[++kar],
&(Opt->oform));
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-mapfile") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a name after -mapfile \n");
exit (1);
}
Opt->s = SUMA_Extension(argv[++kar],".niml.M2M", NOPE);
if (!SUMA_filexists(Opt->s)) {
SUMA_S_Errv("File %s not found\n"
, Opt->s);
exit(1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-proj_dir") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a name after -proj_dir \n");
exit (1);
}
Opt->in_1D = argv[++kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-make_consistent") == 0))
{
Opt->fix_winding = 1;
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
fprintf (SUMA_STDERR,
"Error %s:\n"
"Option %s not understood. Try -help for usage\n",
FuncName, argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}
/* set default for NearestNode if nothing has been set */
if (Opt->NearestNode < 1) Opt->NearestNode = 3;
if (!Opt->out_prefix) Opt->out_prefix = SUMA_copy_string("SurfToSurf");
if (Opt->in_1D && Opt->s) {
SUMA_S_Err("Cannot use -proj_dir along with -mapfile");
exit(1);
}
SUMA_RETURN(Opt);
}
int main( int argc , char *argv[] )
{
MRI_shindss *shd ;
int ids , nopt , kk ;
char *prefix = "EIC" ;
char *fname=NULL , *buf ;
MRI_vectim *mv ; THD_3dim_dataset *dset ;
/*--- official AFNI startup stuff ---*/
mainENTRY("3dExtractGroupInCorr"); machdep();
AFNI_logger("3dExtractGroupInCorr",argc,argv);
PRINT_VERSION("3dExtractGroupInCorr"); AUTHOR("RW Cox");
/*-- process options --*/
nopt = 1 ;
while( nopt < argc && argv[nopt][0] == '-' ){
if( strcasecmp(argv[nopt],"-prefix") == 0 ){
nopt++ ;
if( strcasecmp(argv[nopt],"NULL") == 0 ) prefix = NULL ;
else prefix = strdup(argv[nopt]) ;
nopt++ ; continue ;
}
ERROR_message("Unknown option: '%s'",argv[nopt]) ;
suggest_best_prog_option(argv[0], argv[nopt]);
exit(1);
}
if( argc < 2 ){ usage_3dExtractGroupInCorr(2) ; exit(0) ; }
/* check for errors */
if( nopt >= argc ) ERROR_exit("No input filename on command line?!") ;
/*-- read input file --*/
fname = strdup(argv[nopt]) ;
if( STRING_HAS_SUFFIX(fname,".data") ){
strcpy(fname+strlen(fname)-5,".niml") ;
WARNING_message("EIC: Replaced '.data' with '.niml' in filename") ;
} else if( STRING_HAS_SUFFIX(fname,".grpincorr") ){
fname = (char *)realloc(fname,strlen(fname)+16) ;
strcat(fname,".niml") ;
INFO_message("EIC: Added '.niml' to end of filename") ;
} else if( STRING_HAS_SUFFIX(fname,".grpincorr.") ){
fname = (char *)realloc(fname,strlen(fname)+16) ;
strcat(fname,"niml") ;
INFO_message("EIC: Added 'niml' to end of filename") ;
}
shd = GRINCOR_read_input( fname ) ;
if( shd == NULL ) ERROR_exit("EIC: Cannot continue after input error") ;
INFO_message("EIC: file opened, contains %d datasets, %d time series, %s bytes",
shd->ndset , shd->nvec , commaized_integer_string(shd->nbytes) ) ;
/*-- process input file --*/
fprintf(stderr,"++ %d datasets: ",shd->ndset) ;
for( ids=0 ; ids < shd->ndset ; ids++ ){
fprintf(stderr,"%d",ids+1) ;
dset = GRINCOR_extract_dataset( shd, ids, prefix ) ; fprintf(stderr,".") ;
DSET_write(dset) ;
DSET_delete(dset) ;
}
fprintf(stderr,"\n") ; exit(0) ;
}
int main(int argc, char *argv[])
{
int CHECK = 0;
int iarg;
char *Fname_input = NULL;
char *Fname_output = NULL;
char *Fname_outputBV = NULL;
char *Fname_bval = NULL;
int opt;
FILE *fin=NULL, *fout=NULL, *finbv=NULL, *foutBV=NULL;
int i,j,k;
int BZER=0,idx=0,idx2=0;
MRI_IMAGE *flim=NULL;
MRI_IMAGE *preREADIN=NULL;
MRI_IMAGE *preREADBVAL=NULL;
float *READIN=NULL;
float *READBVAL=NULL;
float OUT_MATR[MAXGRADS][7]; // b- or g-matrix
