コード例 #1
0
ファイル: 3dmask_tool.c プロジェクト: LJWilliams/Neuroimaging
/*
 * 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(&params->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, &params->IND,1,params->verb);
      if( ! params->dsets[iset] ) RETURN(1);
   } 

   DSET_delete(dfirst); /* and nuke */

   RETURN(0);
}
コード例 #2
0
ファイル: SUMA_SegOpts.c プロジェクト: Gilles86/afni
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);
}
コード例 #3
0
ファイル: R_io.c プロジェクト: CesarCaballeroGaudes/afni
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);
}
コード例 #4
0
ファイル: R_io.c プロジェクト: CesarCaballeroGaudes/afni
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);
}
コード例 #5
0
ファイル: 3dTto1D.c プロジェクト: CesarCaballeroGaudes/afni
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);
}
コード例 #6
0
ファイル: 3dmask_tool.c プロジェクト: LJWilliams/Neuroimaging
/*
 * 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);
}
コード例 #7
0
ファイル: 3dSatCheck.c プロジェクト: LJWilliams/Neuroimaging
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) ;
}
コード例 #8
0
ファイル: afni_filer.c プロジェクト: Gilles86/afni
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 ;
}
コード例 #9
0
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) ;
}
コード例 #10
0
ファイル: 3dTto1D.c プロジェクト: CesarCaballeroGaudes/afni
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);
}
コード例 #11
0
ファイル: 3dmask_tool.c プロジェクト: LJWilliams/Neuroimaging
/*--------------- 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, &params->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, &params->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);
}
コード例 #12
0
ファイル: 3dmask_tool.c プロジェクト: LJWilliams/Neuroimaging
/*
 * 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);
}
コード例 #13
0
ファイル: 3dToyProg.c プロジェクト: CesarCaballeroGaudes/afni
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 ;
}
コード例 #14
0
ファイル: afni_lock.c プロジェクト: Gilles86/afni
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 ;
}
コード例 #15
0
ファイル: 3dmask_tool.c プロジェクト: LJWilliams/Neuroimaging
/* 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);
}
コード例 #16
0
ファイル: R_io.c プロジェクト: CesarCaballeroGaudes/afni
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;
}
コード例 #17
0
ファイル: afni_lock.c プロジェクト: Gilles86/afni
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 ;
}
コード例 #18
0
ファイル: edt_coerce.c プロジェクト: ccraddock/afni
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 ;
}
コード例 #19
0
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 ;
}
コード例 #20
0
ファイル: 3dmask_tool.c プロジェクト: LJWilliams/Neuroimaging
/*
 * 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);
}
コード例 #21
0
ファイル: 3dmask_tool.c プロジェクト: LJWilliams/Neuroimaging
/*
 * 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);
}
コード例 #22
0
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 ;
}
コード例 #23
0
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) ;
}
コード例 #24
0
ファイル: 3dRSFC.c プロジェクト: ccraddock/afni
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) ;
}
コード例 #25
0
ファイル: 3dmask_tool.c プロジェクト: LJWilliams/Neuroimaging
/* ----------------------------------------------------------------------
 * 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(&params->IND, 0);
   init_int_list(&params->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(&params->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(&params->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);
}
コード例 #26
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) ;
}
コード例 #27
0
int main(int argc, char *argv[]) {
	int i,j,k,m,n,aa,ii,jj,kk,mm,rr;
	int iarg;
	int nmask1=0;
	int nmask2=0;
	THD_3dim_dataset *insetFA = NULL, *insetV1 = NULL, 
		*insetMD = NULL, *insetL1 = NULL;
	THD_3dim_dataset *insetEXTRA=NULL; 
	THD_3dim_dataset *mset2=NULL; 
	THD_3dim_dataset *mset1=NULL; 
	THD_3dim_dataset *outsetMAP=NULL, *outsetMASK=NULL;
	char *prefix="tracky";
	int LOG_TYPE=0;
	char in_FA[300];
	char in_V1[300];
	char in_MD[300];
	char in_L1[300];
	int EXTRAFILE=0; // switch for whether other file is input as WM map

	char OUT_bin[300];
	char OUT_tracstat[300];
	char prefix_mask[300];
	char prefix_map[300];

	// FACT algopts
	FILE *fout0;
	float MinFA=0.2,MaxAngDeg=45,MinL=20.0;
	float MaxAng;
	int SeedPerV[3]={2,2,2};
	int ArrMax=0;
	float tempvmagn;
  
	int Nvox=-1;   // tot number vox
	int Dim[3]={0,0,0}; // dim in each dir
	int Nseed=0,M=30,bval=1000;
	int DimSeed[3]; // number of seeds there will be
	float Ledge[3]; // voxel edge lengths

	int *ROI1, *ROI2;
	short int *temp_arr;
	char *temp_byte; 
	int **Tforw, **Tback;
	int **Ttot;
	float **flTforw, **flTback;
	float ****coorded;
	int ****INDEX;
	int len_forw, len_back; // int count of num of squares through
	float phys_forw[1], phys_back[1];
	int idx;

	float ave_tract_len, ave_tract_len_phys;
	int inroi1, inroi2, KEEPIT; // switches for detecting
	int in[3]; // to pass to trackit
	float physin[3]; // also for trackit, physical loc, 
	int totlen; 
	float totlen_phys;
	int Numtract;

	int READS_in;
	float READS_fl;
	int end[2][3];
	int test_ind[2][3];

	int  roi3_ct=0, id=0;
	float roi3_mu_MD = 0.,roi3_mu_RD = 0.,roi3_mu_L1 = 0.,roi3_mu_FA = 0.;  
	float roi3_sd_MD = 0.,roi3_sd_RD = 0.,roi3_sd_L1 = 0.,roi3_sd_FA = 0.;  
	float tempMD,tempFA,tempRD,tempL1;
	char dset_or[4] = "RAI";
	THD_3dim_dataset *dsetn;
	int TV_switch[3] = {0,0,0};
	TAYLOR_BUNDLE *tb=NULL;
	TAYLOR_TRACT *tt=NULL;
	char *mode = "NI_fast_binary";
	NI_element *nel=NULL;
	int dump_opts=0;

	tv_io_header header1 = {.id_string = "TRACK\0", 
				.origin = {0,0,0},   
				.n_scalars = 3,
				.scal_n[0] = "FA",
				.scal_n[1] = "MD",
				.scal_n[2] = "L1",
				.n_properties = 0,
				.vox_to_ras = {{0.,0.,0.,0.},{0.,0.,0.,0.},
					       {0.,0.,0.,0.},{0.,0.,0.,0.}},
				// reset this later based on actual data set
				.voxel_order = "RAI\0", 
				.invert_x = 0,
				.invert_y = 0,
				.invert_z = 0,
				.swap_xy = 0,
				.swap_yz = 0,
				.swap_zx = 0,
				.n_count = 0,
				.version = 2,
				.hdr_size = 1000};
	
  	// for testing names...
	char *postfix[4]={"+orig.HEAD\0",".nii.gz\0",".nii\0","+tlrc.HEAD\0"};
  	int FOUND =-1;
	int RECORD_ORIG = 0; 
	float Orig[3] = {0.0,0.0,0.0};

	mainENTRY("3dTrackID"); machdep(); 
  
	// ****************************************************************
	// ****************************************************************
	//                    load AFNI stuff
	// ****************************************************************
	// ****************************************************************

	INFO_message("version: MU");

