nifti_tool.c

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         ac++;
         CHECK_NEXT_OPT(ac, argc, "-debug");
         opts->debug = atoi(argv[ac]);
      }
      else if( ! strncmp(argv[ac], "-diff_hdr", 8) )
         opts->diff_hdr = 1;
      else if( ! strncmp(argv[ac], "-diff_nim", 8) )
         opts->diff_nim = 1;
      else if( ! strncmp(argv[ac], "-disp_exts", 7) )
         opts->disp_exts = 1;
      else if( ! strncmp(argv[ac], "-disp_hdr", 8) )
         opts->disp_hdr = 1;
      else if( ! strncmp(argv[ac], "-disp_nim", 8) )
         opts->disp_nim = 1;
      else if( ! strncmp(argv[ac], "-dci_lines", 6) ||   /* before -dts */ 
               ! strncmp(argv[ac], "-dts_lines", 6) ) 
      {
         opts->dci_lines = 1;
      }
      else if( ! strncmp(argv[ac], "-disp_collapsed_image", 10) ||
               ! strncmp(argv[ac], "-disp_ci", 8) )
      {
         /* we need to read in the 7 dimension values */
         int index;
         opts->ci_dims[0] = 0;
         for( index = 1; index < 8; index++ )
         {
            ac++;
            CHECK_NEXT_OPT_MSG(ac,argc,"-disp_ci",
                               "7 dimension values are requred");
            if( ! isdigit(argv[ac][0]) && strcmp(argv[ac],"-1") ){
               fprintf(stderr,"** -disp_ci param %d (= '%s') is not a valid\n"
                       "   consider: 'nifti_tool -help'\n",index,argv[ac]);
               return -1;
            }
            opts->ci_dims[index] = atoi(argv[ac]);
         }

         opts->dci = 1;
      }
      else if( ! strncmp(argv[ac], "-disp_ts", 10) ||
               ! strncmp(argv[ac], "-dts", 4) )
      {
         /* we need to read in the ijk indices into the ci_dims array */
         int index;
         for( index = 1; index <= 3; index++ )
         {
            ac++;
            CHECK_NEXT_OPT_MSG(ac,argc,"-dts","i,j,k indices are requied\n");
            if( ! isdigit(argv[ac][0]) ){
               fprintf(stderr,"** -dts param %d (= '%s') is not a number\n"
                       "   consider: 'nifti_tool -help'\n",index,argv[ac]);
               return -1;
            }
            opts->ci_dims[index] = atoi(argv[ac]);
         }
         /* and fill the rest of the array */
         opts->ci_dims[0] = 0;
         for( index = 4; index < 8; index++ ) opts->ci_dims[index] = -1;

