/*
* for each input dataset name
* open (check dims, etc.)
* dilate (zeropad, make binary, dilate, unpad, apply)
* fill list of bytemask datasets
*
* also, count total volumes
*/
int process_input_dsets(param_t * params)
{
THD_3dim_dataset * dset, * dfirst=NULL;
int iset, nxyz;
ENTRY("process_input_dsets");
if( !params ) ERROR_exit("NULL inputs to PID");
if( params->ndsets <= 0 ) {
ERROR_message("process_input_dsets: no input datasets");
RETURN(1);
}
/* allocate space for dsets array */
params->dsets = (THD_3dim_dataset **)malloc(params->ndsets*
sizeof(THD_3dim_dataset*));
if( !params->dsets ) ERROR_exit("failed to allocate dset pointers");
if( params->verb ) INFO_message("processing %d input datasets...",
params->ndsets);
/* warn user of dilations */
if(params->verb && params->ndsets) {
int pad = needed_padding(¶ms->IND);
INFO_message("padding all datasets by %d (for dilations)", pad);
}
/* process the datasets */
nxyz = 0;
for( iset=0; iset < params->ndsets; iset++ ) {
/* open and verify dataset */
dset = THD_open_dataset(params->inputs[iset]);
if( !dset ) ERROR_exit("failed to open mask dataset '%s'",
params->inputs[iset]);
DSET_load(dset); CHECK_LOAD_ERROR(dset);
if( params->verb>1 ) INFO_message("loaded dset %s, with %d volumes",
DSET_PREFIX(dset), DSET_NVALS(dset));
if( nxyz == 0 ) { /* make an empty copy of the first dataset */
nxyz = DSET_NVOX(dset);
dfirst = EDIT_empty_copy(dset);
}
/* check for consistency in voxels and grid */
if( DSET_NVOX(dset) != nxyz ) ERROR_exit("nvoxel mis-match");
if( ! EQUIV_GRIDS(dset, dfirst) )
WARNING_message("grid from dset %s does not match that of dset %s",
DSET_PREFIX(dset), DSET_PREFIX(dfirst));
/* apply dilations to all volumes, returning bytemask datasets */
params->dsets[iset] = apply_dilations(dset, ¶ms->IND,1,params->verb);
if( ! params->dsets[iset] ) RETURN(1);
}
DSET_delete(dfirst); /* and nuke */
RETURN(0);
}
THD_3dim_dataset *Seg_load_dset_eng( char *set_name, char *view )
{
static char FuncName[]={"Seg_load_dset_eng"};
THD_3dim_dataset *dset=NULL, *sdset=NULL;
int i=0;
byte make_cp=0;
int verb=0;
char sprefix[THD_MAX_PREFIX+10], *stmp=NULL;
SUMA_ENTRY;
dset = THD_open_dataset( set_name );
if( !ISVALID_DSET(dset) ){
fprintf(stderr,"**ERROR: can't open dataset %s\n",set_name) ;
SUMA_RETURN(NULL);
}
DSET_mallocize(dset) ; DSET_load(dset);
for (i=0; i<DSET_NVALS(dset); ++i) {
if (DSET_BRICK_TYPE(dset,i) != MRI_short) {
if (verb) INFO_message("Sub-brick %d in %s not of type short.\n"
"Creating new short copy of dset ",
i, DSET_PREFIX(dset));
make_cp=1; break;
}
}
if (make_cp) {
if (!SUMA_ShortizeDset(&dset, -1.0)) {
SUMA_S_Err("**ERROR: Failed to shortize");
SUMA_RETURN(NULL);
}
}
if (DSET_IS_MASTERED(dset)) {
if (verb) INFO_message("Dset is mastered, making copy...");
stmp = SUMA_ModifyName(set_name, "append", ".cp", NULL);
sdset = dset;
dset = EDIT_full_copy(sdset, stmp);
free(stmp); DSET_delete(sdset); sdset = NULL;
}
if (view) {
if (view) {
if (!strstr(view,"orig"))
EDIT_dset_items(dset,ADN_view_type, VIEW_ORIGINAL_TYPE, ADN_none);
else if (!strstr(view,"acpc"))
EDIT_dset_items(dset,ADN_view_type, VIEW_ACPCALIGNED_TYPE, ADN_none);
else if (!strstr(view,"tlrc"))
EDIT_dset_items(dset ,ADN_view_type, VIEW_TALAIRACH_TYPE, ADN_none);
else SUMA_S_Errv("View of %s is rubbish", view);
}
}
SUMA_RETURN(dset);
}
SEXP R_SUMA_HistString (SEXP SCallingFunc, SEXP Sarg, SEXP Shold) {
char *CallingFunc=NULL;
SEXP Rname = R_NilValue;
char *fname = NULL, *hold=NULL, **arg=NULL, *res=NULL;
int debug=0, nprot=0, narg=0, i= 0;
if (!debug) debug = get_odebug();
if (isNull(SCallingFunc) || isNull(Sarg)) {
ERROR_message("Null input to R_SUMA_HistString");
return(Rname);
}
/* get the executable name */
PROTECT(SCallingFunc = AS_CHARACTER(SCallingFunc)); ++nprot;
fname = R_alloc(strlen(CHAR(STRING_ELT(SCallingFunc,0)))+1, sizeof(char));
strcpy(fname, CHAR(STRING_ELT(SCallingFunc,0)));
if (debug) INFO_message("filename %s\n", fname);
/* get the arg */
PROTECT(Sarg = AS_CHARACTER(Sarg)); ++nprot;
narg = (LENGTH(Sarg));
arg = (char **)calloc(narg+1, sizeof(char *));
if (fname) arg[0] = strdup(fname);
else arg[0] = strdup("UnChevalSansNom");
for (i=1; i<=narg; ++i) {
arg[i] = (char *)calloc(strlen(CHAR(STRING_ELT(Sarg,i-1)))+1,
sizeof(char));
strcpy(arg[i], CHAR(STRING_ELT(Sarg,i-1)));
if (debug) INFO_message("arg %d/%d %s\t", i, narg, arg[i]);
}
/* any old history ? */
if (!isNull(Shold)) {
PROTECT(Shold = AS_CHARACTER(Shold)); ++nprot;
hold = R_alloc(strlen(CHAR(STRING_ELT(Shold,0)))+1, sizeof(char));
strcpy(hold, CHAR(STRING_ELT(Shold,0)));
if (debug) INFO_message("hold %s\n", hold);
}
if (( res = SUMA_HistString (fname, narg+1, arg, hold))) {
PROTECT(Rname = allocVector(STRSXP, 1)); ++nprot;
SET_STRING_ELT(Rname, 0, mkChar(res));
if (debug) INFO_message("hist is %s\n", res);
SUMA_free(res); res=NULL;
} else {
ERROR_message("Call to SUMA_HistString %s failed", fname);
}
for (i=0; i<=narg; ++i) { if (arg[i]) free(arg[i]); } free(arg); arg=NULL;
UNPROTECT(nprot);
return(Rname);
}
SEXP R_SUMA_ParseModifyName(SEXP Sfname, SEXP Swhat, SEXP Sval, SEXP Scwd)
{
SEXP Rname = R_NilValue;
char *fname = NULL, *what=NULL, *val=NULL, *cwd=NULL, *res=NULL;
int debug=0, nprot=0;
if (!debug) debug = get_odebug();
if (isNull(Sfname) || isNull(Swhat) || isNull(Sval)) {
ERROR_message("Null input to R_SUMA_ModifyName");
return(Rname);
}
/* get the filename */
PROTECT(Sfname = AS_CHARACTER(Sfname)); ++nprot;
fname = R_alloc(strlen(CHAR(STRING_ELT(Sfname,0)))+1, sizeof(char));
strcpy(fname, CHAR(STRING_ELT(Sfname,0)));
if (debug) INFO_message("filename %s\n", fname);
/* get the what */
PROTECT(Swhat = AS_CHARACTER(Swhat)); ++nprot;
what = R_alloc(strlen(CHAR(STRING_ELT(Swhat,0)))+1, sizeof(char));
strcpy(what, CHAR(STRING_ELT(Swhat,0)));
if (debug) INFO_message("what %s\n", what);
/* get the val */
PROTECT(Sval = AS_CHARACTER(Sval)); ++nprot;
val = R_alloc(strlen(CHAR(STRING_ELT(Sval,0)))+1, sizeof(char));
strcpy(val, CHAR(STRING_ELT(Sval,0)));
if (debug) INFO_message("val %s\n", val);
/* get the cwd */
if (!isNull(Scwd)) {
PROTECT(Scwd = AS_CHARACTER(Scwd)); ++nprot;
cwd = R_alloc(strlen(CHAR(STRING_ELT(Scwd,0)))+1, sizeof(char));
strcpy(cwd, CHAR(STRING_ELT(Scwd,0)));
if (debug) INFO_message("cwd %s\n", cwd);
}
if (debug) INFO_message("Modifying %s\n", fname);
if ((res = SUMA_ModifyName(fname, what, val, cwd))) {
PROTECT(Rname = allocVector(STRSXP, 1)); ++nprot;
SET_STRING_ELT(Rname, 0, mkChar(res));
SUMA_free(res); res=NULL;
} else {
ERROR_message("Call to SUMA_ModifyName %s %s %s failed", fname, what, val);
}
UNPROTECT(nprot);
return(Rname);
}
int fill_mask(options_t * opts)
{
THD_3dim_dataset * mset;
int nvox;
ENTRY("fill_mask");
if( opts->automask ) {
if( opts->verb ) INFO_message("creating automask...");
opts->mask = THD_automask(opts->inset);
if( ! opts->mask ) {
ERROR_message("failed to apply -automask");
RETURN(1);
}
RETURN(0);
}
if( opts->mask_name ) {
if( opts->verb )
INFO_message("reading mask dset from %s...", opts->mask_name);
mset = THD_open_dataset( opts->mask_name );
if( ! mset ) ERROR_exit("cannot open mask dset '%s'", opts->mask_name);
nvox = DSET_NVOX(opts->inset);
if( DSET_NVOX(mset) != nvox ) {
ERROR_message("mask does not have the same voxel count as input");
RETURN(1);
}
/* fill mask array and mask_nxyz, remove mask dset */
DSET_load(mset); CHECK_LOAD_ERROR(mset);
opts->mask = THD_makemask(mset, 0, 1, 0);
DSET_delete(mset);
if( ! opts->mask ) {
ERROR_message("cannot make mask from '%s'", opts->mask_name);
RETURN(1);
}
if( opts->verb > 1 )
INFO_message("have mask with %d voxels", nvox);
}
RETURN(0);
}
/*
* A hole is defined as a connected set of zero voxels that does
* not reach an edge.
*
* The core functionality was added to libmri.a in THD_mask_fill_holes.
