00001 /******************************* 3dAFNItoRaw **************************************/
00002 #include "mrilib.h"
00003 
00004 static char outfname[THD_MAX_PREFIX] = "rawxyz.dat";
00005 
00006 /*! convert three sub-briks to a raw dataset with consecutive triplets */
00007 int main( int argc , char * argv[] )
00008 {
00009    THD_3dim_dataset * old_dset;  /* input dataset */
00010    int nopt, nxyz;
00011    int force_float = 0;
00012    float voxval;
00013    int ival;
00014    short sval;
00015    double dval;
00016    byte bval;
00017    void *voxptr;
00018    int i,j;
00019    FILE *fout;
00020    double fac;
00021    MRI_IMAGE *data_im = NULL;
00022    MRI_TYPE out_kind = MRI_float;
00023    int statcode;
00024 
00025    /*----- Read command line -----*/
00026    if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
00027       printf("Usage: 3dAFNItoRaw [options] dataset\n"
00028              "Convert an AFNI brik file with multiple sub-briks to a raw file with\n"
00029              "  each sub-brik voxel concatenated voxel-wise.\n"
00030              "For example, a dataset with 3 sub-briks X,Y,Z with elements x1,x2,x3,...,xn,\n"
00031              "  y1,y2,y3,...,yn and z1,z2,z3,...,zn will be converted to a raw dataset with\n"
00032              "  elements x1,y1,z1, x2,y2,z2, x3,y3,z3, ..., xn,yn,zn \n"
00033              "The dataset is kept in the original data format (float/short/int)\n"
00034              "Options:\n"
00035              "  -output / -prefix = name of the output file (not an AFNI dataset prefix)\n"
00036              "    the default output name will be rawxyz.dat\n\n"
00037              "  -datum float = force floating point output. Floating point forced if any\n"
00038              "    sub-brik scale factors not equal to 1.\n\n"
00039              );
00040      printf("\n" MASTER_SHORTHELP_STRING ) ;
00041       exit(0) ;
00042    }
00043 
00044    mainENTRY("3dAFNItoRaw main"); machdep(); AFNI_logger("3dAFNItoRaw",argc,argv);
00045    PRINT_VERSION("3dAFNItoRaw") ;
00046    nopt = 1;
00047    while( nopt < argc && argv[nopt][0] == '-' ){
00048     if( (strcmp(argv[nopt],"-output") == 0 ) || (strcmp(argv[nopt],"-prefix")==0))
00049       {
00050        if (++nopt >= argc)
00051          {
00052           fprintf (stderr, "*** Error - output / prefix needs an argument!\n");
00053           exit (1);
00054          }
00055        MCW_strncpy (outfname, argv[nopt], THD_MAX_PREFIX);      /* change name from default prefix */
00056        if (!THD_filename_ok (outfname))
00057          {
00058           fprintf (stderr, "*** Error - %s is not a valid output name!\n", outfname);
00059           exit (1);
00060          }
00061        if (THD_is_file(outfname))
00062         {
00063           fprintf (stderr, "*** Error - %s already exists!\n", outfname);
00064           exit (1);
00065          }
00066        fout = fopen (outfname, "w") ;
00067        if( fout == NULL ){
00068           fprintf (stderr, "*** Error - can not create %s for some reason!\n", outfname);
00069           exit (1);
00070          }
00071        nopt++; continue;
00072       }
00073     if (strcmp(argv[nopt],"-datum")==0) {
00074        if (strcmp(argv[++nopt],"float")==0)
00075           force_float = 1;
00076        else {
00077           fprintf (stderr, \
00078             "*** Error - can only specify float; otherwise, original format assumed!\n");
00079           exit (1);
00080          }
00081        nopt++; continue;
00082       }
00083      fprintf(stderr, "*** Error - unknown option %s\n", argv[nopt]);
00084      exit(1);
00085    }
00086  
00087    old_dset = THD_open_dataset (argv[nopt]);
00088 
00089  
00090    if (!ISVALID_DSET (old_dset)){
00091       fprintf (stderr, "*** Error - Can not open dataset %s\n", argv[nopt]);
00092       exit (1);
00093    }
00094 
00095    /* expect at least 2 values per voxel - otherwise what's the point? */
00096    if (DSET_NVALS (old_dset) < 2){
00097       fprintf (stderr, "*** Error - Dataset must have at least two sub-briks.\n");
00098       exit (1);
00099    }
00100 
00101    nxyz = DSET_NVOX(old_dset) ; /* number of voxels in dataset */
00102 
00103    fout = fopen (outfname, "w") ;
00104    if( fout == NULL ){
00105       fprintf (stderr, "*** Error - can not create %s for some reason!\n", outfname);
00106       exit (1);
00107    }
00108  
00109    if(force_float==0) {
