THD_3dim_dataset * EDIT_full_copy( THD_3dim_dataset *dset , char *new_prefix ) { THD_3dim_dataset *new_dset ; int ival , ityp , nbytes , nvals ; void *new_brick , *old_brick ; ENTRY("EDIT_full_copy") ; /*-- sanity check --*/ if( ! ISVALID_3DIM_DATASET(dset) ) RETURN(NULL) ; /*-- make the empty copy --*/ new_dset = EDIT_empty_copy( dset ) ; /* copy is set to MALLOC memory */ /*-- change its name? --*/ if( new_prefix != NULL ) EDIT_dset_items( new_dset , ADN_prefix , new_prefix , ADN_label1 , new_prefix , ADN_none ) ; /*-- make brick(s) for this dataset --*/ if( !DSET_LOADED(dset) ) DSET_load(dset) ; /* make sure is in memory */ nvals = DSET_NVALS(dset) ; for( ival=0 ; ival < nvals ; ival++ ){ ityp = DSET_BRICK_TYPE(new_dset,ival) ; /* type of data */ nbytes = DSET_BRICK_BYTES(new_dset,ival) ; /* how much data */ new_brick = malloc( nbytes ) ; /* make room */ if( new_brick == NULL ){ THD_delete_3dim_dataset( new_dset , False ) ; RETURN(NULL) ; } EDIT_substitute_brick( new_dset , ival , ityp , new_brick ) ; /*-- copy data from old brick to new brick --*/ old_brick = DSET_BRICK_ARRAY(dset,ival) ; if( old_brick == NULL ){ THD_delete_3dim_dataset( new_dset , False ) ; RETURN(NULL) ; } memcpy( new_brick , old_brick , nbytes ) ; } if (0) { /* For DG to activate */ THD_copy_labeltable_atr( new_dset->dblk, dset->dblk); } RETURN( new_dset ); }
int main( int argc , char *argv[] ) { THD_3dim_dataset *dset , *oset=NULL , *tset=NULL ; int nvals , iv , nxyz , ii,jj,kk , iarg , kz,kzold ; float cut1=2.5,cut2=4.0 , sq2p,sfac , fq ; MRI_IMAGE *flim ; char *prefix="despike" , *tprefix=NULL ; int corder=-1 , nref , ignore=0 , polort=2 , nuse , nomask=0 ; int nspike, nbig, nproc ; float **ref ; float c21,ic21 , pspike,pbig ; short *sar , *qar ; byte *tar , *mask=NULL ; float *zar , *yar ; int datum ; int localedit=0 ; /* 04 Apr 2007 */ int verb=1 ; int do_NEW = 0 ; /* 29 Nov 2013 */ MRI_IMAGE *NEW_psinv=NULL ; int dilate = 4 ; /* 04 Dec 2013 */ int ctim = 0 ; /*----- Read command line -----*/ AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */ if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ printf("Usage: 3dDespike [options] dataset\n" "Removes 'spikes' from the 3D+time input dataset and writes\n" "a new dataset with the spike values replaced by something\n" "more pleasing to the eye.\n" "\n" "Method:\n" " * L1 fit a smooth-ish curve to each voxel time series\n" " [see -corder option for description of the curve]\n" " [see -NEW option for a different & faster fitting method]\n" " * Compute the MAD of the difference between the curve and\n" " the data time series (the residuals).\n" " * Estimate the standard deviation 'sigma' of the residuals\n" " as sqrt(PI/2)*MAD.\n" " * For each voxel value, define s = (value-curve)/sigma.\n" " * Values with s > c1 are replaced with a value that yields\n" " a modified s' = c1+(c2-c1)*tanh((s-c1)/(c2-c1)).\n" " * c1 is the threshold value of s for a 'spike' [default c1=2.5].\n" " * c2 is the upper range of the allowed deviation from the curve:\n" " s=[c1..infinity) is mapped to s'=[c1..c2) [default c2=4].\n" "\n" "Options:\n" " -ignore I = Ignore the first I points in the time series:\n" " these values will just be copied to the\n" " output dataset [default I=0].\n" " -corder L = Set the curve fit order to L:\n" " the curve that is fit to voxel data v(t) is\n" "\n" " k=L [ (2*PI*k*t) (2*PI*k*t) ]\n" " f(t) = a+b*t+c*t*t + SUM [ d * sin(--------) + e * cos(--------) ]\n" " k=1 [ k ( T ) k ( T ) ]\n" "\n" " where T = duration of time series;\n" " the a,b,c,d,e parameters are chosen to minimize\n" " the sum over t of |v(t)-f(t)| (L1 regression);\n" " this type of fitting is is insensitive to large\n" " spikes in the data. The default value of L is\n" " NT/30, where NT = number of time points.\n" "\n" " -cut c1 c2 = Alter default values for the spike cut values\n" " [default c1=2.5, c2=4.0].\n" " -prefix pp = Save de-spiked dataset with prefix 'pp'\n" " [default pp='despike']\n" " -ssave ttt = Save 'spikiness' measure s for each voxel into a\n" " 3D+time dataset with prefix 'ttt' [default=no save]\n" " -nomask = Process all voxels\n" " [default=use a mask of high-intensity voxels, ]\n" " [as created via '3dAutomask -dilate 4 dataset'].\n" " -dilate nd = Dilate 'nd' times (as in 3dAutomask). The default\n" " value of 'nd' is 4.\n" " -q[uiet] = Don't print '++' informational messages.