void RT_test_callback(void *junk) { RT_status *rts = GLOBAL_library.realtime_status ; int cc , nval,nbr ; if( rts == NULL ){ ERROR_message("bad call to RT_test_callback"); return; } INFO_message("RT_test_callback: numchan=%d status=%d numdset=%d", rts->numchan , rts->status , rts->numdset ) ; for( cc=0 ; cc < rts->numdset ; cc++ ){ /* print out some dataset info */ if( !ISVALID_DSET(rts->dset[cc]) ){ ININFO_message(" dset[%d] invalid!",cc) ; /* should never happen */ } else { nval = DSET_NVALS(rts->dset[cc]) ; /* number of bricks */ nbr = THD_count_databricks(rts->dset[cc]->dblk) ; /* number with data */ ININFO_message(" dset[%d] '%s': nvals=%d nbr=%d", cc , DSET_HEADNAME(rts->dset[cc]) , nval,nbr ) ; } } return ; }
static int * PLUTO_4D_to_nothing (THD_3dim_dataset * old_dset , int ignore , int detrend , generic_func * user_func, void * user_data ) { 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) */ complex ** cptr = NULL ; float * fxar = NULL ; /* array loaded from input dataset */ float * fac = NULL ; /* array of brick scaling factors */ float * dtr = NULL ; /* will be array of detrending coeff */ float val , d0fac , d1fac , x0,x1; double tzero=0.0 , tdelta , ts_mean , ts_slope ; int ii , old_datum , nuse , use_fac , iz,izold, nxy,nvox ; static int retval; register int kk ; /*----------------------------------------------------------*/ /*----- Check inputs to see if they are reasonable-ish -----*/ if( ! ISVALID_3DIM_DATASET(old_dset) ) return NULL ; if( user_func == NULL ) return NULL ; if( ignore < 0 ) ignore = 0 ; /*--------- set up pointers to each sub-brick in the input dataset ---------*/ old_datum = DSET_BRICK_TYPE( old_dset , 0 ) ; /* get old dataset datum */ nuse = DSET_NUM_TIMES(old_dset) - ignore ; /* # of points on time axis */ if( nuse < 2 ) return NULL ; DSET_load( old_dset ) ; /* must be in memory before we get pointers to it */ kk = THD_count_databricks( old_dset->dblk ) ; /* check if it was */ if( kk < DSET_NVALS(old_dset) ){ /* loaded correctly */ DSET_unload( old_dset ) ; return NULL ; } switch( old_datum ){ /* pointer type depends on input datum type */ default: /** don't know what to do **/ DSET_unload( old_dset ) ; return NULL ; /** create array of pointers into old dataset sub-bricks **/ /*--------- input is bytes ----------*/ /* voxel #i at time #k is bptr[k][i] */ /* for i=0..nvox-1 and k=0..nuse-1. */ case MRI_byte: bptr = (byte **) malloc( sizeof(byte *) * nuse ) ; if( bptr == NULL ) return NULL ; for( kk=0 ; kk < nuse ; kk++ ) bptr[kk] = (byte *) DSET_ARRAY(old_dset,kk+ignore) ; break ; /*--------- input is shorts ---------*/ /* voxel #i at time #k is sptr[k][i] */ /* for i=0..nvox-1 and k=0..nuse-1. */ case MRI_short: sptr = (short **) malloc( sizeof(short *) * nuse ) ; if( sptr == NULL ) return NULL ; for( kk=0 ; kk < nuse ; kk++ ) sptr[kk] = (short *) DSET_ARRAY(old_dset,kk+ignore) ; break ; /*--------- input is floats ---------*/ /* voxel #i at time #k is fptr[k][i] */ /* for i=0..nvox-1 and k=0..nuse-1. */ case MRI_float: fptr = (float **) malloc( sizeof(float *) * nuse ) ; if( fptr == NULL ) return NULL ; for( kk=0 ; kk < nuse ; kk++ ) fptr[kk] = (float *) DSET_ARRAY(old_dset,kk+ignore) ; break ; /*--------- input is complex ---------*/ /* voxel #i at time #k is cptr[k][i] */ /* for i=0..nvox-1 and k=0..nuse-1. */ case MRI_complex: cptr = (complex **) malloc( sizeof(complex *) * nuse ) ; if( cptr == NULL ) return NULL ; for( kk=0 ; kk < nuse ; kk++ ) cptr[kk] = (complex *) DSET_ARRAY(old_dset,kk+ignore) ; break ; } /* end of switch on input type */ nvox = old_dset->daxes->nxx * old_dset->daxes->nyy * old_dset->daxes->nzz ; /*---- allocate space for 1 voxel timeseries ----*/ fxar = (float *) malloc( sizeof(float) * nuse ) ; /* voxel timeseries */ if( fxar == NULL ){ ZFREE_WORKSPACE ; return NULL ; } /*--- get scaling factors for sub-bricks ---*/ fac = (float *) malloc( sizeof(float) * nuse ) ; /* factors */ if( fac == NULL ){ ZFREE_WORKSPACE ; return NULL ; } use_fac = 0 ; for( kk=0 ; kk < nuse ; kk++ ){ fac[kk] = DSET_BRICK_FACTOR(old_dset,kk+ignore) ; if( fac[kk] != 0.0 ) use_fac++ ; else fac[kk] = 1.0 ; } if( !use_fac ) ZFREEUP(fac) ; /*--- setup for detrending ---*/ dtr = (float *) malloc( sizeof(float) * nuse ) ; if( dtr == NULL ){ ZFREE_WORKSPACE ; return NULL ; } d0fac = 1.0 / nuse ; d1fac = 12.0 / nuse / (nuse*nuse - 1.0) ; for( kk=0 ; kk < nuse ; kk++ ) dtr[kk] = kk - 0.5 * (nuse-1) ; /* linear trend, orthogonal to 1 */ /*----- set up to find time at each voxel -----*/ tdelta = old_dset->taxis->ttdel ; if( DSET_TIMEUNITS(old_dset) == UNITS_MSEC_TYPE ) tdelta *= 0.001 ; if( tdelta == 0.0 ) tdelta = 1.0 ; izold = -666 ; nxy = old_dset->daxes->nxx * old_dset->daxes->nyy ; /*----------------------------------------------------*/ /*----- Setup has ended. Now do some real work. -----*/ /* start notification */ #if 0 user_func( 0.0 , 0.0 , nvox , NULL,0.0,0.0 , user_data ) ; #else { void (*uf)(double,double,int,float *,double,double,void *) = (void (*)(double,double,int,float *,double,double,void *))(user_func) ; uf( 0.0l,0.0l , nvox , NULL , 0.0l,0.0l , user_data ) ; } #endif /***** loop over voxels *****/ for( ii=0 ; ii < nvox ; ii++ ){ /* 1 time series at a time */ /*** load data from input dataset, depending on type ***/ switch( old_datum ){ /*** input = bytes ***/ case MRI_byte: for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = bptr[kk][ii] ; break ; /*** input = shorts ***/ case MRI_short: for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = sptr[kk][ii] ; break ; /*** input = floats ***/ case MRI_float: for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = fptr[kk][ii] ; break ; /*** input = complex (note we use absolute value) ***/ case MRI_complex: for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = CABS(cptr[kk][ii]) ; break ; } /* end of switch over input type */ /*** scale? ***/ if( use_fac ) for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] *= fac[kk] ; /** compute mean and slope **/ x0 = x1 = 0.0 ; for( kk=0 ; kk < nuse ; kk++ ){ x0 += fxar[kk] ; x1 += fxar[kk] * dtr[kk] ; } x0 *= d0fac ; x1 *= d1fac ; /* factors to remove mean and trend */ ts_mean = x0 ; ts_slope = x1 / tdelta ; /** detrend? **/ if( detrend ) for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] -= (x0 + x1 * dtr[kk]) ; /** compute start time of this timeseries **/ /* The info computed here is not being used in this version*/ iz = ii / nxy ; /* which slice am I in? */ if( iz != izold ){ /* in a new slice? */ tzero = THD_timeof( ignore , old_dset->daxes->zzorg + iz*old_dset->daxes->zzdel , old_dset->taxis ) ; izold = iz ; if( DSET_TIMEUNITS(old_dset) == UNITS_MSEC_TYPE ) tzero *= 0.001 ; } /*** Send data to user function ***/ #if 0 user_func( tzero,tdelta , nuse,fxar,ts_mean,ts_slope , user_data) ; #else { void (*uf)(double,double,int,float *,double,double,void *) = (void (*)(double,double,int,float *,double,double,void *))(user_func) ; uf( tzero,tdelta , nuse,fxar,ts_mean,ts_slope , user_data) ; } #endif } /* end of outer loop over 1 voxels at a time */ DSET_unload( old_dset ) ; /* end notification */ #if 0 user_func( 0.0 , 0.0 , 0 , NULL,0.0,0.0 , user_data ) ; #else { void (*uf)(double,double,int,float *,double,double,void *) = (void (*)(double,double,int,float *,double,double,void *))(user_func) ; uf( 0.0l,0.0l, 0 , NULL,0.0l,0.0l, user_data ) ; } #endif /*-------------- Cleanup and go home ----------------*/ ZFREE_WORKSPACE ; retval = 0; return &retval; /* this value is not used for now .... */ }