*/
int fill_holes(THD_3dim_dataset * dset, int verb)
{
short * sptr; /* to for filling holes */
byte * bmask; /* computed result */
int nfilled;
int nx, ny, nz, nvox, index, fill=0;
ENTRY("fill_holes");
bmask = THD_makemask(dset, 0, 1, 0); /* copy input as byte mask */
nx = DSET_NX(dset); ny = DSET_NY(dset); nz = DSET_NZ(dset);
nvox = DSET_NVOX(dset);
/* created filled mask */
nfilled = THD_mask_fill_holes(nx,ny,nz, bmask, verb);
if( nfilled < 0 ) { ERROR_message("failed to fill holes"); RETURN(1); }
/* apply to short volume */
sptr = DBLK_ARRAY(dset->dblk, 0);
for( index = 0; index < nvox; index++ )
if( !sptr[index] && bmask[index] ) { fill++; sptr[index] = 1; }
if(verb>2) INFO_message("final check: fill=%d, nfilled=%d", fill, nfilled);
RETURN(0);
}
int main( int argc , char *argv[] )
{
THD_3dim_dataset *dset ; int aa,ll ; char *cpt ; float val ;
if( argc < 2 ){
printf("Usage: 3dSatCheck dataset [...]\n"
"\n"
"Prints the 'raw' initial transient (saturation) check\n"
"value for each dataset on the command line. Round this\n"
"number to the nearest integer to get an estimate of\n"
"how many non-saturated time points start a dataset.\n"
) ;
exit(0) ;
}
for( aa=1 ; aa < argc ; aa++ ){
dset = THD_open_dataset( argv[aa] ) ; if( !ISVALID_DSET(dset) ) continue ;
if( DSET_NVALS(dset) < 9 ) continue ;
DSET_load(dset) ; if( !DSET_LOADED(dset) ) continue ;
val = THD_saturation_check( dset , NULL , 0,0 ) ;
ll = strlen(argv[aa]) ;
cpt = (ll <= 50) ? argv[aa] : argv[aa]+(ll-50) ;
INFO_message("%-50.50s = %.3f",cpt,val) ;
DSET_delete(dset) ;
}
exit(0) ;
}
void AFNI_coord_filer_setup( Three_D_View *im3d )
{
char ename[32] , *eval ; int ic ;
ENTRY("AFNI_coord_filer_setup") ;
if( !IM3D_OPEN(im3d) ) EXRETURN ;
ic = AFNI_controller_index(im3d) ;
if( ic < 0 || ic >= MAX_CONTROLLERS || fpc[ic] != NULL ) EXRETURN ;
sprintf(ename,"AFNI_FILE_COORDS_%c",abet[ic]) ;
eval = my_getenv(ename) ;
if( eval == NULL || *eval == '\0' ){ fpc[ic] = NULL ; EXRETURN ; }
if( strcmp(eval,"-") == 0 || strncmp(eval,"stdout",6) == 0 )
fpc[ic] = stdout ;
else {
fpc[ic] = fopen( eval , "w" ) ;
if( fpc[ic] == NULL ){
ERROR_message("Unable to open file %s from %s",eval,ename) ;
EXRETURN ;
}
}
AFNI_receive_init( im3d , RECEIVE_VIEWPOINT_MASK ,
AFNI_filer_viewpoint_CB ,
im3d , "AFNI_filer_viewpoint_CB" ) ;
INFO_message("Logging [%c] viewpoint changes to '%s'",abet[ic],eval) ;
EXRETURN ;
}
int main( int argc , char *argv[] )
{
int ndset=0 , ii ;
THD_3dim_dataset **dset ;
if( argc < 3 || strcasecmp(argv[1],"-help") == 0 ){
printf(
"** Program 3dConformist reads in a collection of datasets and\n"
" zero pads them to the same size.\n"
"** The output volume size is the smallest region that includes\n"
" all datasets (i.e., the minimal covering box).\n"
"** If the datasets cannot be processed (e.g., different grid\n"
" spacings), then nothing will happen except for error messages.\n"
"** The purpose of this program is to be used in scripts that\n"
" process lots of datasets and needs to make them all conform\n"
" to the same size for collective voxel-wise analyses.\n"
"** The input datasets ARE ALTERED (embiggened)! <<<<<<------******\n"
" Therefore, don't use this program casually.\n"
) ;
exit(0) ;
}
mainENTRY("3dConformist") ; machdep() ; PRINT_VERSION("3dConformist") ;
ndset = argc-1 ;
dset = (THD_3dim_dataset **)malloc(sizeof(THD_3dim_dataset *)*ndset) ;
for( ii=0 ; ii < ndset ; ii++ ){
dset[ii] = THD_open_dataset(argv[ii+1]) ;
CHECK_OPEN_ERROR(dset[ii],argv[ii+1]) ;
}
ii = THD_conformist(ndset,dset,CONFORM_REWRITE,NULL) ;
switch(ii){
default: INFO_message ("3dConformist: Re-wrote %d datasets",ii) ; break ;
case 0: INFO_message ("3dConformist: all datasets matched OK") ; break ;
case -1: ERROR_message("3dConformist: bad input") ; break ;
case -2: ERROR_message("3dConformist: bad inputs") ; break ;
case -3: ERROR_message("3dConformist: can't match grids") ; break ;
}
exit(0) ;
}
int write_results(options_t * opts)
{
FILE * fp;
int c;
ENTRY("write_results");
if( ! opts->result ) {
ERROR_message("no results to write!");
RETURN(1);
}
if( ! opts->prefix ) fp = stdout;
else if ( !strcmp(opts->prefix, "-") ) fp = stdout;
else if ( !strcmp(opts->prefix, "stdout") ) fp = stdout;
else if ( !strcmp(opts->prefix, "stderr") ) fp = stderr;
else {
fp = fopen(opts->prefix, "w");
if( ! fp ) {
ERROR_message("failed to open '%s' for writing", opts->prefix);
RETURN(1);
}
}
if( opts->verb ) {
if ( fp == stdout ) INFO_message("writing to stdout...");
else if( fp == stdout ) INFO_message("writing to stderr...");
else if( opts->prefix ) INFO_message("writing to '%s'...", opts->prefix);
else INFO_message("writing to unknown?!?");
}
/* actually write results */
for( c=0; c < opts->nt; c++ )
fprintf(fp, "%f\n", opts->result[c]);
if( fp != stdout && fp != stderr )
fclose(fp);
RETURN(0);
}
/*--------------- main routine ---------------*/
int main( int argc, char *argv[] )
{
THD_3dim_dataset * countset=NULL;
param_t * params = &g_params;
int rv, limit;
if( argc < 1 ) { show_help(); return 0; }
/* general stuff */
mainENTRY("3dmask_tool"); machdep(); AFNI_logger("3dmask_tool",argc,argv);
enable_mcw_malloc();
/* process options: a negative return is considered an error */
rv = process_opts(params, argc, argv);
if( rv ) RETURN(rv < 0);
/* open, convert to byte, zeropad, dilate, unzeropad */
if( process_input_dsets(params) ) RETURN(1);
/* create mask count dataset and return num volumes (delete old dsets) */
if( count_masks(params->dsets, params->ndsets, params->verb,
&countset, ¶ms->nvols) ) RETURN(1);
/* limit to frac of nvols (if not counting, convert to 0/1 mask) */
limit = ceil((params->frac>1) ? params->frac : params->nvols*params->frac );
if( params->verb )
INFO_message("frac %g over %d volumes gives min count %d\n",
params->frac, params->nvols, limit);
if( limit <= 0 ) limit = 1;
/* if not counting, result is binary 0/1 */
if( limit_to_frac(countset, limit, params->count, params->verb) )
RETURN(1);
/* maybe apply dilations to output */
if( params->RESD.num > 0 ) {
countset = apply_dilations(countset, ¶ms->RESD, 0, params->verb);
if( !countset ) RETURN(1);
}
/* maybe fill any remaining holes */
if( params->fill )
if ( fill_holes(countset, params->verb) ) RETURN(1);
/* create output */
if( write_result(params, countset, argc, argv) ) RETURN(1);
/* clean up a little memory */
DSET_delete(countset);
free(params->dsets);
RETURN(0);
}
/*
* check count against limit
* - clear small values
* - if not count, set large values to 1
*/
int limit_to_frac(THD_3dim_dataset * cset, int limit, int count, int verb)
{
short * dptr;
int index, nsub, nsuper;
ENTRY("limit_to_frac");
if( ! ISVALID_3DIM_DATASET(cset) ) {
ERROR_message("invalid count dataset");
RETURN(1);
} else if( DSET_BRICK_TYPE(cset, 0) != MRI_short ) {
ERROR_message("count dataset not of type short");
RETURN(1);
}
if(verb > 1) INFO_message("limiting to %d (count = %d)\n",limit,count);
/* note how many voxels are affected, just for kicks */
dptr = DBLK_ARRAY(cset->dblk, 0);
nsub = nsuper = 0;
for(index = 0; index < DSET_NVOX(cset); index++, dptr++) {
if( ! *dptr ) continue; /* 0, so skip */
else if( *dptr < limit ) { /* small, so clear */
*dptr = 0;
nsub++;
}
else { /* big enough */
if ( ! count ) *dptr = 1;
nsuper++;
}
}
/* entertain the user */
if( verb )
INFO_message("voxel limits: %d clipped, %d survived, %d were zero\n",
nsub, nsuper, DSET_NVOX(cset)-nsub-nsuper);
RETURN(0);
}
static void toy_tsfunc( double tzero, double tdelta ,
int npts, float ts[],
double ts_mean , double ts_slope ,
void *ud, int nbriks, float *val )
{
static complex *comp_array=NULL;
float mag=0, pow=0, pow6=0;
int jj;
TOY_UD *rpud = (TOY_UD *)ud;
if( val == NULL ){
INFO_message("toy_tsfunc: %s notification call, npts=%d\n",
npts?"Start":"End", npts);
if( npts > 0 ){ /* the "start notification" */
/* This is when you perform any setup you don't want to repeat
each time the function is called for a new voxel.
Such a setup typically involves allocating for temporary
arrays */
/* allocate for fft array */
comp_array = (complex *) calloc( sizeof(complex) , rpud->nfft);
} else { /* the "end notification" */
/* Last call, meant for cleanup */
if (comp_array) free(comp_array); comp_array = NULL;
}
return ;
}
/* if we get here then we have data to process */
/* Load time series */
for( jj=0 ; jj < npts ; jj++ ) {
comp_array[jj].r = ts[jj]; comp_array[jj].i = 0.0f ;
}
/* zero pad */
for( jj=npts ; jj < rpud->nfft ; jj++ )
comp_array[jj].r = comp_array[jj].i = 0.0f ;
csfft_cox( -1 , rpud->nfft, comp_array ) ; /* DFT */
for( jj=0 ; jj < rpud->nfft ; jj++ ) {
mag = CABS(comp_array[jj]) ;
pow += mag*mag;
if (jj<rpud->nfft/6) pow6 += mag*mag ;
}
val[0] = pow;
val[1] = pow6;
return ;
}
void AFNI_pbar_lock_carryout( Three_D_View *im3d )
{
Three_D_View *qq3d ;
static int busy = 0 ; /* !=0 if this routine is "busy" */
int glock , cc,ii ;
ENTRY("AFNI_pbar_lock_carryout") ;
/* first, determine if there is anything to do */
glock = GLOBAL_library.controller_lock ; /* not a handgun */
if( busy ) EXRETURN; /* routine already busy */
if( glock == 0 ) EXRETURN; /* nothing to do */
if( !IM3D_OPEN(im3d) ) EXRETURN; /* bad input */
if( GLOBAL_library.ignore_lock ) EXRETURN; /* ordered not to do anything */
if( !AFNI_check_pbar_lock() ) EXRETURN; /* not locked? */
ii = AFNI_controller_index(im3d) ; /* which one am I? */
if( ii < 0 ) EXRETURN ; /* nobody? bad input! */
if( ((1<<ii) & glock) == 0 ) EXRETURN ; /* input not locked */
#if 0
INFO_message("AFNI_pbar_lock_carryout( %d ) ******************* ",ii) ;
TRACEBACK ;
#endif
/* something to do? */
busy = 1 ; /* don't let this routine be called recursively */
/* loop through other controllers:
for those that ARE open, ARE NOT the current one, and ARE locked */
for( cc=0 ; cc < MAX_CONTROLLERS ; cc++ ){
qq3d = GLOBAL_library.controllers[cc] ; /* controller */
if( IM3D_OPEN(qq3d) && qq3d != im3d && ((1<<cc) & glock) != 0 ){
#if 0
ININFO_message(" equate_pbars( %d )",cc) ;
#endif
AFNI_equate_pbars( qq3d , im3d ) ;
}
}
busy = 0 ; /* OK, let this routine be activated again */
EXRETURN ;
}
/* convert by hand, since no scaling will be done
* (byte seems inappropriate and float does not need it) */
int write_result(param_t * params, THD_3dim_dataset * oset,
int argc, char * argv[])
{
short * sptr;
int nvox = DSET_NVOX(oset), ind;
ENTRY("write_results");
EDIT_dset_items(oset, ADN_prefix, params->prefix, ADN_none);
if( params->verb )
INFO_message("writing result %s...\n", DSET_PREFIX(oset));
switch( params->datum ) {
default: ERROR_exit("invalid datum for result: %d", params->datum);
case MRI_short: break; /* nothing to do */
case MRI_float: {
float * data = (float *)malloc(nvox*sizeof(float));
sptr = DBLK_ARRAY(oset->dblk, 0);
if( ! data ) ERROR_exit("failed to alloc %d output floats\n", nvox);
for( ind = 0; ind < nvox; ind++ ) data[ind] = (float)sptr[ind];
EDIT_substitute_brick(oset, 0, params->datum, data);
}
break;
case MRI_byte: {
byte * data = (byte *)malloc(nvox*sizeof(byte));
int errs = 0;
sptr = DBLK_ARRAY(oset->dblk, 0);
if( ! data ) ERROR_exit("failed to alloc %d output bytes\n", nvox);
for( ind = 0; ind < nvox; ind++ ) {
if( sptr[ind] > 255 ) { /* watch for overflow */
data[ind] = (byte)255;
errs++;
} else data[ind] = (byte)sptr[ind];
}
EDIT_substitute_brick(oset, 0, params->datum, data);
if(errs) WARNING_message("convert to byte: %d truncated voxels",errs);
}
break;
}
tross_Make_History( "3dmask_tool", argc, argv, oset );
DSET_write(oset);
WROTE_DSET(oset);
RETURN(0);
}
SEXP getListElement(SEXP list, const char *str)
{
int debug=0;
R_len_t i;
SEXP elmt = R_NilValue, names = getAttrib(list, R_NamesSymbol);
if (!debug) debug = get_odebug();
for ( i = 0; i < length(list); i++) {
if (debug) INFO_message("Element %d/%d: named %s\n",
i, length(list), CHAR(STRING_ELT(names, i)));
if(strcmp(CHAR(STRING_ELT(names, i)), str) == 0) {
elmt = VECTOR_ELT(list, i);
break;
}
}
return elmt;
}
void AFNI_all_locks_carryout( Three_D_View *im3d )
{
static int busy = 0 ; /* !=0 if this routine is "busy" */
ENTRY("AFNI_all_locks_carryout") ;