	/** scan args **/
	if (argc == 1) { usage_TrackID(1); exit(0); }
	iarg = 1;
	while( iarg < argc && argv[iarg][0] == '-' ){
		if( strcmp(argv[iarg],"-help") == 0 || 
			 strcmp(argv[iarg],"-h") == 0 ) {
			usage_TrackID(strlen(argv[iarg])>3 ? 2:1);
			exit(0);
		}
    
		if( strcmp(argv[iarg],"-verb") == 0) {
			if( ++iarg >= argc ) 
				ERROR_exit("Need argument after '-verb'") ;
			set_tract_verb(atoi(argv[iarg]));
			iarg++ ; continue ;
		}

		if( strcmp(argv[iarg],"-write_opts") == 0) {
			dump_opts=1;
			iarg++ ; continue ;
		}
    
		if( strcmp(argv[iarg],"-rec_orig") == 0) {
			RECORD_ORIG=1;
			iarg++ ; continue ;
		}
    
		if( strcmp(argv[iarg],"-tract_out_mode") == 0) {
			if( ++iarg >= argc ) 
				ERROR_exit("Need argument after '-tract_out_mode'") ;
			if (strcmp(argv[iarg], "NI_fast_binary") &&
				 strcmp(argv[iarg], "NI_fast_text") &&
				 strcmp(argv[iarg], "NI_slow_binary") &&
				 strcmp(argv[iarg], "NI_slow_text") ) {
				ERROR_message("Bad value (%s) for -tract_out_mode",argv[iarg]);
				exit(1);
			}  
			mode = argv[iarg];
			iarg++ ; continue ;
		}
    
		if( strcmp(argv[iarg],"-mask1") == 0 ){
			if( ++iarg >= argc ) 
				ERROR_exit("Need argument after '-mask1'") ;
			mset1 = THD_open_dataset( argv[iarg] ) ;
			if( mset1 == NULL ) 
				ERROR_exit("Can't open mask1 dataset '%s'", argv[iarg]) ;
			DSET_load(mset1) ; CHECK_LOAD_ERROR(mset1) ;
			nmask1 = DSET_NVOX(mset1) ;

			iarg++ ; continue ;
		}
		if( strcmp(argv[iarg],"-mask2") == 0 ){
			if( ++iarg >= argc ) 
				ERROR_exit("Need argument after '-mask2'") ;
			mset2 = THD_open_dataset( argv[iarg] ) ;
			if( mset2 == NULL ) 
				ERROR_exit("Can't open mask2 dataset '%s'",
							  argv[iarg]) ;
			DSET_load(mset2) ; CHECK_LOAD_ERROR(mset2) ;
			nmask2 = DSET_NVOX(mset2) ;
		
			iarg++ ; continue ;
		}
	 
		if( strcmp(argv[iarg],"-prefix") == 0 ){
			iarg++ ; if( iarg >= argc ) 
							ERROR_exit("Need argument after '-prefix'");
			prefix = strdup(argv[iarg]) ;
			if( !THD_filename_ok(prefix) ) 
				ERROR_exit("Illegal name after '-prefix'");
			iarg++ ; continue ;
		}
	 
		if( strcmp(argv[iarg],"-input") == 0 ){
			iarg++ ; if( iarg >= argc ) 
							ERROR_exit("Need argument after '-input'");

			for( i=0 ; i<4 ; i++) {
				sprintf(in_FA,"%s_FA%s", argv[iarg],postfix[i]); 
				if(THD_is_ondisk(in_FA)) {
					FOUND = i;
					break;
				}
			}
			insetFA = THD_open_dataset(in_FA) ;
			if( (insetFA == NULL ) || (FOUND==-1))
				ERROR_exit("Can't open dataset '%s': for FA.",in_FA);
			
			DSET_load(insetFA) ; CHECK_LOAD_ERROR(insetFA) ;
			Nvox = DSET_NVOX(insetFA) ;
			Dim[0] = DSET_NX(insetFA); Dim[1] = DSET_NY(insetFA); 
			Dim[2] = DSET_NZ(insetFA); 
			Ledge[0] = fabs(DSET_DX(insetFA)); Ledge[1] = fabs(DSET_DY(insetFA)); 
			Ledge[2] = fabs(DSET_DZ(insetFA)); 
			Orig[0] = DSET_XORG(insetFA); Orig[1] = DSET_YORG(insetFA);
			Orig[2] = DSET_ZORG(insetFA);

			// check tot num vox match (as proxy for dims...)
			if( (Nvox != nmask1) || (Nvox != nmask2) )
				ERROR_exit("Input dataset does not match both mask volumes!");
		
      
			// this stores the original data file orientation for later use,
			// as well since we convert everything to RAI temporarily, as
			// described below
			header1.voxel_order[0]=ORIENT_typestr[insetFA->daxes->xxorient][0];
			header1.voxel_order[1]=ORIENT_typestr[insetFA->daxes->yyorient][0];
			header1.voxel_order[2]=ORIENT_typestr[insetFA->daxes->zzorient][0];
			for( i=0 ; i<3 ; i++) {
				header1.dim[i] = Dim[i];
				header1.voxel_size[i] = Ledge[i];
				// will want this when outputting file later for TrackVis.
				TV_switch[i] = !(dset_or[i]==header1.voxel_order[i]);
			}
			dset_or[3]='\0';
      
			FOUND = -1;
			for( i=0 ; i<4 ; i++) {
				sprintf(in_V1,"%s_V1%s", argv[iarg],postfix[i]); 
				if(THD_is_ondisk(in_V1)) {
					FOUND = i;
					break;
				}
			}
			insetV1 = THD_open_dataset(in_V1);
			if( insetV1 == NULL ) 
				ERROR_exit("Can't open dataset '%s':V1",in_V1);
			DSET_load(insetV1) ; CHECK_LOAD_ERROR(insetV1) ;
		
			FOUND = -1;
			for( i=0 ; i<4 ; i++) {
				sprintf(in_L1,"%s_L1%s", argv[iarg],postfix[i]); 
				if(THD_is_ondisk(in_L1)) {
					FOUND = i;
					break;
				}
			}
			insetL1 = THD_open_dataset(in_L1);
			if( insetL1 == NULL ) 
				ERROR_exit("Can't open dataset '%s':L1",in_L1);
			DSET_load(insetL1) ; CHECK_LOAD_ERROR(insetL1) ;

			FOUND = -1;
			for( i=0 ; i<4 ; i++) {
				sprintf(in_MD,"%s_MD%s", argv[iarg],postfix[i]); 
				if(THD_is_ondisk(in_MD)) {
					FOUND = i;
					break;
				}
			}
			insetMD = THD_open_dataset(in_MD);
			if( insetMD == NULL ) 
				ERROR_exit("Can't open dataset '%s':MD",in_MD);
			DSET_load(insetMD) ; CHECK_LOAD_ERROR(insetMD) ;

			iarg++ ; continue ;
		}

		if( strcmp(argv[iarg],"-algopt") == 0 ){
			iarg++ ; 
			if( iarg >= argc ) 
				ERROR_exit("Need argument after '-algopt'");
		
			if (!(nel = ReadTractAlgOpts(argv[iarg]))) {
				ERROR_message("Failed to read options in %s\n", argv[iarg]);
				exit(19);
			}
			if (NI_getTractAlgOpts(nel, &MinFA, &MaxAngDeg, &MinL, 
										  SeedPerV, &M, &bval)) {
				ERROR_message("Failed to get options");
				exit(1);
			}
			NI_free_element(nel); nel=NULL;
      
			iarg++ ; continue ;
		}

		if( strcmp(argv[iarg],"-logic") == 0 ){
			iarg++ ; if( iarg >= argc ) 
							ERROR_exit("Need argument after '-logic'");

			INFO_message("ROI logic type is: %s",argv[iarg]);
			if( strcmp(argv[iarg],"AND") == 0 ) 
				LOG_TYPE = 1;
			else if( strcmp(argv[iarg],"OR") == 0 ) 
				LOG_TYPE = 0;
			else if( strcmp(argv[iarg],"ALL") == 0 )
				LOG_TYPE = -1;
			else 
				ERROR_exit("Illegal after '-logic': need 'OR' or 'AND'");
			iarg++ ; continue ;
		}
    