\n" "\n" " -localedit = Change the editing process to the following:\n" " If a voxel |s| value is >= c2, then replace\n" " the voxel value with the average of the two\n" " nearest non-spike (|s| < c2) values; the first\n" " one previous and the first one after.\n" " Note that the c1 cut value is not used here.\n" "\n" " -NEW = Use the 'new' method for computing the fit, which\n" " should be faster than the L1 method for long time\n" " series (200+ time points); however, the results\n" " are similar but NOT identical. [29 Nov 2013]\n" " * You can also make the program use the 'new'\n" " method by setting the environment variable\n" " AFNI_3dDespike_NEW\n" " to the value YES; as in\n" " setenv AFNI_3dDespike_NEW YES (csh)\n" " export AFNI_3dDespike_NEW=YES (bash)\n" " * If this variable is set to YES, you can turn off\n" " the '-NEW' processing by using the '-OLD' option.\n" " -->>* For time series more than 500 points long, the\n" " '-OLD' algorithm is tremendously slow. You should\n" " use the '-NEW' algorith in such cases.\n" " ** At some indeterminate point in the future, the '-NEW'\n" " method will become the default!\n" " -->>* As of 29 Sep 2016, '-NEW' is the default if there\n" " is more than 500 points in the time series dataset.\n" "\n" " -NEW25 = A slightly more aggressive despiking approach than\n" " the '-NEW' method.\n" "\n" "Caveats:\n" "* Despiking may interfere with image registration, since head\n" " movement may produce 'spikes' at the edge of the brain, and\n" " this information would be used in the registration process.\n" " This possibility has not been explored or calibrated.\n" "* [LATER] Actually, it seems like the registration problem\n" " does NOT happen, and in fact, despiking seems to help!\n" "* Check your data visually before and after despiking and\n" " registration!\n" " [Hint: open 2 AFNI controllers, and turn Time Lock on.]\n" ) ; PRINT_AFNI_OMP_USAGE("3dDespike",NULL) ; PRINT_COMPILE_DATE ; exit(0) ; } /** AFNI package setup and logging **/ mainENTRY("3dDespike main"); machdep(); AFNI_logger("3dDespike",argc,argv); PRINT_VERSION("3dDespike") ; AUTHOR("RW Cox") ; /** parse options **/ if( AFNI_yesenv("AFNI_3dDespike_NEW") ) do_NEW = 1 ; /* 29 Nov 2013 */ iarg = 1 ; while( iarg < argc && argv[iarg][0] == '-' ){ if( strncmp(argv[iarg],"-q",2) == 0 ){ /* 04 Apr 2007 */ verb = 0 ; iarg++ ; continue ; } if( strncmp(argv[iarg],"-v",2) == 0 ){ verb++ ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-NEW") == 0 ){ /* 29 Nov 2013 */ do_NEW = 1 ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-NEW25") == 0 ){ /* 29 Sep 2016 */ do_NEW = 1 ; use_des25 = 1 ; cut1 = 2.5f ; cut2 = 3.2f ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-OLD") == 0 ){ do_NEW = 0 ; iarg++ ; continue ; } /** -localedit **/ if( strcmp(argv[iarg],"-localedit") == 0 ){ /* 04 Apr 2007 */ localedit = 1 ; iarg++ ; continue ; } /** don't use masking **/ if( strcmp(argv[iarg],"-nomask") == 0 ){ nomask = 1 ; iarg++ ; continue ; } /** dilation count [04 Dec 2013] **/ if( strcmp(argv[iarg],"-dilate") == 0 ){ dilate = (int)strtod(argv[++iarg],NULL) ; if( dilate <= 0 ) dilate = 1 ; else if( dilate > 99 ) dilate = 99 ; iarg++ ; continue ; } /** output dataset prefix **/ if( strcmp(argv[iarg],"-prefix") == 0 ){ prefix = argv[++iarg] ; if( !THD_filename_ok(prefix) ) ERROR_exit("-prefix is not good"); iarg++ ; continue ; } /** ratio dataset prefix **/ if( strcmp(argv[iarg],"-ssave") == 0 ){ tprefix = argv[++iarg] ; if( !THD_filename_ok(tprefix) ) ERROR_exit("-ssave prefix is not good"); iarg++ ; continue ; } /** trigonometric polynomial order **/ if( strcmp(argv[iarg],"-corder") == 0 ){ corder = strtol( argv[++iarg] , NULL , 10 ) ; if( corder < 0 ) ERROR_exit("Illegal value of -corder"); iarg++ ; continue ; } /** how much to ignore at start **/ if( strcmp(argv[iarg],"-ignore") == 0 ){ ignore = strtol( argv[++iarg] , NULL , 10 ) ; if( ignore < 0 ) ERROR_exit("Illegal value of -ignore"); iarg++ ; continue ; } /** thresholds for s ratio **/ if( strcmp(argv[iarg],"-cut") == 0 ){ cut1 = strtod( argv[++iarg] , NULL ) ; cut2 = strtod( argv[++iarg] , NULL ) ; if( cut1 < 1.0 || cut2 < cut1+0.5 ) ERROR_exit("Illegal values after -cut"); iarg++ ; continue ; } ERROR_exit("Unknown option: %s",argv[iarg]) ; } c21 = cut2-cut1 ; ic21 = 1.0/c21 ; /*----- read input dataset -----*/ if( iarg >= argc ) ERROR_exit("No input dataset!!??"); dset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(dset,argv[iarg]) ; datum = DSET_BRICK_TYPE(dset,0) ; if( (datum != MRI_short && datum != MRI_float) || !DSET_datum_constant(dset) ) ERROR_exit("Can't process non-short, non-float dataset!") ; if( verb ) INFO_message("Input data type = %s\n",MRI_TYPE_name[datum]) ; nvals = DSET_NUM_TIMES(dset) ; nuse = nvals - ignore ; if( nuse < 15 ) ERROR_exit("Can't use dataset with < 15 time points per voxel!") ; if( nuse > 500 && !do_NEW ){ INFO_message("Switching to '-NEW' method since number of time points = %d > 500",nuse) ; do_NEW = 1 ; } if( use_des25 && nuse < 99 ) use_des25 = 0 ; if( verb ) INFO_message("ignoring first %d time points, using last %d",ignore,nuse); if( corder > 0 && 4*corder+2 > nuse ){ ERROR_exit("-corder %d is too big for NT=%d",corder,nvals) ; } else if( corder < 0 ){ corder = rint(nuse/30.0) ; if( corder > 50 && !do_NEW ) corder = 50 ; if( verb ) INFO_message("using %d time points => -corder %d",nuse,corder) ; } else { if( verb ) INFO_message("-corder %d set from command line",corder) ; } nxyz = DSET_NVOX(dset) ; if( verb ) INFO_message("Loading dataset %s",argv[iarg]) ; DSET_load(dset) ; CHECK_LOAD_ERROR(dset) ; /*-- create automask --*/ if( !nomask ){ mask = THD_automask( dset ) ; if( verb ){ ii = THD_countmask( DSET_NVOX(dset) , mask ) ; INFO_message("%d voxels in the automask [out of %d in dataset]",ii,DSET_NVOX(dset)) ; } for( ii=0 ; ii < dilate ; ii++ ) THD_mask_dilate( DSET_NX(dset), DSET_NY(dset), DSET_NZ(dset), mask, 3 ) ; if( verb ){ ii = THD_countmask( DSET_NVOX(dset) , mask ) ; INFO_message("%d voxels in the dilated automask [out of %d in dataset]",ii,DSET_NVOX(dset)) ; } } else { if( verb ) INFO_message("processing all %d voxels in dataset",DSET_NVOX(dset)) ; } /*-- create empty despiked dataset --*/ oset = EDIT_empty_copy( dset ) ; EDIT_dset_items( oset , ADN_prefix , prefix , ADN_brick_fac , NULL , ADN_datum_all , datum , ADN_none ) ; if( THD_deathcon() && THD_is_file(DSET_HEADNAME(oset)) ) ERROR_exit("output dataset already exists: %s",DSET_HEADNAME(oset)); tross_Copy_History( oset , dset ) ; tross_Make_History( "3dDespike" , argc , argv , oset ) ; /* create bricks (will be filled with zeros) */ for( iv=0 ; iv < nvals ; iv++ ) EDIT_substitute_brick( oset , iv , datum , NULL ) ; /* copy the ignored bricks */ switch( datum ){ case MRI_short: for( iv=0 ; iv < ignore ; iv++ ){ sar = DSET_ARRAY(oset,iv) ; qar = DSET_ARRAY(dset,iv) ; memcpy( sar , qar , DSET_BRICK_BYTES(dset,iv) ) ; DSET_unload_one(dset,iv) ; } break ; case MRI_float: for( iv=0 ; iv < ignore ; iv++ ){ zar = DSET_ARRAY(oset,iv) ; yar = DSET_ARRAY(dset,iv) ; memcpy( zar , yar , DSET_BRICK_BYTES(dset,iv) ) ; DSET_unload_one(dset,iv) ; } break ; } /*-- setup to save a threshold statistic dataset, if desired --*/ if( tprefix != NULL ){ float *fac ; tset = EDIT_empty_copy( dset ) ; fac = (float *) malloc( sizeof(float) * nvals ) ; for( ii=0 ; ii < nvals ; ii++ ) fac[ii] = TFAC ; EDIT_dset_items( tset , ADN_prefix , tprefix , ADN_brick_fac , fac , ADN_datum_all , MRI_byte , ADN_func_type , FUNC_FIM_TYPE , ADN_none ) ; free(fac) ; tross_Copy_History( tset , dset ) ; tross_Make_History( "3dDespike" , argc , argv , tset ) ; #if 0 if( THD_is_file(DSET_HEADNAME(tset)) ) ERROR_exit("-ssave dataset already exists"); #endif tross_Copy_History( tset , dset ) ; tross_Make_History( "3dDespike" , argc , argv , tset ) ; for( iv=0 ; iv < nvals ; iv++ ) EDIT_substitute_brick( tset , iv , MRI_byte , NULL ) ; } /*-- setup to find spikes --*/ sq2p = sqrt(0.5*PI) ; sfac = sq2p / 1.4826f ; /* make ref functions */ nref = 2*corder+3 ; ref = (float **) malloc( sizeof(float *) * nref ) ; for( jj=0 ; jj < nref ; jj++ ) ref[jj] = (float *) malloc( sizeof(float) * nuse ) ; /* r(t) = 1 */ for( iv=0 ; iv < nuse ; iv++ ) ref[0][iv] = 1.0 ; jj = 1 ; /* r(t) = t - tmid */ { float tm = 0.5 * (nuse-1.0) ; float fac = 2.0 / nuse ; for( iv=0 ; iv < nuse ; iv++ ) ref[1][iv] = (iv-tm)*fac ; jj = 2 ; /* r(t) = (t-tmid)**jj */ for( ; jj <= polort ; jj++ ) for( iv=0 ; iv < nuse ; iv++ ) ref[jj][iv] = pow( (iv-tm)*fac , (double)jj ) ; } for( kk=1 ; kk <= corder ; kk++ ){ fq = (2.0*PI*kk)/nuse ; /* r(t) = sin(2*PI*k*t/N) */ for( iv=0 ; iv < nuse ; iv++ ) ref[jj][iv] = sin(fq*iv) ; jj++ ; /* r(t) = cos(2*PI*k*t/N) */ for( iv=0 ; iv < nuse ; iv++ ) ref[jj][iv] = cos(fq*iv) ; jj++ ; } /****** setup for the NEW solution method [29 Nov 2013] ******/ if( do_NEW ){ NEW_psinv = DES_get_psinv(nuse,nref,ref) ; INFO_message("Procesing