         opts->dts = 1;
      }
      else if( ! strncmp(argv[ac], "-field", 2) )
      {
         ac++;
         CHECK_NEXT_OPT(ac, argc, "-field");
         if( add_string(&opts->flist, argv[ac]) ) return -1; /* add field */
      }
      else if( ! strncmp(argv[ac], "-infiles", 3) )
      {
         int count;
         /* for -infiles, get all next arguments until a '-' or done */
         ac++;
         for( count = 0; (ac < argc) && (argv[ac][0] != '-'); ac++, count++ )
            if( add_string(&opts->infiles, argv[ac]) ) return -1;/* add field */
         if( count > 0 && ac < argc ) ac--;  /* more options to process */
         if( g_debug > 2 ) fprintf(stderr,"+d have %d file names\n", count);
      }
      else if( ! strncmp(argv[ac], "-make_image", 8) )
      {
         opts->make_im = 1;  /* will setup later, as -cbl and MAKE_IM */
      }
      else if( ! strncmp(argv[ac], "-mod_field", 6) )
      {
         ac++;
         CHECK_NEXT_OPT(ac, argc, "-mod_field");
         if( add_string(&opts->flist, argv[ac]) ) return -1; /* add field */
         ac++;
         CHECK_NEXT_OPT(ac, argc, "-mod_field (2)");
         if( add_string(&opts->vlist, argv[ac]) ) return -1; /* add value */
      }
      else if( ! strncmp(argv[ac], "-mod_hdr", 7) )
         opts->mod_hdr = 1;
      else if( ! strncmp(argv[ac], "-mod_nim", 7) )
         opts->mod_nim = 1;
      else if( ! strncmp(argv[ac], "-keep_hist", 5) )
         opts->keep_hist = 1;
      else if( ! strncmp(argv[ac], "-new_dim", 8) )
      {
         /* we need to read in the 8 dimension values */
         int index;
         for( index = 0; index < 8; index++ )
         {
            ac++;
            CHECK_NEXT_OPT_MSG(ac,argc,"-new_dim","8 dim values are requred");
            if( ! isdigit(argv[ac][0]) && strcmp(argv[ac],"-1") ){
               fprintf(stderr,"** -new_dim param %d (= '%s') is not a valid\n"
                       "   consider: 'nifti_tool -help'\n",index,argv[ac]);
               return -1;
            }
            opts->new_dim[index] = atoi(argv[ac]);
         }
      }
      else if( ! strncmp(argv[ac], "-new_datatype", 10) )
      {
         ac++;
         CHECK_NEXT_OPT(ac, argc, "-new_datatype");
         opts->new_datatype = atoi(argv[ac]);
      }
      else if( ! strncmp(argv[ac], "-overwrite", 6) )
         opts->overwrite = 1;
      else if( ! strncmp(argv[ac], "-prefix", 4) )
      {
         ac++;
         CHECK_NEXT_OPT(ac, argc, "-prefix");
         opts->prefix = argv[ac];
      }
      else if( ! strncmp(argv[ac], "-quiet", 3) )
         opts->debug = 0;
      else if( ! strncmp(argv[ac], "-rm_ext", 7) )
      {
         ac++;
         CHECK_NEXT_OPT(ac, argc, "-rm_ext");
         if( strcmp(argv[ac],"ALL") == 0 )  /* special case, pass -1 */
         {
            if( add_string(&opts->elist, "-1") ) return -1;
         }
         else
         {
            int index = atoi(argv[ac]);
            if( (index != -1) && ((index > 1000) || !isdigit(*argv[ac])) ){
               fprintf(stderr,
                    "** '-rm_ext' requires an extension index (read '%s')\n",
                    argv[ac]);
               return -1;
            }
            if( add_string(&opts->elist, argv[ac]) ) return -1;
         }
         opts->rm_exts = 1;
      }
      else if( ! strncmp(argv[ac], "-strip_extras", 6) )
         opts->strip = 1;
      else
      {
         fprintf(stderr,"** unknown option: '%s'\n", argv[ac]);
         return -1;
      }
   }

   if( opts->make_im )
   {
      if( opts->infiles.len > 0 )
      {
         fprintf(stderr,"** -infiles is invalid when using -make_im\n");
         return -1;
      }
      /* apply -make_im via -cbl and "MAKE_IM" */
      opts->cbl = 1;
      if( add_string(&opts->infiles, NT_MAKE_IM_NAME) ) return -1;
   }

   /* verify for programming purposes */
   if( opts->add_exts && ( opts->elist.len != opts->etypes.len ) )
   {
      fprintf(stderr,"** ext list length (%d) != etype length (%d)\n",
              opts->elist.len, opts->etypes.len);
      return -1;
   }

   g_debug = opts->debug;
   nifti_set_debug_level(g_debug);

   fill_cmd_string(opts, argc, argv);  /* copy this command */

   if( g_debug > 2 ) disp_nt_opts("options read: ", opts);

   return 0;
}


/*----------------------------------------------------------------------
 * verify that the options make sense
 *----------------------------------------------------------------------*/
int verify_opts( nt_opts * opts, char * prog )
{
   int ac, errs = 0;   /* number of requested action types */

