virtual void updt_params(params_ref const & p) {
m_smt_params.updt_params(p);
m_params.copy(p);
m_context.updt_params(p);
smt_params_helper smth(p);
m_core_extend_patterns = smth.core_extend_patterns();
m_core_extend_patterns_max_distance = smth.core_extend_patterns_max_distance();
m_core_extend_nonlocal_patterns = smth.core_extend_nonlocal_patterns();
}
int main(int argc, char** argv)
{
GradSoft::Logger log;
try{
GradSoft::DirectoryEntry smth("cyrilic");
do {
std::cerr << smth.name() << std::endl;
std::string s = "cyrilic/";
s += smth.name();
if (strcmp(smth.name(),".")&&strcmp(smth.name(),"..")) {
std::cerr << " Logging to file \"" << s.c_str()
<< "\" its filename (encoding ÂÈÍÄÎÑ / „Ž‘ / ëïé8 )." << std::endl;
log.setOutputFile(s.c_str());
log.infos() << smth.name() << std::endl;
}
} while (smth.next());
} catch (const GradSoft::DirectoryException& ex) {
std::cerr << ex.what() << std::endl;
}
return 0;
}
int main( int argc , char * argv[] )
{
void (*smth)(int,float *) = linear3_func ; /* default filter */
char prefix[256] = "smooth" ;
int new_datum = ILLEGAL_TYPE , old_datum ;
int nopt ;
THD_3dim_dataset * old_dset , * new_dset ;
int ii,kk , nxyz , ntime , use_fac , ityp , nbytes ;
void * new_brick ;
byte ** bptr = NULL ; /* one of these will be the array of */
short ** sptr = NULL ; /* pointers to input dataset sub-bricks */
float ** fptr = NULL ; /* (depending on input datum type) */
byte ** new_bptr = NULL ; /* one of these will be the array of */
short ** new_sptr = NULL ; /* pointers to output dataset sub-bricks */
float ** new_fptr = NULL ; /* (depending on output datum type) */
float * fxar = NULL ; /* array loaded from input dataset */
float * fac = NULL ; /* array of brick scaling factors */
float * faci = NULL ;
#define BLACKMAN 1
#define HAMMING 2
#define CUSTOM 3
#define EXTEND 77
#define ZERO 78
#define TREND 79
int ntap=0 ; /* 01 Mar 2001 */
float *ftap=NULL ;
int nwin=0,nfil=EXTEND ; /* 03 Mar 2001 */
void (*lfil)(int,float *,int,float *) = linear_filter_extend ;
float * (*lwin)(int) = NULL ;
/* start of code */
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf("Usage: 3dTsmooth [options] dataset\n"
"Smooths each voxel time series in a 3D+time dataset and produces\n"
"as output a new 3D+time dataset (e.g., lowpass filter in time).\n"
"\n"
"*** Also see program 3dBandpass ***\n"
"\n"
"General Options:\n"
" -prefix ppp = Sets the prefix of the output dataset to be 'ppp'.\n"
" [default = 'smooth']\n"
" -datum type = Coerce output dataset to be stored as the given type.\n"
" [default = input data type]\n"
"\n"
"Three Point Filtering Options [07 July 1999]\n"
"--------------------------------------------\n"
"The following options define the smoothing filter to be used.\n"
"All these filters use 3 input points to compute one output point:\n"
" Let a = input value before the current point\n"
" b = input value at the current point\n"
" c = input value after the current point\n"
" [at the left end, a=b; at the right end, c=b]\n"
"\n"
" -lin = 3 point linear filter: 0.15*a + 0.70*b + 0.15*c\n"
" [This is the default smoother]\n"