		//@@
		if( strcmp(argv[iarg],"-extra_set") == 0) {
			if( ++iarg >= argc ) 
				ERROR_exit("Need argument after '-extra_set'");
			EXTRAFILE = 1; // switch on

			insetEXTRA = THD_open_dataset(argv[iarg]);
			if( (insetEXTRA == NULL ) )
				ERROR_exit("Can't open dataset '%s': for extra set.",argv[iarg]);
			DSET_load(insetEXTRA) ; CHECK_LOAD_ERROR(insetEXTRA) ;

			if( !((Dim[0] == DSET_NX(insetEXTRA)) && (Dim[1] == DSET_NY(insetEXTRA)) && (Dim[2] == DSET_NZ(insetEXTRA))))
				ERROR_exit("Dimensions of extra set '%s' don't match those of the DTI prop ones ('%s', etc.).",argv[iarg], in_FA);
			
			iarg++ ; continue ;
		}


		ERROR_message("Bad option '%s'\n",argv[iarg]) ;
		suggest_best_prog_option(argv[0], argv[iarg]);
		exit(1);
	}
	 
	if (iarg < 4) {
		ERROR_message("Too few options. Try -help for details.\n");
		exit(1);
	}
	 
	if (dump_opts) {
      nel = NI_setTractAlgOpts(NULL, &MinFA, &MaxAngDeg, &MinL, 
										 SeedPerV, &M, &bval);
      WriteTractAlgOpts(prefix, nel);
      NI_free_element(nel); nel=NULL;
	}
	 
        
	// Process the options a little 
	for( i=0 ; i<3 ; i++)
		DimSeed[i] = Dim[i]*SeedPerV[i];
	Nseed = Nvox*SeedPerV[0]*SeedPerV[1]*SeedPerV[2];
	 
	// convert to cos of rad value for comparisons, instead of using acos()
	MaxAng = cos(CONV*MaxAngDeg); 
	 
	// switch to add header-- option for now, added Sept. 2012
	// for use with map_TrackID to map tracks to different space
	if(RECORD_ORIG) {
		for( i=0 ; i<3 ; i++)
			header1.origin[i] = Orig[i];
	}
	 
	// at some point, we will have to convert indices into
	// pseudo-locations; being forced into this choice means that
	// different data set orientations would be represented differently
	// and incorrectly in some instances... so, for now, we'll resample
	// everything to RAI, and then resample back later.  guess this will
	// just slow things down slightly.
	 
	// have all be RAI for processing here
	if(TV_switch[0] || TV_switch[1] || TV_switch[2]) {
		dsetn = r_new_resam_dset(insetFA, NULL, 0.0, 0.0, 0.0,
										 dset_or, RESAM_NN_TYPE, NULL, 1, 0);
		DSET_delete(insetFA); 
		insetFA=dsetn;
		dsetn=NULL;
		
		dsetn = r_new_resam_dset(insetMD, NULL, 0.0, 0.0, 0.0,
										 dset_or, RESAM_NN_TYPE, NULL, 1, 0);
		DSET_delete(insetMD); 
		insetMD=dsetn;
		dsetn=NULL;
		
		dsetn = r_new_resam_dset(insetV1, NULL, 0.0, 0.0, 0.0,
										 dset_or, RESAM_NN_TYPE, NULL, 1, 0);
		DSET_delete(insetV1); 
		insetV1=dsetn;
		dsetn=NULL;
		
		dsetn = r_new_resam_dset(insetL1, NULL, 0.0, 0.0, 0.0,
										 dset_or, RESAM_NN_TYPE, NULL, 1, 0);
		DSET_delete(insetL1); 
		insetL1=dsetn;
		dsetn=NULL;
		
		dsetn = r_new_resam_dset(mset1, NULL, 0.0, 0.0, 0.0,
										 dset_or, RESAM_NN_TYPE, NULL, 1, 0);
		DSET_delete(mset1); 
		mset1=dsetn;
		dsetn=NULL;
		
		dsetn = r_new_resam_dset(mset2, NULL, 0.0, 0.0, 0.0,
										 dset_or, RESAM_NN_TYPE, NULL, 1, 0);
		DSET_delete(mset2); 
		mset2=dsetn;
		dsetn=NULL;

		if(EXTRAFILE) {
			dsetn = r_new_resam_dset(insetEXTRA, NULL, 0.0, 0.0, 0.0,
											 dset_or, RESAM_NN_TYPE, NULL, 1, 0);
			DSET_delete(insetEXTRA); 
			insetEXTRA=dsetn;
			dsetn=NULL;
		}


	}
	 
	 

	// ****************************************************************
	// ****************************************************************
	//                    make arrays for tracking
	// ****************************************************************
	// ****************************************************************

	// for temp storage array, just a multiple of longest dimension!
	if(Dim[0] > Dim[1])
		ArrMax = Dim[0] * 4;
	else
		ArrMax = Dim[1] * 4;
	if(4*Dim[2] > ArrMax)
		ArrMax = Dim[2] * 4;

	ROI1 = (int *)calloc(Nvox, sizeof(int)); 
	ROI2 = (int *)calloc(Nvox, sizeof(int)); 
	temp_arr = (short int *)calloc(Nvox, sizeof(short int)); 
	temp_byte = (char *)calloc(Nvox, sizeof(char)); 
	// temp storage whilst tracking
	Tforw = calloc(ArrMax, sizeof(Tforw)); 
	for(i=0 ; i<ArrMax ; i++) 
		Tforw[i] = calloc(3, sizeof(int)); 
	Ttot = calloc(2*ArrMax , sizeof(Ttot)); 
	for(i=0 ; i<2*ArrMax ; i++) 
		Ttot[i] = calloc(3, sizeof(int)); 
	Tback = calloc(ArrMax, sizeof(Tback)); 
	for(i=0 ; i<ArrMax ; i++) 
		Tback[i] = calloc(3, sizeof(int)); 
	// temp storage whilst tracking, physical loc
	flTforw = calloc(ArrMax, sizeof(flTforw)); 
	for(i=0 ; i<ArrMax ; i++) 
		flTforw[i] = calloc(3, sizeof(int)); 
	flTback = calloc(ArrMax,sizeof(flTback)); 
	for(i=0 ; i<ArrMax ; i++) 
		flTback[i] = calloc(3, sizeof(int)); 
	if( (ROI1 == NULL) || (ROI2 == NULL) || (temp_arr == NULL) 
		 || (Tforw == NULL) || (Tback == NULL) || (flTforw == NULL) 
		 || (flTback == NULL) || (Ttot == NULL)) {
		fprintf(stderr, "\n\n MemAlloc failure.\n\n");
		exit(12);
	}
  
	coorded = (float ****) calloc( Dim[0], sizeof(float ***) );
	for ( i = 0 ; i < Dim[0] ; i++ ) 
		coorded[i] = (float ***) calloc( Dim[1], sizeof(float **) );
	for ( i = 0 ; i < Dim[0] ; i++ ) 
		for ( j = 0 ; j < Dim[1] ; j++ ) 
			coorded[i][j] = (float **) calloc( Dim[2], sizeof(float *) );
	for ( i=0 ; i<Dim[0] ; i++ ) 
		for ( j=0 ; j<Dim[1] ; j++ ) 
			for ( k= 0 ; k<Dim[2] ; k++ ) //3 comp of V1 and FA
				coorded[i][j][k] = (float *) calloc( 4, sizeof(float) ); 
  
	INDEX = (int ****) calloc( Dim[0], sizeof(int ***) );
	for ( i = 0 ; i < Dim[0] ; i++ ) 
		INDEX[i] = (int ***) calloc( Dim[1], sizeof(int **) );
	for ( i = 0 ; i < Dim[0] ; i++ ) 
		for ( j = 0 ; j < Dim[1] ; j++ ) 
			INDEX[i][j] = (int **) calloc( Dim[2], sizeof(int *) );
	for ( i=0 ; i<Dim[0] ; i++ ) 
		for ( j=0 ; j<Dim[1] ; j++ ) 
			for ( k= 0 ; k<Dim[2] ; k++ ) 
				INDEX[i][j][k] = (int *) calloc( 4,  sizeof(int) );