if( busy || !IM3D_VALID(im3d) ) EXRETURN ;
if( GLOBAL_library.ignore_lock ) EXRETURN ;
#if 0
INFO_message("AFNI_all_locks_carryout: im3d index = %d",AFNI_controller_index(im3d)) ;
#endif
AFNI_lock_carryout ( im3d ) ;
AFNI_time_lock_carryout ( im3d ) ;
AFNI_thresh_lock_carryout( im3d ) ;
AFNI_pbar_lock_carryout ( im3d ) ;
AFNI_range_lock_carryout ( im3d ) ;
AFNI_sleep(1) ; busy = 0 ; EXRETURN ;
}
void EDIT_misfit_report( char *name, int ib,
int nxyz, float fac, short *sar, float *far )
{
float mf ;
int im ;
static char *msg[5] = { "* Caution" , "** Take Care" ,
"*** Beware" , "**** Red Alert ****" ,
"***** Purple Alert! *****"
} ;
static int first=1 ;
mf = 100.0f * EDIT_scale_misfit( nxyz , fac , sar , far ) ;
if( mf <= 9.0f ) return ; /* OK */
if( mf <= 13.0f ) im = 0 ;
else if( mf <= 19.0f ) im = 1 ;
else if( mf <= 27.0f ) im = 2 ;
else if( mf <= 39.0f ) im = 3 ;
else im = 4 ;
if( first )
WARNING_message("+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++");
WARNING_message("%s[%d] scale to shorts mean misfit error = %.1f%% -- %s",
name , ib , mf , msg[im] ) ;
if( first ) {
ININFO_message("a) Numerical precision has been lost when truncating results\n"
" from 32-bit floating point to 16-bit integers (shorts)." );
ININFO_message("b) Consider writing datasets out in float format.\n"
" In most AFNI programs, use the '-float' option.");
ININFO_message("c) This warning is a new message, but is an old issue\n"
" that arises when storing results in an integer format." );
ININFO_message("d) Don't panic! These messages likely originate in peripheral\n"
" or unimportant voxels. They mean that you must examine your output.\n"
" \"Assess the situation and keep a calm head about you,\n"
" because it doesn't do anybody any good to panic.\"\n" ) ;
INFO_message("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++");
first = 0 ;
}
return ;
}
void RT_test_callback(void *junk)
{
RT_status *rts = GLOBAL_library.realtime_status ;
int cc , nval,nbr ;
if( rts == NULL ){ ERROR_message("bad call to RT_test_callback"); return; }
INFO_message("RT_test_callback: numchan=%d status=%d numdset=%d",
rts->numchan , rts->status , rts->numdset ) ;
for( cc=0 ; cc < rts->numdset ; cc++ ){ /* print out some dataset info */
if( !ISVALID_DSET(rts->dset[cc]) ){
ININFO_message(" dset[%d] invalid!",cc) ; /* should never happen */
} else {
nval = DSET_NVALS(rts->dset[cc]) ; /* number of bricks */
nbr = THD_count_databricks(rts->dset[cc]->dblk) ; /* number with data */
ININFO_message(" dset[%d] '%s': nvals=%d nbr=%d",
cc , DSET_HEADNAME(rts->dset[cc]) , nval,nbr ) ;
}
}
return ;
}
/*
* create empty count dataset
* for each input dataset and each sub-volume
* for each voxel, if set: increment
* close datasets as they are processed
*/
int count_masks(THD_3dim_dataset * dsets[], int ndsets, int verb, /* inputs */
THD_3dim_dataset ** cset, int * nvol) /* outputs */
{
THD_3dim_dataset * dset;
short * counts = NULL; /* will become data for returned cset */
byte * bptr; /* always points to mask volumes */
int nxyz, iset, ivol, ixyz;
ENTRY("count_masks");
if( !dsets || !cset || !nvol )
ERROR_exit("NULL inputs to count_masks");
if( ndsets <= 0 ) {
ERROR_message("count_masks: no input datasets");
RETURN(1);
}
*nvol = 0;
nxyz = DSET_NVOX(dsets[0]);
/* allocate memory for the counts */
counts = (short *)calloc(nxyz, sizeof(short));
if( !counts ) ERROR_exit("failed to malloc %d shorts", nxyz);
/* for each volume of each dataset, count set voxels */
for( iset=0; iset < ndsets; iset++ ) {
dset = dsets[iset];
*nvol += DSET_NVALS(dset); /* accumulate num volumes */
/* for each volume in this dataset, count set voxels */
for( ivol=0; ivol < DSET_NVALS(dset); ivol++ ) {
if( DSET_BRICK_TYPE(dset, ivol) != MRI_byte )
ERROR_exit("in count_masks with non-byte data (set %d, vol %d)",
iset, ivol);
bptr = DBLK_ARRAY(dset->dblk, ivol);
for( ixyz = 0; ixyz < nxyz; ixyz++ )
if( bptr[ixyz] ) counts[ixyz]++;
}
if( iset > 0 ) DSET_delete(dset); /* close the first one at end */
} /* dataset */
if( verb > 1 ) {
int maxval;
for( maxval=counts[0], ixyz=1; ixyz < nxyz; ixyz++ )
if( counts[ixyz] > maxval ) maxval = counts[ixyz];
INFO_message("counted %d mask volumes in %d datasets (%d voxels)\n",
*nvol, ndsets, nxyz);
INFO_message(" (maximum overlap = %d)\n", maxval);
}
if( *nvol >= (1<<15) )
WARNING_message("too many volumes to count as shorts: %d", *nvol);
/* create output dataset */
*cset = EDIT_empty_copy(dsets[0]);
EDIT_dset_items(*cset, ADN_nvals, 1, ADN_ntt, 0, ADN_none);
EDIT_substitute_brick(*cset, 0, MRI_short, counts);
DSET_delete(dsets[0]); /* now finished with first dataset */
RETURN(0);
}
/*
* 1. zeropad (if needed for dilations)
* 2. make byte copy of dataset (if not already)
* 3. dilate (using binary mask)
* 4. if not converting, modify original data
* 5. undo any zeropad
* 6. return new dataset (might be same as old)
*
* dilations are passed as a list of +/- integers (- means erode)
*
* convert: flag specifying whether dset should be converted to MRI_byte
*
* note: the dilations list should not be long (does more than 2 even
* make any sense?), but here they will be treated generically
* - foreach dilation: dilate or erode, as specified by sign
*/
THD_3dim_dataset * apply_dilations(THD_3dim_dataset * dset, int_list * D,
int convert, int verb)
{
THD_3dim_dataset * dnew = NULL;
byte * bdata = NULL;
int index, ivol, id, dsize, datum, pad;
int nx, ny, nz, nvox;
ENTRY("apply_dilations");
if( !dset || !D ) ERROR_exit("missing inputs to apply_dilations");
/* note and apply any needed zeropadding */
pad = needed_padding(D);
if(verb > 3 && pad) INFO_message("padding by %d (for dilations)", pad);
if( pad ) dnew = THD_zeropad(dset, pad, pad, pad, pad, pad, pad, "pad", 0);
else dnew = dset;
/* note geometry */
nx = DSET_NX(dnew); ny = DSET_NY(dnew); nz = DSET_NZ(dnew);
nvox = nx*ny*nz;
/* now apply the actual dilations */
if(verb>1) INFO_message("applying dilation list to dataset");
for( ivol=0; ivol < DSET_NVALS(dnew); ivol++ ) {
datum = DSET_BRICK_TYPE(dnew, ivol);
/* if non-byte data (short/float), make byte mask of volume */
if( datum == MRI_byte )
bdata = DBLK_ARRAY(dnew->dblk, ivol);
else if ( datum == MRI_float || datum == MRI_short )
bdata = THD_makemask(dnew, ivol, 1, 0);
else {
ERROR_message("invalid datum for result: %d", datum);
RETURN(NULL);
}
if( !bdata ) {
ERROR_message("failed to make as mask");
RETURN(NULL);
}
for( index=0; index < D->num; index++ ) {
dsize = D->list[index];
if(verb>2) INFO_message("... dilating vol %d by %d\n", ivol, dsize);
if( dsize > 0 ) {
for( id=0; id < dsize; id++ )
THD_mask_dilate(nx, ny, nz, bdata, 1);
} else if( dsize < 0 ) {
for( id=0; id > dsize; id-- )
THD_mask_erode_sym(nx, ny, nz, bdata, 1);
}
}
/* if we are converting, just replace the old data */
if( convert && (datum == MRI_short || datum == MRI_float) ) {
if( verb > 2 ) INFO_message("applying byte result from dilate");
EDIT_substitute_brick(dnew, ivol, MRI_byte, bdata);
/* explicit set needed on an Fedora 8 system? 5 Jun 2012 */
DSET_BRICK_TYPE(dnew, ivol) = MRI_byte;
continue; /* so nothing more to do */
}
/* if short or float data, apply mask changes to data */
if( datum == MRI_short ) {
short * dptr = DBLK_ARRAY(dnew->dblk, ivol);
int nfill=0;
if( verb > 2 ) INFO_message("applying dilate result to short data");
for( index = 0; index < nvox; index++ )
if( ! dptr[index] && bdata[index] ){ dptr[index] = 1; nfill++; }
if( verb > 1 ) INFO_message("AD: filled %d voxels", nfill);
free(bdata);
}
else if( datum == MRI_float ) {
float * dptr = DBLK_ARRAY(dnew->dblk, ivol);
if( verb > 2 ) INFO_message("applying dilate result to float data");
for( index = 0; index < nvox; index++ )
if( ! dptr[index] && bdata[index] ) dptr[index] = 1.0;
free(bdata);
}
}
/* undo any zeropadding (delete original and temporary datasets) */
if( pad ) {
DSET_delete(dset);
dset = THD_zeropad(dnew, -pad, -pad, -pad, -pad, -pad, -pad, "pad", 0);
DSET_delete(dnew);
dnew = dset;
}
RETURN(dnew);
}
MRI_shindss * GRINCOR_read_input( char *fname )
{
NI_element *nel=NULL ;
char *dfname=NULL , *atr ;
NI_float_array *facar ; NI_int_array *nvar, *nnode=NULL, *ninmask=NULL;
MRI_shindss *shd ;
long long nbytes_needed , nbytes_dfname=0 ; int fdes ;
void *var ; int ids , nvmax , nvtot ;
int datum , datum_size ;
char *geometry_string=NULL ;
THD_3dim_dataset *tdset=NULL; int nvox;
int no_ivec=0 , *ivec=NULL , *nvals=NULL , nvec,ndset ; float *fac=NULL ;
NI_str_array *slabar=NULL ;
if( fname == NULL || *fname == '\0' ) GQUIT(NULL) ;
/* get data element */
if (!THD_is_ondisk(fname))
GQUIT("not on disk") ;
nelshd = nel = NI_read_element_fromfile(fname) ;
if( nel == NULL || nel->type != NI_ELEMENT_TYPE )
GQUIT("not properly formatted") ;
if( strcmp(nel->name,"3dGroupInCorr") != 0 )
GQUIT("data element name is not '3dGroupInCorr'") ;
/* no data vector ==> using all voxels */
no_ivec = ( nel->vec_num < 1 ||
nel->vec_len < 1 || nel->vec_typ[0] != NI_INT ) ;
/* number of vectors in each dataset */
atr = NI_get_attribute(nel,"nvec");
if( atr == NULL ) GQUIT("nvec attribute missing?") ;
nvec = (int)strtod(atr,NULL) ;
if( nvec < 2 || (!no_ivec && nel->vec_len != nvec) )
GQUIT("nvec attribute has illegal value") ;
/* number of datasets */
atr = NI_get_attribute(nel,"ndset");
if( atr == NULL ) GQUIT("ndset attribute missing") ;
ndset = (int)strtod(atr,NULL) ;
if( ndset < 1 ) GQUIT("ndset attribute has illegal value") ;
/* number of time points in each dataset (varies with dataset) */
atr = NI_get_attribute(nel,"nvals");
if( atr == NULL ) GQUIT("nvals attribute missing") ;
nvar = NI_decode_int_list(atr,",") ;
if( nvar == NULL || nvar->num < ndset )
GQUIT("nvals attribute doesn't match ndset") ;
nvals = nvar->ar ; nvar->ar = NULL ; NI_delete_int_array(nvar) ;
nvmax = nvtot = nvals[0] ;
for( ids=1 ; ids < ndset ; ids++ ){ /* Feb 2011 */
nvtot += nvals[ids] ;
if( nvals[ids] > nvmax ) nvmax = nvals[ids] ;
}
/* dataset labels [23 May 2010] */
atr = NI_get_attribute(nel,"dset_labels") ;
if( atr != NULL ){
slabar = NI_decode_string_list(atr,";,") ;
if( slabar == NULL || slabar->num < ndset )
GQUIT("dset_labels attribute invalid") ;
}
/* datum of datasets */
atr = NI_get_attribute(nel,"datum") ;
if( atr != NULL && strcasecmp(atr,"byte") == 0 ){
datum = 1 ; datum_size = sizeof(sbyte) ;
} else {
datum = 2 ; datum_size = sizeof(short) ;
}
/* number of bytes needed:
sizeof(datum) * number of vectors per dataset
* number of datasets
* sum of per dataset vector lengths */
nbytes_needed = 0 ;
for( ids=0 ; ids < ndset ; ids++ ) nbytes_needed += nvals[ids] ;
nbytes_needed *= ((long long)nvec) * datum_size ;
if( nbytes_needed >= twogig &&
( sizeof(void *) < 8 || sizeof(size_t) < 8 ) ) /* too much for 32-bit */
GQUIT("datafile size exceeds 2 GB -- you need a 64-bit computer!") ;
/* scale factor for each dataset */
atr = NI_get_attribute(nel,"fac") ;
if( atr == NULL ) GQUIT("fac attribute missing") ;
facar = NI_decode_float_list(atr,",") ;
if( facar == NULL || facar->num < ndset )
GQUIT("can't decode fac attribute") ;
fac = facar->ar ; facar->ar = NULL ; NI_delete_float_array(facar) ;
for( ids=0 ; ids < ndset ; ids++ ) if( fac[ids] <= 0.0f ) fac[ids] = 1.0f ;
/* grid definition */
atr = NI_get_attribute(nel,"geometry") ;
if( atr == NULL ) GQUIT("geometry attribute missing") ;
geometry_string = strdup(atr) ;
tdset = EDIT_geometry_constructor( geometry_string , "GrpInCorr" ) ;
if( tdset == NULL ) GQUIT("can't decode geometry attribute") ;
nvox = DSET_NVOX(tdset) ;
if( no_ivec && nvox != nvec )
GQUIT("geometry attribute doesn't match nvec attribute") ;
if( !no_ivec && nvox < nvec )
GQUIT("geometry attribute specifies too few voxels") ;
/* name of data file: check its size against what's needed */
#if 0
atr = NI_get_attribute(nel,"datafile") ;
if( atr != NULL ){
dfname = strdup(atr) ; nbytes_dfname = THD_filesize(dfname) ;
if( nbytes_dfname <= 0 && strstr(dfname,"/") != NULL ){
char *tnam = THD_trailname(atr,0) ;
nbytes_dfname = THD_filesize(tnam) ;
if( nbytes_dfname > 0 ){ free(dfname); dfname = strdup(tnam); }
}
}
#endif
if( nbytes_dfname <= 0 && strstr(fname,".niml") != NULL ){