THD_3dim_dataset * MAKER_4D_to_typed_fim( THD_3dim_dataset * old_dset , char * new_prefix , int new_datum , int ignore , int detrend , generic_func * user_func , void * user_data ) { THD_3dim_dataset * new_dset ; /* output dataset */ 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) */ complex ** cptr = NULL ; float * fxar = NULL ; /* array loaded from input dataset */ float * fac = NULL ; /* array of brick scaling factors */ float * fout = NULL ; /* will be array of output floats */ float * dtr = NULL ; /* will be array of detrending coeff */ float val , d0fac , d1fac , x0,x1; double tzero=0 , tdelta , ts_mean , ts_slope ; int ii , old_datum , nuse , use_fac , iz,izold, nxy,nvox , nbad ; register int kk ; void (*ufunc)(double,double,int,float *,double,double,void *,float *) = (void (*)(double,double,int,float *,double,double,void *,float *)) user_func ; /*----------------------------------------------------------*/ /*----- Check inputs to see if they are reasonable-ish -----*/ if( ! ISVALID_3DIM_DATASET(old_dset) ) return NULL ; if( new_datum >= 0 && new_datum != MRI_byte && new_datum != MRI_short && new_datum != MRI_float ) return NULL ; if( user_func == NULL ) return NULL ; if( ignore < 0 ) ignore = 0 ; /*--------- set up pointers to each sub-brick in the input dataset ---------*/ old_datum = DSET_BRICK_TYPE( old_dset , 0 ) ; /* get old dataset datum */ nuse = DSET_NUM_TIMES(old_dset) - ignore ; /* # of points on time axis */ if( nuse < 2 ) return NULL ; if( new_datum < 0 ) new_datum = old_datum ; /* output datum = input */ if( new_datum == MRI_complex ) return NULL ; /* but complex = bad news */ DSET_load( old_dset ) ; /* must be in memory before we get pointers to it */ kk = THD_count_databricks( old_dset->dblk ) ; /* check if it was */ if( kk < DSET_NVALS(old_dset) ){ /* loaded correctly */ DSET_unload( old_dset ) ; return NULL ; } switch( old_datum ){ /* pointer type depends on input datum type */ default: /** don't know what to do **/ DSET_unload( old_dset ) ; return NULL ; /** create array of pointers into old dataset sub-bricks **/ /*--------- input is bytes ----------*/ /* voxel #i at time #k is bptr[k][i] */ /* for i=0..nvox-1 and k=0..nuse-1. */ case MRI_byte: bptr = (byte **) malloc( sizeof(byte *) * nuse ) ; if( bptr == NULL ) return NULL ; for( kk=0 ; kk < nuse ; kk++ ) bptr[kk] = (byte *) DSET_ARRAY(old_dset,kk+ignore) ; break ; /*--------- input is shorts ---------*/ /* voxel #i at time #k is sptr[k][i] */ /* for i=0..nvox-1 and k=0..nuse-1. */ case MRI_short: sptr = (short **) malloc( sizeof(short *) * nuse ) ; if( sptr == NULL ) return NULL ; for( kk=0 ; kk < nuse ; kk++ ) sptr[kk] = (short *) DSET_ARRAY(old_dset,kk+ignore) ; break ; /*--------- input is floats ---------*/ /* voxel #i at time #k is fptr[k][i] */ /* for i=0..nvox-1 and k=0..nuse-1. */ case MRI_float: fptr = (float **) malloc( sizeof(float *) * nuse ) ; if( fptr == NULL ) return NULL ; for( kk=0 ; kk < nuse ; kk++ ) fptr[kk] = (float *) DSET_ARRAY(old_dset,kk+ignore) ; break ; /*--------- input is complex ---------*/ /* voxel #i at time #k is cptr[k][i] */ /* for i=0..nvox-1 and k=0..nuse-1. */ case MRI_complex: cptr = (complex **) malloc( sizeof(complex *) * nuse ) ; if( cptr == NULL ) return NULL ; for( kk=0 ; kk < nuse ; kk++ ) cptr[kk] = (complex *) DSET_ARRAY(old_dset,kk+ignore) ; break ; } /* end of switch on input type */ /*---- allocate space for 1 voxel timeseries ----*/ fxar = (float *) malloc( sizeof(float) * nuse ) ; /* voxel timeseries */ if( fxar == NULL ){ FREE_WORKSPACE ; return NULL ; } /*--- get scaling factors for sub-bricks ---*/ fac = (float *) malloc( sizeof(float) * nuse ) ; /* factors */ if( fac == NULL ){ FREE_WORKSPACE ; return NULL ; } use_fac = 0 ; for( kk=0 ; kk < nuse ; kk++ ){ fac[kk] = DSET_BRICK_FACTOR(old_dset,kk+ignore) ; if( fac[kk] != 0.0 ) use_fac++ ; else fac[kk] = 1.0 ; } if( !use_fac ) FREEUP(fac) ; /*--- setup for detrending ---*/ dtr = (float *) malloc( sizeof(float) * nuse ) ; if( dtr == NULL ){ FREE_WORKSPACE ; return NULL ; } d0fac = 1.0 / nuse ; d1fac = 12.0 / nuse / (nuse*nuse - 1.0) ; for( kk=0 ; kk < nuse ; kk++ ) dtr[kk] = kk - 0.5 * (nuse-1) ; /* linear trend, orthogonal to 1 */ /*---------------------- make a new dataset ----------------------*/ new_dset = EDIT_empty_copy( old_dset ) ; /* start with copy of old one */ /*-- edit some of its internal parameters --*/ ii = EDIT_dset_items( new_dset , ADN_prefix , new_prefix , /* filename prefix */ ADN_malloc_type , DATABLOCK_MEM_MALLOC , /* store in memory */ ADN_datum_all , new_datum , /* atomic datum */ ADN_nvals , 1 , /* # sub-bricks */ ADN_ntt , 0 , /* # time points */ ADN_type , ISHEAD(old_dset) /* dataset type */ ? HEAD_FUNC_TYPE : GEN_FUNC_TYPE , ADN_func_type , FUNC_FIM_TYPE , /* function type */ ADN_none ) ; if( ii != 0 ){ ERROR_message("Error creating dataset '%s'",new_prefix) ; THD_delete_3dim_dataset( new_dset , False ) ; /* some error above */ FREE_WORKSPACE ; return NULL ; } /*------ make floating point output brick (only at the end will scale to byte or shorts) ------*/ nvox = old_dset->daxes->nxx * old_dset->daxes->nyy * old_dset->daxes->nzz ; fout = (float *) malloc( sizeof(float) * nvox ) ; /* ptr to brick */ if( fout == NULL ){ THD_delete_3dim_dataset( new_dset , False ) ; FREE_WORKSPACE ; return NULL ; } /*----- set up to find time at each voxel -----*/ tdelta = old_dset->taxis->ttdel ; if( DSET_TIMEUNITS(old_dset) == UNITS_MSEC_TYPE ) tdelta *= 0.001 ; if( tdelta == 0.0 ) tdelta = 1.0 ; izold = -666 ; nxy = old_dset->daxes->nxx * old_dset->daxes->nyy ; /*----------------------------------------------------*/ /*----- Setup has ended. Now do some real work. -----*/ /* start notification */ #if 0 user_func( 0.0 , 0.0 , nvox , NULL,0.0,0.0 , user_data , NULL ) ; #else ufunc( 0.0 , 0.0 , nvox , NULL,0.0,0.0 , user_data , NULL ) ; #endif /***** loop over voxels *****/ for( ii=0 ; ii < nvox ; ii++ ){ /* 1 time series at a time */ /*** load data from input dataset, depending on type ***/ switch( old_datum ){ /*** input = bytes ***/ case MRI_byte: for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = bptr[kk][ii] ; break ; /*** input = shorts ***/ case MRI_short: for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = sptr[kk][ii] ; break ; /*** input = floats ***/ case MRI_float: for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = fptr[kk][ii] ; break ; /*** input = complex (note we use absolute value) ***/ case MRI_complex: for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = CABS(cptr[kk][ii]) ; break ; } /* end of switch over input