	// this statement will never be executed if allocation fails above
	if( (INDEX == NULL) || (coorded == NULL) ) { 
		fprintf(stderr, "\n\n MemAlloc failure.\n\n");
		exit(122);
	}
  
	for(i=0 ; i<Nvox ; i++) {
		if(THD_get_voxel( mset1, i, 0) >0.5){
			ROI1[i] = 1;
		}
		if(THD_get_voxel( mset2, i, 0) >0.5)
			ROI2[i] = 1;
	}

	// set up eigvecs in 3D coord sys,
	// mark off where ROIs are and keep index handy
	idx=0;
	for( k=0 ; k<Dim[2] ; k++ ) 
		for( j=0 ; j<Dim[1] ; j++ ) 
			for( i=0 ; i<Dim[0] ; i++ ) {
				for( m=0 ; m<3 ; m++ ) 
					coorded[i][j][k][m] = THD_get_voxel(insetV1, idx, m);
				if(EXTRAFILE)
					coorded[i][j][k][3] = THD_get_voxel(insetEXTRA, idx, 0); 
				else
					coorded[i][j][k][3] = THD_get_voxel(insetFA, idx, 0); 
   
				// make sure that |V1| == 1 for all eigenvects, otherwise it's
				/// a problem in the tractography; currently, some from
				// 3dDWItoDT do not have this property...
				tempvmagn = sqrt(coorded[i][j][k][0]*coorded[i][j][k][0]+
									  coorded[i][j][k][1]*coorded[i][j][k][1]+
									  coorded[i][j][k][2]*coorded[i][j][k][2]);
				if( tempvmagn<0.99 ) 
					for( m=0 ; m<3 ; m++ ) 
						coorded[i][j][k][m]/= tempvmagn;
   
				INDEX[i][j][k][0] =idx; // first value is the index itself
				if( ROI1[idx]==1 ) 
					INDEX[i][j][k][1]=1; // second value identifies ROI1 mask
				else
					INDEX[i][j][k][1]=0;
				if( ROI2[idx]==1 )
					INDEX[i][j][k][2]=1; // third value identifies ROI2 mask
				else
					INDEX[i][j][k][2]=0;

				// fourth value will be counter for number of kept tracks
				// passing through
				INDEX[i][j][k][3] = 0;  
				idx+= 1;
			}
  
	// *************************************************************
	// *************************************************************
	//                    Beginning of main loop
	// *************************************************************
	// *************************************************************

	Numtract = 0;
	ave_tract_len = 0.;
	ave_tract_len_phys = 0.;
 
	sprintf(OUT_bin,"%s.trk",prefix);
	if( (fout0 = fopen(OUT_bin, "w")) == NULL) {
		fprintf(stderr, "Error opening file %s.",OUT_bin);
		exit(16);
	}
	fwrite(&header1,sizeof(tv_io_header),1,fout0);
  
	if (get_tract_verb()) {
		INFO_message("Begin tracking...");
	}

	tb = AppCreateBundle(NULL, 0, NULL, insetFA); // start bundle
	id = 0;
	for( k=0 ; k<Dim[2] ; k++ ) 
		for( j=0 ; j<Dim[1] ; j++ ) 
			for( i=0 ; i<Dim[0] ; i++ ) 
				if(coorded[i][j][k][3] >= MinFA) { 
					for( ii=0 ; ii<SeedPerV[0] ; ii++ ) 
						for( jj=0 ; jj<SeedPerV[1] ; jj++ ) 
							for( kk=0 ; kk<SeedPerV[2] ; kk++ ) {

								in[0] = i;
								in[1] = j;
								in[2] = k;
								physin[0] = ((float) in[0] + 
												 (0.5 + (float) ii)/SeedPerV[0])*Ledge[0];
								physin[1] = ((float) in[1] + 
												 (0.5 + (float) jj)/SeedPerV[1])*Ledge[1];
								physin[2] = ((float) in[2] + 
												 (0.5 + (float) kk)/SeedPerV[2])*Ledge[2];
      
								len_forw = TrackIt(coorded, in, physin, Ledge, Dim, 
														 MinFA, MaxAng, ArrMax, Tforw, 
														 flTforw, 1, phys_forw);
      
								// reset, because it's changed in TrackIt func
								in[0] = i; 
								in[1] = j;
								in[2] = k;

								physin[0] = ((float) in[0] + 
												 (0.5 + (float) ii)/SeedPerV[0])*Ledge[0];
								physin[1] = ((float) in[1] + 
												 (0.5 + (float) jj)/SeedPerV[1])*Ledge[1];
								physin[2] = ((float) in[2] + 
												 (0.5 + (float) kk)/SeedPerV[2])*Ledge[2];

								len_back = TrackIt(coorded, in, physin, Ledge, Dim, 
														 MinFA, MaxAng, ArrMax, Tback, 
														 flTback, -1, phys_back);
            
								KEEPIT = 0; // a simple switch

								totlen = len_forw+len_back-1; // NB: overlap of starts
								totlen_phys = phys_forw[0] + phys_back[0];
		
								if( totlen_phys >= MinL ) {
		  
									// glue together for simpler notation later
									for( n=0 ; n<len_back ; n++) { // all of this
										rr = len_back-n-1; // read in backward
										for(m=0;m<3;m++)
											Ttot[rr][m] = Tback[n][m];
									}
									for( n=1 ; n<len_forw ; n++){// skip first->overlap
										rr = n+len_back-1; // put after
										for(m=0;m<3;m++)
											Ttot[rr][m] = Tforw[n][m];
									}
									// <<So close and orthogonal condition>>:
									// test projecting ends, to see if they abut ROI.  
									for(m=0;m<3;m++) { 
										//actual projected ends
										end[1][m] = 2*Ttot[totlen-1][m]-Ttot[totlen-2][m];
										end[0][m] = 2*Ttot[0][m]-Ttot[1][m];
										// default choice, just retest known ends 
										// as default
										test_ind[1][m] = test_ind[0][m] = Ttot[0][m];
									}
		  
									tt = Create_Tract(len_back, flTback, len_forw, 
															flTforw, id, insetFA); ++id; 
        
									if (LOG_TYPE == -1) {
										KEEPIT = 1; 
									} else {
										inroi1 = 0;
										// check forw
										for( n=0 ; n<len_forw ; n++) {
											if(INDEX[Tforw[n][0]][Tforw[n][1]][Tforw[n][2]][1]==1){
												inroi1 = 1;
												break;
											} else
												continue;
										}
										if( inroi1==0 ){// after 1st half, check 2nd half
											for( m=0 ; m<len_back ; m++) {
												if(INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][1]==1){
													inroi1 = 1;
													break;
												} else
													continue;
											}
										}
										// after 1st&2nd halves, check bound/neigh
										if( inroi1==0 ) {
											if(INDEX[test_ind[1][0]][test_ind[1][1]][test_ind[1][2]][1]==1)
												inroi1 = 1;
											if(INDEX[test_ind[0][0]][test_ind[0][1]][test_ind[0][2]][1]==1)
												inroi1 = 1;
										}
			 
										if( ((LOG_TYPE ==0) && (inroi1 ==0)) || 
											 ((LOG_TYPE ==1) && (inroi1 ==1))) {
											// have to check in ROI2
				
											inroi2 = 0;
											// check forw
											for( n=0 ; n<len_forw ; n++) {
												if(INDEX[Tforw[n][0]][Tforw[n][1]][Tforw[n][2]][2]==1){
													inroi2 = 1;
													break;
												} else
													continue;
											}
											//after 1st half, check 2nd half
											if( inroi2==0 ) { 
												for( m=0 ; m<len_back ; m++) {
													if(INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][2]==1){
														inroi2 = 1;
														break;
													} else
														continue;
												}
											}
											// after 1st&2nd halves, check bound/neigh
											if( inroi2==0 ) { 
												if(INDEX[test_ind[1][0]][test_ind[1][1]][test_ind[1][2]][2]==1)
													inroi2 = 1;
												if(INDEX[test_ind[0][0]][test_ind[0][1]][test_ind[0][2]][2]==1)
													inroi2 = 1;
											}
				