if( dfname != NULL ) free(dfname) ;
dfname = strdup(fname) ; strcpy(dfname+strlen(dfname)-5,".data") ;
nbytes_dfname = THD_filesize(dfname) ;
}
if( nbytes_dfname <= 0 ){
char mess[THD_MAX_NAME+256] ;
sprintf(mess,"datafile is missing (%s)",dfname) ; GQUIT(mess) ;
} else if( nbytes_dfname < nbytes_needed ){
char mess[THD_MAX_NAME+1024] ;
sprintf(mess,"datafile %s has %s bytes but needs at least %s",
dfname ,
commaized_integer_string(nbytes_dfname) ,
commaized_integer_string(nbytes_needed) ) ;
GQUIT(mess) ;
} else {
INFO_message("EIC: data file %s found with %s bytes of data",
dfname , commaized_integer_string(nbytes_dfname) ) ;
}
fdes = open( dfname , O_RDWR ) ;
if( fdes < 0 ){
char mess[THD_MAX_NAME+256] ;
sprintf(mess,"can't open datafile (%s)",dfname) ; GQUIT(mess) ;
}
NI_set_attribute( nelshd , "datafile" , dfname ) ;
/* ivec[i] is the voxel spatial index of the i-th vector */
if( no_ivec ){
ivec = NULL ; /* means all voxels: ivec[i] == i */
} else {
ivec = (int *)nel->vec[0] ; /* copy pointer */
nel->vec[0] = NULL ; /* NULL out in element so won't be free-ed */
}
/* And stuff for LR surface pairs ZSS Jan 09*/
if ((atr=NI_get_attribute(nel,"LRpair_nnode"))) {
nnode = NI_decode_int_list(atr,",") ;
}
if ((atr=NI_get_attribute(nel,"LRpair_ninmask"))) {
ninmask = NI_decode_int_list(atr,",") ;
}
/* create output struct */
shd = (MRI_shindss *)malloc(sizeof(MRI_shindss)) ;
shd->nvals = nvals ; shd->nvals_max = nvmax ; shd->nvals_tot = nvtot ;
shd->nvec = nvec ;
shd->ndset = ndset ;
shd->geometry_string = geometry_string ;
shd->tdset = tdset ;
shd->dfname = dfname ;
shd->nvox = nvox ;
shd->nx = DSET_NX(tdset); shd->ny = DSET_NY(tdset); shd->nz = DSET_NZ(tdset);
shd->ivec = ivec ;
shd->fac = fac ;
/* and surface fields... ZSS Jan 09 */
if (nnode) {
if (nnode->num != 2) GQUIT("LRpair_nnode must have 2 values");
shd->nnode[0] = nnode->ar[0];
shd->nnode[1] = nnode->ar[1];
NI_delete_int_array(nnode); nnode=NULL;
} else {
shd->nnode[0] = shd->nnode[1] = -1 ;
}
if (ninmask) {
if (ninmask->num != 2) GQUIT("LRpair_ninmask must have 2 values");
shd->ninmask[0] = ninmask->ar[0];
shd->ninmask[1] = ninmask->ar[1];
NI_delete_int_array(ninmask); ninmask=NULL;
} else {
shd->ninmask[0] = shd->ninmask[1] = -1 ;
}
/*--- 07 Apr 2010: setup default use list (all of them) ---*/
shd->nuse = ndset ;
shd->use = (int *)malloc(sizeof(int)*ndset) ;
for( ids=0 ; ids < ndset ; ids++ ) shd->use[ids] = ids ;
shd->dslab = (slabar != NULL) ? slabar->str : NULL ; /* 23 May 2010 */
/*--- now have to map data from disk ---*/
var = mmap( 0 , (size_t)nbytes_needed ,
PROT_WRITE , THD_MMAP_FLAG , fdes , 0 ) ;
close(fdes) ; /* close file descriptor does not unmap data */
if( var == (void *)(-1) ){ /* this is bad */
ERROR_message(
"EIC: file %s: can't mmap() datafile -- memory space exhausted?" , dfname ) ;
free(shd) ; return NULL ;
}
/*-- create array of pointers to each dataset's data array --*/
shd->datum = datum ;
if( datum == 2 ){ /* shorts */
shd->sv = (short **)malloc(sizeof(short *)*ndset) ;
shd->bv = NULL ;
shd->sv[0] = (short *)var ;
for( ids=1 ; ids < ndset ; ids++ )
shd->sv[ids] = shd->sv[ids-1] + nvals[ids-1]*nvec ;
} else { /* sbytes */
shd->sv = NULL ;
shd->bv = (sbyte **)malloc(sizeof(sbyte *)*ndset) ;
shd->bv[0] = (sbyte *)var ;
for( ids=1 ; ids < ndset ; ids++ )
shd->bv[ids] = shd->bv[ids-1] + nvals[ids-1]*nvec ;
}
shd->nbytes = nbytes_needed ;
return shd ;
}
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 do_norm=0 , qdet=2 , have_freq=0 , do_automask=0 ;
float dt=0.0f , fbot=0.0f,ftop=999999.9f , blur=0.0f ;
MRI_IMARR *ortar=NULL ; MRI_IMAGE *ortim=NULL ;
THD_3dim_dataset **ortset=NULL ; int nortset=0 ;
THD_3dim_dataset *inset=NULL , *outset=NULL;
char *prefix="RSFC" ;
byte *mask=NULL ;
int mask_nx=0,mask_ny=0,mask_nz=0,nmask , verb=1 ,
nx,ny,nz,nvox , nfft=0 , kk ;
float **vec , **ort=NULL ; int nort=0 , vv , nopt , ntime ;
MRI_vectim *mrv ;
float pvrad=0.0f ; int nosat=0 ;
int do_despike=0 ;
// @@ non-BP variables
float fbotALL=0.0f, ftopALL=999999.9f; // do full range version
int NumDen = 0; // switch for doing numerator or denom
THD_3dim_dataset *outsetALL=NULL ;
int m, mm;
float delf; // harmonics
int ind_low,ind_high,N_ny, ctr;
float sqnt,nt_fac;
gsl_fft_real_wavetable *real1, *real2; // GSL stuff
gsl_fft_real_workspace *work;
double *series1, *series2;
double *xx1,*xx2;
float numer,denom,val;
float *alff=NULL,*malff=NULL,*falff=NULL,
*rsfa=NULL,*mrsfa=NULL,*frsfa=NULL; // values
float meanALFF=0.0f,meanRSFA=0.0f; // will be for mean in brain region
THD_3dim_dataset *outsetALFF=NULL;
THD_3dim_dataset *outsetmALFF=NULL;
THD_3dim_dataset *outsetfALFF=NULL;
THD_3dim_dataset *outsetRSFA=NULL;
THD_3dim_dataset *outsetmRSFA=NULL;
THD_3dim_dataset *outsetfRSFA=NULL;
char out_lff[300];
char out_alff[300];
char out_malff[300];
char out_falff[300];
char out_rsfa[300];
char out_mrsfa[300];
char out_frsfa[300];
char out_unBP[300];
int SERIES_OUT = 1;
int UNBP_OUT = 0;
int DO_RSFA = 1;
int BP_LAST = 0; // option for only doing filter to LFFs at very end of proc
float de_rsfa=0.0f,nu_rsfa=0.0f;
double pow1=0.0,pow2=0.0;
/*-- help? --*/
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf(
"\n Program to calculate common resting state functional connectivity (RSFC)\n"
" parameters (ALFF, mALFF, fALFF, RSFA, etc.) for resting state time\n"
" series. This program is **heavily** based on the existing\n"
" 3dBandPass by RW Cox, with the amendments to calculate RSFC\n"
" parameters written by PA Taylor (July, 2012).\n"
" This program is part of FATCAT (Taylor & Saad, 2013) in AFNI. Importantly,\n"
" its functionality can be included in the `afni_proc.py' processing-script \n"
" generator; see that program's help file for an example including RSFC\n"
" and spectral parameter calculation via the `-regress_RSFC' option.\n"
"\n"
"* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n"
"\n"
" All options of 3dBandPass may be used here (with a couple other\n"
" parameter options, as well): essentially, the motivation of this\n"
" program is to produce ALFF, etc. values of the actual RSFC time\n"
" series that you calculate. Therefore, all the 3dBandPass processing\n"
" you normally do en route to making your final `resting state time\n"
" series' is done here to generate your LFFs, from which the\n"
" amplitudes in the LFF band are calculated at the end. In order to\n"
" calculate fALFF, the same initial time series are put through the\n"
" same processing steps which you have chosen but *without* the\n"
" bandpass part; the spectrum of this second time series is used to\n"
" calculate the fALFF denominator.\n"
" \n"
" For more information about each RSFC parameter, see, e.g.: \n"
" ALFF/mALFF -- Zang et al. (2007),\n"
" fALFF -- Zou et al. (2008),\n"
" RSFA -- Kannurpatti & Biswal (2008).\n"
"\n"
"* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n"
"\n"
" + USAGE: 3dRSFC [options] fbot ftop dataset\n"
"\n"
"* One function of this program is to prepare datasets for input\n"
" to 3dSetupGroupInCorr. Other uses are left to your imagination.\n"
"\n"
"* 'dataset' is a 3D+time sequence of volumes\n"
" ++ This must be a single imaging run -- that is, no discontinuities\n"
" in time from 3dTcat-ing multiple datasets together.\n"
"\n"
"* fbot = lowest frequency in the passband, in Hz\n"
" ++ fbot can be 0 if you want to do a lowpass filter only;\n"
" HOWEVER, the mean and Nyquist freq are always removed.\n"
"\n"
"* ftop = highest frequency in the passband (must be > fbot)\n"
" ++ if ftop > Nyquist freq, then it's a highpass filter only.\n"
"\n"
"* Set fbot=0 and ftop=99999 to do an 'allpass' filter.\n"
" ++ Except for removal of the 0 and Nyquist frequencies, that is.\n"
"\n"
"* You cannot construct a 'notch' filter with this program!\n"
" ++ You could use 3dRSFC followed by 3dcalc to get the same effect.\n"
" ++ If you are understand what you are doing, that is.\n"
" ++ Of course, that is the AFNI way -- if you don't want to\n"
" understand what you are doing, use Some other PrograM, and\n"
" you can still get Fine StatisticaL maps.\n"
"\n"
"* 3dRSFC will fail if fbot and ftop are too close for comfort.\n"
" ++ Which means closer than one frequency grid step df,\n"
" where df = 1 / (nfft * dt) [of course]\n"
"\n"
"* The actual FFT length used will be printed, and may be larger\n"
" than the input time series length for the sake of efficiency.\n"
" ++ The program will use a power-of-2, possibly multiplied by\n"
" a power of 3 and/or 5 (up to and including the 3rd power of\n"
" each of these: 3, 9, 27, and 5, 25, 125).\n"
"\n"
"* Note that the results of combining 3dDetrend and 3dRSFC will\n"
" depend on the order in which you run these programs. That's why\n"
" 3dRSFC has the '-ort' and '-dsort' options, so that the\n"
" time series filtering can be done properly, in one place.\n"
"\n"
"* The output dataset is stored in float format.\n"
"\n"
"* The order of processing steps is the following (most are optional), and\n"
" for the LFFs, the bandpass is done between the specified fbot and ftop,\n"
" while for the `whole spectrum' (i.e., fALFF denominator) the bandpass is:\n"
" done only to exclude the time series mean and the Nyquist frequency:\n"
" (0) Check time series for initial transients [does not alter data]\n"
" (1) Despiking of each time series\n"
" (2) Removal of a constant+linear+quadratic trend in each time series\n"
" (3) Bandpass of data time series\n"
" (4) Bandpass of -ort time series, then detrending of data\n"
" with respect to the -ort time series\n"
" (5) Bandpass and de-orting of the -dsort dataset,\n"
" then detrending of the data with respect to -dsort\n"
" (6) Blurring inside the mask [might be slow]\n"
" (7) Local PV calculation [WILL be slow!]\n"
" (8) L2 normalization [will be fast.]\n"
" (9) Calculate spectrum and amplitudes, for RSFC parameters.\n"
"\n"
"* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n"
"--------\n"
"OPTIONS:\n"
"--------\n"
" -despike = Despike each time series before other processing.\n"
" ++ Hopefully, you don't actually need to do this,\n"
" which is why it is optional.\n"
" -ort f.1D = Also orthogonalize input to columns in f.1D\n"
" ++ Multiple '-ort' options are allowed.\n"
" -dsort fset = Orthogonalize each voxel to the corresponding\n"
" voxel time series in dataset 'fset', which must\n"
" have the same spatial and temporal grid structure\n"
" as the main input dataset.\n"
" ++ At present, only one '-dsort' option is allowed.\n"
" -nodetrend = Skip the quadratic detrending of the input that\n"
" occurs before the FFT-based bandpassing.\n"
" ++ You would only want to do this if the dataset\n"
" had been detrended already in some other program.\n"
" -dt dd = set time step to 'dd' sec [default=from dataset header]\n"
" -nfft N = set the FFT length to 'N' [must be a legal value]\n"
" -norm = Make all output time series have L2 norm = 1\n"
" ++ i.e., sum of squares = 1\n"
" -mask mset = Mask dataset\n"
" -automask = Create a mask from the input dataset\n"
" -blur fff = Blur (inside the mask only) with a filter\n"
" width (FWHM) of 'fff' millimeters.\n"
" -localPV rrr = Replace each vector by the local Principal Vector\n"
" (AKA first singular vector) from a neighborhood\n"
" of radius 'rrr' millimiters.\n"
" ++ Note that the PV time series is L2 normalized.\n"
" ++ This option is mostly for Bob Cox to have fun with.\n"
"\n"
" -input dataset = Alternative way to specify input dataset.\n"
" -band fbot ftop = Alternative way to specify passband frequencies.\n"
"\n"
" -prefix ppp = Set prefix name of output dataset. Name of filtered time\n"
" series would be, e.g., ppp_LFF+orig.*, and the parameter\n"
" outputs are named with obvious suffices.\n"
" -quiet = Turn off the fun and informative messages. (Why?)\n"
" -no_rs_out = Don't output processed time series-- just output\n"
" parameters (not recommended, since the point of\n"
" calculating RSFC params here is to have them be quite\n"
" related to the time series themselves which are used for\n"
" further analysis)."