time series with NEW model fit algorithm") ; } else { INFO_message("Procesing time series with OLD model fit algorithm") ; } /*--- loop over voxels and do work ---*/ #define Laplace_t2p(val) ( 1.0 - nifti_stat2cdf( (val), 15, 0.0, 1.4427 , 0.0 ) ) if( verb ){ if( !localedit ){ INFO_message("smash edit thresholds: %.1f .. %.1f MADs",cut1*sq2p,cut2*sq2p) ; ININFO_message(" [ %.3f%% .. %.3f%% of normal distribution]", 200.0*qg(cut1*sfac) , 200.0*qg(cut2*sfac) ) ; ININFO_message(" [ %.3f%% .. %.3f%% of Laplace distribution]" , 100.0*Laplace_t2p(cut1) , 100.0*Laplace_t2p(cut2) ) ; } else { INFO_message("local edit threshold: %.1f MADS",cut2*sq2p) ; ININFO_message(" [ %.3f%% of normal distribution]", 200.0*qg(cut2*sfac) ) ; ININFO_message(" [ %.3f%% of Laplace distribution]", 100.0*Laplace_t2p(cut1) ) ; } INFO_message("%d slices to process",DSET_NZ(dset)) ; } kzold = -1 ; nspike = 0 ; nbig = 0 ; nproc = 0 ; ctim = NI_clock_time() ; AFNI_OMP_START ; #pragma omp parallel if( nxyz > 6666 ) { int ii , iv , iu , id , jj ; float *far , *dar , *var , *fitar , *ssp , *fit , *zar ; short *sar , *qar ; byte *tar ; float fsig , fq , cls , snew , val ; float *NEW_wks=NULL ; #pragma omp critical (DESPIKE_malloc) { far = (float *) malloc( sizeof(float) * nvals ) ; dar = (float *) malloc( sizeof(float) * nvals ) ; var = (float *) malloc( sizeof(float) * nvals ) ; fitar = (float *) malloc( sizeof(float) * nvals ) ; ssp = (float *) malloc( sizeof(float) * nvals ) ; fit = (float *) malloc( sizeof(float) * nref ) ; if( do_NEW ) NEW_wks = (float *)malloc(sizeof(float)*DES_workspace_size(nuse,nref)) ; } #ifdef USE_OMP INFO_message("start OpenMP thread #%d",omp_get_thread_num()) ; #endif #pragma omp for for( ii=0 ; ii < nxyz ; ii++ ){ /* ii = voxel index */ if( mask != NULL && mask[ii] == 0 ) continue ; /* skip this voxel */ #ifndef USE_OMP kz = DSET_index_to_kz(dset,ii) ; /* starting a new slice */ if( kz != kzold ){ if( verb ){ fprintf(stderr, "++ start slice %2d",kz ) ; if( nproc > 0 ){ pspike = (100.0*nspike)/nproc ; pbig = (100.0*nbig )/nproc ; fprintf(stderr, "; so far %d data points, %d edits [%.3f%%], %d big edits [%.3f%%]", nproc,nspike,pspike,nbig,pbig ) ; } fprintf(stderr,"\n") ; } kzold = kz ; } #else if( verb && ii % 2345 == 1234 ) fprintf(stderr,".") ; #endif /*** extract ii-th time series into far[] ***/ switch( datum ){ case MRI_short: for( iv=0 ; iv < nuse ; iv++ ){ qar = DSET_ARRAY(dset,iv+ignore) ; /* skip ignored data */ far[iv] = (float)qar[ii] ; } break ; case MRI_float: for( iv=0 ; iv < nuse ; iv++ ){ zar = DSET_ARRAY(dset,iv+ignore) ; far[iv] = zar[ii] ; } break ; } AAmemcpy(dar,far,sizeof(float)*nuse) ; /* copy time series into dar[] */ /*** solve for L1 fit ***/ if( do_NEW ) cls = DES_solve( NEW_psinv , far , fit , NEW_wks ) ; /* 29 Nov 2013 */ else cls = cl1_solve( nuse , nref , far , ref , fit,0 ) ; /* the slow part */ if( cls < 0.0f ){ /* fit failed! */ #if 0 fprintf(stderr,"curve fit fails at voxel %d %d %d\n", DSET_index_to_ix(dset,ii) , DSET_index_to_jy(dset,ii) , DSET_index_to_kz(dset,ii) ) ; #endif continue ; /* skip this voxel */ } for( iv=0 ; iv < nuse ; iv++ ){ /* detrend */ val = fit[0] + fit[1]*ref[1][iv] /* quadratic part of curve fit */ + fit[2]*ref[2][iv] ; for( jj=3 ; jj < nref ; jj++ ) /* rest of curve fit */ val += fit[jj] * ref[jj][iv] ; fitar[iv] = val ; /* save curve fit value */ var[iv] = dar[iv]-val ; /* remove fitted value = resid */ far[iv] = fabsf(var[iv]) ; /* abs value of resid */ } /*** compute estimate standard deviation of detrended data ***/ fsig = sq2p * qmed_float(nuse,far) ; /* also mangles far array */ /*** process time series for spikes, editing data in dar[] ***/ if( fsig > 0.0f ){ /* data wasn't fit perfectly */ /* find spikiness for each point in time */ fq = 1.0f / fsig ; for( iv=0 ; iv < nuse ; iv++ ){ ssp[iv] = fq * var[iv] ; /* spikiness s = how many sigma out */ } /* save spikiness in -ssave datset */ if( tset != NULL ){ for( iv=0 ; iv < nuse ; iv++ ){ tar = DSET_ARRAY(tset,iv+ignore) ; snew = ITFAC*fabsf(ssp[iv]) ; /* scale for byte storage */ tar[ii] = BYTEIZE(snew) ; /* cf. mrilib.h */ } } /* process values of |s| > cut1, editing dar[] */ for( iv=0 ; iv < nuse ; iv++ ){ /* loop over time points */ if( !localedit ){ /** classic 'smash' edit **/ if( ssp[iv] > cut1 ){ snew = cut1 + c21*mytanh((ssp[iv]-cut1)*ic21) ; /* edit s down */ dar[iv] = fitar[iv] + snew*fsig ; #pragma omp critical (DESPIKE_counter) { nspike++ ; if( ssp[iv] > cut2 ) nbig++ ; } } else if( ssp[iv] < -cut1 ){ snew = -cut1 + c21*mytanh((ssp[iv]+cut1)*ic21) ; /* edit s up */ dar[iv] = fitar[iv] + snew*fsig ; #pragma omp critical (DESPIKE_counter) { nspike++ ; if( ssp[iv] < -cut2 ) nbig++ ; } } } else { /** local edit: 04 Apr 2007 **/ if( ssp[iv] >= cut2 || ssp[iv] <= -cut2 ){ for( iu=iv+1 ; iu < nuse ; iu++ ) /* find non-spike above */ if( ssp[iu] < cut2 && ssp[iu] > -cut2 ) break ; for( id=iv-1 ; id >= 0 ; id-- ) /* find non-spike below */ if( ssp[id] < cut2 && ssp[id] > -cut2 ) break ; switch( (id>=0) + 2*(iu<nuse) ){ /* compute replacement val */ case 3: val = 0.5*(dar[iu]+dar[id]); break; /* iu and id OK */ case 2: val = dar[iu] ; break; /* only iu OK */ case 1: val = dar[id] ; break; /* only id OK */ default: val = fitar[iv] ; break; /* shouldn't be */ } dar[iv] = val ; #pragma omp critical (DESPIKE_counter) { nspike++ ; nbig++ ; } } } } /* end of loop over time points */ #pragma omp atomic nproc += nuse ; /* number data points processed */ } /* end of processing time series when fsig is positive */ /* put dar[] time series (possibly edited above) into output bricks */ switch( datum ){ case MRI_short: for( iv=0 ; iv < nuse ; iv++ ){ sar = DSET_ARRAY(oset,iv+ignore) ; /* output brick */ sar[ii] = (short)dar[iv] ; /* original or mutated data */ } break ; case MRI_float: for( iv=0 ; iv < nuse ; iv++ ){ zar = DSET_ARRAY(oset,iv+ignore) ; /* output brick */ zar[ii] = dar[iv] ; /* original or mutated data */ } break ; } } /* end of loop over voxels #ii */ #pragma omp critical (DESPIKE_malloc) { free(fit); free(ssp); free(fitar); free(var); free(dar); free(far); if( do_NEW ) free(NEW_wks) ; } } /* end OpenMP */ AFNI_OMP_END ; #ifdef USE_OMP if( verb ) fprintf(stderr,"\n") ; #endif ctim = NI_clock_time() - ctim ; INFO_message( "Elapsed despike time = %s" , nice_time_string(ctim) ) ; if( ctim > 345678 && !do_NEW ) ININFO_message("That was SLOW -- try the '-NEW' option for a speedup") ; #ifdef USE_OMP if( verb ) fprintf(stderr,"\n") ; #endif /*--- finish up ---*/ if( do_NEW ) mri_free(NEW_psinv) ; DSET_delete(dset) ; /* delete input dataset */ if( verb ){ if( nproc > 0 ){ pspike = (100.0*nspike)/nproc ; pbig = (100.0*nbig )/nproc ; INFO_message("FINAL: %d data points, %d edits [%.3f%%], %d big edits [%.3f%%]", nproc,nspike,pspike,nbig,pbig ) ; } else { INFO_message("FINAL: no good voxels found to process!!??") ; } } /* write results */ DSET_write(oset) ; if( verb ) WROTE_DSET(oset) ; DSET_delete(oset) ; if( tset != NULL ){ DSET_write(tset) ; if( verb ) WROTE_DSET(tset) ; DSET_delete(tset) ; } exit( THD_get_write_error_count() ) ; }
THD_3dim_dataset * fim3d_fimmer_compute ( THD_3dim_dataset * dset_time , time_series_array * ref_ts , time_series_array * ort_ts , int itbot, char * new_prefix, float max_percent /* 19 May 1997 */ ) { THD_3dim_dataset * new_dset ; int ifim , it,iv , nvox=0 , ngood_ref , ntime , it1 , dtyp , nxyz; float * vval , * tsar , * aval , * rbest , * abest ; int * indx=NULL ; short * bar ; void * ptr ; float stataux[MAX_STAT_AUX]; float fthr , topval ; int nx_ref , ny_ref , ivec , nnow ; PCOR_references ** pc_ref ; PCOR_voxel_corr ** pc_vc ; int save_resam ; int fim_nref , nx_ort , ny_ort=0 , internal_ort ; /* 10 Dec 1996 */ static float * ref_vec = NULL ; static int nref_vec = -666 ; float * ref_ts_min = NULL, * ref_ts_max = NULL, * baseline = NULL; /* 19 May 1997 */ int i; int nupdt = 0 , /* number of updates done yet */ min_updt = 5 ; /* min number needed for display */ /*--- check for legal inputs ---*/ /* 14 Jan 1998 */ if (!DSET_GRAPHABLE(dset_time)) { fprintf (stderr, "Error: Invalid 3d+time input data file \n"); RETURN (NULL); } if (ref_ts == NULL) { fprintf (stderr, "Error: No ideal time series \n"); RETURN (NULL); } for (i = 0; i < ref_ts->num; i++) if (ref_ts->tsarr[i]->len < DSET_NUM_TIMES(dset_time)) { fprintf (stderr, "Error: ideal time series is too short: ntime=%d num_ts=%d \n", DSET_NUM_TIMES(dset_time), ref_ts->tsarr[i]->len); RETURN (NULL) ; } /** 10 Dec 1996: allow for orts **/ if( ort_ts->num > 0 ) /** 05 Sept 1997 **/ { internal_ort = 0; ny_ort = ort_ts->num; for (i = 0; i < ny_ort; i++) { nx_ort = ort_ts->tsarr[i]->len ; if (nx_ort < DSET_NUM_TIMES(dset_time)) /* 14 Jan 1998 */ { fprintf (stderr, "Error: ort time series is too short: ntime=%d ort_ts=%d \n", DSET_NUM_TIMES(dset_time), ort_ts->tsarr[i]->len); RETURN (NULL) ; } } } else { internal_ort = 1 ; } fim_nref = (internal_ort) ? 