float OUT_GRAD[MAXGRADS][4]; // b- or g-matrix
int INV[3] = {1,1,1}; // if needing to switch
int FLAG[MAXGRADS];
float temp;
int YES_B = 0;
int EXTRA_ZEROS=0;
int HAVE_BVAL = 0;
int BVAL_OUT = 0;
int BVAL_OUT_SEP = 0;
float BMAX_REF = 1; // i.e., essentially zero
int IN_FORM = 0; // 0 for row, 1 for col
int OUT_FORM = 1; // 1 for col, 2 for bmatr
int HAVE_BMAX_REF=0 ; // referring to user input value
int count_in=0, count_out=0;
THD_3dim_dataset *dwset=NULL, *dwout=NULL;
int Nbrik = 0;
char *prefix=NULL ;
float **temp_arr=NULL, **temp_grad=NULL;
int Ndwi = 0, dwi=0, Ndwout = 0, Ndwi_final = 0, Ndwout_final = 0;
int Nvox = 0;
int DWI_COMP_FAC = 0;
int ct_dwi = 0;
float MaxDP = 0;
mainENTRY("1dDW_Grad_o_Mat"); machdep();
if (argc == 1) { usage_1dDW_Grad_o_Mat(1); exit(0); }
iarg = 1;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 ||
strcmp(argv[iarg],"-h") == 0 ) {
usage_1dDW_Grad_o_Mat(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
if( strcmp(argv[iarg],"-flip_x") == 0) {
INV[0] = -1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-flip_y") == 0) {
INV[1] = -1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-flip_z") == 0) {
INV[2] = -1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-keep_b0s") == 0) {
YES_B = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-put_zeros_top") == 0) {
EXTRA_ZEROS = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_grad_rows") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_grad_rows'\n") ;
Fname_input = argv[iarg];
count_in++;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_grad_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_grad_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_gmatT_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_matT_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 2;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_gmatA_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_matA_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 3;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_bmatT_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_matT_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 4;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_bmatA_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_matA_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 5;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_grad_rows") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_grad_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 0;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_grad_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_grad_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_gmatT_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_gmatT_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 2;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_gmatA_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_gmatA_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 3;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_bmatT_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_bmatT_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 4;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_bmatA_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_bmatA_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 5;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_bvals") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_bvals'\n") ;
Fname_bval = argv[iarg];
