00004 {
00005    int iarg=1 , dcode=0 , maxgap=9 , nftot=0 ;
00006    char * prefix="rowfillin" , * dstr=NULL;
00007    THD_3dim_dataset * inset , * outset ;
00008    MRI_IMAGE * brim ;
00009    int verb=0 ;
00010 
00011    if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
00012       printf("Usage: 3dRowFillin [options] dataset\n"
00013              "Extracts 1D rows in the given direction from a 3D dataset,\n"
00014              "searches for blank (zero) regions, and fills them in if\n"
00015              "the blank region isn't too large and it is flanked by\n"
00016              "the same value on either edge.  For example:\n"
00017              "     input row = 0 1 2 0 0 2 3 0 3 0 0 4 0\n"
00018              "    output row = 0 1 2 2 2 2 3 3 3 0 0 4 0\n"
00019              "\n"
00020              "OPTIONS:\n"
00021              " -maxgap N  = set the maximum length of a blank region that\n"
00022              "                will be filled in to 'N' [default=9].\n"
00023              " -dir D     = set the direction of fill to 'D', which can\n"
00024              "                be one of the following:\n"
00025              "                  A-P, P-A, I-S, S-I, L-R, R-L, x, y, z\n"
00026              "                The first 6 are anatomical directions;\n"
00027              "                the last 3 are reference to the dataset\n"
00028              "                internal axes [no default value].\n"
00029              " -prefix P  = set the prefix to 'P' for the output dataset.\n"
00030              "\n"
00031              "N.B.: If the input dataset has more than one sub-brick,\n"
00032              "      only the first one will be processed.\n"
00033              "\n"
00034              "The intention of this program is to let you fill in slice gaps\n"
00035              "made when drawing ROIs with the 'Draw Dataset' plugin.  If you\n"
00036              "draw every 5th coronal slice, say, then you could fill in using\n"
00037              "  3dRowFillin -maxgap 4 -dir A-P -prefix fredfill fred+orig\n"
00038              "\n"
00039             ) ;
00040       exit(0) ;
00041    }
00042 
00043    mainENTRY("3dRowFillin main"); machdep(); AFNI_logger("3dRowFillin",argc,argv);
00044    PRINT_VERSION("3dRowFillin") ;
00045 
00046    /*-- scan args --*/
00047 
00048    while( iarg < argc && argv[iarg][0] == '-' ){
00049 
00050       if( strncmp(argv[iarg],"-verb",5) == 0 ){
00051          verb++ ; iarg++ ; continue ;
00052       }
00053 
00054       if( strcmp(argv[iarg],"-prefix") == 0 ){
00055          prefix = argv[++iarg] ;
00056          if( !THD_filename_ok(prefix) ){
00057             fprintf(stderr,"*** Illegal string after -prefix!\n"); exit(1) ;
00058          }
00059          iarg++ ; continue ;
00060       }
00061 
00062       if( strcmp(argv[iarg],"-maxgap") == 0 ){
00063          maxgap = strtol( argv[++iarg] , NULL , 10 ) ;
00064          if( maxgap < 1 ){
00065             fprintf(stderr,"*** Illegal value after -maxgap!\n"); exit(1);
00066          }
00067          iarg++ ; continue ;
00068       }
00069 
00070       if( strcmp(argv[iarg],"-dir") == 0 ){
00071          dstr = argv[++iarg] ;
00072          iarg++ ; continue ;
00073       }
00074 
00075       fprintf(stderr,"*** Illegal option: %s\n",argv[iarg]) ; exit(1) ;
00076    }
00077 
00078    if( dstr == NULL ){
00079       fprintf(stderr,"*** No -dir option on command line!\n"); exit(1);
00080    }
00081    if( iarg >= argc ){
00082       fprintf(stderr,"*** No input dataset on command line!\n"); exit(1);
00083    }
00084 
00085    inset = THD_open_dataset( argv[iarg] ) ;
00086    if( inset == NULL ){
00087       fprintf(stderr,"*** Can't open dataset %s\n",argv[iarg]); exit(1);
00088    }
00089 
00090    outset = EDIT_empty_copy( inset ) ;
00091    EDIT_dset_items( outset , ADN_prefix , prefix , ADN_none ) ;
00092    if( THD_is_file( DSET_HEADNAME(outset) ) ){
00093       fprintf(stderr,"** Output file %s exists -- cannot overwrite!\n",
00094               DSET_HEADNAME(outset) ) ;
00095       exit(1) ;
00096    }
00097 
00098    tross_Copy_History( inset , outset ) ;
00099    tross_Make_History( "3dRowFillin" , argc,argv , outset ) ;
00100 
00101    if( DSET_NVALS(inset) > 1 ){
00102       fprintf(stderr,"++ WARNING: input dataset has more than one sub-brick!\n");
00103       EDIT_dset_items( outset ,
00104                          ADN_ntt   , 0 ,
00105                          ADN_nvals , 1 ,
00106                        ADN_none ) ;
00107    }
00108 
00109    if( DSET_BRICK_TYPE(outset,0) != MRI_short &&
00110        DSET_BRICK_TYPE(outset,0) != MRI_byte    ){
00111 
00112       fprintf(stderr,"*** This program only works on byte and short dataset!\n");
00113       exit(1) ;
00114    }
00115 
00116    switch( *dstr ){
00117       case 'x': dcode = 1 ; break ;
00118       case 'y': dcode = 2 ; break ;
00119       case 'z': dcode = 3 ; break ;
00120 
00121       default:
00122         if( *dstr == ORIENT_tinystr[outset->daxes->xxorient][0] ||
00123             *dstr == ORIENT_tinystr[outset->daxes->xxorient][1]   ) dcode = 1 ;
00124 
00125         if( *dstr == ORIENT_tinystr[outset->daxes->yyorient][0] ||
00126             *dstr == ORIENT_tinystr[outset->daxes->yyorient][1]   ) dcode = 2 ;
00127 
00128         if( *dstr == ORIENT_tinystr[outset->daxes->zzorient][0] ||
00129             *dstr == ORIENT_tinystr[outset->daxes->zzorient][1]   ) dcode = 3 ;
00130       break ;
00131    }
00132    if( dcode == 0 ){
00133       fprintf(stderr,"*** Illegal -dir direction!\n") ; exit(1) ;
00134    }
00135    if( verb )
00136       fprintf(stderr,"++ Direction = axis %d in dataset\n",dcode) ;
00137 
00138    DSET_load(inset) ;
00139    if( !DSET_LOADED(inset) ){
00140       fprintf(stderr,"*** Can't load dataset %s\n",argv[iarg]); exit(1);
00141    }
00142    brim = mri_copy( DSET_BRICK(inset,0) ) ;
00143    DSET_unload(inset) ;
00144    EDIT_substitute_brick( outset , 0 , brim->kind , mri_data_pointer(brim) ) ;
00145    nftot = THD_dataset_rowfillin( outset , 0 , dcode , maxgap ) ;
00146    fprintf(stderr,"++ Number of voxels filled = %d\n",nftot) ;
00147    DSET_write(outset) ;
00148    exit(0) ;
00149 }