3 : (ny_ort+3) ; if( nref_vec < fim_nref ) { ref_vec = (float *) malloc (sizeof(float)*fim_nref) ; nref_vec = fim_nref; } /* arrays to store maximum change in the ideal time series */ if (max_percent > 0.0) /* 19 May 1997 */ { ref_ts_max = (float *) malloc (sizeof(float) * (ref_ts->num)); ref_ts_min = (float *) malloc (sizeof(float) * (ref_ts->num)); } nx_ref = ref_ts->tsarr[0]->len; ny_ref = ref_ts->num; ntime = DSET_NUM_TIMES(dset_time) ; ngood_ref = 0 ; it1 = -1 ; for( ivec=0 ; ivec < ny_ref ; ivec++ ){ tsar = ref_ts->tsarr[ivec]->ts; ifim = 0 ; if (max_percent > 0.0) /* 19 May 1997 */ { ref_ts_min[ivec] = (float) SO_BIG; ref_ts_max[ivec] = - (float) SO_BIG; } for( it=itbot ; it < ntime ; it++ ) { if( tsar[it] < SO_BIG ) { ifim++ ; if( it1 < 0 ) it1 = it ; if (max_percent > 0.0) /* 19 May 1997 */ { if (tsar[it] > ref_ts_max[ivec]) ref_ts_max[ivec] = tsar[it]; if (tsar[it] < ref_ts_min[ivec]) ref_ts_min[ivec] = tsar[it]; } } } if( ifim < min_updt ){ STATUS("ref_ts has too few good entries!") ; RETURN(NULL) ; } ngood_ref = MAX( ifim , ngood_ref ) ; } /** at this point, ngood_ref = max number of good reference points, and it1 = index of first point used in first reference **/ dtyp = DSET_BRICK_TYPE(dset_time,it1) ; if( ! AFNI_GOOD_FUNC_DTYPE(dtyp) ){ STATUS("illegal input data type!") ; RETURN(NULL) ; } #ifdef AFNI_DEBUG { char str[256] ; sprintf(str,"new prefix = %s",new_prefix) ; STATUS(str) ; } #endif /*--- FIM: find values above threshold to fim ---*/ DSET_load(dset_time); CHECK_LOAD_ERROR(dset_time); nxyz = dset_time->dblk->diskptr->dimsizes[0] * dset_time->dblk->diskptr->dimsizes[1] * dset_time->dblk->diskptr->dimsizes[2] ; /** find the mean of the first array, compute the threshold (fthr) from it, make indx[i] be the 3D index of the i-th voxel above threshold **/ switch( dtyp ){ case MRI_short:{ short * dar = (short *) DSET_ARRAY(dset_time,it1) ; for( iv=0,fthr=0.0 ; iv < nxyz ; iv++ ) fthr += abs(dar[iv]) ; fthr = FIM_THR * fthr / nxyz ; for( iv=0,nvox=0 ; iv < nxyz ; iv++ ) if( abs(dar[iv]) > fthr ) nvox++ ; indx = (int *) malloc( sizeof(int) * nvox ) ; if( indx == NULL ){ fprintf(stderr,"\n*** indx malloc failure in fim3d_fimmer_compute\n") ; RETURN(NULL) ; } for( iv=0,nvox=0 ; iv < nxyz ; iv++ ) if( abs(dar[iv]) > fthr ) indx[nvox++] = iv ; } break ; case MRI_float:{ float * dar = (float *) DSET_ARRAY(dset_time,it1) ; for( iv=0,fthr=0.0 ; iv < nxyz ; iv++ ) fthr += fabs(dar[iv]) ; fthr = FIM_THR * fthr / nxyz ; for( iv=0,nvox=0 ; iv < nxyz ; iv++ ) if( fabs(dar[iv]) > fthr ) nvox++ ; indx = (int *) malloc( sizeof(int) * nvox ) ; if( indx == NULL ){ fprintf(stderr,"\n*** indx malloc failure in fim3d_fimmer_compute\n") ; RETURN(NULL) ; } for( iv=0,nvox=0 ; iv < nxyz ; iv++ ) if( fabs(dar[iv]) > fthr ) indx[nvox++] = iv ; } break ; case MRI_byte:{ byte * dar = (byte *) DSET_ARRAY(dset_time,it1) ; for( iv=0,fthr=0.0 ; iv < nxyz ; iv++ ) fthr += dar[iv] ; fthr = FIM_THR * fthr / nxyz ; for( iv=0,nvox=0 ; iv < nxyz ; iv++ ) if( dar[iv] > fthr ) nvox++ ; indx = (int *) malloc( sizeof(int) * nvox ) ; if( indx == NULL ){ fprintf(stderr,"\n*** indx malloc failure in fim3d_fimmer_compute\n") ; RETURN(NULL) ; } for( iv=0,nvox=0 ; iv < nxyz ; iv++ ) if( dar[iv] > fthr ) indx[nvox++] = iv ; } break ; } /** allocate space for voxel values **/ vval = (float *) malloc( sizeof(float) * nvox) ; if( vval == NULL ){ fprintf(stderr,"\n*** vval malloc failure in fim3d_fimmer_compute\n") ; free(indx) ; RETURN(NULL) ; } /*----- allocate space for baseline values -----*/ if (max_percent > 0.0) /* 19 May 1997 */ { baseline = (float *) malloc (sizeof(float) * nvox); if (baseline == NULL) { fprintf(stderr, "\n*** baseline malloc failure in fim3d_fimmer_compute\n") ; free(indx) ; free(vval); RETURN(NULL) ; } else /* initialize baseline values to zero */ for (iv = 0; iv < nvox; iv++) baseline[iv] = 0.0; } /** allocate extra space for comparing results from multiple ref vectors **/ if( ny_ref > 1 ){ aval = (float *) malloc( sizeof(float) * nvox) ; rbest = (float *) malloc( sizeof(float) * nvox) ; abest = (float *) malloc( sizeof(float) * nvox) ; if( aval==NULL || rbest==NULL || abest==NULL ){ fprintf(stderr,"\n*** abest malloc failure in fim3d_fimmer_compute\n") ; free(vval) ; free(indx) ; if( aval != NULL ) free(aval) ; if( rbest != NULL ) free(rbest) ; if( abest != NULL ) free(abest) ; RETURN(NULL) ; } } else { aval = rbest = abest = NULL ; } #ifdef AFNI_DEBUG { char str[256] ; sprintf(str,"nxyz = %d nvox = %d",nxyz,nvox) ; STATUS(str) ; } #endif /*--- FIM: initialize recursive updates ---*/ pc_ref = (PCOR_references **) malloc( sizeof(PCOR_references *) * ny_ref ) ; pc_vc = (PCOR_voxel_corr **) malloc( sizeof(PCOR_voxel_corr *) * ny_ref ) ; if( pc_ref == NULL || pc_vc == NULL ){ free(vval) ; free(indx) ; free(pc_ref) ; free(pc_vc) ; if( aval != NULL ) free(aval) ; if( rbest != NULL ) free(rbest) ; if( abest != NULL ) free(abest) ; fprintf(stderr,"\n*** FIM initialization fails in fim3d_fimmer_compute\n") ; RETURN(NULL) ; } ifim = 0 ; for( ivec=0 ; ivec < ny_ref ; ivec++ ){ pc_ref[ivec] = new_PCOR_references( fim_nref ) ; pc_vc[ivec] = new_PCOR_voxel_corr( nvox , fim_nref ) ; if( pc_ref[ivec] == NULL || pc_vc[ivec] == NULL ) ifim++ ; } if( ifim > 0 ){ for( ivec=0 ; ivec < ny_ref ; ivec++ ){ free_PCOR_references(pc_ref[ivec]) ; free_PCOR_voxel_corr(pc_vc[ivec]) ; } free(vval) ; free(indx) ; free(pc_ref) ; free(pc_vc) ; if( aval != NULL ) free(aval) ; if( rbest != NULL ) free(rbest) ; if( abest != NULL ) free(abest) ; fprintf(stderr,"\n*** FIM initialization fails in fim3d_fimmer_compute\n") ; RETURN(NULL) ; } /*--- Make a new dataset to hold the output ---*/ new_dset = EDIT_empty_copy( dset_time ) ; it = EDIT_dset_items( new_dset , ADN_prefix , new_prefix , ADN_malloc_type , DATABLOCK_MEM_MALLOC , ADN_type , ISHEAD(dset_time) ? HEAD_FUNC_TYPE : GEN_FUNC_TYPE , ADN_func_type , FUNC_COR_TYPE , ADN_nvals , FUNC_nvals[FUNC_COR_TYPE] , ADN_datum_all , MRI_short , ADN_ntt , 0 , ADN_none ) ; if( it > 0 ){ fprintf(stderr, "\n*** EDIT_dset_items error %d in fim3d_fimmer_compute\n",it) ; THD_delete_3dim_dataset( new_dset , False ) ; for( ivec=0 ; ivec < ny_ref ; ivec++ ){ free_PCOR_references(pc_ref[ivec]) ; free_PCOR_voxel_corr(pc_vc[ivec]) ; } free(vval) ; free(indx) ; free(pc_ref) ; free(pc_vc) ; if( aval != NULL ) free(aval) ; if( rbest != NULL ) free(rbest) ; if( abest != NULL ) free(abest) ; RETURN(NULL) ; } for( iv=0 ; iv < new_dset->dblk->nvals ; iv++ ){ ptr = malloc( DSET_BRICK_BYTES(new_dset,iv) ) ; mri_fix_data_pointer( ptr , DSET_BRICK(new_dset,iv) ) ; } if( THD_count_databricks(new_dset->dblk) < new_dset->dblk->nvals ){ fprintf(stderr, "\n*** failure to malloc new bricks in fim3d_fimmer_compute\n") ; THD_delete_3dim_dataset( new_dset , False ) ; for( ivec=0 ; ivec < ny_ref ; ivec++ ){ free_PCOR_references(pc_ref[ivec]) ; free_PCOR_voxel_corr(pc_vc[ivec]) ; } free(vval) ; free(indx) ; free(pc_ref) ; free(pc_vc) ; if( aval != NULL ) free(aval) ; if( rbest != NULL ) free(rbest) ; if( abest != NULL ) free(abest) ; RETURN(NULL) ; } /*--- FIM: do recursive updates ---*/ for( it=itbot ; it < ntime ; it++ ){ nnow = 0 ; for( ivec=0 ; ivec < ny_ref ; ivec++ ){ tsar = ref_ts->tsarr[ivec]->ts ; if( tsar[it] >= SO_BIG ) continue ; /* skip this */ ref_vec[0] = 1.0 ; /* we always supply orts */ ref_vec[1] = (float) it ; /* for mean and linear trend */ if (internal_ort) /* 10 Dec 1996 */ { ref_vec[2] = tsar[it] ; } else { for( iv=0 ; iv < ny_ort ; iv++ ) ref_vec[iv+2] = ort_ts->tsarr[iv]->ts[it]; ref_vec[ny_ort+2] = tsar[it] ; } #ifdef AFNI_DEBUG { char str[256] ; sprintf(str,"time index=%d ideal[%d]=%f" , it,ivec,tsar[it] ) ; if (ivec == 0) STATUS(str) ; } #endif update_PCOR_references( ref_vec , pc_ref[ivec] ) ; switch( dtyp ){ case MRI_short:{ short * dar = (short *) DSET_ARRAY(dset_time,it) ; for( iv=0 ; iv < nvox ; iv++ ) vval[iv] = (float) dar[indx[iv]] ; } break ; case MRI_float:{ float * dar = (float *) DSET_ARRAY(dset_time,it) ; for( iv=0 ; iv < nvox ; iv++ ) vval[iv] = (float) dar[indx[iv]] ; } break ; case MRI_byte:{ byte * dar = (byte *) DSET_ARRAY(dset_time,it) ; for( iv=0 ; iv < nvox ; iv++ ) vval[iv] = (float) dar[indx[iv]] ; } break ; } PCOR_update_float( vval , pc_ref[ivec] , pc_vc[ivec] ) ; nnow++ ; /*----- update baseline value calculation -----*/ if (max_percent > 0.0) /* 19 May 1997 */ if (ivec == 0) for (iv = 0; iv < nvox; iv++) baseline[iv] += vval[iv] / ngood_ref; } if( nnow > 0 ) nupdt++ ; /*--- Load results into the dataset and redisplay it ---*/ if( nupdt == ngood_ref ) { /*--- set the statistical parameters ---*/ stataux[0] = nupdt ; /* number of points used */ stataux[1] = (ny_ref==1) ? 