HAVE_BVAL = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-bmax_ref") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-bmax_ref'\n");
BMAX_REF = atof(argv[iarg]);
HAVE_BMAX_REF = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_bval_col") == 0) {
BVAL_OUT = 1;
iarg++ ; continue ;
}
// May,2015
if( strcmp(argv[iarg],"-out_bval_row_sep") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_bval_row_sep'\n") ;
Fname_outputBV = argv[iarg];
BVAL_OUT_SEP = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-proc_dset") == 0 ){ // in DWIs
if( ++iarg >= argc )
ERROR_exit("Need argument after '-proc_dset'") ;
dwset = THD_open_dataset( argv[iarg] ) ;
if( dwset == NULL )
ERROR_exit("Can't open DWI dataset '%s'", argv[iarg]) ;
DSET_load(dwset) ; CHECK_LOAD_ERROR(dwset) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-pref_dset") == 0 ){ // will be output
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-pref_dset'");
prefix = strdup(argv[iarg]) ;
if( !THD_filename_ok(prefix) )
ERROR_exit("Illegal name after '-pref_dset'");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-dwi_comp_fac") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-dwi_comp_fac'\n");
DWI_COMP_FAC = atoi(argv[iarg]);
if (DWI_COMP_FAC <=1)
ERROR_exit("The compression factor after '-dwi_comp_fac'"
"must be >1!");
iarg++ ; continue ;
}
ERROR_message("Bad option '%s'\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * *
if( (Fname_input == NULL) ) {
fprintf(stderr,
"\n\tBad Command-lining! Option '-in_*' requires argument.\n");
exit(1);
}
if( (Fname_output == NULL) ) {
fprintf(stderr,
"\n\tBad Command-lining! Option '-out_*' requires arg.\n");
exit(2);
}
if( count_in > 1 ) {
fprintf(stderr,
"\n\tBad Command-lining! Can't have >1 vec file input.\n");
exit(3);
}
if( count_out > 1 ) {
fprintf(stderr,
"\n\tBad Command-lining! Can't have >1 output file opt.\n");
exit(4);
}
if(YES_B && dwset) {
fprintf(stderr,
"\n** Bad Command-lining! "
"Can't have '-keep_b0s' and '-proc_dset' together.\n");
exit(5);
}
if( !prefix && dwset) {
fprintf(stderr,
"\n** Bad Command-lining! "
"Need an output '-pref_dset' when using '-proc_dset'.\n");
exit(6);
}
if(YES_B && DWI_COMP_FAC) {
fprintf(stderr,
"\n** Bad Command-lining! "
"Can't have '-keep_b0s' and '-dwi_comp_fac' together.\n");
exit(7);
}
if(!HAVE_BVAL && (BVAL_OUT || BVAL_OUT_SEP)) {
fprintf(stderr,
"\n** Bad Command-lining! "
"Can't have ask for outputting bvals with no '-in_bvals FILE'.\n");
exit(8);
}
// ********************************************************************
// ************************* start reading ****************************
// ********************************************************************
flim = mri_read_1D (Fname_input);
if (flim == NULL) {
ERROR_exit("Error reading gradient vector file");
}
if( IN_FORM )
preREADIN = mri_transpose(flim); // effectively *undoes* autotranspose
else
preREADIN = mri_copy(flim);
mri_free(flim);
idx = preREADIN->ny;
if( HAVE_BVAL ) {
flim = mri_read_1D (Fname_bval);
if (flim == NULL) {
ERROR_exit("Error reading b-value file");
}
if( flim->ny == 1)
preREADBVAL = mri_transpose(flim); // effectively *undoes* autotransp
else
preREADBVAL = mri_copy(flim);
mri_free(flim);
idx2 = preREADBVAL->ny;
}
if(idx>= MAXGRADS ) {
printf("Error, too many input grads.\n");
mri_free (preREADIN);
if( HAVE_BVAL ) mri_free (preREADBVAL);
exit(4);
}
if( ( (preREADIN->nx != 3 ) && (preREADIN->ny != 3 )) &&
(preREADIN->nx != 6 ) )
printf("Probably an error, "
"because there aren't 3 or 6 numbers in columns!\n");
if( HAVE_BVAL && ( idx != idx2 ) ) {