" -med = 3 point median filter: median(a,b,c)\n"
" -osf = 3 point order statistics filter:\n"
" 0.15*min(a,b,c) + 0.70*median(a,b,c) + 0.15*max(a,b,c)\n"
"\n"
" -3lin m = 3 point linear filter: 0.5*(1-m)*a + m*b + 0.5*(1-m)*c\n"
" Here, 'm' is a number strictly between 0 and 1.\n"
"\n"
"General Linear Filtering Options [03 Mar 2001]\n"
"----------------------------------------------\n"
" -hamming N = Use N point Hamming or Blackman windows.\n"
" -blackman N (N must be odd and bigger than 1.)\n"
" -custom coeff_filename.1D (odd # of coefficients must be in a \n"
" single column in ASCII file)\n"
" (-custom added Jan 2003)\n"
" WARNING: If you use long filters, you do NOT want to include the\n"
" large early images in the program. Do something like\n"
" 3dTsmooth -hamming 13 'fred+orig[4..$]'\n"
" to eliminate the first 4 images (say).\n"
" The following options determing how the general filters treat\n"
" time points before the beginning and after the end:\n"
" -EXTEND = BEFORE: use the first value; AFTER: use the last value\n"
" -ZERO = BEFORE and AFTER: use zero\n"
" -TREND = compute a linear trend, and extrapolate BEFORE and AFTER\n"
" The default is -EXTEND. These options do NOT affect the operation\n"
" of the 3 point filters described above, which always use -EXTEND.\n"
) ;
printf("\n" MASTER_SHORTHELP_STRING ) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
mainENTRY("3dTsmooth main"); machdep(); AFNI_logger("3dTsmooth",argc,argv);
PRINT_VERSION("3dTsmooth") ;
/* parse options */
nopt = 1 ;
while( nopt < argc && argv[nopt][0] == '-' ){
if( strcmp(argv[nopt],"-EXTEND") == 0 ){ /* 03 Mar 2001 */
nfil = EXTEND ; lfil = linear_filter_extend ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-ZERO") == 0 ){ /* 03 Mar 2001 */
nfil = ZERO ; lfil = linear_filter_zero ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-TREND") == 0 ){ /* 03 Mar 2001 */
nfil = TREND ; lfil = linear_filter_trend ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-hamming") == 0 ){
if( ++nopt >= argc ){fprintf(stderr,"*** Illegal -hamming!\n");exit(1);}
ntap = (int) strtod(argv[nopt],NULL) ;
if( ntap < 3 || ntap%2 != 1 ){fprintf(stderr,"*** Illegal -hamming!\n");exit(1);}
nwin = HAMMING ; lwin = hamming_window ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-blackman") == 0 ){
if( ++nopt >= argc ){fprintf(stderr,"*** Illegal -blackman!\n");exit(1);}
ntap = (int) strtod(argv[nopt],NULL) ;
if( ntap < 3 || ntap%2 != 1 ){fprintf(stderr,"*** Illegal -blackman!\n");exit(1);}
nwin = BLACKMAN ; lwin = blackman_window ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-custom") == 0 ){
if( ++nopt >= argc ){fprintf(stderr,"*** Illegal -custom!\n");exit(1);}
strcpy(custom_file, argv[nopt]) ;
nwin = CUSTOM ; lwin = custom_filter ;
ntap = 1;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-prefix") == 0 ){
if( ++nopt >= argc ){fprintf(stderr,"*** Illegal -prefix!\n");exit(1);}
strcpy(prefix,argv[nopt]) ;
if( !THD_filename_ok(prefix) ){fprintf(stderr,"*** Illegal -prefix!\n");exit(1);}
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-datum") == 0 ){