											// for both cases, need to see it here to keep
											if( inroi2 ==1 )
												KEEPIT = 1; // otherwise, it's gone
				
										} else if((LOG_TYPE ==0) && (inroi1 ==1))
											KEEPIT = 1;
									}
								}
      
								// by now, we *know* if we're keeping this or not.
								if( KEEPIT == 1 ) {
									tb = AppCreateBundle(tb, 1, tt, NULL); 
									tt = Free_Tracts(tt, 1);
        
									READS_in = totlen;
									fwrite(&READS_in,sizeof(READS_in),1,fout0);
									for( n=0 ; n<len_back ; n++) {
										//put this one in backwords, to make it connect
										m = len_back - 1 - n; 
										for(aa=0 ; aa<3 ; aa++) {
											// recenter phys loc for trackvis, if nec...
											// just works this way (where they define 
											// origin)
											READS_fl = flTback[m][aa];
											if(!TV_switch[aa])
												READS_fl = Ledge[aa]*Dim[aa]-READS_fl;
											fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
										}
										mm = INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][0];
										READS_fl =THD_get_voxel(insetFA, mm, 0); // FA
										fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
										READS_fl =THD_get_voxel(insetMD, mm, 0); // MD
										fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
										READS_fl =THD_get_voxel(insetL1, mm, 0); // L1
										fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
										// count this voxel for having a tract
										INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][3]+= 1; 
									}
        
									for( m=1 ; m<len_forw ; m++) {
										for(aa=0 ; aa<3 ; aa++) {
											// recenter phys loc for trackvis, if nec...
											READS_fl = flTforw[m][aa];
											if(!TV_switch[aa])
												READS_fl = Ledge[aa]*Dim[aa]-READS_fl;
											fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
										}
										mm = INDEX[Tforw[m][0]][Tforw[m][1]][Tforw[m][2]][0];
										READS_fl =THD_get_voxel(insetFA, mm, 0); // FA
										fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
										READS_fl =THD_get_voxel(insetMD, mm, 0); // MD
										fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
										READS_fl =THD_get_voxel(insetL1, mm, 0); // L1 
										fwrite(&READS_fl,sizeof(READS_fl),1,fout0);
										// count this voxel for having a tract
										INDEX[Tforw[m][0]][Tforw[m][1]][Tforw[m][2]][3]+= 1; 
									}
        
									ave_tract_len+= totlen;
									ave_tract_len_phys+= totlen_phys;
									Numtract+=1;
								}   
							}
				}
	fclose(fout0); 
  
	if (get_tract_verb()) {
		INFO_message("Done tracking, have %d tracks.", tb->N_tracts);
		Show_Taylor_Bundle(tb, NULL, 3);
	}

	if (!Write_Bundle(tb,prefix,mode)) {
		ERROR_message("Failed to write the bundle");
	}
   
	// **************************************************************
	// **************************************************************
	//                    Some simple stats on ROIs and outputs
	// **************************************************************
	// **************************************************************

	for( k=0 ; k<Dim[2] ; k++ ) 
		for( j=0 ; j<Dim[1] ; j++ ) 
			for( i=0 ; i<Dim[0] ; i++ ) {
				if( INDEX[i][j][k][3]>=1 ) {
					tempMD = THD_get_voxel(insetMD,INDEX[i][j][k][0],0);
					tempFA = THD_get_voxel(insetFA,INDEX[i][j][k][0],0);
					tempL1 = THD_get_voxel(insetL1,INDEX[i][j][k][0],0);
					tempRD = 0.5*(3*tempMD-tempL1);
					roi3_mu_MD+= tempMD;
					roi3_mu_FA+= tempFA;
					roi3_mu_L1+= tempL1;
					roi3_mu_RD+= tempRD;
					roi3_sd_MD+= tempMD*tempMD;
					roi3_sd_FA+= tempFA*tempFA;
					roi3_sd_L1+= tempL1*tempL1;
					roi3_sd_RD+= tempRD*tempRD;
					roi3_ct+= 1;
				}
			}
  
	if(roi3_ct > 0 ) { // !!!! make into afni file
		roi3_mu_MD/= (float) roi3_ct; 
		roi3_mu_FA/= (float) roi3_ct;
		roi3_mu_L1/= (float) roi3_ct;
		roi3_mu_RD/= (float) roi3_ct;
    
		roi3_sd_MD-= roi3_ct*roi3_mu_MD*roi3_mu_MD;
		roi3_sd_FA-= roi3_ct*roi3_mu_FA*roi3_mu_FA;
		roi3_sd_L1-= roi3_ct*roi3_mu_L1*roi3_mu_L1;
		roi3_sd_RD-= roi3_ct*roi3_mu_RD*roi3_mu_RD;
		roi3_sd_MD/= (float) roi3_ct-1; 
		roi3_sd_FA/= (float) roi3_ct-1;
		roi3_sd_L1/= (float) roi3_ct-1;
		roi3_sd_RD/= (float) roi3_ct-1;
		roi3_sd_MD = sqrt(roi3_sd_MD); 
		roi3_sd_FA = sqrt(roi3_sd_FA);
		roi3_sd_L1 = sqrt(roi3_sd_L1);
		roi3_sd_RD = sqrt(roi3_sd_RD);
  
		sprintf(OUT_tracstat,"%s.stats",prefix);
		if( (fout0 = fopen(OUT_tracstat, "w")) == NULL) {
			fprintf(stderr, "Error opening file %s.",OUT_tracstat);
			exit(19);
		}
		fprintf(fout0,"%d\t%d\n",Numtract,roi3_ct);
		fprintf(fout0,"%.3f\t%.3f\n",ave_tract_len/Numtract,
				  ave_tract_len_phys/Numtract);
		// as usual, these next values would have to be divided by the
		// bval to get their actual value in standard phys units
		fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_FA,roi3_sd_FA);
		fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_MD,roi3_sd_MD);
		fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_RD,roi3_sd_RD);
		fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_L1,roi3_sd_L1);
		fclose(fout0);

		sprintf(prefix_map,"%s_MAP",prefix); 
		sprintf(prefix_mask,"%s_MASK",prefix); 

		outsetMAP = EDIT_empty_copy( mset1 ) ;
		EDIT_dset_items( outsetMAP ,
							  ADN_datum_all , MRI_short , 
							  ADN_prefix    , prefix_map ,
							  ADN_none ) ;
		if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMAP)) )
			ERROR_exit("Can't overwrite existing dataset '%s'",
						  DSET_HEADNAME(outsetMAP));
    
		outsetMASK = EDIT_empty_copy( mset1 ) ;
		EDIT_dset_items( outsetMASK ,
							  ADN_datum_all , MRI_byte , 
							  ADN_prefix    , prefix_mask ,
							  ADN_none ) ;
		if(!THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMASK)) )
			ERROR_exit("Can't overwrite existing dataset '%s'",
						  DSET_HEADNAME(outsetMASK));
    
		m=0;
		for( k=0 ; k<Dim[2] ; k++ ) 
			for( j=0 ; j<Dim[1] ; j++ ) 
				for( i=0 ; i<Dim[0] ; i++ ) {
					temp_arr[m]=INDEX[i][j][k][3];
					if(temp_arr[m]>0.5)
						temp_byte[m]=1;
					else
						temp_byte[m]=0;
					m++;
				}
    