1 : 2 ; /* number of references */ stataux[2] = fim_nref - 1 ; /* number of orts */ /* 12 Dec 96 */ for( iv=3 ; iv < MAX_STAT_AUX ; iv++ ) stataux[iv] = 0.0 ; STATUS("setting statistical parameters") ; (void) EDIT_dset_items( new_dset , ADN_stat_aux , stataux , ADN_none ) ; /*** Compute brick arrays for new dataset ***/ if( ny_ref == 1 ){ /*** Just 1 ref vector --> load values directly into dataset ***/ /*--- get alpha (coef) into vval, find max value, scale into brick array ---*/ STATUS("getting 1 ref alpha") ; PCOR_get_coef( pc_ref[0] , pc_vc[0] , vval ) ; /*--- replace alpha with percentage change, if so requested ---*/ if (max_percent > 0.0) /* 19 May 1997 */ { for (iv = 0; iv < nvox; iv++) { vval[iv] *= 100.0 * (ref_ts_max[0] - ref_ts_min[0]); if (fabs(vval[iv]) < max_percent * fabs(baseline[iv])) vval[iv] = fabs( vval[iv] / baseline[iv] ); else vval[iv] = max_percent; } topval = max_percent; } else { topval = 0.0 ; for( iv=0 ; iv < nvox ; iv++ ) if( fabs(vval[iv]) > topval ) topval = fabs(vval[iv]) ; } bar = DSET_ARRAY( new_dset , FUNC_ival_fim[FUNC_COR_TYPE] ) ; memset( bar , 0 , sizeof(short)*nxyz ) ; if( topval > 0.0 ){ topval = MRI_TYPE_maxval[MRI_short] / topval ; for( iv=0 ; iv < nvox ; iv++ ) bar[indx[iv]] = (short)(topval * vval[iv] + 0.499) ; stataux[0] = 1.0/topval ; } else { stataux[0] = 0.0 ; } /*--- get correlation coefficient (pcor) into vval, scale into brick array (with fixed scaling factor) ---*/ STATUS("getting 1 ref pcor") ; PCOR_get_pcor( pc_ref[0] , pc_vc[0] , vval ) ; bar = DSET_ARRAY( new_dset , FUNC_ival_thr[FUNC_COR_TYPE] ) ; memset( bar , 0 , sizeof(short)*nxyz ) ; for( iv=0 ; iv < nvox ; iv++ ) bar[indx[iv]] = (short)(FUNC_COR_SCALE_SHORT * vval[iv] + 0.499) ; stataux[1] = 1.0 / FUNC_COR_SCALE_SHORT ; } else { /*** Multiple references --> find best correlation at each voxel ***/ /*--- get first ref results into abest and rbest (best so far) ---*/ PCOR_get_coef( pc_ref[0] , pc_vc[0] , abest ) ; /*--- modify alpha for percentage change calculation ---*/ if (max_percent > 0.0) /* 19 May 1997 */ for (iv = 0; iv < nvox; iv++) abest[iv] *= 100.0 * (ref_ts_max[0] - ref_ts_min[0]); PCOR_get_pcor( pc_ref[0] , pc_vc[0] , rbest ) ; /*--- for each succeeding ref vector, get results into aval and vval, if |vval| > |rbest|, then use that result instead ---*/ for( ivec=1 ; ivec < ny_ref ; ivec++ ){ PCOR_get_coef( pc_ref[ivec] , pc_vc[ivec] , aval ) ; PCOR_get_pcor( pc_ref[ivec] , pc_vc[ivec] , vval ) ; for( iv=0 ; iv < nvox ; iv++ ){ if( fabs(vval[iv]) > fabs(rbest[iv]) ){ rbest[iv] = vval[iv] ; abest[iv] = aval[iv] ; /*--- modify alpha for percentage change calculation ---*/ if (max_percent > 0.0) /* 19 May 1997 */ abest[iv] *= 100.0 * (ref_ts_max[ivec] - ref_ts_min[ivec]); } } } /*--- at this point, abest and rbest are the best results, so scale them into the dataset bricks ---*/ /*--- finish percentage change calculation, if so requested ---*/ if (max_percent > 0.0) /* 19 May 1997 */ { for (iv = 0; iv < nvox; iv++) { if (fabs(abest[iv]) < max_percent * fabs(baseline[iv])) abest[iv] = fabs( abest[iv] / baseline[iv] ); else abest[iv] = max_percent; } topval = max_percent; } else { topval = 0.0 ; for( iv=0 ; iv < nvox ; iv++ ) if( fabs(abest[iv]) > topval ) topval = fabs(abest[iv]) ; } bar = DSET_ARRAY( new_dset , FUNC_ival_fim[FUNC_COR_TYPE] ) ; memset( bar , 0 , sizeof(short)*nxyz ) ; if( topval > 0.0 ){ topval = MRI_TYPE_maxval[MRI_short] / topval ; for( iv=0 ; iv < nvox ; iv++ ) bar[indx[iv]] = (short)(topval * abest[iv] + 0.499) ; stataux[0] = 1.0/topval ; } else { stataux[0] = 0.0 ; } bar = DSET_ARRAY( new_dset , FUNC_ival_thr[FUNC_COR_TYPE] ) ; memset( bar , 0 , sizeof(short)*nxyz ) ; for( iv=0 ; iv < nvox ; iv++ ) bar[indx[iv]] = (short)(FUNC_COR_SCALE_SHORT * rbest[iv] + 0.499) ; stataux[1] = 1.0 / FUNC_COR_SCALE_SHORT ; } STATUS("setting brick_fac") ; (void) EDIT_dset_items( new_dset , ADN_brick_fac , stataux , ADN_none ) ; } } /*--- End of recursive updates; now free temporary workspaces ---*/ for( ivec=0 ; ivec < ny_ref ; ivec++ ){ free_PCOR_references(pc_ref[ivec]) ; free_PCOR_voxel_corr(pc_vc[ivec]) ; } free(vval) ; free(indx) ; free(pc_ref) ; free(pc_vc) ; if( aval != NULL ) free(aval) ; if( rbest != NULL ) free(rbest) ; if( abest != NULL ) free(abest) ; if (ref_ts_min != NULL) free (ref_ts_min); /* 19 May 1997 */ if (ref_ts_max != NULL) free (ref_ts_max); if (baseline != NULL) free (baseline); /* --- load the statistics --- */ THD_load_statistics (new_dset); /*--- Return new dataset ---*/ RETURN(new_dset) ; }
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) ; } }