00001 #include "mrilib.h"
00002 
00003 /*------------------------------------------------------------------------*/
00004 
00005 int main( int argc , char * argv[] )
00006 {
00007    float irad=1.5 ;
00008    int nrep=1 ;
00009    char *prefix = "MedianFilter" ;
00010    int iarg , verb=0 , do_mask=0 ;
00011    THD_3dim_dataset *inset , *outset ;
00012    MRI_IMAGE *imout ;
00013    byte *mask=NULL ;
00014 
00015    if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
00016       printf("Usage: 3dMedianFilter [options] dataset\n"
00017              "Computes the median in a spherical nbhd around each point in the\n"
00018              "input to produce the output.\n"
00019              "\n"
00020              "Options:\n"
00021              "  -irad x    = Radius in voxels of spherical regions\n"
00022              "  -verb      = Be verbose during run\n"
00023              "  -prefix pp = Use 'pp' for prefix of output dataset\n"
00024              "  -automask  = Create a mask (a la 3dAutomask)\n"
00025              "\n"
00026              "Output dataset is always stored in float format.  If the input\n"
00027              "dataset has more than 1 sub-brick, only sub-brick #0 is processed.\n"
00028              "\n"
00029              "-- Feb 2005 - RWCox\n"
00030             ) ;
00031       exit(0) ;
00032    }
00033 
00034    mainENTRY("3dMedianFilter main"); machdep(); AFNI_logger("3dMedianFilter",argc,argv);
00035    PRINT_VERSION("3dMedianFilter") ;
00036 
00037    /*-- scan command line --*/
00038 
00039    iarg = 1 ;
00040    while( iarg < argc && argv[iarg][0] == '-' ){
00041 
00042       if( strncmp(argv[iarg],"-automask",5) == 0 ){
00043         do_mask++ ; iarg++ ; continue ;
00044       }
00045 
00046       if( strncmp(argv[iarg],"-verb",5) == 0 ){
00047         verb++ ; iarg++ ; continue ;
00048       }
00049 
00050       if( strcmp(argv[iarg],"-irad") == 0 ){
00051          irad = strtod( argv[++iarg] , NULL ) ;
00052          if( irad < 1.0 ){
00053             fprintf(stderr,"*** Illegal value after -irad!\n"); exit(1);
00054          }
00055          iarg++ ; continue ;
00056       }
00057 
00058       if( strcmp(argv[iarg],"-prefix") == 0 ){
00059          prefix = argv[++iarg] ;
00060          if( !THD_filename_ok(prefix) ){
00061             fprintf(stderr,"*** Illegal value after -prefix!\n"); exit(1);
00062          }
00063          iarg++ ; continue ;
00064       }
00065 
00066       fprintf(stderr,"*** Unknown option: %s\n",argv[iarg]); exit(1) ;
00067    }
00068 
00069    if( iarg >= argc ){
00070       fprintf(stderr,"*** No dataset name on command line?\n"); exit(1);
00071    }
00072 
00073    /*-- read input --*/
00074 
00075    inset = THD_open_dataset( argv[iarg] ) ;
00076    if( inset == NULL ){
00077      fprintf(stderr,"**  ERROR: Can't open dataset %s\n",argv[iarg]); exit(1);
00078    }
00079    DSET_load( inset ) ;
00080    if( !DSET_LOADED(inset) ){
00081      fprintf(stderr,"** ERROR: can't load dataset %s\n",argv[iarg]); exit(1);
00082    }
00083    if( DSET_NVALS(inset) > 1 ){
00084      fprintf(stderr,"++ WARNING: only processing sub-brick #0\n") ;
00085    }
00086 
00087    if( do_mask ){
00088      THD_automask_verbose( verb ) ;
00089      THD_automask_extclip( 1 ) ;
00090      mask = THD_automask( inset ) ;
00091    }
00092 
00093    imout = mri_medianfilter( DSET_BRICK(inset,0) , irad , mask , verb ) ;
00094    free((void *)mask) ;
00095 
00096    outset = EDIT_empty_copy( inset )  ;
00097    EDIT_dset_items( outset ,
00098                        ADN_prefix , prefix ,
00099                        ADN_nvals  , 1 ,
00100                        ADN_ntt    , 0 ,
00101                     ADN_none ) ;
00102    EDIT_substitute_brick( outset , 0 , MRI_float , MRI_FLOAT_PTR(imout) ) ;
00103    tross_Copy_History( inset , outset ) ;
00104    tross_Make_History( "3dMedianFilter" , argc,argv , outset ) ;
00105    DSET_write(outset) ;
00106    fprintf(stderr,"++ output dataset: %s\n",DSET_BRIKNAME(outset)) ;
00107    exit(0) ;
00108 }