		// re-orient the data as original inputs 
		// (this function copies the pointer)
		EDIT_substitute_brick(outsetMAP, 0, MRI_short, temp_arr); 
		temp_arr=NULL;
		if(TV_switch[0] || TV_switch[1] || TV_switch[2]) {
			dsetn = r_new_resam_dset(outsetMAP, NULL, 0.0, 0.0, 0.0,
											 header1.voxel_order, RESAM_NN_TYPE, 
											 NULL, 1, 0);
			DSET_delete(outsetMAP); 
			outsetMAP=dsetn;
			dsetn=NULL;
		}
		EDIT_dset_items( outsetMAP ,
							  ADN_prefix , prefix_map ,
							  ADN_none ) ;
		THD_load_statistics(outsetMAP );
		if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMAP)) )
			ERROR_exit("Can't overwrite existing dataset '%s'",
						  DSET_HEADNAME(outsetMAP));
		tross_Make_History( "3dTrackID" , argc , argv ,  outsetMAP) ;
		THD_write_3dim_dataset(NULL, NULL, outsetMAP, True);
		// re-orient the data as original inputs
		EDIT_substitute_brick(outsetMASK, 0, MRI_byte, temp_byte);
		temp_byte=NULL;
		if(TV_switch[0] || TV_switch[1] || TV_switch[2]) {
			dsetn = r_new_resam_dset(outsetMASK, NULL, 0.0, 0.0, 0.0,
											 header1.voxel_order, RESAM_NN_TYPE, 
											 NULL, 1, 0);
			DSET_delete(outsetMASK); 
			outsetMASK=dsetn;
			dsetn=NULL;
		}
		EDIT_dset_items( outsetMASK ,
							  ADN_prefix , prefix_mask ,
							  ADN_none ) ;
		THD_load_statistics(outsetMASK);
		if(!THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMASK)) )
			ERROR_exit("Can't overwrite existing dataset '%s'",
						  DSET_HEADNAME(outsetMASK));
		tross_Make_History( "3dTrackID" , argc , argv ,  outsetMASK) ;
		THD_write_3dim_dataset(NULL, NULL, outsetMASK, True);

		INFO_message("Number of tracts found = %d",Numtract) ;
	}
	else 
		INFO_message("\n No Tracts Found!!!\n");
  

	// ************************************************************
	// ************************************************************
	//                    Freeing
	// ************************************************************
	// ************************************************************

	// !!! need to free afni-sets?
	DSET_delete(insetFA);
	DSET_delete(insetMD);
	DSET_delete(insetL1);
	DSET_delete(insetV1);
	DSET_delete(insetEXTRA);
	//DSET_delete(outsetMAP);  
	//DSET_delete(outsetMASK);
	DSET_delete(mset2);
	DSET_delete(mset1);

	free(prefix);
	free(insetV1);
	free(insetFA);
	free(mset1);
	free(mset2);
  	free(insetEXTRA);

	free(ROI1);
	free(ROI2);
	free(temp_byte);
  
	for( i=0 ; i<ArrMax ; i++) {
		free(Tforw[i]);
		free(Tback[i]);
		free(flTforw[i]);
		free(flTback[i]);
	}
	free(Tforw);
	free(Tback);
	free(flTforw);
	free(flTback);
  
	for( i=0 ; i<Dim[0] ; i++) 
		for( j=0 ; j<Dim[1] ; j++) 
			for( k=0 ; k<Dim[2] ; k++) 
				free(coorded[i][j][k]);
	for( i=0 ; i<Dim[0] ; i++) 
		for( j=0 ; j<Dim[1] ; j++) 
			free(coorded[i][j]);
	for( i=0 ; i<Dim[0] ; i++) 
		free(coorded[i]);
	free(coorded);

	for( i=0 ; i<Dim[0] ; i++) 
		for( j=0 ; j<Dim[1] ; j++) 
			for( k=0 ; k<Dim[2] ; k++) 
				free(INDEX[i][j][k]);
	for( i=0 ; i<Dim[0] ; i++) 
		for( j=0 ; j<Dim[1] ; j++) 
			free(INDEX[i][j]);
	for( i=0 ; i<Dim[0] ; i++) 
		free(INDEX[i]);
	free(INDEX);

	free(temp_arr); // need to free
	for( i=0 ; i<2*ArrMax ; i++) 
		free(Ttot[i]);
	free(Ttot);

	//free(mode);
	
	return 0;
}
コード例 #28
0
ファイル: powell_int.c プロジェクト: LJWilliams/Neuroimaging
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 ;
}
コード例 #29
0
ファイル: rsfc.c プロジェクト: ccraddock/afni
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);
}
コード例 #30
0
int main( int argc , char *argv[] )
{
   THD_3dim_dataset *inset=NULL , *outset ;
   THD_3dim_dataset **insar=NULL ; int nsar=0 ;
   int iarg=1 , ii,kk , ids ;
   MCW_cluster *nbhd=NULL ;
   char *prefix="./localhistog" ;
   int ntype=0 ; float na=0.0f,nb=0.0f,nc=0.0f ;
   int verb=1 , do_prob=0 ;
   int nx=0,ny=0,nz=0,nvox=0, rbot,rtop ;
   char *labfile=NULL ; NI_element *labnel=NULL ;
   int nlab=0 , *labval=NULL ; char **lablab=NULL ; char buf[THD_MAX_SBLABEL] ;
   UINT32 *ohist , *mhist=NULL ; char *ohist_name=NULL ; int ohzadd=0 ;
   int *rlist , numval ; float mincount=0.0f ; int mcc ;
   int *exlist=NULL, numex=0 ;
   int do_excNONLAB=0 ;

   /*---- for the clueless who wish to become clued-in ----*/

   if( argc == 1 ){ usage_3dLocalHistog(1); exit(0); } /* Bob's help shortcut */

   /*---- official startup ---*/

#if defined(USING_MCW_MALLOC) && !defined(USE_OMP)
   enable_mcw_malloc() ;
#endif

   PRINT_VERSION("3dLocalHistog"); mainENTRY("3dLocalHistog main"); machdep();
   AFNI_logger("3dLocalHistog",argc,argv);
   if( getpid()%2 ) AUTHOR("Bilbo Baggins"); else AUTHOR("Thorin Oakenshield");
   AFNI_SETUP_OMP(0) ;  /* 24 Jun 2013 */

   /*---- loop over options ----*/

   while( iarg < argc && argv[iarg][0] == '-' ){

     if( strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0){
        usage_3dLocalHistog(strlen(argv[iarg])>3 ? 2:1);
        exit(0);
     }

     if( strncmp(argv[iarg],"-qu",3) == 0 ){
       verb = 0 ; iarg++ ; continue ;
     }
     if( strncmp(argv[iarg],"-verb",5) == 0 ){
       verb++ ; iarg++ ; continue ;
     }