" -un_bp_out = Output the un-bandpassed series as well (default is not \n"
" to). Name would be, e.g., ppp_unBP+orig.* .\n"
" with suffix `_unBP'.\n"
" -no_rsfa = If you don't want RSFA output (default is to do so).\n"
" -bp_at_end = A (probably unnecessary) switch to have bandpassing be \n"
" the very last processing step that is done in the\n"
" sequence of steps listed above; at Step 3 above, only \n"
" the time series mean and nyquist are BP'ed out, and then\n"
" the LFF series is created only after Step 9. NB: this \n"
" probably makes only very small changes for most\n"
" processing sequences (but maybe not, depending usage).\n"
"\n"
" -notrans = Don't check for initial positive transients in the data:\n"
" *OR* ++ The test is a little slow, so skipping it is OK,\n"
" -nosat if you KNOW the data time series are transient-free.\n"
" ++ Or set AFNI_SKIP_SATCHECK to YES.\n"
" ++ Initial transients won't be handled well by the\n"
" bandpassing algorithm, and in addition may seriously\n"
" contaminate any further processing, such as inter-\n"
" voxel correlations via InstaCorr.\n"
" ++ No other tests are made [yet] for non-stationary \n"
" behavior in the time series data.\n"
"\n"
"* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n"
"\n"
" If you use this program, please reference the introductory/description\n"
" paper for the FATCAT toolbox:\n"
" Taylor PA, Saad ZS (2013). FATCAT: (An Efficient) Functional\n"
" And Tractographic Connectivity Analysis Toolbox. Brain \n"
" Connectivity 3(5):523-535.\n"
"____________________________________________________________________________\n"
);
PRINT_AFNI_OMP_USAGE(
" 3dRSFC" ,
" * At present, the only part of 3dRSFC that is parallelized is the\n"
" '-blur' option, which processes each sub-brick independently.\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
/*-- startup --*/
mainENTRY("3dRSFC"); machdep();
AFNI_logger("3dRSFC",argc,argv);
PRINT_VERSION("3dRSFC (from 3dBandpass by RW Cox): version THETA");
AUTHOR("PA Taylor");
nosat = AFNI_yesenv("AFNI_SKIP_SATCHECK") ;
nopt = 1 ;
while( nopt < argc && argv[nopt][0] == '-' ){
if( strcmp(argv[nopt],"-despike") == 0 ){ /* 08 Oct 2010 */
do_despike++ ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-nfft") == 0 ){
int nnup ;
if( ++nopt >= argc ) ERROR_exit("need an argument after -nfft!") ;
nfft = (int)strtod(argv[nopt],NULL) ;
nnup = csfft_nextup_even(nfft) ;
if( nfft < 16 || nfft != nnup )
ERROR_exit("value %d after -nfft is illegal! Next legal value = %d",nfft,nnup) ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-blur") == 0 ){
if( ++nopt >= argc ) ERROR_exit("need an argument after -blur!") ;
blur = strtod(argv[nopt],NULL) ;
if( blur <= 0.0f ) WARNING_message("non-positive blur?!") ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-localPV") == 0 ){
if( ++nopt >= argc ) ERROR_exit("need an argument after -localpv!") ;
pvrad = strtod(argv[nopt],NULL) ;
if( pvrad <= 0.0f ) WARNING_message("non-positive -localpv?!") ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-prefix") == 0 ){
if( ++nopt >= argc ) ERROR_exit("need an argument after -prefix!") ;
prefix = strdup(argv[nopt]) ;
if( !THD_filename_ok(prefix) ) ERROR_exit("bad -prefix option!") ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-automask") == 0 ){
if( mask != NULL ) ERROR_exit("Can't use -mask AND -automask!") ;
do_automask = 1 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-mask") == 0 ){
THD_3dim_dataset *mset ;
if( ++nopt >= argc ) ERROR_exit("Need argument after '-mask'") ;
if( mask != NULL || do_automask ) ERROR_exit("Can't have two mask inputs") ;
mset = THD_open_dataset( argv[nopt] ) ;
CHECK_OPEN_ERROR(mset,argv[nopt]) ;
DSET_load(mset) ; CHECK_LOAD_ERROR(mset) ;
mask_nx = DSET_NX(mset); mask_ny = DSET_NY(mset); mask_nz = DSET_NZ(mset);
mask = THD_makemask( mset , 0 , 0.5f, 0.0f ) ; DSET_delete(mset) ;
if( mask == NULL ) ERROR_exit("Can't make mask from dataset '%s'",argv[nopt]) ;
nmask = THD_countmask( mask_nx*mask_ny*mask_nz , mask ) ;
if( verb ) INFO_message("Number of voxels in mask = %d",nmask) ;
if( nmask < 1 ) ERROR_exit("Mask is too small to process") ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-norm") == 0 ){
do_norm = 1 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-quiet") == 0 ){
verb = 0 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-no_rs_out") == 0 ){ // @@
SERIES_OUT = 0 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-un_bp_out") == 0 ){ // @@
UNBP_OUT = 1 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-no_rsfa") == 0 ){ // @@
DO_RSFA = 0 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-bp_at_end") == 0 ){ // @@
BP_LAST = 1 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-notrans") == 0 || strcmp(argv[nopt],"-nosat") == 0 ){
nosat = 1 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-ort") == 0 ){
if( ++nopt >= argc ) ERROR_exit("need an argument after -ort!") ;
if( ortar == NULL ) INIT_IMARR(ortar) ;
ortim = mri_read_1D( argv[nopt] ) ;
if( ortim == NULL ) ERROR_exit("can't read from -ort '%s'",argv[nopt]) ;
mri_add_name(argv[nopt],ortim) ;
ADDTO_IMARR(ortar,ortim) ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-dsort") == 0 ){
THD_3dim_dataset *qset ;
if( ++nopt >= argc ) ERROR_exit("need an argument after -dsort!") ;
if( nortset > 0 ) ERROR_exit("only 1 -dsort option is allowed!") ;
qset = THD_open_dataset(argv[nopt]) ;
CHECK_OPEN_ERROR(qset,argv[nopt]) ;
ortset = (THD_3dim_dataset **)realloc(ortset,
sizeof(THD_3dim_dataset *)*(nortset+1)) ;
ortset[nortset++] = qset ;
nopt++ ; continue ;
}
if( strncmp(argv[nopt],"-nodetrend",6) == 0 ){
qdet = 0 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-dt") == 0 ){
if( ++nopt >= argc ) ERROR_exit("need an argument after -dt!") ;
dt = (float)strtod(argv[nopt],NULL) ;
if( dt <= 0.0f ) WARNING_message("value after -dt illegal!") ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-input") == 0 ){
if( inset != NULL ) ERROR_exit("Can't have 2 -input options!") ;
if( ++nopt >= argc ) ERROR_exit("need an argument after -input!") ;
inset = THD_open_dataset(argv[nopt]) ;
CHECK_OPEN_ERROR(inset,argv[nopt]) ;
nopt++ ; continue ;
}
if( strncmp(argv[nopt],"-band",5) == 0 ){
if( ++nopt >= argc-1 ) ERROR_exit("need 2 arguments after -band!") ;
if( have_freq ) WARNING_message("second -band option replaces first one!") ;
fbot = strtod(argv[nopt++],NULL) ;
ftop = strtod(argv[nopt++],NULL) ;
have_freq = 1 ; continue ;
}
ERROR_exit("Unknown option: '%s'",argv[nopt]) ;
}
/** check inputs for reasonablositiness **/
if( !have_freq ){
if( nopt+1 >= argc )
ERROR_exit("Need frequencies on command line after options!") ;
fbot = (float)strtod(argv[nopt++],NULL) ;
ftop = (float)strtod(argv[nopt++],NULL) ;
}
if( inset == NULL ){
if( nopt >= argc )
ERROR_exit("Need input dataset name on command line after options!") ;
inset = THD_open_dataset(argv[nopt]) ;
CHECK_OPEN_ERROR(inset,argv[nopt]) ;
nopt++ ;
}
DSET_UNMSEC(inset) ;
if( fbot < 0.0f ) ERROR_exit("fbot value can't be negative!") ;
if( ftop <= fbot ) ERROR_exit("ftop value %g must be greater than fbot value %g!",ftop,fbot) ;
ntime = DSET_NVALS(inset) ;
if( ntime < 9 ) ERROR_exit("Input dataset is too short!") ;
if( nfft <= 0 ){
nfft = csfft_nextup_even(ntime) ;
if( verb ) INFO_message("Data length = %d FFT length = %d",ntime,nfft) ;
(void)THD_bandpass_set_nfft(nfft) ;
} else if( nfft < ntime ){
ERROR_exit("-nfft %d is less than data length = %d",nfft,ntime) ;
} else {
kk = THD_bandpass_set_nfft(nfft) ;
if( kk != nfft && verb )
INFO_message("Data length = %d FFT length = %d",ntime,kk) ;
}
if( dt <= 0.0f ){
dt = DSET_TR(inset) ;
if( dt <= 0.0f ){
WARNING_message("Setting dt=1.0 since input dataset lacks a time axis!") ;
dt = 1.0f ;
}
}
ftopALL = 1./dt ;// Aug,2016: should solve problem of a too-large
// value for THD_bandpass_vectors(), while still
// being >f_{Nyquist}
if( !THD_bandpass_OK(ntime,dt,fbot,ftop,1) ) ERROR_exit("Can't continue!") ;
nx = DSET_NX(inset); ny = DSET_NY(inset); nz = DSET_NZ(inset); nvox = nx*ny*nz;
/* check mask, or create it */
if( verb ) INFO_message("Loading input dataset time series" ) ;
DSET_load(inset) ;
if( mask != NULL ){
if( mask_nx != nx || mask_ny != ny || mask_nz != nz )
ERROR_exit("-mask dataset grid doesn't match input dataset") ;
} else if( do_automask ){
mask = THD_automask( inset ) ;
if( mask == NULL )
ERROR_message("Can't create -automask from input dataset?") ;
nmask = THD_countmask( DSET_NVOX(inset) , mask ) ;
if( verb ) INFO_message("Number of voxels in automask = %d",nmask);
if( nmask < 1 ) ERROR_exit("Automask is too small to process") ;
} else {
mask = (byte *)malloc(sizeof(byte)*nvox) ; nmask = nvox ;
memset(mask,1,sizeof(byte)*nvox) ;
// if( verb ) // @@ alert if aaaalllllll vox are going to be analyzed!
INFO_message("No mask ==> processing all %d voxels",nvox);
}
/* A simple check of dataset quality [08 Feb 2010] */
if( !nosat ){
float val ;
INFO_message(
"Checking dataset for initial transients [use '-notrans' to skip this test]") ;
val = THD_saturation_check(inset,mask,0,0) ; kk = (int)(val+0.54321f) ;
if( kk > 0 )
ININFO_message(
"Looks like there %s %d non-steady-state initial time point%s :-(" ,
((kk==1) ? "is" : "are") , kk , ((kk==1) ? " " : "s") ) ;
else if( val > 0.3210f ) /* don't ask where this threshold comes from! */
ININFO_message(
"MAYBE there's an initial positive transient of 1 point, but it's hard to tell\n") ;
else
ININFO_message("No widespread initial positive transient detected :-)") ;
}
/* check -dsort inputs for match to inset */
for( kk=0 ; kk < nortset ; kk++ ){
if( DSET_NX(ortset[kk]) != nx ||
DSET_NY(ortset[kk]) != ny ||
DSET_NZ(ortset[kk]) != nz ||
DSET_NVALS(ortset[kk]) != ntime )
ERROR_exit("-dsort %s doesn't match input dataset grid" ,
DSET_BRIKNAME(ortset[kk]) ) ;
}
/* convert input dataset to a vectim, which is more fun */
// @@ convert BP'ing ftop/bot into indices for the DFT (below)
delf = 1.0/(ntime*dt);
ind_low = (int) rint(fbot/delf);
ind_high = (int) rint(ftop/delf);
if( ntime % 2 ) // nyquist number
N_ny = (ntime-1)/2;
else
N_ny = ntime/2;
sqnt = sqrt(ntime);
nt_fac = sqrt(ntime*(ntime-1));
// @@ if BP_LAST==0:
// now we go through twice, doing LFF bandpass for NumDen==0 and
// `full spectrum' processing for NumDen==1.