00110      for(j=0;j<DSET_NVALS(old_dset);j++) {
00111          fac = DSET_BRICK_FACTOR(old_dset, j); /* get scale factor for each sub-brik*/
00112          if(fac==0.0) fac=1.0;
00113          if(fac!=1.0) {
00114            force_float = 1;                /* if even one scale factor != 1, put output in float */
00115            break;
00116          }
00117      }
00118    }
00119  
00120 
00121    DSET_mallocize (old_dset);
00122    DSET_load (old_dset);                        /* load dataset */
00123 
00124    for(i=0;i<nxyz;i++) {                   /* for every voxel in each sub-brik */
00125      for(j=0;j<DSET_NVALS(old_dset);j++) {  /*   for each sub-brik */
00126        data_im = DSET_BRICK (old_dset, j);      /* set pointer to the jth sub-brik of the dataset */
00127        fac = DSET_BRICK_FACTOR(old_dset, j); /* get scale factor for each sub-brik*/
00128        if(fac==0.0) fac=1.0;
00129               switch( data_im->kind ){
00130                case MRI_short:{
00131                   short *ar = mri_data_pointer(data_im) ;
00132                   voxval = ar[i];
00133                }
00134                break ;
00135 
00136                case MRI_byte:{
00137                   byte *ar = mri_data_pointer(data_im) ;
00138                   voxval = ar[i];
00139                }
00140                break ;
00141 
00142                case MRI_float:{
00143                   float *ar = mri_data_pointer(data_im) ;
00144                   voxval = ar[i];
00145                }
00146                break ;
00147 
00148               case MRI_double:{
00149                   double *ar = mri_data_pointer(data_im) ;
00150                   voxval = ar[i];
00151                }
00152                break ;
00153 
00154               case MRI_int:{
00155                   int *ar = mri_data_pointer(data_im) ;
00156                   voxval = ar[i];
00157                }
00158                break ;
00159 
00160               case MRI_complex:{
00161                   complex *ar = mri_data_pointer(data_im) ;
00162                   voxval = CABS(ar[i]);
00163                }
00164                break ;
00165 
00166               case MRI_rgb:{
00167                   byte *ar = mri_data_pointer(data_im) ;
00168                   voxval = 0.299*ar[3*i]+0.587*ar[3*i+1]+0.114*ar[3*i+2];
00169                }
00170                break ;
00171 
00172               default:                          /* unknown type */
00173                  voxval = 0.0;                   /* ignore this voxel */
00174                  fprintf(stderr,"Unknown type, %s, in sub-brik %d\n", MRI_TYPE_name[data_im->kind], i);
00175                break;
00176             }
00177 
00178        voxval = voxval * fac;
00179 
00180        if(force_float!=0)
00181          out_kind = MRI_float;
00182        else
00183          out_kind = data_im->kind;
00184        
00185        switch(out_kind) {
00186           case MRI_short:{
00187              sval  = voxval;
00188              voxptr = &sval;
00189           }
00190           break ;
00191 
00192           case MRI_byte:{
00193              bval  = voxval;
00194              voxptr = &sval;
00195           }
00196           break ;
00197 
00198           case MRI_float:{
00199              voxptr = &voxval;
00200           }
00201           break ;
00202 
00203           case MRI_double:{
00204              dval = voxval;
00205              voxptr = &dval;
00206           }
00207           break ;
00208 
00209           case MRI_int:{
00210              ival = voxval;
00211              voxptr = &ival;
00212           }
00213           break ;
00214  
00215           default:                          /* unknown type */
00216               fprintf(stderr,"Can't handle type, %s, in sub-brik %d\n",\
00217                 MRI_TYPE_name[data_im->kind], j);
00218               fclose(fout);
00219               exit(1);
00220           break;
00221        }             
00222 
00223        statcode = fwrite(voxptr, sizeof(out_kind), 1,fout);  /* write one voxel value at a time */
00224        if(statcode!=1) {
00225          fprintf(stderr, "*** Error - writing output file!\n");
00226          fclose(fout);
00227          exit(1);
00228        }
00229      }
00230    }
00231 
00232    fprintf(stderr, "File output format is %s\n", MRI_TYPE_name[out_kind]);
00233    fclose(fout);
00234    exit(0);
00235 }