if( ++nopt >= argc ){fprintf(stderr,"*** Illegal -datum!\n");exit(1);}
if( strcmp(argv[nopt],"short") == 0 ){
new_datum = MRI_short ;
} else if( strcmp(argv[nopt],"float") == 0 ){
new_datum = MRI_float ;
} else if( strcmp(argv[nopt],"byte") == 0 ){
new_datum = MRI_byte ;
} else {
fprintf(stderr,"*** Illegal -datum!\n");exit(1);
}
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-lin") == 0 ){
bf = 0.70 ; af = cf = 0.15 ;
smth = linear3_func ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-med") == 0 ){
smth = median3_func ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-osf") == 0 ){
smth = osfilt3_func ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-3lin") == 0 ){
if( ++nopt >= argc ){fprintf(stderr,"*** Illegal -3lin!\n");exit(1);}
bf = strtod( argv[nopt] , NULL ) ;
if( bf <= 0.0 || bf >= 1.0 ){fprintf(stderr,"*** Illegal -3lin!\n");exit(1);}
af = cf = 0.5*(1.0-bf) ;
smth = linear3_func ;
nopt++ ; continue ;
}
fprintf(stderr,"*** Unknown option: %s\n",argv[nopt]) ; exit(1) ;
} /* end of loop over options */
if( nopt >= argc ){
fprintf(stderr,"*** No input dataset?!\n") ; exit(1) ;
}
/* open dataset */
old_dset = THD_open_dataset( argv[nopt] ) ;
if( old_dset == NULL ){
fprintf(stderr,"*** Can't open dataset %s\n",argv[nopt]) ; exit(1) ;
}
ntime = DSET_NVALS(old_dset) ;
nxyz = DSET_NVOX(old_dset) ;
if( ntime < 4 ){
fprintf(stderr,"*** Can't smooth dataset with less than 4 time points!\n") ;
exit(1) ;
}
DSET_load(old_dset) ; CHECK_LOAD_ERROR(old_dset) ;
old_datum = DSET_BRICK_TYPE(old_dset,0) ;
if( new_datum < 0 ) new_datum = old_datum ;
switch( old_datum ){ /* pointer type depends on input datum type */
/** create array of pointers into old dataset sub-bricks **/
/*--------- input is bytes ----------*/
/* voxel #i at time #k is bptr[k][i] */
/* for i=0..nxyz-1 and k=0..ntime-1. */
case MRI_byte:
bptr = (byte **) malloc( sizeof(byte *) * ntime ) ;
for( kk=0 ; kk < ntime ; kk++ )
bptr[kk] = (byte *) DSET_ARRAY(old_dset,kk) ;
break ;
/*--------- input is shorts ---------*/
/* voxel #i at time #k is sptr[k][i] */
/* for i=0..nxyz-1 and k=0..ntime-1. */
case MRI_short:
sptr = (short **) malloc( sizeof(short *) * ntime ) ;
for( kk=0 ; kk < ntime ; kk++ )
sptr[kk] = (short *) DSET_ARRAY(old_dset,kk) ;
break ;
/*--------- input is floats ---------*/
/* voxel #i at time #k is fptr[k][i] */
/* for i=0..nxyz-1 and k=0..ntime-1. */
case MRI_float:
fptr = (float **) malloc( sizeof(float *) * ntime ) ;
for( kk=0 ; kk < ntime ; kk++ )
fptr[kk] = (float *) DSET_ARRAY(old_dset,kk) ;
break ;
} /* end of switch on input type */
/*---- allocate space for 1 voxel timeseries ----*/
fxar = (float *) malloc( sizeof(float) * ntime ) ; /* voxel timeseries */
/*--- get scaling factors for sub-bricks ---*/
fac = (float *) malloc( sizeof(float) * ntime ) ; /* factors */
use_fac = 0 ;
for( kk=0 ; kk < ntime ; kk++ ){
fac[kk] = DSET_BRICK_FACTOR(old_dset,kk) ;
if( fac[kk] != 0.0 ) use_fac++ ;
else fac[kk] = 1.0 ;
}
if( !use_fac ){
free(fac) ; fac == NULL ;
} else {
faci = (float *) malloc( sizeof(float) * ntime ) ;
for( kk=0 ; kk < ntime ; kk++ ) faci[kk] = 1.0 / fac[kk] ;
}