printf("Error, because the number of bvecs (%d)\n"
"and bvals (%d) don't appear to match!\n", idx, idx2);
mri_free (preREADIN);
mri_free (preREADBVAL);
exit(3);
}
if(dwset) {
Nbrik = DSET_NVALS(dwset);
if( idx != Nbrik ) {
fprintf(stderr,
"\n** ERROR: the number of bvecs (%d) does not match the "
"number of briks in '-proc_dset' (%d).\n", idx, Nbrik);
exit(4);
}
}
READIN = MRI_FLOAT_PTR( preREADIN );
if( HAVE_BVAL )
READBVAL = MRI_FLOAT_PTR( preREADBVAL );
// 0 is grad row;
// 1 is grad col;
// 2 is gmatrRow col T;
// 3 is gmatrDiag col A;
// 4 is bmatrRow col T;
// 5 is bmatrDiag col A;
//if( IN_FORM == 0 ) // grad rows, no binfo
// for( i=0; i<idx ; i++ )
// for ( j=0; j<3 ; j++ )
// OUT_GRAD[i][j+1] = *(READIN +j*idx +i) ;
//else
if ( IN_FORM <= 1 ) // grad cols, no binfo
for( i=0; i<idx ; i++ )
for ( j=0; j<3 ; j++ )
OUT_GRAD[i][j+1] = *(READIN + 3*i+j);
// A/row/3dDWItoDT: Bxx, Byy, Bzz, Bxy, Bxz, Byz
// T/diag/TORTOISE: b_xx 2b_xy 2b_xz b_yy 2b_yz b_zz
else if ( (IN_FORM == 3) || (IN_FORM ==5 ) ) { // diag matr
for( i=0; i<idx ; i++ ) {
for( j=0; j<3 ; j++ ) {
OUT_MATR[i][j+1] = *(READIN+6*i+j);
OUT_MATR[i][3+j+1] = *(READIN+6*i+3+j);
}
for( j=0; j<3 ; j++ )
if(OUT_MATR[i][j] < 0 )
CHECK++;
}
if(CHECK > 0)
INFO_message("Warning: you *said* you input a mat'T',"
" but the matr diagonals don't appear to be uniformly"
" positive. If input cols 0, 3 and 5 are positive,"
" then you might have meant mat'A'?");
}
else if ( (IN_FORM ==2 ) || (IN_FORM ==4 ) ) { // row matr
CHECK = 0;
for( i=0; i<idx ; i++ ) {
OUT_MATR[i][1] = *(READIN +6*i);
OUT_MATR[i][2] = *(READIN +6*i+3);
OUT_MATR[i][3] = *(READIN +6*i+5);
OUT_MATR[i][4] = *(READIN +6*i+1)/2.;
OUT_MATR[i][5] = *(READIN +6*i+2)/2.;
OUT_MATR[i][6] = *(READIN +6*i+4)/2.;
}
for( i=0; i<idx ; i++ )
for( j=0; j<3 ; j++ )
if(OUT_MATR[i][j] < 0 )
CHECK++;
if(CHECK > 0)
INFO_message("Warning: you *said* you input a mat'A',"
" but the matr diagonals don't appear to be uniformly"
" positive. If input cols 0, 1 and 2 are positive,"
" then you might have meant mat'T'?");
}
else{
fprintf(stderr, "Coding error with format number (%d), not allowed.\n",
IN_FORM);
exit(2);
}
// get bval info
if( ( (IN_FORM ==4 ) || (IN_FORM ==5 ) ) ) { //bval
for( i=0; i<idx ; i++ ) {
OUT_MATR[i][0] = OUT_GRAD[i][0] =
OUT_MATR[i][1] + OUT_MATR[i][2] + OUT_MATR[i][3];
if( OUT_MATR[i][0] > 0.000001)
for( j=1 ; j<7 ; j++ )
OUT_MATR[i][j]/= OUT_MATR[i][0];
}
}
else if ( HAVE_BVAL )
for( i=0; i<idx ; i++ ) {
OUT_MATR[i][0] = OUT_GRAD[i][0] = *(READBVAL + i);
}
else if ( OUT_FORM > 3 || BVAL_OUT || BVAL_OUT_SEP || HAVE_BMAX_REF ) {
fprintf(stderr, "ERROR: you asked for b-value dependent output, "
"but gave me no bvals to work with.\n");
exit(2);
}
// * * * ** * * * * * * * * ** ** * * ** * * ** * ** * ** * * *
// at this point, all IN_FORM >1 cases which need bval have led to:
// + grad[0] has bval
// + matr[0] has bval
// + matr file normalized and in diagonal form
// * * * ** * * * * * * * * ** ** * * ** * * ** * ** * ** * * *
for( i=0; i<idx ; i++ )
if( IN_FORM > 1)
j = GradConv_Gsign_from_BmatA( OUT_GRAD[i]+1, OUT_MATR[i]+1);
else
j = GradConv_BmatA_from_Gsign( OUT_MATR[i]+1, OUT_GRAD[i]+1);
// flip if necessary
for( i=0 ; i<idx ; i++) {
for( j=0 ; j<3 ; j++)
OUT_GRAD[i][j+1]*= INV[j];
OUT_MATR[i][4]*= INV[0]*INV[1];
OUT_MATR[i][5]*= INV[0]*INV[2];
OUT_MATR[i][6]*= INV[1]*INV[2];
}
BZER=0;
for( i=0 ; i<idx ; i++) {
if( HAVE_BVAL || (IN_FORM ==4) || (IN_FORM ==5) )
if( OUT_GRAD[i][0] >= BMAX_REF )
FLAG[i] = 1;
else{
if( YES_B )