// if BP_LAST==1:
// now we go through once, doing only `full spectrum' processing
for( NumDen=0 ; NumDen<2 ; NumDen++) {
//if( NumDen==1 ){ // full spectrum
// fbot = fbotALL;
// ftop = ftopALL;
//}
// essentially, just doesn't BP here, and the perfect filtering at end
// is used for both still; this makes the final output spectrum
// contain only frequencies in range of 0.01-0.08
if( BP_LAST==1 )
INFO_message("Only doing filtering to LFFs at end!");
mrv = THD_dset_to_vectim( inset , mask , 0 ) ;
if( mrv == NULL ) ERROR_exit("Can't load time series data!?") ;
if( NumDen==1 )
DSET_unload(inset) ; // @@ only unload on 2nd pass
/* similarly for the ort vectors */
if( ortar != NULL ){
for( kk=0 ; kk < IMARR_COUNT(ortar) ; kk++ ){
ortim = IMARR_SUBIM(ortar,kk) ;
if( ortim->nx < ntime )
ERROR_exit("-ort file %s is shorter than input dataset time series",
ortim->name ) ;
ort = (float **)realloc( ort , sizeof(float *)*(nort+ortim->ny) ) ;
for( vv=0 ; vv < ortim->ny ; vv++ )
ort[nort++] = MRI_FLOAT_PTR(ortim) + ortim->nx * vv ;
}
}
/* all the real work now */
if( do_despike ){
int_pair nsp ;
if( verb ) INFO_message("Testing data time series for spikes") ;
nsp = THD_vectim_despike9( mrv ) ;
if( verb ) ININFO_message(" -- Squashed %d spikes from %d voxels",nsp.j,nsp.i) ;
}
if( verb ) INFO_message("Bandpassing data time series") ;
if( (BP_LAST==0) && (NumDen==0) )
(void)THD_bandpass_vectim( mrv , dt,fbot,ftop , qdet , nort,ort ) ;
else
(void)THD_bandpass_vectim( mrv , dt,fbotALL,ftopALL, qdet,nort,ort ) ;
/* OK, maybe a little more work */
if( nortset == 1 ){
MRI_vectim *orv ;
orv = THD_dset_to_vectim( ortset[0] , mask , 0 ) ;
if( orv == NULL ){
ERROR_message("Can't load -dsort %s",DSET_BRIKNAME(ortset[0])) ;
} else {
float *dp , *mvv , *ovv , ff ;
if( verb ) INFO_message("Orthogonalizing to bandpassed -dsort") ;
//(void)THD_bandpass_vectim( orv , dt,fbot,ftop , qdet , nort,ort ) ; //@@
if( (BP_LAST==0) && (NumDen==0) )
(void)THD_bandpass_vectim(orv,dt,fbot,ftop,qdet,nort,ort);
else
(void)THD_bandpass_vectim(orv,dt,fbotALL,ftopALL,qdet,nort,ort);
THD_vectim_normalize( orv ) ;
dp = malloc(sizeof(float)*mrv->nvec) ;
THD_vectim_vectim_dot( mrv , orv , dp ) ;
for( vv=0 ; vv < mrv->nvec ; vv++ ){
ff = dp[vv] ;
if( ff != 0.0f ){
mvv = VECTIM_PTR(mrv,vv) ; ovv = VECTIM_PTR(orv,vv) ;
for( kk=0 ; kk < ntime ; kk++ ) mvv[kk] -= ff*ovv[kk] ;
}
}
VECTIM_destroy(orv) ; free(dp) ;
}
}
if( blur > 0.0f ){
if( verb )
INFO_message("Blurring time series data spatially; FWHM=%.2f",blur) ;
mri_blur3D_vectim( mrv , blur ) ;
}
if( pvrad > 0.0f ){
if( verb )
INFO_message("Local PV-ing time series data spatially; radius=%.2f",pvrad) ;
THD_vectim_normalize( mrv ) ;
THD_vectim_localpv( mrv , pvrad ) ;
}
if( do_norm && pvrad <= 0.0f ){
if( verb ) INFO_message("L2 normalizing time series data") ;
THD_vectim_normalize( mrv ) ;
}
/* create output dataset, populate it, write it, then quit */
if( (NumDen==0) ) { // @@ BP'ed version; will do filt if BP_LAST
if(BP_LAST) // do bandpass here for BP_LAST
(void)THD_bandpass_vectim(mrv,dt,fbot,ftop,qdet,0,NULL);
if( verb ) INFO_message("Creating output dataset in memory, then writing it") ;
outset = EDIT_empty_copy(inset) ;
if(SERIES_OUT){
sprintf(out_lff,"%s_LFF",prefix);
EDIT_dset_items( outset , ADN_prefix,out_lff , ADN_none ) ;
tross_Copy_History( inset , outset ) ;
tross_Make_History( "3dBandpass" , argc,argv , outset ) ;
}
for( vv=0 ; vv < ntime ; vv++ )
EDIT_substitute_brick( outset , vv , MRI_float , NULL ) ;
#if 1
THD_vectim_to_dset( mrv , outset ) ;
#else
AFNI_OMP_START ;
#pragma omp parallel
{ float *far , *var ; int *ivec=mrv->ivec ; int vv,kk ;
#pragma omp for
for( vv=0 ; vv < ntime ; vv++ ){
far = DSET_BRICK_ARRAY(outset,vv) ; var = mrv->fvec + vv ;
for( kk=0 ; kk < nmask ; kk++ ) far[ivec[kk]] = var[kk*ntime] ;
}
}
AFNI_OMP_END ;
#endif
VECTIM_destroy(mrv) ;
if(SERIES_OUT){ // @@
DSET_write(outset) ; if( verb ) WROTE_DSET(outset) ;
}
}
else{ // @@ non-BP'ed version
if( verb ) INFO_message("Creating output dataset 2 in memory") ;
// do this here because LFF version was also BP'ed at end.
if(BP_LAST) // do bandpass here for BP_LAST
(void)THD_bandpass_vectim(mrv,dt,fbotALL,ftopALL,qdet,0,NULL);
outsetALL = EDIT_empty_copy(inset) ;
if(UNBP_OUT){
sprintf(out_unBP,"%s_unBP",prefix);
EDIT_dset_items( outsetALL, ADN_prefix, out_unBP, ADN_none );
tross_Copy_History( inset , outsetALL ) ;
tross_Make_History( "3dRSFC" , argc,argv , outsetALL ) ;
}
for( vv=0 ; vv < ntime ; vv++ )
EDIT_substitute_brick( outsetALL , vv , MRI_float , NULL ) ;
#if 1
THD_vectim_to_dset( mrv , outsetALL ) ;
#else
AFNI_OMP_START ;
#pragma omp parallel
{ float *far , *var ; int *ivec=mrv->ivec ; int vv,kk ;
#pragma omp for
for( vv=0 ; vv < ntime ; vv++ ){
far = DSET_BRICK_ARRAY(outsetALL,vv) ; var = mrv->fvec + vv ;
for( kk=0 ; kk < nmask ; kk++ ) far[ivec[kk]] = var[kk*ntime] ;
}
}
AFNI_OMP_END ;
#endif
VECTIM_destroy(mrv) ;
if(UNBP_OUT){
DSET_write(outsetALL) ; if( verb ) WROTE_DSET(outsetALL) ;
}
}
}// end of NumDen loop
// @@
INFO_message("Starting the (f)ALaFFel calcs") ;
// allocations
series1 = (double *)calloc(ntime,sizeof(double));
series2 = (double *)calloc(ntime,sizeof(double));
xx1 = (double *)calloc(2*ntime,sizeof(double));
xx2 = (double *)calloc(2*ntime,sizeof(double));
alff = (float *)calloc(nvox,sizeof(float));
malff = (float *)calloc(nvox,sizeof(float));
falff = (float *)calloc(nvox,sizeof(float));
if( (series1 == NULL) || (series2 == NULL)
|| (xx1 == NULL) || (xx2 == NULL)
|| (alff == NULL) || (malff == NULL) || (falff == NULL)) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(122);
}
if(DO_RSFA) {
rsfa = (float *)calloc(nvox,sizeof(float));
mrsfa = (float *)calloc(nvox,sizeof(float));
frsfa = (float *)calloc(nvox,sizeof(float));
if( (rsfa == NULL) || (mrsfa == NULL) || (frsfa == NULL)) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(123);
}
}
work = gsl_fft_real_workspace_alloc (ntime);
real1 = gsl_fft_real_wavetable_alloc (ntime);
real2 = gsl_fft_real_wavetable_alloc (ntime);
gsl_complex_packed_array compl_freqs1 = xx1;
gsl_complex_packed_array compl_freqs2 = xx2;
// *********************************************************************
// *********************************************************************
// ************** Falafelling = ALFF/fALFF calcs *****************
// *********************************************************************
// *********************************************************************
// Be now have the BP'ed data set (outset) and the non-BP'ed one
// (outsetALL). now we'll FFT both, get amplitudes in appropriate
// ranges, and calculate: ALFF, mALFF, fALFF,
ctr = 0;
for( kk=0; kk<nvox ; kk++) {
if(mask[kk]) {
// BP one, and unBP one, either for BP_LAST or !BP_LAST
for( m=0 ; m<ntime ; m++ ) {
series1[m] = THD_get_voxel(outset,kk,m);
series2[m] = THD_get_voxel(outsetALL,kk,m);
}
mm = gsl_fft_real_transform(series1, 1, ntime, real1, work);
mm = gsl_fft_halfcomplex_unpack(series1, compl_freqs1, 1, ntime);
mm = gsl_fft_real_transform(series2, 1, ntime, real2, work);
mm = gsl_fft_halfcomplex_unpack(series2, compl_freqs2, 1, ntime);
numer = 0.0f;
denom = 0.0f;
de_rsfa = 0.0f;
nu_rsfa = 0.0f;
for( m=1 ; m<N_ny ; m++ ) {
mm = 2*m;
pow2 = compl_freqs2[mm]*compl_freqs2[mm] +
compl_freqs2[mm+1]*compl_freqs2[mm+1]; // power
//pow2*=2;// factor of 2 since ampls are even funcs
denom+= (float) sqrt(pow2); // amplitude
de_rsfa+= (float) pow2;
if( ( m>=ind_low ) && ( m<=ind_high ) ){
pow1 = compl_freqs1[mm]*compl_freqs1[mm]+
compl_freqs1[mm+1]*compl_freqs1[mm+1];
//pow1*=2;
numer+= (float) sqrt(pow1);
nu_rsfa+= (float) pow1;
}
}
if( denom>0.000001 )
falff[kk] = numer/denom;
else
falff[kk] = 0.;
alff[kk] = 2*numer/sqnt;// factor of 2 since ampl is even funct
meanALFF+= alff[kk];
if(DO_RSFA){
nu_rsfa = sqrt(2*nu_rsfa); // factor of 2 since ampls
de_rsfa = sqrt(2*de_rsfa); // are even funcs
if( de_rsfa>0.000001 )
frsfa[kk] = nu_rsfa/de_rsfa;
else
frsfa[kk]=0.;
rsfa[kk] = nu_rsfa/nt_fac;
meanRSFA+= rsfa[kk];
}
ctr+=1;
}
}
meanALFF/= ctr;
meanRSFA/= ctr;
gsl_fft_real_wavetable_free(real1);
gsl_fft_real_wavetable_free(real2);
gsl_fft_real_workspace_free(work);
// ALFFs divided by mean of brain value
for( kk=0 ; kk<nvox ; kk++ )
if(mask[kk]){
malff[kk] = alff[kk]/meanALFF;
if(DO_RSFA)
mrsfa[kk] = rsfa[kk]/meanRSFA;
}
// **************************************************************
// **************************************************************
// Store and output
// **************************************************************
// **************************************************************
outsetALFF = EDIT_empty_copy( inset ) ;
sprintf(out_alff,"%s_ALFF",prefix);
EDIT_dset_items( outsetALFF,
ADN_nvals, 1,
ADN_datum_all , MRI_float ,
ADN_prefix , out_alff,
ADN_none ) ;
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetALFF)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outsetALFF));
EDIT_substitute_brick(outsetALFF, 0, MRI_float, alff);
alff=NULL;
THD_load_statistics(outsetALFF);
tross_Make_History("3dRSFC", argc, argv, outsetALFF);
THD_write_3dim_dataset(NULL, NULL, outsetALFF, True);
outsetfALFF = EDIT_empty_copy( inset ) ;
sprintf(out_falff,"%s_fALFF",prefix);
EDIT_dset_items( outsetfALFF,
ADN_nvals, 1,
ADN_datum_all , MRI_float ,
ADN_prefix , out_falff,
ADN_none ) ;
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetfALFF)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outsetfALFF));
EDIT_substitute_brick(outsetfALFF, 0, MRI_float, falff);
falff=NULL;
THD_load_statistics(outsetfALFF);
tross_Make_History("3dRSFC", argc, argv, outsetfALFF);
THD_write_3dim_dataset(NULL, NULL, outsetfALFF, True);
outsetmALFF = EDIT_empty_copy( inset ) ;
sprintf(out_malff,"%s_mALFF",prefix);
EDIT_dset_items( outsetmALFF,
ADN_nvals, 1,
ADN_datum_all , MRI_float ,
ADN_prefix , out_malff,
ADN_none ) ;
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetmALFF)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outsetmALFF));
EDIT_substitute_brick(outsetmALFF, 0, MRI_float, malff);
malff=NULL;
THD_load_statistics(outsetmALFF);
tross_Make_History("3dRSFC", argc, argv, outsetmALFF);
THD_write_3dim_dataset(NULL, NULL, outsetmALFF, True);
if(DO_RSFA){
outsetRSFA = EDIT_empty_copy( inset ) ;
sprintf(out_rsfa,"%s_RSFA",prefix);
EDIT_dset_items( outsetRSFA,
ADN_nvals, 1,
ADN_datum_all , MRI_float ,
ADN_prefix , out_rsfa,
ADN_none ) ;
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetRSFA)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outsetRSFA));
EDIT_substitute_brick(outsetRSFA, 0, MRI_float, rsfa);
rsfa=NULL;
THD_load_statistics(outsetRSFA);
tross_Make_History("3dRSFC", argc, argv, outsetRSFA);
THD_write_3dim_dataset(NULL, NULL, outsetRSFA, True);
outsetfRSFA = EDIT_empty_copy( inset ) ;
sprintf(out_frsfa,"%s_fRSFA",prefix);
EDIT_dset_items( outsetfRSFA,
ADN_nvals, 1,
ADN_datum_all , MRI_float ,
ADN_prefix , out_frsfa,
ADN_none ) ;
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetfRSFA)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outsetfRSFA));
EDIT_substitute_brick(outsetfRSFA, 0, MRI_float, frsfa);
frsfa=NULL;
THD_load_statistics(outsetfRSFA);
tross_Make_History("3dRSFC", argc, argv, outsetfRSFA);
THD_write_3dim_dataset(NULL, NULL, outsetfRSFA, True);
outsetmRSFA = EDIT_empty_copy( inset ) ;
sprintf(out_mrsfa,"%s_mRSFA",prefix);
EDIT_dset_items( outsetmRSFA,
ADN_nvals, 1,
ADN_datum_all , MRI_float ,
ADN_prefix , out_mrsfa,
ADN_none ) ;
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetmRSFA)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outsetmRSFA));
EDIT_substitute_brick(outsetmRSFA, 0, MRI_float, mrsfa);
mrsfa=NULL;
THD_load_statistics(outsetmRSFA);
tross_Make_History("3dRSFC", argc, argv, outsetmRSFA);
THD_write_3dim_dataset(NULL, NULL, outsetmRSFA, True);
}
// ************************************************************
// ************************************************************
// Freeing
// ************************************************************
// ************************************************************
DSET_delete(inset);
DSET_delete(outsetALL);
DSET_delete(outset);
DSET_delete(outsetALFF);
