if((ptr)==NULL) \
( estPDF_error ("Cannot allocate memory") )

00083 {
00084   printf 
00085     (
00086      "This program estimates the PDF for a dataset.\n\n"
00087      "Usage: \n"
00088      "3destpdf \n"
00089      "-anat filename    Filename of anat dataset to be segmented            \n"
00090       );
00091   
00092   exit(0);
00093 }

00054 {
00055   fprintf (stderr, "\n");
00056   fprintf (stderr, "%s Error: %s \n", PROGRAM_NAME, message);
00057   exit(1);
00058 }

00107 {
00108   int nopt = 1;                     /* input option argument counter */
00109   int ival, index;                  /* integer input */
00110   float fval;                       /* float input */
00111   char message[MAX_STRING_LENGTH];  /* error message */
00112 
00113 
00114   /*----- does user request help menu? -----*/
00115   if (argc < 2 || strncmp(argv[1], "-help", 5) == 0)  display_help_menu();  
00116    
00117 
00118   /*----- main loop over input options -----*/
00119   while (nopt < argc )
00120     {
00121 
00122       /*-----   -anat filename   -----*/
00123       if (strncmp(argv[nopt], "-anat", 5) == 0)
00124         {
00125           nopt++;
00126           if (nopt >= argc)  estPDF_error ("need argument after -anat ");
00127           anat_filename = malloc (sizeof(char) * MAX_STRING_LENGTH);
00128           MTEST (anat_filename);
00129           strcpy (anat_filename, argv[nopt]);
00130 
00131           anat = THD_open_one_dataset (anat_filename);
00132           if (!ISVALID_3DIM_DATASET (anat))
00133             {
00134               sprintf (message, "Can't open dataset: %s\n", anat_filename); 
00135               estPDF_error (message); 
00136             } 
00137           THD_load_datablock (anat->dblk); 
00138           if (DSET_ARRAY(anat,0) == NULL)
00139             {
00140               sprintf (message, "Can't access data: %s\n", anat_filename); 
00141               estPDF_error (message); 
00142             }
00143 
00144           nopt++;
00145           continue;
00146         }
00147       
00148 
00149       /*----- unknown command -----*/
00150       sprintf(message,"Unrecognized command line option: %s\n", argv[nopt]);
00151       estPDF_error (message);
00152       
00153     }
00154 
00155   
00156 }

00170 {
00171   float parameters [DIMENSION];    /* parameters for PDF estimation */
00172   Boolean ok = TRUE;               /* flag for successful PDF estimation */
00173 
00174   int nx, ny, nz, nxy, nxyz, ixyz;       /* voxel counters */
00175   int n;                                 /* histogram bin index */
00176   short * sfim = NULL;                   /* pointer to anat data */
00177   short * rfim = NULL;                   /* truncated data */ 
00178   int icount;
00179   int lower_cutoff = 25;
00180 
00181   /*----- Get operator inputs -----*/
00182   get_options (argc, argv);
00183 
00184 
00185   /*----- Initialize local variables -----*/
00186   if (anat == NULL)  estPDF_error ("Unable to read anat dataset");
00187   nx = DSET_NX(anat);   ny = DSET_NY(anat);   nz = DSET_NZ(anat);
00188   nxy = nx*ny;   nxyz = nxy*nz;
00189   sfim  = (short *) DSET_BRICK_ARRAY(anat,0) ;
00190   if (sfim == NULL)  estPDF_error ("Unable to read anat dataset");
00191   rfim = (short *) malloc (sizeof(short) * nxyz);   MTEST (rfim);
00192 
00193 
00194   /*----- Just use voxels whose intensity is above the lower cutoff -----*/
00195   icount = 0;
00196   for (ixyz = 0;  ixyz < nxyz;  ixyz++)
00197     if (sfim[ixyz] > lower_cutoff)
00198       {
00199         rfim[icount] = sfim[ixyz];
00200         icount++;
00201       }
00202   printf ("%d voxels above lower cutoff = %d \n", icount, lower_cutoff);
00203 
00204 
00205   /*----- Get PDF estimate and set voxel intensity limits -----*/
00206   estpdf_short (icount, rfim, parameters);
00207   min_val_float = parameters[4] - 2.0*parameters[5];
00208   max_val_float = parameters[7] + 2.0*parameters[8];
00209   
00210    
00211   if (! quiet)
00212     {
00213       printf ("\n");
00214       printf ("Control inputs: \n");
00215       printf ("anat filename = %s \n", anat_filename);
00216       printf ("min value = %f \n", min_val_float);
00217       printf ("max value = %f \n", max_val_float);
00218     }
00219 
00220 
00221 }

00235 {
00236 
00237   /*----- Identify software -----*/
00238   printf ("\n\n");
00239   printf ("Program: %s \n", PROGRAM_NAME);
00240   printf ("Author:  %s \n", PROGRAM_AUTHOR);
00241   printf ("Date:    %s \n", PROGRAM_DATE);
00242   printf ("\n");
00243 
00244   
00245   /*----- Program initialization -----*/
00246   initialize_program (argc, argv);
00247 
00248   
00249 
00250 }