FLAG[i] = 1;
BZER++;
}
else {
temp = 0.;
for( j=1 ; j<4 ; j++)
temp+= pow(OUT_GRAD[i][j],2);
if( temp > 0.1 )
FLAG[i] = 1;
else{
if( YES_B )
FLAG[i] = 1;
BZER++;
}
}
}
if(YES_B) {
printf("\tChose to *keep* %d b0s,\tas well as \t%d grads\n",
BZER,idx-BZER);
BZER=0;
}
else {
printf("\tGetting rid of %d b0s,\tleaving the %d grads\n",
BZER,idx-BZER);
Ndwi = idx-BZER;
}
Ndwi_final = idx-BZER; // default: all DWIs
if( DWI_COMP_FAC ) {
if( Ndwi % DWI_COMP_FAC != 0 ) {
fprintf(stderr, "\n** ERROR can't compress: "
"Ndwi=%d, and %d/%d has a nonzero remainder (=%d).\n",
Ndwi,Ndwi,DWI_COMP_FAC, Ndwi % DWI_COMP_FAC );
exit(1);
}
else {
Ndwi_final = Ndwi/DWI_COMP_FAC;
INFO_message("You have chosen a compression factor of %d, "
"with %d DWIs,\n"
"\tso that afterward there will be %d DWIs.",
DWI_COMP_FAC, Ndwi, Ndwi_final);
}
}
if(BVAL_OUT_SEP)
if( (foutBV = fopen(Fname_outputBV, "w")) == NULL) {
fprintf(stderr, "\n\nError opening file %s.\n",Fname_outputBV);
exit(1);
}
if( (fout = fopen(Fname_output, "w")) == NULL) {
fprintf(stderr, "\n\nError opening file %s.\n",Fname_output);
exit(1);
}
// 0 is grad row;
// 1 is grad col;
// 2 is gmatrRow col T;
// 3 is gmatrDiag col A;
// 4 is bmatrRow col T;
// 5 is bmatrDiag col A;
if( OUT_FORM>0) {
if( EXTRA_ZEROS ) {
if( BVAL_OUT )
fprintf(fout,"%8d ", 0);
if( BVAL_OUT_SEP )
fprintf(foutBV,"%8d ", 0);
if( OUT_FORM == 1 )
for( k=1 ; k<4 ; k++ )
fprintf(fout,"%11.5f ", 0.0);
else if ( OUT_FORM > 1 ) // bit superfluous at this point
for( k=1 ; k<7 ; k++ )
fprintf(fout,"%11.5f ", 0.0);
fprintf(fout,"\n");
}
ct_dwi = 0;
for(i=0 ; i<idx ; i++){
if(FLAG[i]) {
if( BVAL_OUT )
fprintf(fout,"%8d ", (int) OUT_GRAD[i][0]);
if( BVAL_OUT_SEP )
fprintf(foutBV,"%8d ", (int) OUT_GRAD[i][0]);
if( (OUT_FORM == 4) || (OUT_FORM ==5) )
for( k=1 ; k<7 ; k++ )
OUT_MATR[i][k]*= OUT_MATR[i][0];
if( OUT_FORM == 1 ) // grad col
for( k=1 ; k<4 ; k++ )
fprintf(fout,"%11.5f ", OUT_GRAD[i][k]);
else if( (OUT_FORM == 3) || (OUT_FORM == 5) ) { // gmat
for( k=1 ; k<6 ; k++ )
fprintf(fout,"%11.5f ", OUT_MATR[i][k]);
fprintf(fout,"%11.5f", OUT_MATR[i][k]);
}
else if ( (OUT_FORM == 2 ) || (OUT_FORM ==4)) { // bmat
fprintf(fout,"%11.5f ", OUT_MATR[i][1]);
fprintf(fout,"%11.5f ", 2*OUT_MATR[i][4]);
fprintf(fout,"%11.5f ", 2*OUT_MATR[i][5]);
fprintf(fout,"%11.5f ", OUT_MATR[i][2]);
fprintf(fout,"%11.5f ", 2*OUT_MATR[i][6]);
fprintf(fout,"%11.5f", OUT_MATR[i][3]);
}
fprintf(fout,"\n");
ct_dwi++;
}
if( (ct_dwi == Ndwi_final) && DWI_COMP_FAC ) {
INFO_message("Reached compression level: DWI number %d",
Ndwi_final);
break;
}
}
}
else if(OUT_FORM ==0) {
if(BVAL_OUT)
WARNING_message("Ignoring '-out_bval_col' option, since "
" you are outputting in rows.");
for( k=1 ; k<4 ; k++ ) {
if(EXTRA_ZEROS){
fprintf(fout,"% -11.5f ", 0.0);
if( (k==1) && BVAL_OUT_SEP ) // only output 1 zeroin bval file
fprintf(foutBV,"%8d ", 0);
}
ct_dwi = 0;
for(i=0 ; i<idx ; i++) {
if(FLAG[i]) {
fprintf(fout,"% -11.5f ", OUT_GRAD[i][k]);
if( (k==1) && BVAL_OUT_SEP )// only output 1 zeroin bval file
fprintf(foutBV,"%8d ", (int) OUT_GRAD[i][0]);
ct_dwi++;
}
if( (ct_dwi == Ndwi_final) && DWI_COMP_FAC ) {
INFO_message("Reached compression level: DWI number %d",
Ndwi_final);
break;
}
}
fprintf(fout,"\n");
}
}
fclose(fout);
if( BVAL_OUT_SEP ) {
fprintf(foutBV,"\n");
fclose(foutBV);
}
if(dwset) {
INFO_message("Processing the B0+DWI file now.");
if(!BZER) {
fprintf(stderr, "\n** Error in processing data set: "
"no b=0 values from bvecs/bval info!\n");
exit(5);
}
// FLAG marks where DWIs are if not using '-keep_b0s'!