DSET_delete(outsetmALFF);
DSET_delete(outsetfALFF);
DSET_delete(outsetRSFA);
DSET_delete(outsetmRSFA);
DSET_delete(outsetfRSFA);
free(inset);
free(outsetALL);
free(outset);
free(outsetALFF);
free(outsetmALFF);
free(outsetfALFF);
free(outsetRSFA);
free(outsetmRSFA);
free(outsetfRSFA);
free(rsfa);
free(mrsfa);
free(frsfa);
free(alff);
free(malff);
free(falff);
free(mask);
free(series1);
free(series2);
free(xx1);
free(xx2);
exit(0) ;
}
/* ----------------------------------------------------------------------
* fill the param_t struct
* return 1 on (acceptable) termination
* 0 on continue
* -1 on error
*/
int process_opts(param_t * params, int argc, char * argv[] )
{
int ac, ival;
ENTRY("process_opts");
memset(params, 0, sizeof(param_t)); /* init everything to 0 */
params->inputs = NULL;
params->prefix = "combined_mask";
init_int_list(¶ms->IND, 0);
init_int_list(¶ms->RESD, 0);
params->frac = -1.0;
params->datum = MRI_byte;
params->verb = 1;
params->ndsets = 0;
if( argc < 2 ) { show_help(); RETURN(1); }
ac = 1;
while( ac < argc ) {
/* check for terminal options */
if( strcmp(argv[ac],"-help") == 0 ) {
show_help();
RETURN(1);
} else if( strcmp(argv[ac],"-hist") == 0 ) {
int c, len = sizeof(g_history)/sizeof(char *);
for( c = 0; c < len; c++) fputs(g_history[c], stdout);
putchar('\n');
RETURN(1);
} else if( strcmp(argv[ac],"-ver") == 0 ) {
puts(g_version);
RETURN(1);
}
/* the remaining options are alphabetical */
else if( strcmp(argv[ac],"-count") == 0 ) {
params->count = 1;
ac++; continue;
}
else if( strcmp(argv[ac],"-datum") == 0 ) {
if( ++ac >= argc ) ERROR_exit("need argument after '-datum'");
/* output datum can be byte, short or float */
if ( ! strcmp(argv[ac],"byte") ) params->datum = MRI_byte;
else if( ! strcmp(argv[ac],"short") ) params->datum = MRI_short;
else if( ! strcmp(argv[ac],"float") ) params->datum = MRI_float;
else ERROR_exit("-datum '%s' is not supported", argv[ac]);
ac++; continue;
}
/* read in a list of dilations (negatives are erosions) */
else if( strncmp(argv[ac],"-dilate_in", 10) == 0 ) {
char * rptr; /* return pointer for strtol */
int ndilates = 0;
if( ++ac >= argc ) ERROR_exit("need argument after '-dilate_inputs'");
ival = strtol(argv[ac], &rptr, 10);
while( ac < argc && rptr > argv[ac] ) {
if( ! add_to_int_list(¶ms->IND, ival, 1) ) RETURN(-1);
ndilates++;
if( ++ac >= argc ) break;
ival = strtol(argv[ac], &rptr, 10);
}
if( ndilates == 0 )
ERROR_exit("no integral dilations found after -dilate_inputs");
/* ac is already past last number */ continue;
}
/* read in a list of dilations (negatives are erosions) */
else if( strncmp(argv[ac],"-dilate_result", 11) == 0 ) {
char * rptr; /* return pointer for strtol */
int ndilates = 0;
if( ++ac >= argc ) ERROR_exit("need argument after '-dilate_result'");
ival = strtol(argv[ac], &rptr, 10);
while( ac < argc && rptr > argv[ac] ) {
if( ! add_to_int_list(¶ms->RESD, ival, 1) ) RETURN(-1);
ndilates++;
if( ++ac >= argc ) break;
ival = strtol(argv[ac], &rptr, 10);
}
if( ndilates == 0 )
ERROR_exit("no integral dilations found after -dilate_result");
/* ac is already past last number */ continue;
}
/* overlap: -frac, -inter, -union */
else if( strncmp(argv[ac],"-frac", 5) == 0 ) {
if( ++ac >= argc ) ERROR_exit("need argument after '-frac'");
params->frac = atof(argv[ac]);
if( params->frac < 0.0 )
ERROR_exit("have -frac < 0 (from %s)", argv[ac]);
ac++; continue;
}
else if( strncmp(argv[ac],"-inter", 6) == 0 ) {
params->frac = 1.0;
ac++; continue;
}
else if( strcmp(argv[ac],"-union") == 0 ) {
params->frac = 0.0;
ac++; continue;
}
else if( strcmp(argv[ac],"-fill_holes") == 0 ) {
params->fill = 1;
ac++; continue;
}
else if( strncmp(argv[ac],"-inputs", 4) == 0 ) {
/* store list of names from argv */
ac++;
params->inputs = argv+ac; /* pointer to first name */
params->ndsets = 0; /* number of datasets */
while( ac < argc && argv[ac][0] != '-' ){ params->ndsets++; ac++; }
if( params->ndsets == 0 ) ERROR_exit("need datasets after '-inputs'");
/* already incremented: ac++; */ continue;
}
else if( strcmp(argv[ac],"-prefix") == 0 ) {
if( ++ac >= argc ) ERROR_exit("need argument after '-prefix'");
params->prefix = argv[ac];
if( !THD_filename_ok(params->prefix) )
ERROR_exit("Illegal name after -prefix: %s", argv[ac]);
ac++; continue;
}
else if( strcmp(argv[ac],"-quiet") == 0 ) { /* -quiet means -verb 0 */
params->verb = 0;
ac++; continue;
}
else if( strcmp(argv[ac],"-verb") == 0 ) {
if( ++ac >= argc ) ERROR_exit("need argument after '-verb'");
params->verb = atoi(argv[ac]);
ac++; continue;
}
ERROR_message("** unknown option '%s'\n",argv[ac]);
RETURN(-1);
}
if( !dilations_are_valid(& params->IND) ||
!dilations_are_valid(& params->RESD) ) RETURN(-1);
if( params->ndsets <= 0 ) ERROR_exit("missing -input dataset list");
if( !params->prefix ) ERROR_exit("missing -prefix option");
if( params->frac < 0.0 ) {
if( params->verb ) INFO_message("no -frac option: defaulting to -union");
params->frac = 0.0;
}
if( params->verb > 1 )
INFO_message("%d datasets, frac = %g, %d IN dilation(s), %d OUT D(s)\n",
params->ndsets, params->frac, params->IND.num, params->RESD.num);
RETURN(0);
}
THD_3dim_dataset * THD_localhistog( int nsar , THD_3dim_dataset **insar ,
int numval , int *rlist , MCW_cluster *nbhd ,
int do_prob , int verb )
{
THD_3dim_dataset *outset=NULL , *inset ;
int nvox=DSET_NVOX(insar[0]) ;
int ids, iv, bb, nnpt=nbhd->num_pt ;
MRI_IMAGE *bbim ; int btyp ;
float **outar , **listar ;
ENTRY("THD_localhistog") ;
/*---- create output dataset ----*/
outset = EDIT_empty_copy(insar[0]) ;
EDIT_dset_items( outset ,
ADN_nvals , numval ,
ADN_datum_all , MRI_float ,
ADN_nsl , 0 ,
ADN_brick_fac , NULL ,
ADN_none ) ;
outar = (float **)malloc(sizeof(float *)*numval) ;
for( bb=0 ; bb < numval ; bb++ ){
EDIT_substitute_brick( outset , bb , MRI_float , NULL ) ;
outar[bb] = DSET_BRICK_ARRAY(outset,bb) ;
}
/*---- make mapping between values and arrays to get those values ----*/
listar = (float **)malloc(sizeof(float *)*TWO16) ;
for( bb=0 ; bb < TWO16 ; bb++ ) listar[bb] = outar[0] ;
for( bb=1 ; bb < numval ; bb++ ){
listar[ rlist[bb] + TWO15 ] = outar[bb] ;
}
/*----------- loop over datasets, add in counts for all voxels -----------*/
for( ids=0 ; ids < nsar ; ids++ ){ /* dataset loop */
inset = insar[ids] ; DSET_load(inset) ;
for( iv=0 ; iv < DSET_NVALS(inset) ; iv++ ){ /* sub-brick loop */
if( verb ) fprintf(stderr,".") ;
bbim = DSET_BRICK(inset,iv) ; btyp = bbim->kind ;
if( nnpt == 1 ){ /* only 1 voxel in nbhd */
int qq,ii,jj,kk,ib,nb ;
switch( bbim->kind ){
case MRI_short:{
short *sar = MRI_SHORT_PTR(bbim) ;
for( qq=0 ; qq < nvox ; qq++ ) listar[sar[qq]+TWO15][qq]++ ;
}
break ;
case MRI_byte:{
byte *bar = MRI_BYTE_PTR(bbim) ;
for( qq=0 ; qq < nvox ; qq++ ) listar[bar[qq]+TWO15][qq]++ ;
}
break ;
case MRI_float:{
float *far = MRI_FLOAT_PTR(bbim) ; short ss ;
for( qq=0 ; qq < nvox ; qq++ ){ ss = SHORTIZE(far[qq]); listar[ss+TWO15][qq]++; }
}
break ;
}
} else { /* multiple voxels in nbhd */
AFNI_OMP_START ;
#pragma omp parallel
{ int qq,ii,jj,kk,ib,nb ; void *nar ; short *sar,ss ; byte *bar ; float *far ;
nar = malloc(sizeof(float)*nnpt) ;
sar = (short *)nar ; bar = (byte *)nar ; far = (float *)nar ;
#pragma omp for
for( qq=0 ; qq < nvox ; qq++ ){ /* qq=voxel index */
ii = DSET_index_to_ix(inset,qq) ;
jj = DSET_index_to_jy(inset,qq) ;
kk = DSET_index_to_kz(inset,qq) ;
nb = mri_get_nbhd_array( bbim , NULL , ii,jj,kk , nbhd , nar ) ;
if( nb == 0 ) continue ;
switch( btyp ){
case MRI_short:
for( ib=0 ; ib < nb ; ib++ ) listar[sar[ib]+TWO15][qq]++ ;
break ;
case MRI_byte:
for( ib=0 ; ib < nb ; ib++ ) listar[bar[ib]+TWO15][qq]++ ;
break ;
case MRI_float:
for( ib=0 ; ib < nb ; ib++ ){ ss = SHORTIZE(far[ib]); listar[ss+TWO15][qq]++; }
break ;
}
} /* end of voxel loop */
free(nar) ;
} /* end of OpenMP */
AFNI_OMP_END ;
}
} /* end of sub-brick loop */
DSET_unload(inset) ;
} /* end of dataset loop */
if( verb ) fprintf(stderr,"\n") ;
free(listar) ;
/*---- post-process output ---*/
if( do_prob ){
byte **bbar ; int pp ;
if( verb ) INFO_message("Conversion to probabilities") ;
AFNI_OMP_START ;
#pragma omp parallel
{ int qq , ib ; float pfac , val ; byte **bbar ;
#pragma omp for
for( qq=0 ; qq < nvox ; qq++ ){
pfac = 0.0001f ;
for( ib=0 ; ib < numval ; ib++ ) pfac += outar[ib][qq] ;
pfac = 250.0f / pfac ;
for( ib=0 ; ib < numval ; ib++ ){
val = outar[ib][qq]*pfac ; outar[ib][qq] = BYTEIZE(val) ;
}
}
} /* end OpenMP */
AFNI_OMP_END ;
bbar = (byte **)malloc(sizeof(byte *)*numval) ;
for( bb=0 ; bb < numval ; bb++ ){
bbar[bb] = (byte *)malloc(sizeof(byte)*nvox) ;
for( pp=0 ; pp < nvox ; pp++ ) bbar[bb][pp] = (byte)outar[bb][pp] ;
EDIT_substitute_brick(outset,bb,MRI_byte,bbar[bb]) ;
EDIT_BRICK_FACTOR(outset,bb,0.004f) ;
}
free(bbar) ;
} /* end of do_prob */
free(outar) ;
RETURN(outset) ;
}
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 powell_newuoa_constrained( int ndim, double *x, double *cost ,
double *xbot, double *xtop ,
int nrand, int nkeep, int ntry ,
double rstart , double rend ,
int maxcall , double (*ufunc)(int,double *) )
{
integer n , npt , icode , maxfun ;
doublereal rhobeg , rhoend , *w ;
int ii,tt , tbest , ntot=0 , nx01 ;
double **x01 , *x01val , vbest ;
/*--- check inputs for stupidity ---*/
if( ndim < 1 ) return -2 ;
if( x == NULL ) return -3 ;
if( ufunc == NULL ) return -5 ;
if( xbot == NULL || xtop == NULL ) return -6 ;
/*--- edit inputs for idiocy ---*/
if( rstart <= rend || rstart <= 1.e-4 || rstart > 0.333 ){
rstart = 0.1 ; rend = 1.e-4 ;
}
/* if this call is totally vanilla, then call the older function */
if( nrand == 0 && nkeep == 0 && ntry < 2 )
return powell_newuoa_con( ndim , x,xbot,xtop ,
0 , rstart,rend , maxcall , ufunc ) ;
if( maxcall < 10+5*ndim ) maxcall = 10+5*ndim ;
if( ntry < 1 ) ntry = 1 ;
if( nkeep < 1 && nrand > 0 ) nkeep = 1 ;
if( nkeep > 0 && nrand <= 2*nkeep ) nrand = 2*nkeep+1 ;
/*--- set up newuoa parameters and workspace ---*/
n = ndim ;
npt = (int)(mfac*n+afac) ; if( npt < n+2 ) npt = n+2 ;
icode = (n+1)*(n+2)/2 ; if( npt > icode ) npt = icode ;
maxfun = maxcall ;
rhobeg = (doublereal)rstart ;
rhoend = (doublereal)rend ;
icode = (npt+14)*(npt+n) + 3*n*(n+3)/2 + 666 ;
w = (doublereal *)malloc(sizeof(doublereal)*icode) ; /* workspace */
userfun = ufunc ; /* store pointer to user's function in global variable */
/*-- To enforce constraints:
(a) scale each variable to be in the range 0..1, in x01[] array;
(b) in calfun_(), if an input variable drifts outside the 0..1
range, bring it back into that range with the PRED01() macro;
(c) then scale that 0..1 value back to the 'true' value
before calling ufunc() to evaluate objective function. -------*/
scalx = 1 ; /* signal to calfun_() to apply scaling */
sxmin = (double *)malloc(sizeof(double)*ndim) ; /* copy xbot for calfun_ */
sxsiz = (double *)malloc(sizeof(double)*ndim) ; /* = xtop - xbot */
sx = (double *)malloc(sizeof(double)*ndim) ; /* workspace for calfun_ */
for( ii=0 ; ii < ndim ; ii++ ){
sxmin[ii] = xbot[ii] ;
sxsiz[ii] = xtop[ii] - xbot[ii]; if( sxsiz[ii] <= 0.0 ) sxsiz[ii] = 1.0 ;
}
/*-- set up the first starting vector from x[] array --*/
nx01 = nkeep+2 ;
x01 = (double **)malloc(sizeof(double *)*nx01) ; /* array of vectors */
for( tt=0 ; tt < nx01 ; tt++ )
x01[tt] = (double *)malloc(sizeof(double)*ndim) ; /* tt-th keeper vector */
x01val = (double *)malloc(sizeof(double)*nx01) ; /* cost func values */
for( tt=0 ; tt < nx01 ; tt++ ) x01val[tt] = BIGVAL; /* mark as unready */
/* copy x[] into x01[0], scaling to 0..1 range */
for( ii=0 ; ii < ndim ; ii++ ){
x01[0][ii] = (x[ii] - sxmin[ii]) / sxsiz[ii] ;
x01[0][ii] = PRED01(x01[0][ii]) ; /* make sure is in range 0..1 */
}
(void)calfun_(&n,x01[0],x01val+0) ; /* value of keeper #0 = input vector */
ntot++ ; /* number of times calfun_() is called */
/*-- do a random search for the best starting vector? --*/
if( nrand > 0 ){
double *xtest , *qpar,*cpar , ftest , rb,re , dist ;
int qq,jj ; integer mf ;
static int seed=1 ;
if( seed ){ srand48((long)time(NULL)+(long)getpid()); seed=0; }
xtest = (double *)malloc(sizeof(double)*ndim) ;
/* Step 1: search nrand start vectors, keeping the
nkeep-th best values we find on the way.