#ifdef ALLOW_PROB
     if( strncmp(argv[iarg],"-prob",5) == 0 ){
       do_prob = 1 ; iarg++ ; continue ;
     }
#endif

     if( strcmp(argv[iarg],"-exclude") == 0 ){
       int ebot=-6666666,etop=-6666666 , ee ;
       if( ++iarg >= argc ) ERROR_exit("Need argument after '-exclude'") ;
       sscanf(argv[iarg],"%d..%d",&ebot,&etop) ;
       if( ebot >= -TWO15 && ebot <= TWO15 ){
         if( etop < -TWO15 || etop > TWO15 || etop < ebot ) etop = ebot ;
         exlist = (int *)realloc(exlist,sizeof(int)*(etop-ebot+1+numex+1)) ;
         for( ee=ebot ; ee <= etop ; ee++ ){ if( ee != 0 ) exlist[numex++] = ee ; }
       }
       iarg++ ; continue ;
     }

     if( strcmp(argv[iarg],"-excNONLAB") == 0 ){
       do_excNONLAB = 1 ; iarg++ ; continue ;
     }

     if( strcmp(argv[iarg],"-prefix") == 0 ){
       if( ++iarg >= argc ) ERROR_exit("Need argument after '-prefix'") ;
       prefix = strdup(argv[iarg]) ;
       if( !THD_filename_ok(prefix) ) ERROR_exit("Bad -prefix!") ;
       iarg++ ; continue ;
     }

     if( strcmp(argv[iarg],"-hsave") == 0 ){
       if( ++iarg >= argc ) ERROR_exit("Need argument after '-hsave'") ;
       ohist_name = strdup(argv[iarg]) ;
       if( !THD_filename_ok(ohist_name) ) ERROR_exit("Bad -hsave!") ;
       iarg++ ; continue ;
     }

     if( strcmp(argv[iarg],"-mincount") == 0 ){
       char *cpt ;
       if( ++iarg >= argc ) ERROR_exit("Need argument after '-mincount'") ;
       mincount = (float)strtod(argv[iarg],&cpt) ;
#if 0
       if( mincount > 0.0f && mincount < 50.0f && *cpt == '%' )  /* percentage */
         mincount = -0.01f*mincount ;
#endif
       iarg++ ; continue ;
     }

     if( strcmp(argv[iarg],"-nbhd") == 0 ){
       char *cpt ;
       if( ntype  >  0    ) ERROR_exit("Can't have 2 '-nbhd' options") ;
       if( ++iarg >= argc ) ERROR_exit("Need argument after '-nbhd'") ;

       cpt = argv[iarg] ;
       if( strncasecmp(cpt,"SPHERE",6) == 0 ){
         sscanf( cpt+7 , "%f" , &na ) ;
         ntype = NTYPE_SPHERE ;
       } else if( strncasecmp(cpt,"RECT",4) == 0 ){
         sscanf( cpt+5 , "%f,%f,%f" , &na,&nb,&nc ) ;
         if( na == 0.0f && nb == 0.0f && nc == 0.0f )
           ERROR_exit("'RECT(0,0,0)' is not a legal neighborhood") ;
         ntype = NTYPE_RECT ;
       } else if( strncasecmp(cpt,"RHDD",4) == 0 ){
         sscanf( cpt+5 , "%f" , &na ) ;
         if( na == 0.0f ) ERROR_exit("Can't have a RHDD of radius 0") ;
         ntype = NTYPE_RHDD ;
       } else if( strncasecmp(cpt,"TOHD",4) == 0 ){
         sscanf( cpt+5 , "%f" , &na ) ;
         if( na == 0.0f ) ERROR_exit("Can't have a TOHD of radius 0") ;
         ntype = NTYPE_TOHD ;
       } else {
         ERROR_exit("Unknown -nbhd shape: '%s'",cpt) ;
       }
       iarg++ ; continue ;
     }

     if( strcmp(argv[iarg],"-lab_file") == 0 || strcmp(argv[iarg],"-labfile") == 0 ){
       char **labnum ; int nbad=0 ;
       if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]) ;
       if( labfile != NULL ) ERROR_exit("Can't use '%s' twice!",argv[iarg-1]) ;
       labfile = strdup(argv[iarg]) ;
       labnel = THD_string_table_read(labfile,0) ;
       if( labnel == NULL || labnel->vec_num < 2 )
         ERROR_exit("Can't read label file '%s'",labfile) ;
       nlab   = labnel->vec_len ;
       labnum = (char **)labnel->vec[0] ;
       lablab = (char **)labnel->vec[1] ;
       labval = (int *)calloc(sizeof(int),nlab) ;
       for( ii=0 ; ii < nlab ; ii++ ){
         if( labnum[ii] != NULL ){
           labval[ii] = (int)strtod(labnum[ii],NULL) ;
           if( labval[ii] < -TWO15 || labval[ii] > TWO15 ){ labval[ii] = 0; nbad++; }
         }
       }
       if( nbad > 0 )
         ERROR_message("%d label values are outside the range %d..%d :-(" ,
         nbad , -TWO15 , TWO15 ) ;
       iarg++ ; continue ;
     }

     ERROR_message("** 3dLocalHistog: Illegal option: '%s'",argv[iarg]) ;
     suggest_best_prog_option(argv[0], argv[iarg]);
     exit(1) ;

   } /*--- end of loop over options ---*/

   /*---- check for stupid user inputs ----*/

   if( iarg >= argc ) ERROR_exit("No datasets on command line?") ;

   if( ohist_name == NULL && strcmp(prefix,"NULL") == 0 )
     ERROR_exit("-prefix NULL is only meaningful if you also use -hsave :-(") ;

   /*------------ scan input datasets, built overall histogram ------------*/

   nsar  = argc - iarg ;
   insar = (THD_3dim_dataset **)malloc(sizeof(THD_3dim_dataset *)*nsar) ;

   if( verb ) fprintf(stderr,"Scanning %d datasets ",nsar) ;

   ohist = (UINT32 *)calloc(sizeof(UINT32),TWO16) ;

   for( ids=iarg ; ids < argc ; ids++ ){                      /* dataset loop */
     insar[ids-iarg] = inset = THD_open_dataset(argv[ids]) ;
     CHECK_OPEN_ERROR(inset,argv[ids]) ;
     if( ids == iarg ){
       nx = DSET_NX(inset); ny = DSET_NY(inset); nz = DSET_NZ(inset); nvox = nx*ny*nz;
     } else if( nx != DSET_NX(inset) ||
                ny != DSET_NY(inset) || nz != DSET_NZ(inset) ){
       ERROR_exit("Dataset %s grid doesn't match!",argv[ids]) ;
     }
     if( !THD_datum_constant(inset->dblk) )
       ERROR_exit("Dataset %s doesn't have a fixed data type! :-(",argv[ids]) ;
     if( THD_need_brick_factor(inset) )
       ERROR_exit("Dataset %s has scale factors! :-(",argv[ids]) ;
     if( DSET_BRICK_TYPE(inset,0) != MRI_byte  &&
         DSET_BRICK_TYPE(inset,0) != MRI_short &&
         DSET_BRICK_TYPE(inset,0) != MRI_float    )
       ERROR_exit("Dataset %s is not byte- or short-valued! :-(",argv[ids]) ;
     DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ;

     for( ii=0 ; ii < DSET_NVALS(inset) ; ii++ ){ /* add to overall histogram */
       if( verb ) fprintf(stderr,".") ;
       switch( DSET_BRICK_TYPE(inset,ii) ){
         case MRI_short:{
           short *sar = (short *)DSET_BRICK_ARRAY(inset,ii) ;
           for( kk=0 ; kk < nvox ; kk++ ) ohist[ sar[kk]+TWO15 ]++ ;
         }
         break ;
         case MRI_byte:{
           byte *bar = (byte *)DSET_BRICK_ARRAY(inset,ii) ;
           for( kk=0 ; kk < nvox ; kk++ ) ohist[ bar[kk]+TWO15 ]++ ;
         }
         break ;
         case MRI_float:{
           float *far = (float *)DSET_BRICK_ARRAY(inset,ii) ; short ss ;
           for( kk=0 ; kk < nvox ; kk++ ){ ss = SHORTIZE(far[kk]); ohist[ss+TWO15]++; }
         }
         break ;
       }
     } /* end of sub-brick loop */

     DSET_unload(inset) ;  /* will re-load later, as needed */

   } /* end of dataset loop */

   if( verb ) fprintf(stderr,"\n") ;