/*---------------------- make a new dataset ----------------------*/
new_dset = EDIT_empty_copy( old_dset ) ;
tross_Copy_History( old_dset , new_dset ) ;
tross_Make_History( "3dTsmooth" , argc,argv , new_dset ) ;
/*-- edit some of its internal parameters --*/
EDIT_dset_items( new_dset ,
ADN_prefix , prefix ,
ADN_malloc_type , DATABLOCK_MEM_MALLOC ,
ADN_datum_all , new_datum ,
ADN_none ) ;
/*-- make brick(s) for this dataset --*/
switch( new_datum ){
case MRI_byte:
new_bptr = (byte **) malloc( sizeof(byte *) * ntime ) ;
break ;
case MRI_short:
new_sptr = (short **) malloc( sizeof(short *) * ntime ) ;
break ;
case MRI_float:
new_fptr = (float **) malloc( sizeof(float *) * ntime ) ;
break ;
}
for( kk=0 ; kk < ntime ; kk++ ){
ityp = DSET_BRICK_TYPE(new_dset,kk) ; /* type of data */
nbytes = DSET_BRICK_BYTES(new_dset,kk) ; /* how much data */
new_brick = malloc( nbytes ) ; /* make room */
if( new_brick == NULL ){
fprintf(stderr,"*** Can't get memory for output dataset!\n") ; exit(1) ;
}
EDIT_substitute_brick( new_dset , kk , ityp , new_brick ) ;
switch( new_datum ){
case MRI_byte: new_bptr[kk] = (byte * ) new_brick ; break ;
case MRI_short: new_sptr[kk] = (short *) new_brick ; break ;
case MRI_float: new_fptr[kk] = (float *) new_brick ; break ;
}
}
if( lwin != NULL && ntap > 0 ){ /* 03 Mar 2001 */
ftap = lwin(ntap) ;
if( lfil == NULL ) lfil = linear_filter_extend ;
if( nwin == CUSTOM ) ntap = custom_ntaps ;
}
/*----------------------------------------------------*/
/*----- Setup has ended. Now do some real work. -----*/
/***** loop over voxels *****/
for( ii=0 ; ii < nxyz ; ii++ ){ /* 1 time series at a time */
/*** load data from input dataset, depending on type ***/
switch( old_datum ){
case MRI_byte:
for( kk=0 ; kk < ntime ; kk++ ) fxar[kk] = bptr[kk][ii] ;
break ;
case MRI_short:
for( kk=0 ; kk < ntime ; kk++ ) fxar[kk] = sptr[kk][ii] ;
break ;
case MRI_float:
for( kk=0 ; kk < ntime ; kk++ ) fxar[kk] = fptr[kk][ii] ;
break ;
} /* end of switch over input type */
if( use_fac )
for( kk=0 ; kk < ntime ; kk++ ) fxar[kk] *= fac[kk] ;
/* do smoothing */
if( ftap != NULL )
lfil( ntap,ftap , ntime,fxar ) ; /* 01 Mar 2001 */
else
smth( ntime , fxar ) ; /* 3 point smoother */
/*** put data into output dataset ***/
switch( new_datum ){
case MRI_byte:
if( use_fac )
for( kk=0 ; kk < ntime ; kk++ ) new_bptr[kk][ii] = (byte)(fxar[kk] * faci[kk]) ;
else
for( kk=0 ; kk < ntime ; kk++ ) new_bptr[kk][ii] = (byte) fxar[kk] ;
break ;
case MRI_short:
if( use_fac )
for( kk=0 ; kk < ntime ; kk++ ) new_sptr[kk][ii] = (short)(fxar[kk] * faci[kk]) ;
else
for( kk=0 ; kk < ntime ; kk++ ) new_sptr[kk][ii] = (short) fxar[kk] ;
break ;
case MRI_float:
if( use_fac )
for( kk=0 ; kk < ntime ; kk++ ) new_fptr[kk][ii] = (float)(fxar[kk] * faci[kk]) ;
else
for( kk=0 ; kk < ntime ; kk++ ) new_fptr[kk][ii] = (float) fxar[kk] ;
break ;
}
} /* end of loop over voxels */
DSET_unload(old_dset) ; free(ftap) ;
if (DSET_write(new_dset) != False) {
fprintf(stderr,"++ output dataset: %s\n",DSET_BRIKNAME(new_dset)) ;
exit(0) ;
} else {
fprintf(stderr,
"** 3dTsmooth: Failed to write output!\n" ) ;
exit(1) ;
}
}