N.B.: we do NOT displace the input vector in x01[0];
therefore, there are nkeep+1 vectors being kept */
if( verb )
INFO_message("Powell: random search of %d vectors in %d-dim space",nrand,ndim);
for( qq=0 ; qq < nrand ; qq++ ){
for( ii=0 ; ii < ndim ; ii++ ) xtest[ii] = drand48() ; /* random pt */
(void)calfun_(&n,xtest,&ftest) ; ntot++ ; /* eval cost func */
for( tt=1 ; tt <= nkeep ; tt++ ){ /* is this better than what */
if( ftest < x01val[tt] ){ /* we've seen thus far? */
for( jj=nkeep-1 ; jj >= tt ; jj-- ){ /* push those above #tt up */
memcpy( x01[jj+1] , x01[jj] , sizeof(double)*ndim ) ; /* in list */
x01val[jj+1] = x01val[jj] ;
}
memcpy( x01[tt] , xtest , sizeof(double)*ndim ) ; /* save in list */
x01val[tt] = ftest ;
break ; /* breaking out of 'tt' loop, having put xtest in list */
}
}
} /* end of random search loop */
free((void *)xtest) ; /* don't need this no more */
/* count number that have valid cost function results */
for( tt=0 ; tt <= nkeep && x01val[tt] < BIGVAL ; tt++ ) ; /* nada */
nkeep = tt ; /** from now on, nkeep = actual number of keepers **/
/* Step 2a: do a little first round optimization on each of the keepers */
if( verb )
INFO_message("Powell: 1st round optimization on %d vectors",nkeep);
rb = 0.05 ; re = 0.005 ; mf = 9*ndim+7 ; tbest = 0 ; vbest = BIGVAL ;
for( tt=0 ; tt < nkeep ; tt++ ){
(void)newuoa_( &n, &npt, (doublereal *)x01[tt], &rb,&re,&mf,w,&icode ) ;
for( ii=0 ; ii < ndim ; ii++ ) x01[tt][ii] = PRED01(x01[tt][ii]) ;
(void)calfun_(&n,x01[tt],x01val+tt) ; ntot += icode+1 ;
if( x01val[tt] < vbest ){ vbest = x01val[tt]; tbest = tt; }
if( verb > 1 )
ININFO_message("%2d: cost = %g %c nfunc=%d",tt,x01val[tt],(tbest==tt)?'*':' ',icode) ;
}
/* Step 2b: sort results by new x01val costs */
qsort_doublestuff( nkeep , x01val , (void **)x01 ) ;
/* Step 2c: cast out those that are too close to better vectors
in the max-norm (we always keep the best vector in x01[0]) */
#undef DTHRESH
#define DTHRESH 0.05 /* max-norm distance threshold for vector reject */
for( tt=1 ; tt < nkeep ; tt++ ){
qpar = x01[tt] ; /* do we keep this vector? */
for( jj=0 ; jj < tt ; jj++ ){ /* loop over previous keepers */
if( x01val[jj] >= BIGVAL ) continue ; /* already rejected */
cpar = x01[jj] ; /* compare qpar to cpar */
for( dist=0.0,ii=0 ; ii < ndim ; ii++ ){
re = fabs(cpar[ii]-qpar[ii]) ; dist = MAX(dist,re) ;
}
if( dist < DTHRESH ){ /* qpar is too close to cpar */
x01val[tt] = BIGVAL ; break ; /* reject qpar vector */
}
}
}
/* Step 2d: sort again (so that the rejected ones rise to the top) */
qsort_doublestuff( nkeep , x01val , (void **)x01 ) ;
for( tt=0 ; tt <= nkeep && x01val[tt] < BIGVAL ; tt++ ) ; /* nada */
nkeep = tt ; /* number of keepers that weren't rejected above */
if( ntry > nkeep ) ntry = nkeep ;
} else { /*------ didn't do random search -----*/
ntry = 1 ; /* can only try the input x[] vector! */
}
/****** fully optimize each of the first ntry-th vectors in x01[] ******/
if( verb )
INFO_message("Powell: 2nd round optimization on %d vectors",ntry) ;
tbest = 0 ; vbest = BIGVAL ;
for( tt=0 ; tt < ntry ; tt++ ){
(void)newuoa_( &n , &npt , (doublereal *)x01[tt] ,
&rhobeg , &rhoend , &maxfun , w , &icode ) ;
for( ii=0 ; ii < ndim ; ii++ ) x01[tt][ii] = PRED01(x01[tt][ii]) ;
(void)calfun_(&n,x01[tt],x01val+tt) ; ntot += icode+1 ;
if( x01val[tt] < vbest ){ vbest = x01val[tt]; tbest = tt; }
if( verb > 1 )
ININFO_message("%2d: cost = %g %c nfunc=%d",tt,x01val[tt],(tbest==tt)?'*':' ',icode) ;
}
/*-- Rescale bestest output vector back to 'true' range --*/
for( ii=0 ; ii < ndim ; ii++ )
x[ii] = sxmin[ii] + x01[tbest][ii] * sxsiz[ii] ;
if( cost != NULL ) *cost = vbest ; /* save cost func */
/*-- toss the trash, and vamoose the ranch --*/
free((void *)sx); free((void *)sxsiz); free((void *)sxmin);
sx = sxmin = sxsiz = NULL ; scalx = 0 ;
for( tt=0 ; tt < nx01 ; tt++ ) free((void *)x01[tt]) ;
free((void *)x01val); free((void *)x01); free((void *)w) ;
return ntot ;
}
int WB_netw_corr(int Do_r,
int Do_Z,
int HAVE_ROIS,
char *prefix,
int NIFTI_OUT,
int *NROI_REF,
int *Dim,
double ***ROI_AVE_TS,
int **ROI_LABELS_REF,
THD_3dim_dataset *insetTIME,
byte *mskd2,
int Nmask,
int argc,
char *argv[])
{
int i,j,k;
float **AVE_TS_fl=NULL; // not great, but another format of TS
char OUT_indiv0[300];
char OUT_indiv[300];
char OUT_indivZ[300];
MRI_IMAGE *mri=NULL;
THD_3dim_dataset *OUT_CORR_MAP=NULL;
THD_3dim_dataset *OUT_Z_MAP=NULL;
float *zscores=NULL;
int Nvox;
Nvox = Dim[0]*Dim[1]*Dim[2];
// make average time series per voxel
AVE_TS_fl = calloc( 1,sizeof(AVE_TS_fl));
for(i=0 ; i<1 ; i++)
AVE_TS_fl[i] = calloc(Dim[3],sizeof(float));
if( (AVE_TS_fl == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure (time series out).\n\n");
exit(123);
}
fprintf(stderr,"\nHAVE_ROIS=%d",HAVE_ROIS);
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++ ) {
fprintf(stderr,"\nNROI_REF[%d]= %d",k,NROI_REF[k]);
for( j=0 ; j<Dim[3] ; j++)
AVE_TS_fl[0][j] = (float) ROI_AVE_TS[k][i][j];
if( NIFTI_OUT )
sprintf(OUT_indiv,"%s/WB_CORR_ROI_%03d.nii.gz",
OUT_indiv0,ROI_LABELS_REF[k][i+1]);
else
sprintf(OUT_indiv,"%s/WB_CORR_ROI_%03d",
OUT_indiv0,ROI_LABELS_REF[k][i+1]);
mri = mri_float_arrays_to_image(AVE_TS_fl,Dim[3],1);
OUT_CORR_MAP = THD_Tcorr1D(insetTIME, mskd2, Nmask,
mri,
"pearson", OUT_indiv);
if(Do_r){
THD_load_statistics(OUT_CORR_MAP);
tross_Copy_History( insetTIME , OUT_CORR_MAP ) ;
tross_Make_History( "3dNetcorr", argc, argv, OUT_CORR_MAP );
if( !THD_ok_overwrite() &&
THD_is_ondisk(DSET_HEADNAME(OUT_CORR_MAP)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(OUT_CORR_MAP));
THD_write_3dim_dataset(NULL, NULL, OUT_CORR_MAP, True);
INFO_message("Wrote dataset: %s\n",DSET_BRIKNAME(OUT_CORR_MAP));
}
if(Do_Z){
if( NIFTI_OUT )
sprintf(OUT_indivZ,"%s/WB_Z_ROI_%03d.nii.gz",
OUT_indiv0,ROI_LABELS_REF[k][i+1]);
else
sprintf(OUT_indivZ,"%s/WB_Z_ROI_%03d",
OUT_indiv0,ROI_LABELS_REF[k][i+1]);
OUT_Z_MAP = EDIT_empty_copy(OUT_CORR_MAP);
EDIT_dset_items( OUT_Z_MAP,
ADN_nvals, 1,
ADN_datum_all , MRI_float ,
ADN_prefix , OUT_indivZ,
ADN_none ) ;
if( !THD_ok_overwrite() &&
THD_is_ondisk(DSET_HEADNAME(OUT_Z_MAP)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(OUT_Z_MAP));
zscores = (float *)calloc(Nvox,sizeof(float));
if( (zscores == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure (zscores).\n\n");
exit(123);
}
for( j=0 ; j<Nvox ; j++ )
if( mskd2[j] ) // control for r ==1
BOBatanhf( THD_get_voxel(OUT_CORR_MAP, j, 0) );
/*
if( THD_get_voxel(OUT_CORR_MAP, j, 0) > MAX_R )
zscores[j] = (float) atanh(MAX_R);
else if ( THD_get_voxel(OUT_CORR_MAP, j, 0) < -MAX_R )
zscores[j] = (float) atanh(-MAX_R);
else
zscores[j] = (float) atanh(THD_get_voxel(OUT_CORR_MAP, j, 0));*/
EDIT_substitute_brick(OUT_Z_MAP, 0, MRI_float, zscores);
zscores=NULL;
THD_load_statistics(OUT_Z_MAP);
tross_Copy_History(insetTIME, OUT_Z_MAP);
tross_Make_History("3dNetcorr", argc, argv, OUT_Z_MAP);
THD_write_3dim_dataset(NULL, NULL, OUT_Z_MAP, True);
INFO_message("Wrote dataset: %s\n",DSET_BRIKNAME(OUT_Z_MAP));
DSET_delete(OUT_Z_MAP);
free(OUT_Z_MAP);
OUT_Z_MAP=NULL;
}
DSET_delete(OUT_CORR_MAP);
free(OUT_CORR_MAP);
OUT_CORR_MAP=NULL;
}
}
free(zscores);
mri_free(mri);
for( i=0 ; i<1 ; i++)
free(AVE_TS_fl[i]);
free(AVE_TS_fl);
RETURN(1);
}
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) ;
}