Nvox = DSET_NVOX(dwset);
Ndwout = Ndwi+1;
temp_arr = calloc( Ndwout,sizeof(temp_arr));
for( i=0 ; i<Ndwout ; i++)
temp_arr[i] = calloc( Nvox,sizeof(float));
temp_grad = calloc( Ndwi,sizeof(temp_grad));
for( i=0 ; i<Ndwi ; i++)
temp_grad[i] = calloc( 3,sizeof(float));
if( (temp_arr == NULL) || (temp_grad == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(123);
}
dwi = 0; // keep track of DWI contraction
for( i=0 ; i<Nbrik ; i++)
if( !FLAG[i] ) // b=0
for( j=0 ; j<Nvox ; j++)
temp_arr[0][j]+= THD_get_voxel(dwset,j,i);
else {
for( j=0 ; j<3 ; j++)
temp_grad[dwi][j]= OUT_GRAD[i][j+1];
dwi++;
for( j=0 ; j<Nvox ; j++)
temp_arr[dwi][j]+= THD_get_voxel(dwset,j,i);
}
if( dwi != Ndwi ) {
fprintf(stderr, "\n** Mismatch in internal DWI counting!\n");
exit(6);
}
// average the values
for( j=0 ; j<Nvox ; j++)
temp_arr[0][j]/= BZER; // can't be zero here.
if( DWI_COMP_FAC ) {
INFO_message("Compressing DWI file");
for( k=1 ; k<DWI_COMP_FAC ; k++)
for( i=0 ; i<Ndwi_final ; i++)
for( j=0 ; j<Nvox ; j++)
temp_arr[1+i][j]+= temp_arr[1+k*Ndwi_final+i][j];
for( i=0 ; i<Ndwi_final ; i++)
for( j=0 ; j<Nvox ; j++)
temp_arr[1+i][j]/= DWI_COMP_FAC;
INFO_message("Checking closeness of compressed gradient values");
MaxDP = GradCloseness(temp_grad, Ndwi, DWI_COMP_FAC);
INFO_message("The max angular difference between matched/compressed\n"
"\tgradients is: %f", MaxDP);
if( MaxDP > 2)
WARNING_message("The max angular difference seem kinda big-- you\n"
" sure about the compression factor?");
}
Ndwout_final = Ndwi_final + 1;
INFO_message("Writing the processed data set.");
dwout = EDIT_empty_copy( dwset );
EDIT_dset_items(dwout,
ADN_nvals, Ndwout_final,
ADN_ntt, 0,
ADN_datum_all, MRI_float ,
ADN_prefix, prefix,
ADN_none );
for( i=0; i<Ndwout_final ; i++) {
EDIT_substitute_brick(dwout, i, MRI_float, temp_arr[i]);
temp_arr[i]=NULL;
}
// if necessary
for( i=Ndwout_final ; i<Ndwout ; i++)
temp_arr[i]=NULL;
THD_load_statistics( dwout );
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(dwout)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(dwout));
tross_Make_History("1dDW_Grad_o_Mat", argc, argv, dwout);
THD_write_3dim_dataset(NULL, NULL, dwout, True);
DSET_delete(dwout);
free(dwout);
DSET_delete(dwset);
free(dwset);
for( i=0 ; i<Ndwout_final ; i++)
free(temp_arr[i]);
free(temp_arr);
}
mri_free(preREADIN);
if( HAVE_BVAL )
mri_free(preREADBVAL);
if(prefix)
free(prefix);
printf("\n\tDone. Check output file '%s' for results",Fname_output);
if(dwset) {
printf("\n\t-> as well as the data_set '%s'",DSET_FILECODE(dwout));
}
if(BVAL_OUT_SEP)
printf("\n\t-> and even the b-value rows '%s'",Fname_outputBV);
printf("\n\n");
exit(0);
}