   /*-------------- process overall histogram for fun and profit -------------*/

   /* if we didn't actually find 0, put it in the histogram now */

   if( ohist[0+TWO15] == 0 ){ ohist[0+TWO15] = 1 ; ohzadd = 1 ; }

   /* excNONLAB? */

   if( nlab > 0 && do_excNONLAB ){
     byte *klist = (byte *)calloc(sizeof(byte),TWO16) ; int nee ;
     for(     ii=0 ; ii < nlab  ; ii++ ){ if( labval[ii] != 0 ) klist[labval[ii]+TWO15] = 1 ; }
     for( nee=ii=0 ; ii < TWO16 ; ii++ ){ if( !klist[ii] ) nee++ ; }
     exlist = (int *)realloc(exlist,sizeof(int)*(numex+nee+1)) ;
     for(     ii=0 ; ii < TWO16 ; ii++ ){ if( ii != TWO15 && !klist[ii] ) exlist[numex++] = ii-TWO15 ; }
     free(klist) ;
   }

   /* make a copy of ohist and edit it for mincount, etc */

   mhist = (UINT32 *)malloc(sizeof(UINT32)*TWO16) ;
   memcpy(mhist,ohist,sizeof(UINT32)*TWO16) ;
   mcc = (mincount < 0.0f) ? (int)(-mincount*nvox) : (int)mincount ;
   if( mcc > 1 ){
     for( ids=ii=0 ; ii < TWO16 ; ii++ ){
       if( ii != TWO15 && mhist[ii] > 0 && mhist[ii] < mcc ){ mhist[ii] = 0; ids++; }
     }
     if( ids > 0 && verb )
       INFO_message("Edited out %d values with overall histogram counts less than %d",ids,mcc) ;
   }
   if( numex > 0 ){
     int ee ;
     for( ids=0,ii=0 ; ii < numex ; ii++ ){
       ee = exlist[ii] ;
       if( mhist[ee+TWO15] > 0 ){ mhist[ee+TWO15] = 0; ids++; }
     }
     free(exlist) ;
     if( ids > 0 && verb )
       INFO_message("Edited out %d values from the exclude list",ids) ;
   }

   /* count number of values with nonzero (edited) counts */

   numval = 0 ;
   for( ii=0 ; ii < TWO16 ; ii++ ) if( mhist[ii] != 0 ) numval++ ;

   if( numval == 0 ) ERROR_exit("Nothing found! WTF?") ;  /* should not happen */

   /* make list of all values with nonzero (edited) count */

   rlist = (int *)malloc(sizeof(int)*numval) ;
   if( verb > 1 ) fprintf(stderr,"++ Include list:") ;
   for( ii=kk=0 ; ii < TWO16 ; ii++ ){
     if( mhist[ii] != 0 ){
       rlist[kk++] = ii-TWO15 ;
       if( verb > 1 ) fprintf(stderr," %d[%u]",ii-TWO15,mhist[ii]) ;
     }
   }
   if( verb > 1 ) fprintf(stderr,"\n") ;

   rbot = rlist[0] ; rtop = rlist[numval-1] ; /* smallest and largest values found */

   if( rbot == rtop ) ERROR_exit("Only one value (%d) found in all inputs!",rbot) ;

   /* if 0 isn't first in rlist, then
      put it in first place and move negative values up by one spot */

   if( rbot < 0 ){
     for( kk=0 ; kk < numval && rlist[kk] != 0 ; kk++ ) ; /*nada*/
     if( kk < numval ){   /* should always be true */
       for( ii=kk-1 ; ii >= 0 ; ii-- ) rlist[ii+1] = rlist[ii] ;
       rlist[0] = 0 ;
     }
   }

   if( verb )
     INFO_message("Value range = %d..%d (%d distinct values)",rbot,rtop,numval );

   /* save overall histogram? */

   if( ohist_name != NULL ){
     FILE *fp = fopen(ohist_name,"w") ; int nl=0 ;
     if( fp == NULL ) ERROR_exit("Can't open -hsave '%s' for output!",ohist_name) ;
     if( ohzadd ) ohist[0+TWO15] = 0 ;
     for( ii=0 ; ii < TWO16 ; ii++ ){
       if( ohist[ii] != 0 ){ fprintf(fp,"%6d %u\n",ii-TWO15,ohist[ii]); nl++; }
     }
     fclose(fp) ;
     if( verb ) INFO_message("Wrote %d lines to -hsave file %s",nl,ohist_name) ;
   }

   free(ohist) ; free(mhist) ; mhist = ohist = NULL ;  /* done with this */

   if( strcmp(prefix,"NULL") == 0 ) exit(0) ;   /* special case */

   /*----------- build the neighborhood mask -----------*/

   if( ntype <= 0 ){         /* default neighborhood */
     ntype = NTYPE_SPHERE ; na = 0.0f ;
     if( verb ) INFO_message("Using default neighborhood = self") ;
   }

   switch( ntype ){
     default:
       ERROR_exit("WTF?  ntype=%d",ntype) ;  /* should not happen */

     case NTYPE_SPHERE:{
       float dx , dy , dz ;
       if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; }
       else           { dx = fabsf(DSET_DX(insar[0])) ;
                        dy = fabsf(DSET_DY(insar[0])) ;
                        dz = fabsf(DSET_DZ(insar[0])) ; }
       nbhd = MCW_spheremask( dx,dy,dz , na ) ;
     }
     break ;

     case NTYPE_RECT:{
       float dx , dy , dz ;
       if( na < 0.0f ){ dx = 1.0f; na = -na; } else dx = fabsf(DSET_DX(insar[0]));
       if( nb < 0.0f ){ dy = 1.0f; nb = -nb; } else dy = fabsf(DSET_DY(insar[0]));
       if( nc < 0.0f ){ dz = 1.0f; nc = -nc; } else dz = fabsf(DSET_DZ(insar[0]));
       nbhd = MCW_rectmask( dx,dy,dz , na,nb,nc ) ;
     }
     break ;

     case NTYPE_RHDD:{
       float dx , dy , dz ;
       if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; }
       else           { dx = fabsf(DSET_DX(insar[0])) ;
                        dy = fabsf(DSET_DY(insar[0])) ;
                        dz = fabsf(DSET_DZ(insar[0])) ; }
       nbhd = MCW_rhddmask( dx,dy,dz , na ) ;
     }
     break ;

     case NTYPE_TOHD:{
       float dx , dy , dz ;
       if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; }
       else           { dx = fabsf(DSET_DX(insar[0])) ;
                        dy = fabsf(DSET_DY(insar[0])) ;
                        dz = fabsf(DSET_DZ(insar[0])) ; }
       nbhd = MCW_tohdmask( dx,dy,dz , na ) ;
     }
     break ;
   }

   if( verb ) INFO_message("Neighborhood comprises %d voxels",nbhd->num_pt) ;

   /*------- actually do some work for a change (is it lunchtime yet?) -------*/

   if( verb ) fprintf(stderr,"Voxel-wise histograms ") ;

   outset = THD_localhistog( nsar,insar , numval,rlist , nbhd , do_prob,verb ) ;

   if( outset == NULL ) ERROR_exit("Function THD_localhistog() fails?!") ;

   /*---- save resulting dataset ----*/

   EDIT_dset_items( outset , ADN_prefix,prefix , ADN_none ) ;

   tross_Copy_History( insar[0] , outset ) ;
   tross_Make_History( "3dLocalHistog" , argc,argv , outset ) ;

   /* but first attach labels to sub-bricks */

   EDIT_BRICK_LABEL(outset,0,"0:Other") ;
   for( kk=1 ; kk < numval ; kk++ ){
     sprintf(buf,"%d:",rlist[kk]) ;
     for( ii=0 ; ii < nlab ; ii++ ){
       if( labval[ii] == rlist[kk] && lablab[ii] != NULL ){
         ids = strlen(buf) ;
         MCW_strncpy(buf+ids,lablab[ii],THD_MAX_SBLABEL-ids) ;
         break ;
       }
     }
     EDIT_BRICK_LABEL(outset,kk,buf) ;
   }

   DSET_write( outset ) ;
   if( verb ) WROTE_DSET( outset ) ;
   exit(0) ;
}