type */ /*** scale? ***/ if( use_fac ) for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] *= fac[kk] ; /** compute mean and slope **/ x0 = x1 = 0.0 ; for( kk=0 ; kk < nuse ; kk++ ){ x0 += fxar[kk] ; x1 += fxar[kk] * dtr[kk] ; } x0 *= d0fac ; x1 *= d1fac ; /* factors to remove mean and trend */ ts_mean = x0 ; ts_slope = x1 / tdelta ; /** detrend? **/ if( detrend ) for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] -= (x0 + x1 * dtr[kk]) ; /** compute start time of this timeseries **/ iz = ii / nxy ; /* which slice am I in? */ if( iz != izold ){ /* in a new slice? */ tzero = THD_timeof( ignore , old_dset->daxes->zzorg + iz*old_dset->daxes->zzdel , old_dset->taxis ) ; izold = iz ; if( DSET_TIMEUNITS(old_dset) == UNITS_MSEC_TYPE ) tzero *= 0.001 ; } /*** compute output ***/ #if 0 user_func( tzero,tdelta , nuse,fxar,ts_mean,ts_slope , user_data , fout+ii ) ; #else ufunc( tzero,tdelta , nuse,fxar,ts_mean,ts_slope , user_data , fout+ii ) ; #endif } /* end of outer loop over 1 voxels at a time */ DSET_unload( old_dset ) ; /* don't need this no more */ /* end notification */ #if 0 user_func( 0.0 , 0.0 , 0 , NULL,0.0,0.0 , user_data , NULL ) ; #else ufunc( 0.0 , 0.0 , 0 , NULL,0.0,0.0 , user_data , NULL ) ; #endif nbad = thd_floatscan( nvox , fout ) ; /* 08 Aug 2000 */ if( nbad > 0 ) fprintf(stderr, "++ Warning: %d bad floats computed in MAKER_4D_to_typed_fim\n\a", nbad ) ; /*------------------------------------------------------------*/ /*------- The output is now in fout[ii], ii=0..nvox-1. We must now put this into the output dataset -------*/ switch( new_datum ){ /*** output is floats is the simplest: we just have to attach the fout brick to the dataset ***/ case MRI_float: EDIT_substitute_brick( new_dset , 0 , MRI_float , fout ) ; fout = NULL ; /* so it won't be freed later */ break ; /*** output is shorts: we have to create a scaled sub-brick from fout ***/ case MRI_short:{ short * bout ; float sfac ; /*-- get output sub-brick --*/ bout = (short *) malloc( sizeof(short) * nvox ) ; if( bout == NULL ){ fprintf(stderr, "\nFinal malloc error in MAKER_4D_to_fim - is memory exhausted?\n\a"); EXIT(1) ; } /*-- find scaling and then scale --*/ sfac = MCW_vol_amax( nvox,1,1 , MRI_float , fout ) ; if( sfac > 0.0 ){ sfac = 32767.0 / sfac ; EDIT_coerce_scale_type( nvox,sfac , MRI_float,fout , MRI_short,bout ) ; sfac = 1.0 / sfac ; } /*-- put output brick into dataset, and store scale factor --*/ EDIT_substitute_brick( new_dset , 0 , MRI_short , bout ) ; EDIT_dset_items( new_dset , ADN_brick_fac , &sfac , ADN_none ) ; } break ; /*** output is bytes (byte = unsigned char) we have to create a scaled sub-brick from fout ***/ case MRI_byte:{ byte * bout ; float sfac ; /*-- get output sub-brick --*/ bout = (byte *) malloc( sizeof(byte) * nvox ) ; if( bout == NULL ){ fprintf(stderr, "\nFinal malloc error in MAKER_4D_to_fim - is memory exhausted?\n\a"); EXIT(1) ; } /*-- find scaling and then scale --*/ sfac = MCW_vol_amax( nvox,1,1 , MRI_float , fout ) ; if( sfac > 0.0 ){ sfac = 255.0 / sfac ; EDIT_coerce_scale_type( nvox,sfac , MRI_float,fout , MRI_byte,bout ) ; sfac = 1.0 / sfac ; } /*-- put output brick into dataset, and store scale factor --*/ EDIT_substitute_brick( new_dset , 0 , MRI_byte , bout ) ; EDIT_dset_items( new_dset , ADN_brick_fac , &sfac , ADN_none ) ; } break ; } /* end of switch on output data type */ /*-------------- Cleanup and go home ----------------*/ FREE_WORKSPACE ; return new_dset ; }
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) ; }