   /* check that only one of disp, diff, mod or add_*_ext is used */
   ac  = (opts->check_hdr || opts->check_nim                   ) ? 1 : 0;
   ac += (opts->diff_hdr  || opts->diff_nim                    ) ? 1 : 0;
   ac += (opts->disp_hdr  || opts->disp_nim  || opts->disp_exts) ? 1 : 0;
   ac += (opts->mod_hdr   || opts->mod_nim                     ) ? 1 : 0;
   ac += (opts->add_exts  || opts->rm_exts                     ) ? 1 : 0;
   ac += (opts->strip                                          ) ? 1 : 0;
   ac += (opts->cbl                                            ) ? 1 : 0;
   ac += (opts->cci                                            ) ? 1 : 0;
   ac += (opts->dts       || opts->dci                         ) ? 1 : 0;

   if( ac < 1 )
   {
      fprintf(stderr,
              "** no action option, so nothing to do...\n"
              "   (try one of '-add...', '-diff...', '-disp...' or '-mod...')\n"
              "   (see '%s -help' for details)\n", prog);
      return 1;
   }
   else if( ac > 1 )
   {
      fprintf(stderr,
         "** only one action option is allowed, please use only one of:\n"
         "        '-add_...', '-check_...', '-diff_...', '-disp_...',\n"
         "        '-mod_...', '-strip', '-dts', '-cbl' or '-cci'\n"
         "   (see '%s -help' for details)\n", prog);
      return 1;
   }

   /* can modify nifti_1_header or nifti_image, but not both */
   if( opts->mod_hdr && opts->mod_nim )
   {
      fprintf(stderr,"** cannot use both '-mod_hdr' and '-mod_nim'\n");
      return 1;
   }

   /* can add or remove extensions, but not both */
   if( opts->add_exts && opts->rm_exts )
   {
      fprintf(stderr,"** cannot use both '-add_*_ext' and '-rm_ext'\n");
      return 1;
   }
   if( (opts->add_exts || opts->rm_exts) && opts->elist.len <= 0 )
   {
      fprintf(stderr,"** missing extensions to add or remove\n");
      return 1;
   }

   /* if modify, then we need fields and corresponding values */
   if( opts->mod_hdr || opts->mod_nim )
   {
      if( opts->flist.len <= 0 )
      {
         fprintf(stderr,"** missing field to modify (need '-mod_field' opt)\n");
         return 1;
      }
      if( opts->flist.len != opts->vlist.len )
      {
         fprintf(stderr,"** error: modifying %d fields with %d values\n",
                 opts->flist.len, opts->vlist.len);
         return 1;
      }
   }

   /* verify the number of files given for each of 4 action types */

   /* -diff_... : require nfiles == 2 */
   if( opts->diff_hdr || opts->diff_nim )
   {
     if( opts->infiles.len != 2 )
     {
      fprintf(stderr,"** '-diff_XXX' options require exactly 2 inputs files\n");
      return 1;
     }
   }
   /* if we are making changes, but not overwriting... */
   else if( (opts->elist.len > 0 || opts->mod_hdr || opts->mod_nim) &&
            !opts->overwrite )
   {
      if( opts->infiles.len > 1 )
      {
         fprintf(stderr,"** without -overwrite, only one input file may be"
                          " modified at a time\n");
         errs++;
      }
      if( ! opts->prefix )
      {
         fprintf(stderr,"** missing -prefix for output file\n");
         errs++;
      }
   }

   if( opts->dci_lines && ! opts->dts && ! opts->dci )
   {
      fprintf(stderr,"** option '-dci_lines' must only be used with '-dts'\n");
      errs++;
   }

   if( opts->infiles.len <= 0 ) /* in any case */
   {
      fprintf(stderr,"** missing input files (see -infiles option)\n");
      errs++;
   }

   if ( opts->overwrite && opts->prefix )
   {
      fprintf(stderr, "** please specify only one of -prefix and -overwrite\n");
      errs++;
   }

   if( errs ) return 1;

   if( g_debug > 1 ) fprintf(stderr,"+d options seem valid\n");

   return 0;
}


/*----------------------------------------------------------------------
 * re-assemble the command string into opts->command
 *----------------------------------------------------------------------*/
int fill_cmd_string( nt_opts * opts, int argc, char * argv[])
{
   char * cp;
   int    len, remain = NT_CMD_LEN;  /* NT_CMD_LEN is max command len */
   int    c, ac;
   int    has_space;  /* arguments containing space must be quoted */
   int    skip = 0;   /* counter to skip some of the arguments     */